Example usage for org.apache.commons.lang RandomStringUtils randomNumeric

Introduction

In this page you can find the example usage for org.apache.commons.lang RandomStringUtils randomNumeric.

Prototype

public static String randomNumeric(int count)

Source Link

Document

Creates a random string whose length is the number of characters specified.

Characters will be chosen from the set of numeric characters.

Usage

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * @param ee/*from  www  .  ja  v  a  2s  .c  o m*/
 */
public void addTestAnalyses(ExpressionExperiment ee) {
    /*
     * Add analyses
     */
    ProbeCoexpressionAnalysis pca = ProbeCoexpressionAnalysis.Factory.newInstance();
    pca.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH));

    pca.setExperimentAnalyzed(ee);

    persisterHelper.persist(pca);

    /*
     * Diff
     */
    DifferentialExpressionAnalysis expressionAnalysis = DifferentialExpressionAnalysis.Factory.newInstance();
    Protocol protocol = Protocol.Factory.newInstance();
    protocol.setName("Differential expression analysis settings");
    protocol.setDescription("qvalue: " + true);
    expressionAnalysis.setProtocol(protocol);
    expressionAnalysis.setExperimentAnalyzed(ee);

    persisterHelper.persist(expressionAnalysis);
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * @return//from w ww . j ava  2s  .  c  o  m
 */
public Gene getTestPeristentGene(Taxon t) {
    Gene gene = Gene.Factory.newInstance();
    gene.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_test");
    gene.setOfficialName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_test");
    gene.setOfficialSymbol(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH).toUpperCase());

    if (t == null) {
        gene.setTaxon(this.getTestNonPersistentTaxon());
    } else {
        gene.setTaxon(t);
    }

    GeneProduct gp = GeneProduct.Factory.newInstance();
    gp.setGene(gene);
    gp.setName(RandomStringUtils.randomNumeric(5) + "_test");
    gene.getProducts().add(gp);
    return (Gene) persisterHelper.persist(gene);
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * Convenience method to provide an ArrayDesign that can be used to fill non-nullable associations in test objects.
 * The ArrayDesign is provided with some CompositeSequenece DesignElements if desired. If composite seequences are
 * created, they are each associated with a single generated Reporter.
 * //  w  w w . j a va2s .c o m
 * @param numCompositeSequences The number of CompositeSequences to populate the ArrayDesign with.
 * @param randomNames If true, probe names will be random strings; otherwise they will be 0_probe_at....N_probe_at
 * @param dosequence If true, biosequences and biosequence2GeneProduct associations are filled in (slower).
 * @return ArrayDesign
 */
public ArrayDesign getTestPersistentArrayDesign(int numCompositeSequences, boolean randomNames,
        boolean dosequence) {
    ArrayDesign ad = ArrayDesign.Factory.newInstance();

    ad.setName("arrayDesign_" + RandomStringUtils.randomAlphabetic(RANDOM_STRING_LENGTH));
    ad.setShortName("AD_" + RandomStringUtils.randomAlphabetic(5));
    ad.setTechnologyType(TechnologyType.ONECOLOR);

    ad.setPrimaryTaxon(this.getTestPersistentTaxon());

    for (int i = 0; i < numCompositeSequences; i++) {

        // Reporter reporter = Reporter.Factory.newInstance();
        CompositeSequence compositeSequence = CompositeSequence.Factory.newInstance();

        if (randomNames) {
            compositeSequence.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testcs");
        } else {
            compositeSequence.setName("probeset_" + i);
        }

        // compositeSequence.getComponentReporters().add( reporter );
        compositeSequence.setArrayDesign(ad);
        ad.getCompositeSequences().add(compositeSequence);

        if (dosequence) {
            BioSequence bioSequence = getTestPersistentBioSequence();
            compositeSequence.setBiologicalCharacteristic(bioSequence);
            bioSequence.setBioSequence2GeneProduct(this.getTestPersistentBioSequence2GeneProducts(bioSequence));
        }
    }

    for (CompositeSequence cs : ad.getCompositeSequences()) {
        cs.setArrayDesign(ad);
    }
    assert (ad.getCompositeSequences().size() == numCompositeSequences);

    return (ArrayDesign) persisterHelper.persist(ad);
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * @param ad//from   w  w  w.  jav a  2 s. c o m
 * @param bm
 * @return
 */
private BioAssay getTestNonPersistentBioAssay(ArrayDesign ad, BioMaterial bm) {
    BioAssay ba = ubic.gemma.model.expression.bioAssay.BioAssay.Factory.newInstance();
    ba.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testbioassay");
    ba.setSampleUsed(bm);
    ba.setArrayDesignUsed(ad);
    ba.setIsOutlier(false);
    ba.setSequencePairedReads(false);
    DatabaseEntry de = DatabaseEntry.Factory.newInstance();

    de.setExternalDatabase(this.geo);
    de.setAccession(ba.getName());
    ba.setAccession(de);

