java.lang.Object
- ubic.gemma.core.util.test.PersistentDummyObjectHelper

@Component
@Transactional
public class PersistentDummyObjectHelper
extends Object

Used to generate test data.

Author:: pavlidis

Constructor Summary

Constructors
Constructor Description

PersistentDummyObjectHelper()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Collection<Analysis>`	`addTestAnalyses(ExpressionExperiment ee)`
`ExperimentalDesign`	`getExperimentalDesign(Collection<FactorValue> allFactorValues)`
`Collection<ExperimentalFactor>`	`getExperimentalFactors(ExperimentalDesign ed)`
`Collection<FactorValue>`	`getFactorValues(ExperimentalFactor ef)`
`protected Set<FactorValue>`	`getFactorValues(ExperimentalFactor ef, Collection<FactorValue> allFactorValues)`
`protected Characteristic`	`getTestCharacteristic(String name, String value)`
`int`	`getTestElementCollectionSize()`
`ExpressionExperiment`	`getTestExpressionExperimentWithAllDependencies()`	Add an expressionExperiment to the database for testing purposes.
`ExpressionExperiment`	`getTestExpressionExperimentWithAllDependencies(boolean doSequence)`	Add an expressionExperiment to the database for testing purposes.
`ExpressionExperiment`	`getTestExpressionExperimentWithAllDependencies(ExpressionExperiment prototype)`
`ExpressionExperiment`	`getTestExpressionExperimentWithAnalysisAndResults()`	Create a test EE with analysis results.
`BioSequence`	`getTestNonPersistentBioSequence(Taxon taxon)`
`GeneProduct`	`getTestNonPersistentGeneProduct(Gene gene)`
`QuantitationType`	`getTestNonPersistentQuantitationType()`	Note that if you want a 'preferred' qt or other special properties you have to set it yourself.
`ArrayDesign`	`getTestPersistentArrayDesign(int numCompositeSequences, boolean randomNames, boolean doSequence)`	Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
`ExpressionExperiment`	`getTestPersistentBasicExpressionExperiment()`
`ExpressionExperiment`	`getTestPersistentBasicExpressionExperiment(ArrayDesign arrayDesign)`
`BibliographicReference`	`getTestPersistentBibliographicReference(String accession)`
`BioAssay`	`getTestPersistentBioAssay(ArrayDesign ad)`
`BioAssay`	`getTestPersistentBioAssay(ArrayDesign ad, BioMaterial bm)`	Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`BioMaterial`	`getTestPersistentBioMaterial()`
`BioMaterial`	`getTestPersistentBioMaterial(Taxon tax)`
`BioSequence`	`getTestPersistentBioSequence()`
`BioSequence`	`getTestPersistentBioSequence(Taxon taxon)`
`Set<BioSequence2GeneProduct>`	`getTestPersistentBioSequence2GeneProducts(BioSequence bioSequence)`
`BlatResult`	`getTestPersistentBlatResult(BioSequence querySequence, Taxon taxon)`
`Contact`	`getTestPersistentContact()`	Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
`DatabaseEntry`	`getTestPersistentDatabaseEntry(String accession, String databaseName)`
`DatabaseEntry`	`getTestPersistentDatabaseEntry(String accession, ExternalDatabase ed)`	Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`DatabaseEntry`	`getTestPersistentDatabaseEntry(ExternalDatabase ed)`	Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
`ExpressionExperiment`	`getTestPersistentExpressionExperiment()`	Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
`ExpressionExperiment`	`getTestPersistentExpressionExperiment(Taxon taxon)`	Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test objects.
`Gene`	`getTestPersistentGene()`
`Gene`	`getTestPersistentGene(Taxon t)`
`GeneProduct`	`getTestPersistentGeneProduct(Gene gene)`
`QuantitationType`	`getTestPersistentQuantitationType()`	Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
`Taxon`	`getTestPersistentTaxon()`
`protected Statement`	`getTestStatement(String name, String value)`
`void`	`resetSeed()`
`void`	`resetTestElementCollectionSize()`
`void`	`setTestElementCollectionSize(int testElementCollectionSize)`	Override the number of elements made in collections.

