Package ubic.gemma.persistence.service.expression.experiment

Class ExpressionExperimentDaoTest

java.lang.Object

org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests

org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests

ubic.gemma.core.util.test.BaseDatabaseTest

ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoTest

All Implemented Interfaces:

Aware, ApplicationContextAware

@ContextConfiguration
@TestExecutionListeners(WithSecurityContextTestExecutionListener.class)
public class ExpressionExperimentDaoTest
extends BaseDatabaseTest

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.core.util.test.BaseDatabaseTest

BaseDatabaseTest.BaseDatabaseTestContextConfiguration

Field Summary

Fields inherited from class ubic.gemma.core.util.test.BaseDatabaseTest

sessionFactory

Fields inherited from class org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests

jdbcTemplate, simpleJdbcTemplate

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

applicationContext, logger

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentDaoTest()

Method Summary

Modifier and Type	Method	Description
void	removeFixtures()
void	removeWithBioAssayDimension()
void	testAddRawDataVectors()
void	testCreateProcessedDataVectors()
void	testCreateProcessedDataVectorsWithPersistentQt()
void	testFilterAndCountByArrayDesign()
void	testGetAllAnnotations()
void	testGetAnnotationsByLevel()
void	testGetAnnotationUsageFrequency()
void	testGetAnnotationUsageFrequencyAsAnonymous()
void	testGetAnnotationUsageFrequencyExcludingFreeTextCategories()
void	testGetAnnotationUsageFrequencyExcludingFreeTextTerms()
void	testGetAnnotationUsageFrequencyExcludingUncategorizedTerms()
void	testGetAnnotationUsageFrequencyRetainMentionedTerm()
void	testGetAnnotationUsageFrequencyWithIds()	No ACL filtering is done when explicit IDs are provided, so this should work without WithMockUser.
void	testGetAnnotationUsageFrequencyWithLargeBatch()
void	testGetAnnotationUsageFrequencyWithUncategorizedCategory()
void	testGetArrayDesignUsageFrequency()
void	testGetCategoriesUsageFrequencyAsAnonymous()
void	testGetCategoriesUsageFrequencyWithIds()	No ACL filtering is done when explicit IDs are provided, so this should work without WithMockUser.
void	testGetCategoriesWithUsageFrequency()
void	testGetFilterableProperties()
void	testGetOriginalPlatformUsageFrequency()
void	testGetPerTaxonCount()
void	testGetTechnologyTypeUsageFrequency()
void	testLoadMultipleReferences()
void	testLoadReference()
void	testRemoveAllRawDataVectors()
void	testRemoveExperimentWithSharedBioMaterial()
void	testRemoveProcessedDataVectors()
void	testRemoveRawDataVectors()
void	testRemoveRawDataVectorsWhenQtIsUnknown()
void	testReplaceProcessedDataVectors()
void	testReplaceProcessedDataVectorsReusingTheSameQT()
void	testReplaceProcessedDataVectorsWithDetachedExperiment()
void	testReplaceRawDataVectors()
void	testSubquery()
void	testSubqueryWithMultipleJointures()
void	testThaw()
void	testThawBioAssays()
void	testThawForFrontEnd()
void	testThawTransientEntity()
void	testThawWithoutVectors()

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

flushAndClearSession

Methods inherited from class org.springframework.test.context.junit4.AbstractTransactionalJUnit4SpringContextTests

countRowsInTable, countRowsInTableWhere, deleteFromTables, dropTables, executeSqlScript, setDataSource, setSqlScriptEncoding

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

Constructor Detail

ExpressionExperimentDaoTest

public ExpressionExperimentDaoTest()

