Examples with CompositeSequence ubic.gemma.model.expression.designElement.CompositeSequence used on opensource projects

Example 11 with CompositeSequence

use of ubic.gemma.model.expression.designElement.CompositeSequence in project Gemma by PavlidisLab.

the class AclAuthorizationTest method setup.

@Before
public void setup() {
    arrayDesign = ArrayDesign.Factory.newInstance();
    arrayDesign.setName(arrayDesignName);
    arrayDesign.setShortName(arrayDesignName);
    arrayDesign.setDescription("A test ArrayDesign from " + this.getClass().getName());
    arrayDesign.setPrimaryTaxon(this.getTaxon("mouse"));
    CompositeSequence cs1 = CompositeSequence.Factory.newInstance();
    cs1.setName(compositeSequenceName1);
    CompositeSequence cs2 = CompositeSequence.Factory.newInstance();
    cs2.setName(compositeSequenceName2);
    Collection<CompositeSequence> col = new HashSet<>();
    col.add(cs1);
    col.add(cs2);
    cs1.setArrayDesign(arrayDesign);
    cs2.setArrayDesign(arrayDesign);
    arrayDesign.setCompositeSequences(col);
    // persister helper
    arrayDesign = (ArrayDesign) persisterHelper.persist(arrayDesign);
    try {
        userManager.loadUserByUsername(aDifferentUsername);
    } catch (UsernameNotFoundException e) {
        userManager.createUser(new UserDetailsImpl("foo", aDifferentUsername, true, null, RandomStringUtils.randomAlphabetic(10) + "@gmail.com", "key", new Date()));
    }
}

Example 12 with CompositeSequence

use of ubic.gemma.model.expression.designElement.CompositeSequence in project Gemma by PavlidisLab.

the class CompositeSequenceGeneMapperServiceTest method testGetCompositeSequencesByGeneId.

/**
 * Tests finding the composite sequences for a given gene id.
 */
@Test
public void testGetCompositeSequencesByGeneId() {
    Collection<Gene> genes = geneService.findByOfficialSymbol(geneOfficialSymbol);
    if (genes == null || genes.isEmpty())
        return;
    Gene g = genes.iterator().next();
    Collection<CompositeSequence> compositeSequences = geneService.getCompositeSequencesById(g.getId());
    assertNotNull(compositeSequences);
    assertEquals(compositeSequences.size(), 1);
    assertEquals((compositeSequences.iterator().next()).getName(), csName);
}

Example 13 with CompositeSequence

use of ubic.gemma.model.expression.designElement.CompositeSequence in project Gemma by PavlidisLab.

the class ExpressionDataDoubleMatrixTest method testConstructExpressionDataDoubleMatrixWithGeoValues.