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

- Constructor Detail
  - PersistentDummyObjectHelper
```
public PersistentDummyObjectHelper()
```
- Method Detail
  - resetSeed
```
public void resetSeed()
```
  - getTestNonPersistentBioSequence
```
public BioSequence getTestNonPersistentBioSequence(Taxon taxon)
```
  - getTestNonPersistentGeneProduct
```
public GeneProduct getTestNonPersistentGeneProduct(Gene gene)
```
  - getTestNonPersistentQuantitationType
```
public QuantitationType getTestNonPersistentQuantitationType()
```
    Note that if you want a 'preferred' qt or other special properties you have to set it yourself.
    
    Returns:
    
    QT
  - addTestAnalyses
```
public Collection<Analysis> addTestAnalyses(ExpressionExperiment ee)
```
  - getExperimentalDesign
```
public ExperimentalDesign getExperimentalDesign(Collection<FactorValue> allFactorValues)
```
    Parameters:
    
    allFactorValues - all factor values
    
    Returns:
    
    Non-persistent ED
  - getExperimentalFactors
```
public Collection<ExperimentalFactor> getExperimentalFactors(ExperimentalDesign ed)
```
  - getFactorValues
```
public Collection<FactorValue> getFactorValues(ExperimentalFactor ef)
```
  - getTestElementCollectionSize
```
public int getTestElementCollectionSize()
```
  - setTestElementCollectionSize
```
public void setTestElementCollectionSize(int testElementCollectionSize)
```
    Override the number of elements made in collections. By default this is quite small, so you can increase it. But please call 'reset' afterwards.
    
    Parameters:
    
    testElementCollectionSize - new size
  - getTestExpressionExperimentWithAllDependencies
```
public ExpressionExperiment getTestExpressionExperimentWithAllDependencies()
```
    Add an expressionExperiment to the database for testing purposes. Includes associations.
    
    Returns:
    
    EE
  - getTestExpressionExperimentWithAllDependencies
```
public ExpressionExperiment getTestExpressionExperimentWithAllDependencies(ExpressionExperiment prototype)
```
  - getTestExpressionExperimentWithAllDependencies
```
public ExpressionExperiment getTestExpressionExperimentWithAllDependencies(boolean doSequence)
```
    Add an expressionExperiment to the database for testing purposes. Includes associations
    
    Parameters:
    
    doSequence - Should the array design get all the sequence information filled in? (true = slower)
    
    Returns:
    
    EE
  - getTestExpressionExperimentWithAnalysisAndResults
```
public ExpressionExperiment getTestExpressionExperimentWithAnalysisAndResults()
```
    Create a test EE with analysis results. The design is simple: two conditions: healthy and sick with 3 replicates Random statistics will be generated for all the probes defined in the provided ArrayDesign.
  - getTestPersistentGene
```
public Gene getTestPersistentGene()
```
    Returns:
    
    with default taxon
  - getTestPersistentGene
```
public Gene getTestPersistentGene(Taxon t)
```
  - getTestPersistentArrayDesign
```
public ArrayDesign getTestPersistentArrayDesign(int numCompositeSequences,
                                                boolean randomNames,
                                                boolean doSequence)
```
    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_probe_at....N_probe_at
    
    doSequence - If true, biosequences and biosequence2GeneProduct associations are filled in (slower).
    
    Returns:
    
    ArrayDesign
  - getTestPersistentBasicExpressionExperiment
```
public ExpressionExperiment getTestPersistentBasicExpressionExperiment()
```
  - getTestPersistentBasicExpressionExperiment
```
public ExpressionExperiment getTestPersistentBasicExpressionExperiment(ArrayDesign arrayDesign)
```
    Parameters:
    
    arrayDesign - AD
    
    Returns:
    
    A lighter-weight EE, with no data, and the ADs have no sequences.
  - getTestPersistentBibliographicReference
```
public BibliographicReference getTestPersistentBibliographicReference(String accession)
```
  - getTestPersistentBioAssay
```
public BioAssay getTestPersistentBioAssay(ArrayDesign ad)
```
  - getTestPersistentBioAssay
```
public BioAssay getTestPersistentBioAssay(ArrayDesign ad,
                                          BioMaterial bm)
```
    Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects.
    