Method Detail

removeFixtures

public void removeFixtures()

testGetFilterableProperties

public void testGetFilterableProperties()

testThawTransientEntity

public void testThawTransientEntity()

testThaw

public void testThaw()

testThawBioAssays

public void testThawBioAssays()

testThawForFrontEnd

public void testThawForFrontEnd()

testThawWithoutVectors

public void testThawWithoutVectors()

testLoadReference

public void testLoadReference()

testLoadMultipleReferences

public void testLoadMultipleReferences()

testGetTechnologyTypeUsageFrequency

@WithMockUser
public void testGetTechnologyTypeUsageFrequency()

testGetArrayDesignUsageFrequency

@WithMockUser
public void testGetArrayDesignUsageFrequency()

testGetOriginalPlatformUsageFrequency

@WithMockUser
public void testGetOriginalPlatformUsageFrequency()

testGetCategoriesWithUsageFrequency

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetCategoriesWithUsageFrequency()

testGetCategoriesUsageFrequencyAsAnonymous

@WithMockUser
public void testGetCategoriesUsageFrequencyAsAnonymous()

testGetCategoriesUsageFrequencyWithIds

public void testGetCategoriesUsageFrequencyWithIds()

No ACL filtering is done when explicit IDs are provided, so this should work without WithMockUser.

testGetAnnotationUsageFrequency

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequency()

testGetAnnotationUsageFrequencyAsAnonymous

@WithMockUser
public void testGetAnnotationUsageFrequencyAsAnonymous()

testGetAnnotationUsageFrequencyWithLargeBatch

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequencyWithLargeBatch()

testGetAnnotationUsageFrequencyRetainMentionedTerm

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequencyRetainMentionedTerm()

testGetAnnotationUsageFrequencyExcludingFreeTextTerms

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequencyExcludingFreeTextTerms()

testGetAnnotationUsageFrequencyExcludingFreeTextCategories

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequencyExcludingFreeTextCategories()

testGetAnnotationUsageFrequencyExcludingUncategorizedTerms

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequencyExcludingUncategorizedTerms()

testGetAnnotationUsageFrequencyWithUncategorizedCategory

@WithMockUser(authorities="GROUP_ADMIN")
public void testGetAnnotationUsageFrequencyWithUncategorizedCategory()

testGetAnnotationUsageFrequencyWithIds

public void testGetAnnotationUsageFrequencyWithIds()

No ACL filtering is done when explicit IDs are provided, so this should work without WithMockUser.

testGetPerTaxonCount

@WithMockUser("bob")
public void testGetPerTaxonCount()

testFilterAndCountByArrayDesign

@WithMockUser
public void testFilterAndCountByArrayDesign()

testSubquery

public void testSubquery()

testSubqueryWithMultipleJointures

public void testSubqueryWithMultipleJointures()

testRemoveExperimentWithSharedBioMaterial

public void testRemoveExperimentWithSharedBioMaterial()

removeWithBioAssayDimension

public void removeWithBioAssayDimension()

testGetAllAnnotations

public void testGetAllAnnotations()

testGetAnnotationsByLevel

public void testGetAnnotationsByLevel()

testAddRawDataVectors

public void testAddRawDataVectors()

testRemoveAllRawDataVectors

public void testRemoveAllRawDataVectors()

testRemoveRawDataVectors

public void testRemoveRawDataVectors()

testRemoveRawDataVectorsWhenQtIsUnknown

public void testRemoveRawDataVectorsWhenQtIsUnknown()

testReplaceRawDataVectors

public void testReplaceRawDataVectors()

testCreateProcessedDataVectors

public void testCreateProcessedDataVectors()

testCreateProcessedDataVectorsWithPersistentQt

public void testCreateProcessedDataVectorsWithPersistentQt()

testRemoveProcessedDataVectors

public void testRemoveProcessedDataVectors()

testReplaceProcessedDataVectors

public void testReplaceProcessedDataVectors()

testReplaceProcessedDataVectorsReusingTheSameQT

public void testReplaceProcessedDataVectorsReusingTheSameQT()

testReplaceProcessedDataVectorsWithDetachedExperiment

public void testReplaceProcessedDataVectorsWithDetachedExperiment()