/**
 * This is a self-contained test. That is, it does not depend on the setup in onSetUpInTransaction}. It tests
 * creating an {@link ExpressionDataDoubleMatrix} using real values from the Gene Expression Omnibus (GEO). That is,
 * we have obtained information from GSE994. The probe sets used are 218120_s_at and 121_at, and the samples used
 * are GSM15697 and GSM15744. Specifically, we the Gemma objects that correspond to the GEO objects are:
 * DesignElement 1 = 218120_s_at, DesignElement 2 = 121_at
 * BioAssay 1 = "Current Smoker 73", BioAssay 2 = "Former Smoker 34"
 * BioMaterial 1 = "GSM15697", BioMaterial 2 = "GSM15744"
 * BioAssayDimension = "GSM15697, GSM15744" (the names of all the biomaterials).
 */
@Test
public void testConstructExpressionDataDoubleMatrixWithGeoValues() {
    ByteArrayConverter bac = new ByteArrayConverter();
    ee = ExpressionExperiment.Factory.newInstance();
    QuantitationType qt = QuantitationType.Factory.newInstance();
    qt.setName("VALUE");
    qt.setIsBackgroundSubtracted(false);
    qt.setIsNormalized(false);
    qt.setIsBackground(false);
    qt.setIsRatio(false);
    qt.setIsPreferred(true);
    qt.setIsMaskedPreferred(false);
    qt.setRepresentation(PrimitiveType.DOUBLE);
    BioAssayDimension bioAssayDimension = BioAssayDimension.Factory.newInstance();
    bioAssayDimension.setName("GSM15697, GSM15744");
    List<BioAssay> assays = new ArrayList<>();
    BioAssay assay1 = BioAssay.Factory.newInstance();
    assay1.setName("Current Smoker 73");
    BioMaterial sample1 = BioMaterial.Factory.newInstance();
    sample1.setName("GSM15697");
    assay1.setSampleUsed(sample1);
    assays.add(assay1);
    BioAssay assay2 = BioAssay.Factory.newInstance();
    assay2.setName("Former Smoker 34");
    BioMaterial sample2 = BioMaterial.Factory.newInstance();
    sample2.setName("GSM15744");
    assay2.setSampleUsed(sample2);
    assays.add(assay2);
    bioAssayDimension.setBioAssays(assays);
    RawExpressionDataVector vector1 = RawExpressionDataVector.Factory.newInstance();
    double[] ddata1 = { 74.9, 101.7 };
    byte[] bdata1 = bac.doubleArrayToBytes(ddata1);
    vector1.setData(bdata1);
    vector1.setQuantitationType(qt);
    vector1.setBioAssayDimension(bioAssayDimension);
    RawExpressionDataVector vector2 = RawExpressionDataVector.Factory.newInstance();
    double[] ddata2 = { 404.6, 318.7 };
    byte[] bdata2 = bac.doubleArrayToBytes(ddata2);
    vector2.setData(bdata2);
    vector2.setQuantitationType(qt);
    vector2.setBioAssayDimension(bioAssayDimension);
    ArrayDesign ad = ArrayDesign.Factory.newInstance();
    ad.setName("test ar");
    CompositeSequence de1 = CompositeSequence.Factory.newInstance();
    de1.setName("218120_s_at");
    vector1.setDesignElement(de1);
    BioSequence bs1 = BioSequence.Factory.newInstance();
    bs1.setName("test1");
    de1.setBiologicalCharacteristic(bs1);
    de1.setArrayDesign(ad);
    CompositeSequence de2 = CompositeSequence.Factory.newInstance();
    de2.setName("121_at");
    BioSequence bs2 = BioSequence.Factory.newInstance();
    bs2.setName("test2");
    de2.setBiologicalCharacteristic(bs2);
    de2.setArrayDesign(ad);
    vector2.setDesignElement(de2);
    Collection<RawExpressionDataVector> eeVectors = new LinkedHashSet<>();
    eeVectors.add(vector1);
    eeVectors.add(vector2);
    ee.setRawExpressionDataVectors(eeVectors);
    ExpressionDataDoubleMatrix expressionDataMatrix = new ExpressionDataDoubleMatrix(eeVectors);
    assertNotNull(expressionDataMatrix);
    assertEquals(expressionDataMatrix.rows(), 2);
    assertEquals(expressionDataMatrix.columns(), 2);
}

Example 14 with CompositeSequence

use of ubic.gemma.model.expression.designElement.CompositeSequence in project Gemma by PavlidisLab.

the class DataUpdaterTest method testAddData.

