Examples with RawExpressionDataVector ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector used on opensource projects

Example 1 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestExpressionExperimentWithAllDependencies.

public ExpressionExperiment getTestExpressionExperimentWithAllDependencies(ExpressionExperiment prototype) {
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setShortName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setName("Expression Experiment " + RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setDescription("A test expression experiment");
    ee.setSource("https://www.ncbi.nlm.nih.gov/geo/");
    DatabaseEntry de1 = this.getTestPersistentDatabaseEntry(PersistentDummyObjectHelper.geo);
    ee.setAccession(de1);
    LocalFile file = LocalFile.Factory.newInstance();
    try {
        file.setLocalURL(new URL("file:///just/a/placeholder/" + ee.getShortName()));
    } catch (MalformedURLException e) {
        log.error("Malformed URL");
    }
    ee.setRawDataFile(file);
    Collection<FactorValue> allFactorValues = new HashSet<>();
    ExperimentalDesign ed = this.getExperimentalDesign(allFactorValues);
    Collection<BioMaterial> bioMaterials = this.getBioMaterials(allFactorValues);
    ee.setExperimentalDesign(ed);
    ee.setOwner(this.getTestPersistentContact());
    List<ArrayDesign> arrayDesignsUsed = new ArrayList<>(eeService.getArrayDesignsUsed(prototype));
    Collection<BioAssay> bioAssays = new HashSet<>();
    Collection<QuantitationType> quantitationTypes = this.addQuantitationTypes(new HashSet<QuantitationType>());
    eeService.thaw(prototype);
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    for (ArrayDesign ad : arrayDesignsUsed) {
        List<BioAssay> bas = this.getBioAssays(bioMaterials, ad);
        bioAssays.addAll(bas);
        ad = this.adService.thaw(ad);
        vectors.addAll(this.getDesignElementDataVectors(ee, quantitationTypes, bas, ad));
    }
    ee.setBioAssays(bioAssays);
    assert quantitationTypes.size() > 0;
    ee.setQuantitationTypes(quantitationTypes);
    ee.setRawExpressionDataVectors(vectors);
    ArrayDesignsForExperimentCache c = persisterHelper.prepare(ee);
    ee = persisterHelper.persist(ee, c);
    return ee;
}

Example 2 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getDesignElementDataVectors.

/**
 * @param bioAssays         BAs
 * @param ad                AD
 * @param ee                EE
 * @param quantitationTypes QTs
 * @return These are non-persistent
 */
private Collection<RawExpressionDataVector> getDesignElementDataVectors(ExpressionExperiment ee, Collection<QuantitationType> quantitationTypes, List<BioAssay> bioAssays, ArrayDesign ad) {
    BioAssayDimension baDim = BioAssayDimension.Factory.newInstance(ee.getShortName() + "_" + RandomStringUtils.randomAlphanumeric(20), null, bioAssays);
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    for (QuantitationType quantType : quantitationTypes) {
        for (CompositeSequence cs : ad.getCompositeSequences()) {
            RawExpressionDataVector vector = RawExpressionDataVector.Factory.newInstance();
            byte[] bdata = this.getDoubleData();
            vector.setData(bdata);
            vector.setDesignElement(cs);
            assert cs.getArrayDesign() != null;
            vector.setExpressionExperiment(ee);
            vector.setQuantitationType(quantType);
            vector.setBioAssayDimension(baDim);
            vectors.add(vector);
        }
    }
    return vectors;
}

Example 3 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestExpressionExperimentWithAllDependencies.

/**
 * Add an expressionExperiment to the database for testing purposes. Includes associations
 *
 * @param doSequence Should the array design get all the sequence information filled in? (true = slower)
 * @return EE
 */
public ExpressionExperiment getTestExpressionExperimentWithAllDependencies(boolean doSequence) {
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setShortName(RandomStringUtils.randomAlphanumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setName("Expression Experiment " + RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setDescription("A test expression experiment");
    ee.setSource("https://www.ncbi.nlm.nih.gov/geo/");
    DatabaseEntry de1 = this.getTestPersistentDatabaseEntry(PersistentDummyObjectHelper.geo);
    ee.setAccession(de1);
    LocalFile file = LocalFile.Factory.newInstance();
    try {
        file.setLocalURL(new URL("file:///just/a/placeholder/" + ee.getShortName()));
    } catch (MalformedURLException e) {
        log.error("Malformed URL");
    }
    ee.setRawDataFile(file);
    ArrayDesign adA = this.getTestPersistentArrayDesign(this.getTestElementCollectionSize(), false, doSequence);
    ArrayDesign adB = this.getTestPersistentArrayDesign(this.getTestElementCollectionSize(), false, doSequence);
    Collection<FactorValue> allFactorValues = new HashSet<>();
    ExperimentalDesign ed = this.getExperimentalDesign(allFactorValues);
    ee.setExperimentalDesign(ed);
    ee.setOwner(this.getTestPersistentContact());
    Collection<BioAssay> bioAssays = new HashSet<>();
    Collection<BioMaterial> bioMaterials = this.getBioMaterials(allFactorValues);
    List<BioAssay> bioAssaysA = this.getBioAssays(bioMaterials, adA);
    List<BioAssay> bioAssaysB = this.getBioAssays(bioMaterials, adB);
    bioAssays.addAll(bioAssaysA);
    bioAssays.addAll(bioAssaysB);
    ee.setBioAssays(bioAssays);
    log.debug("expression experiment => design element data vectors");
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    Collection<QuantitationType> quantitationTypes = this.addQuantitationTypes(new HashSet<QuantitationType>());
    assert quantitationTypes.size() > 0;
    vectors.addAll(this.getDesignElementDataVectors(ee, quantitationTypes, bioAssaysA, adA));
    vectors.addAll(this.getDesignElementDataVectors(ee, quantitationTypes, bioAssaysB, adB));
    ee.setQuantitationTypes(quantitationTypes);
    ee.setRawExpressionDataVectors(vectors);
    ArrayDesignsForExperimentCache c = persisterHelper.prepare(ee);
    ee = persisterHelper.persist(ee, c);
    return ee;
}

Example 4 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector in project Gemma by PavlidisLab.

the class TwoChannelMissingValueTaskImpl method execute.

@Override
public TaskResult execute() {
    ExpressionExperiment ee = taskCommand.getExpressionExperiment();
    Collection<RawExpressionDataVector> missingValueVectors = twoChannelMissingValues.computeMissingValues(ee, taskCommand.getS2n(), taskCommand.getExtraMissingValueIndicators());
    System.out.println("MVs: " + missingValueVectors.size());
    return new TaskResult(taskCommand, missingValueVectors.size());
}

Example 5 with RawExpressionDataVector

use of ubic.gemma.model.expression.bioAssayData.RawExpressionDataVector 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);
}