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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`loadTroubledIds()`
`void`	`removeFixtures()`
`void`	`removeWithBioAssayDimension()`
`void`	`testAddRawDataVectors()`
`void`	`testCreateProcessedDataVectors()`
`void`	`testCreateProcessedDataVectorsWithNonPersistentQt()`
`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`	`testGetArrayDesignUsed()`
`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`	`testGetGenesUsedByProcessedVectors()`
`void`	`testGetOriginalPlatformUsageFrequency()`
`void`	`testGetPerTaxonCount()`
`void`	`testGetRawDataVectors()`
`void`	`testGetTechnologyTypeUsageFrequency()`
`void`	`testLoadMultipleReferences()`
`void`	`testLoadReference()`
`void`	`testLoadValueObjectWithSingleCellData()`
`void`	`testRemoveAllRawDataVectors()`
`void`	`testRemoveExperimentWithSharedBioMaterial()`
`void`	`testRemoveProcessedDataVectors()`
`void`	`testRemoveRawDataVectors()`
`void`	`testRemoveRawDataVectorsWhenQtIsUnknown()`
`void`	`testRemoveRawDataVectorsWithDimension()`
`void`	`testReplaceProcessedDataVectors()`
`void`	`testReplaceProcessedDataVectorsReusingTheSameQT()`
`void`	`testReplaceProcessedDataVectorsWithDetachedExperiment()`
`void`	`testReplaceRawDataVectors()`
`void`	`testReplaceRawDataVectorsWithNewDimension()`
`void`	`testSubquery()`
`void`	`testSubqueryWithMultipleJointures()`
`void`	`testThaw()`
`void`	`testThawLite()`
`void`	`testThawLiter()`
`void`	`testThawTransientEntity()`

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()
```

loadTroubledIds
```
public void loadTroubledIds()
```

testGetFilterableProperties

public void testGetFilterableProperties()

testThawTransientEntity
```
public void testThawTransientEntity()
```

testThaw
```
public void testThaw()
```

testThawLite
```
public void testThawLite()
```

testThawLiter
```
public void testThawLiter()
```

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()

testLoadValueObjectWithSingleCellData

@WithMockUser
public void testLoadValueObjectWithSingleCellData()

testGetAllAnnotations
```
public void testGetAllAnnotations()
```

testGetAnnotationsByLevel

public void testGetAnnotationsByLevel()

testGetRawDataVectors
```
public void testGetRawDataVectors()
```

testAddRawDataVectors
```
public void testAddRawDataVectors()
```

testRemoveAllRawDataVectors

public void testRemoveAllRawDataVectors()

testRemoveRawDataVectors

public void testRemoveRawDataVectors()

testRemoveRawDataVectorsWithDimension

public void testRemoveRawDataVectorsWithDimension()

testRemoveRawDataVectorsWhenQtIsUnknown

public void testRemoveRawDataVectorsWhenQtIsUnknown()

testReplaceRawDataVectors

public void testReplaceRawDataVectors()

testReplaceRawDataVectorsWithNewDimension

public void testReplaceRawDataVectorsWithNewDimension()

testCreateProcessedDataVectors

public void testCreateProcessedDataVectors()

testCreateProcessedDataVectorsWithNonPersistentQt

public void testCreateProcessedDataVectorsWithNonPersistentQt()

testRemoveProcessedDataVectors

public void testRemoveProcessedDataVectors()

testReplaceProcessedDataVectors

public void testReplaceProcessedDataVectors()

testReplaceProcessedDataVectorsReusingTheSameQT

public void testReplaceProcessedDataVectorsReusingTheSameQT()

testReplaceProcessedDataVectorsWithDetachedExperiment

public void testReplaceProcessedDataVectorsWithDetachedExperiment()

testGetGenesUsedByProcessedVectors

public void testGetGenesUsedByProcessedVectors()

testGetArrayDesignUsed
```
public void testGetArrayDesignUsed()
```

Class ExpressionExperimentDaoTest

Nested Class Summary

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

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Constructor Detail

ExpressionExperimentDaoTest

Method Detail

removeFixtures

loadTroubledIds

testGetFilterableProperties

testThawTransientEntity

testThaw

testThawLite

testThawLiter

testLoadReference

testLoadMultipleReferences

testGetTechnologyTypeUsageFrequency

testGetArrayDesignUsageFrequency

testGetOriginalPlatformUsageFrequency

testGetCategoriesWithUsageFrequency

testGetCategoriesUsageFrequencyAsAnonymous

testGetCategoriesUsageFrequencyWithIds

testGetAnnotationUsageFrequency

testGetAnnotationUsageFrequencyAsAnonymous

testGetAnnotationUsageFrequencyWithLargeBatch

testGetAnnotationUsageFrequencyRetainMentionedTerm

testGetAnnotationUsageFrequencyExcludingFreeTextTerms

testGetAnnotationUsageFrequencyExcludingFreeTextCategories

testGetAnnotationUsageFrequencyExcludingUncategorizedTerms

testGetAnnotationUsageFrequencyWithUncategorizedCategory

testGetAnnotationUsageFrequencyWithIds

testGetPerTaxonCount

testFilterAndCountByArrayDesign

testSubquery

testSubqueryWithMultipleJointures

testRemoveExperimentWithSharedBioMaterial

removeWithBioAssayDimension

testLoadValueObjectWithSingleCellData

testGetAllAnnotations

testGetAnnotationsByLevel

testGetRawDataVectors

testAddRawDataVectors

testRemoveAllRawDataVectors

testRemoveRawDataVectors

testRemoveRawDataVectorsWithDimension

testRemoveRawDataVectorsWhenQtIsUnknown

testReplaceRawDataVectors

testReplaceRawDataVectorsWithNewDimension

testCreateProcessedDataVectors

testCreateProcessedDataVectorsWithNonPersistentQt

testRemoveProcessedDataVectors

testReplaceProcessedDataVectors

testReplaceProcessedDataVectorsReusingTheSameQT

testReplaceProcessedDataVectorsWithDetachedExperiment

testGetGenesUsedByProcessedVectors

testGetArrayDesignUsed