@Test
public void testAddData() throws Exception {
    /*
         * Load a regular data set that has no data. Platform is (basically) irrelevant.
         */
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
    ExpressionExperiment ee;
    try {
        // RNA-seq data.
        Collection<?> results = geoService.fetchAndLoad("GSE37646", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        // log.warn( "Test skipped because GSE37646 was not removed from the system prior to test" );
        ee = (ExpressionExperiment) ((List<?>) e.getData()).get(0);
    }
    ee = experimentService.thawLite(ee);
    List<BioAssay> bioAssays = new ArrayList<>(ee.getBioAssays());
    assertEquals(31, bioAssays.size());
    List<BioMaterial> bms = new ArrayList<>();
    for (BioAssay ba : bioAssays) {
        bms.add(ba.getSampleUsed());
    }
    targetArrayDesign = this.getTestPersistentArrayDesign(100, true);
    DoubleMatrix<CompositeSequence, BioMaterial> rawMatrix = new DenseDoubleMatrix<>(targetArrayDesign.getCompositeSequences().size(), bms.size());
    /*
         * make up some fake data on another platform, and match it to those samples
         */
    for (int i = 0; i < rawMatrix.rows(); i++) {
        for (int j = 0; j < rawMatrix.columns(); j++) {
            rawMatrix.set(i, j, (i + 1) * (j + 1) * Math.random() / 100.0);
        }
    }
    List<CompositeSequence> probes = new ArrayList<>(targetArrayDesign.getCompositeSequences());
    rawMatrix.setRowNames(probes);
    rawMatrix.setColumnNames(bms);
    QuantitationType qt = this.makeQt(true);
    ExpressionDataDoubleMatrix data = new ExpressionDataDoubleMatrix(ee, qt, rawMatrix);
    assertNotNull(data.getBestBioAssayDimension());
    assertEquals(rawMatrix.columns(), data.getBestBioAssayDimension().getBioAssays().size());
    assertEquals(probes.size(), data.getMatrix().rows());
    /*
         * Replace it.
         */
    ee = dataUpdater.replaceData(ee, targetArrayDesign, data);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    ee = experimentService.thaw(ee);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    assertEquals(100, ee.getRawExpressionDataVectors().size());
    for (RawExpressionDataVector v : ee.getRawExpressionDataVectors()) {
        assertTrue(v.getQuantitationType().getIsPreferred());
    }
    assertEquals(100, ee.getProcessedExpressionDataVectors().size());
    Collection<DoubleVectorValueObject> processedDataArrays = dataVectorService.getProcessedDataArrays(ee);
    for (DoubleVectorValueObject v : processedDataArrays) {
        assertEquals(31, v.getBioAssays().size());
    }
    /*
         * Test adding data (non-preferred)
         */
    qt = this.makeQt(false);
    ExpressionDataDoubleMatrix moreData = new ExpressionDataDoubleMatrix(ee, qt, rawMatrix);
    ee = dataUpdater.addData(ee, targetArrayDesign, moreData);
    ee = experimentService.thaw(ee);
    try {
        // add preferred data twice.
        dataUpdater.addData(ee, targetArrayDesign, data);
        fail("Should have gotten an exception");
    } catch (IllegalArgumentException e) {
    // okay.
    }
    dataUpdater.deleteData(ee, qt);
}

Example 15 with CompositeSequence

use of ubic.gemma.model.expression.designElement.CompositeSequence in project Gemma by PavlidisLab.

the class AffyProbeReaderTest method testReadInputStream.

/*
     * Class under test for Map read(InputStream)
     */
public final void testReadInputStream() throws Exception {
    is = AffyProbeReaderTest.class.getResourceAsStream("/data/loader/affymetrix-probes-test.txt");
    apr.setSequenceField(5);
    apr.parse(is);
    // 10
    String expectedValue = "GCCCCCGTGAGGATGTCACTCAGAT";
    CompositeSequence cs = this.getProbeMatchingName("1004_at");
    TestCase.assertNotNull("CompositeSequence was null", cs);
    boolean foundIt = false;
    for (Reporter element : apr.get(cs)) {
        if (element.getName().equals("1004_at#2:557:275")) {
            String actualValue = element.getImmobilizedCharacteristic().getSequence();
            TestCase.assertEquals(expectedValue, actualValue);
            foundIt = true;
            break;
        }
    }
    TestCase.assertTrue("Didn't find the probe ", foundIt);
}