Package ubic.gemma.core.util.test

Class PersistentDummyObjectHelper

java.lang.Object
ubic.gemma.core.util.test.PersistentDummyObjectHelper
@Component @Transactional public class PersistentDummyObjectHelper extends Object
Used to generate test data.
Author:
pavlidis

  • Constructor Details

    • PersistentDummyObjectHelper

      public PersistentDummyObjectHelper()

  • Method Details

    • setSeed

      public void setSeed(long seed)
      Set the seed to use to generate random data.

    • resetSeed

      public void resetSeed()
      Reset the seed to the default value.

    • 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

    • getTestPersistentSingleCellExpressionExperiment

      public ExpressionExperiment getTestPersistentSingleCellExpressionExperiment()

    • 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)

    • getTestPersistentBasicExpressionExperiment

      public ExpressionExperiment getTestPersistentBasicExpressionExperiment(@Nullable ArrayDesign arrayDesign, boolean includeRawQts)
      Parameters:
      arrayDesign - platform to use, if null two random platforms are generated
      includeRawQts - include two raw QTs (one being preferred)
      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:
      accession - accession
      ed - ED
      Returns:
      db entry

    • getTestPersistentDatabaseEntry

      public DatabaseEntry getTestPersistentDatabaseEntry(String accession, String databaseName)
      Parameters:
      accession - accession
      databaseName - GEO or PubMed (others could be supported)
      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)