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

Example 86 with Taxon

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

the class TaxonUtilityTest method testIsHuman.

@Test
public void testIsHuman() {
    Taxon humanTax = taxonService.findByCommonName("human");
    assertTrue(TaxonUtility.isHuman(humanTax));
}

Example 87 with Taxon

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

the class TaxonUtilityTest method testIsMouse.

@Test
public void testIsMouse() {
    Taxon mouseTax = taxonService.findByCommonName("mouse");
    assertTrue(TaxonUtility.isMouse(mouseTax));
}

Example 88 with Taxon

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

the class TaxonUtilityTest method testIsRat.

@Test
public void testIsRat() {
    Taxon ratTax = taxonService.findByCommonName("rat");
    assertTrue(TaxonUtility.isRat(ratTax));
}

Example 89 with Taxon

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

the class ExperimentalDesignImporterTestB method setup.

@Before
public void setup() throws Exception {
    super.executeSqlScript("/script/sql/add-fish-taxa.sql", false);
    SimpleExpressionExperimentMetaData metaData = new SimpleExpressionExperimentMetaData();
    Taxon salmon = taxonService.findByCommonName("salmonid");
    // doesn't matter what it is for this test, but the test data are from salmon.
    assertNotNull(salmon);
    metaData.setShortName(RandomStringUtils.randomAlphabetic(10));
    metaData.setDescription("bar");
    metaData.setIsRatio(false);
    metaData.setTaxon(salmon);
    metaData.setQuantitationTypeName("value");
    metaData.setScale(ScaleType.LOG2);
    metaData.setType(StandardQuantitationType.AMOUNT);
    ArrayDesign ad = ArrayDesign.Factory.newInstance();
    ad.setShortName(this.randomName());
    ad.setTechnologyType(TechnologyType.ONECOLOR);
    ad.setName("foobly foo");
    ad.setPrimaryTaxon(salmon);
    metaData.getArrayDesigns().add(ad);
    try (InputStream data = this.getClass().getResourceAsStream("/data/loader/expression/head.Gill2007gemmaExpressionData.txt")) {
        ee = simpleExpressionDataLoaderService.create(metaData, data);
    }
}

Example 90 with Taxon

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

the class SimpleExpressionDataLoaderServiceTest method testLoadB.

@Test
public final void testLoadB() throws Exception {
    Taxon taxon = this.getTaxon("mouse");
    SimpleExpressionExperimentMetaData metaData = new SimpleExpressionExperimentMetaData();
    ArrayDesign ad = ArrayDesign.Factory.newInstance();
    ad.setShortName(RandomStringUtils.randomAlphabetic(5));
    ad.setName(RandomStringUtils.randomAlphabetic(5));
    ad.setPrimaryTaxon(taxon);
    ad.setTechnologyType(TechnologyType.ONECOLOR);
    Collection<ArrayDesign> ads = new HashSet<>();
    ads.add(ad);
    metaData.setArrayDesigns(ads);
    metaData.setTaxon(taxon);
    metaData.setName(RandomStringUtils.randomAlphabetic(5));
    metaData.setShortName(metaData.getName());
    metaData.setDescription("Simple expression data loader service test - load B");
    metaData.setQuantitationTypeName("testing");
    metaData.setGeneralType(GeneralType.QUANTITATIVE);
    metaData.setScale(ScaleType.LOG2);
    metaData.setType(StandardQuantitationType.AMOUNT);
    metaData.setIsRatio(true);
    try (InputStream data = this.getClass().getResourceAsStream("/data/loader/aov.results-2-monocyte-data-bytime.bypat.data.sort")) {
        ee = service.create(metaData, data);
    }
    ee = eeService.thaw(ee);
    assertNotNull(ee);
    assertEquals(200, ee.getRawExpressionDataVectors().size());
    assertEquals(59, ee.getBioAssays().size());
// 
}