    Parameters:
    
    ad - AD
    
    bm - BM
    
    Returns:
    
    BA
  - getTestPersistentBioMaterial
```
public BioMaterial getTestPersistentBioMaterial()
```
  - getTestPersistentBioMaterial
```
public BioMaterial getTestPersistentBioMaterial(Taxon tax)
```
  - getTestPersistentBioSequence
```
public BioSequence getTestPersistentBioSequence()
```
  - getTestPersistentBioSequence
```
public BioSequence getTestPersistentBioSequence(Taxon taxon)
```
  - getTestPersistentBioSequence2GeneProducts
```
public Set<BioSequence2GeneProduct> getTestPersistentBioSequence2GeneProducts(BioSequence bioSequence)
```
    Parameters:
    
    bioSequence - bio sequence
    
    Returns:
    
    bio sequence to gene products
  - getTestPersistentBlatResult
```
public BlatResult getTestPersistentBlatResult(BioSequence querySequence,
                                              Taxon taxon)
```
  - getTestPersistentContact
```
public Contact getTestPersistentContact()
```
    Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
    
    Returns:
    
    contact
  - getTestPersistentDatabaseEntry
```
public DatabaseEntry getTestPersistentDatabaseEntry(ExternalDatabase ed)
```
    Convenience method to provide a DatabaseEntry that can be used to fill non-nullable associations in test objects. The accession is set to a random string
    
    Parameters:
    
    ed - ED
    
    Returns:
    
    db entry
  - getTestPersistentDatabaseEntry
```
public DatabaseEntry getTestPersistentDatabaseEntry(String accession,
                                                    ExternalDatabase ed)
```
    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 - ED
    
    accession - accession
    
    Returns:
    
    db entry
  - getTestPersistentDatabaseEntry
```
public DatabaseEntry getTestPersistentDatabaseEntry(String accession,
                                                    String databaseName)
```
    Parameters:
    
    databaseName - GEO or PubMed (others could be supported)
    
    accession - accession
    
    Returns:
    
    db entry
  - getTestPersistentExpressionExperiment
```
public ExpressionExperiment getTestPersistentExpressionExperiment()
```
    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
```
public ExpressionExperiment getTestPersistentExpressionExperiment(Taxon taxon)
```
    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 - the experiment will have this taxon
    
    Returns:
    
    EE
  - getTestPersistentGeneProduct
```
public GeneProduct getTestPersistentGeneProduct(Gene gene)
```
  - getTestPersistentQuantitationType
```
public QuantitationType getTestPersistentQuantitationType()
```
    Convenience method to provide a QuantitationType that can be used to fill non-nullable associations in test objects.
    
    Returns:
    
    QT
  - getTestPersistentTaxon
```
public Taxon getTestPersistentTaxon()
```
  - resetTestElementCollectionSize
```
public void resetTestElementCollectionSize()
```
  - getFactorValues
```
protected Set<FactorValue> getFactorValues(ExperimentalFactor ef,
                                           Collection<FactorValue> allFactorValues)
```
  - getTestCharacteristic
```
protected Characteristic getTestCharacteristic(String name,
                                               String value)
```
  - getTestStatement
```
protected Statement getTestStatement(String name,
                                     String value)
```

Class PersistentDummyObjectHelper

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

PersistentDummyObjectHelper

Method Detail

resetSeed

getTestNonPersistentBioSequence

getTestNonPersistentGeneProduct

getTestNonPersistentQuantitationType

addTestAnalyses

getExperimentalDesign

getExperimentalFactors

getFactorValues

getTestElementCollectionSize

setTestElementCollectionSize

getTestExpressionExperimentWithAllDependencies

getTestExpressionExperimentWithAllDependencies

getTestExpressionExperimentWithAllDependencies

getTestExpressionExperimentWithAnalysisAndResults

getTestPersistentGene

getTestPersistentGene

getTestPersistentArrayDesign

getTestPersistentBasicExpressionExperiment

getTestPersistentBasicExpressionExperiment

getTestPersistentBibliographicReference

getTestPersistentBioAssay

getTestPersistentBioAssay

getTestPersistentBioMaterial

getTestPersistentBioMaterial

getTestPersistentBioSequence

getTestPersistentBioSequence

getTestPersistentBioSequence2GeneProducts

getTestPersistentBlatResult

getTestPersistentContact

getTestPersistentDatabaseEntry

getTestPersistentDatabaseEntry

getTestPersistentDatabaseEntry

getTestPersistentExpressionExperiment

getTestPersistentExpressionExperiment

getTestPersistentGeneProduct

getTestPersistentQuantitationType

getTestPersistentTaxon

resetTestElementCollectionSize

getFactorValues

getTestCharacteristic

getTestStatement