Examples with Taxon ubic.gemma.model.genome.Taxon used on opensource projects

Example 41 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class GeneServiceTest method testFindByAccessionOther.

@Test
public void testFindByAccessionOther() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    ExternalDatabase ensembl = edbs.findByName("Ensembl");
    DatabaseEntry dbe = DatabaseEntry.Factory.newInstance();
    dbe.setAccession("E129458");
    dbe.setExternalDatabase(ensembl);
    gene.getAccessions().add(dbe);
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    geneDao.create(gene);
    Gene g = geneDao.findByAccession("E129458", ensembl);
    assertNotNull(g);
    assertEquals(g, gene);
    geneDao.remove(gene);
}

Example 42 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class GeneServiceTest method testFindEvenThoughHaveSameSymbol.

@Test
public void testFindEvenThoughHaveSameSymbol() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    gene.setOfficialName(GeneServiceTest.TEST_GENE_NAME);
    gene.setOfficialSymbol(GeneServiceTest.TEST_GENE_NAME);
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    PhysicalLocation pl1 = PhysicalLocation.Factory.newInstance();
    Chromosome chromosome = new Chromosome("X", null, this.getTestPersistentBioSequence(), human);
    chromosome = (Chromosome) persisterHelper.persist(chromosome);
    pl1.setChromosome(chromosome);
    pl1.setNucleotide(10000010L);
    pl1.setNucleotideLength(1001);
    pl1.setStrand("-");
    gene.setPhysicalLocation(pl1);
    gene = geneDao.create(gene);
    Long idWeWant = gene.getId();
    Gene gene2 = Gene.Factory.newInstance();
    gene2.setNcbiGeneId(null);
    gene2.setName(GeneServiceTest.TEST_GENE_NAME);
    gene2.setOfficialName(GeneServiceTest.TEST_GENE_NAME);
    gene2.setOfficialSymbol(GeneServiceTest.TEST_GENE_NAME);
    gene2.setTaxon(human);
    PhysicalLocation pl2 = PhysicalLocation.Factory.newInstance();
    Chromosome chromosome2 = new Chromosome("Y", null, this.getTestPersistentBioSequence(), human);
    chromosome2 = (Chromosome) persisterHelper.persist(chromosome2);
    pl2.setChromosome(chromosome2);
    pl2.setChromosome(chromosome);
    pl2.setNucleotide(10000010L);
    pl2.setNucleotideLength(1001);
    pl2.setStrand("-");
    gene2.setPhysicalLocation(pl2);
    gene2 = geneDao.create(gene2);
    gene.setId(null);
    Gene g = geneDao.find(gene);
    assertNotNull(g);
    assertEquals(idWeWant, g.getId());
    geneDao.remove(g);
    geneDao.remove(gene2);
}

Example 43 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class BlatAssociationServiceTest method testFindBioSequence.

@Test
public final void testFindBioSequence() {
    BioSequence bs = BioSequence.Factory.newInstance();
    Taxon t = Taxon.Factory.newInstance();
    // has to match what the testpersistent object is.
    t.setScientificName("Mus musculus");
    t.setIsSpecies(true);
    t.setIsGenesUsable(true);
    bs.setSequence(testSequence);
    bs.setTaxon(t);
    bs.setName(testSequenceName);
    BioSequence bsIn = this.bioSequenceService.find(bs);
    assertNotNull("Did not find " + bs, bsIn);
    Collection<BlatAssociation> res = this.blatAssociationService.find(bs);
    assertEquals("Was seeking blatresults for sequence " + testSequenceName, 1, res.size());
}

Example 44 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class ArrayDesignServiceTest method testGetTaxon.

/*
     * Test retrieving one taxa for an arraydesign where hibernate query is restricted to return just 1 taxon.
     */
@Test
public void testGetTaxon() {
    ad = (ArrayDesign) persisterHelper.persist(ad);
    Taxon tax = arrayDesignService.getTaxa(ad.getId()).iterator().next();
    assertEquals(ArrayDesignServiceTest.DEFAULT_TAXON, tax.getScientificName());
}

Example 45 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class ExpressionExperimentSetServiceTest method setUp.

@Before
public void setUp() {
    // need persistent entities so that experiment's taxon can be
    // queried from database during methods being tested
    Taxon tax1 = this.getTaxon("human");
    Taxon taxMouse = this.getTaxon("mouse");
    ee1 = this.getTestPersistentExpressionExperiment(tax1);
    ee2 = this.getTestPersistentExpressionExperiment(tax1);
    eeMouse = this.getTestPersistentExpressionExperiment(taxMouse);
    // Make experiment set
    Collection<ExpressionExperiment> ees = new HashSet<>();
    ees.add(ee1);
    ees.add(ee2);
    eeSet = ExpressionExperimentSet.Factory.newInstance();
    eeSet.setName("CreateTest");
    eeSet.setDescription("CreateDesc");
    eeSet.getExperiments().addAll(ees);
    eeSet.setTaxon(tax1);
    eeSet = expressionExperimentSetService.create(eeSet);
    eeSetAutoGen = expressionExperimentSetService.initAutomaticallyGeneratedExperimentSet(ees, tax1);
    eeSetAutoGen = expressionExperimentSetService.create(eeSetAutoGen);
}