    LocalFile file = LocalFile.Factory.newInstance();
    try {
        file.setLocalURL(new URL("file:///tmp/" + ba.getName()));
    } catch (MalformedURLException e) {
    }
    ba.setRawDataFile(file);

    LocalFile fileb = LocalFile.Factory.newInstance();
    try {
        fileb.setLocalURL(new URL("file:///tmp/raw" + ba.getName()));
    } catch (MalformedURLException e) {
    }
    ba.setRawDataFile(file);

    ba.getDerivedDataFiles().add(fileb);

    return ba;
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * Slightly misleading, associations are persistent.
 * /*from w  w  w. jav a  2 s . co m*/
 * @return
 */
private BioMaterial getTestNonPersistentBioMaterial() {
    BioMaterial bm = BioMaterial.Factory.newInstance();
    bm.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testbiomaterial");
    if (geo == null) {
        geo = externalDatabaseService.find("GEO");
        assert geo != null;
    }
    bm.setSourceTaxon(getTestNonPersistentTaxon());
    bm.setExternalAccession(this.getTestPersistentDatabaseEntry(geo));
    return bm;
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * Slightly misleading, associations are persistent.
 * //from  w  w w .  ja v a 2s  .c om
 * @return
 */
private BioMaterial getTestNonPersistentBioMaterial(Taxon tax) {
    BioMaterial bm = BioMaterial.Factory.newInstance();
    bm.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testbiomaterial");
    if (geo == null) {
        geo = externalDatabaseService.find("GEO");
        assert geo != null;
    }
    bm.setSourceTaxon(tax);
    bm.setExternalAccession(this.getTestPersistentDatabaseEntry(geo));
    return bm;
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * @return/* ww w  . j a  v a2  s.c o m*/
 */
public BioSequence getTestNonPersistentBioSequence() {
    BioSequence bs = BioSequence.Factory.newInstance();
    bs.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testbiosequence");
    bs.setSequence(RandomStringUtils.random(40, "ATCG"));
    bs.setTaxon(getTestNonPersistentTaxon());

    if (this.genbank == null) {
        genbank = ExternalDatabase.Factory.newInstance();
        genbank.setName("Genbank");
    }

    DatabaseEntry de = DatabaseEntry.Factory.newInstance();

    de.setExternalDatabase(this.genbank);
    de.setAccession(RandomStringUtils.randomAlphanumeric(10));

    bs.setSequenceDatabaseEntry(de);
    return bs;
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * Convenience method to provide a Contact that can be used to fill non-nullable associations in test objects.
 * //from w  w w  .  ja v a 2s  . co  m
 * @return
 */
public Contact getTestPersistentContact() {
    Contact c = Contact.Factory.newInstance();
    c.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testcontact");
    c.setEmail(c.getName() + "@foo.org");
    c = (Contact) persisterHelper.persist(c);
    return c;
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * 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.
 * /* w  w w.ja v  a  2 s  . co  m*/
 * @return
 */
public DatabaseEntry getTestPersistentDatabaseEntry(String accession, ExternalDatabase ed) {
    DatabaseEntry result = DatabaseEntry.Factory.newInstance();

    if (accession == null) {
        result.setAccession(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testaccession");
    } else {
        result.setAccession(accession);
    }

    if (ed == null) {
        ed = ExternalDatabase.Factory.newInstance();
        ed.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testdb");
        ed = (ExternalDatabase) persisterHelper.persist(ed);
    }

    result.setExternalDatabase(ed);
    return result;
}

From source file:ubic.gemma.testing.PersistentDummyObjectHelper.java

/**
 * 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.
 * /*from w  ww.j a v a  2 s  . c  o m*/
 * @return
 */
public ExpressionExperiment getTestPersistentExpressionExperiment() {
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setName(RandomStringUtils.randomNumeric(RANDOM_STRING_LENGTH) + "_testee");
    ee = (ExpressionExperiment) persisterHelper.persist(ee);
    return ee;
}