Examples with BioAssay ubic.gemma.model.expression.bioAssay.BioAssay used on opensource projects

Example 11 with BioAssay

use of ubic.gemma.model.expression.bioAssay.BioAssay in project Gemma by PavlidisLab.

the class AclTestUtils method checkDeleteEEAcls.

/**
 * CHeck the entire entity graph of an ee for ACL deletion.
 *
 * @param ee ee
 */
public void checkDeleteEEAcls(ExpressionExperiment ee) {
    this.checkDeletedAcl(ee);
    this.checkDeletedAcl(ee.getRawDataFile());
    this.checkDeletedAcl(ee.getExperimentalDesign());
    for (ExperimentalFactor f : ee.getExperimentalDesign().getExperimentalFactors()) {
        this.checkDeletedAcl(f);
        for (FactorValue fv : f.getFactorValues()) {
            this.checkDeletedAcl(fv);
        }
    }
    assertTrue(ee.getBioAssays().size() > 0);
    for (BioAssay ba : ee.getBioAssays()) {
        this.checkDeletedAcl(ba);
        LocalFile rawDataFile = ba.getRawDataFile();
        for (LocalFile f : ba.getDerivedDataFiles()) {
            this.checkDeletedAcl(f);
        }
        if (rawDataFile != null) {
            this.checkDeletedAcl(rawDataFile);
        }
        BioMaterial bm = ba.getSampleUsed();
        this.checkDeletedAcl(bm);
    }
}

Example 12 with BioAssay

use of ubic.gemma.model.expression.bioAssay.BioAssay in project Gemma by PavlidisLab.

the class AclTestUtils method checkEEAcls.

/**
 * Validate ACLs on EE
 *
 * @param ee ee
 */
public void checkEEAcls(ExpressionExperiment ee) {
    ee = expressionExperimentService.thawLite(ee);
    this.checkHasAcl(ee);
    this.checkHasAces(ee);
    ExperimentalDesign experimentalDesign = ee.getExperimentalDesign();
    this.checkHasAcl(experimentalDesign);
    this.checkHasAclParent(experimentalDesign, ee);
    this.checkLacksAces(experimentalDesign);
    if (ee.getRawDataFile() != null) {
        this.checkHasAcl(ee.getRawDataFile());
        this.checkHasAclParent(ee.getRawDataFile(), ee);
        this.checkLacksAces(ee.getRawDataFile());
    }
    for (ExperimentalFactor f : experimentalDesign.getExperimentalFactors()) {
        this.checkHasAcl(f);
        this.checkHasAclParent(f, ee);
        this.checkLacksAces(f);
        for (FactorValue fv : f.getFactorValues()) {
            this.checkHasAcl(fv);
            this.checkHasAclParent(fv, ee);
            this.checkLacksAces(fv);
        }
    }
    // make sure ACLs for the child objects are there
    assertTrue(ee.getBioAssays().size() > 0);
    for (BioAssay ba : ee.getBioAssays()) {
        this.checkHasAcl(ba);
        this.checkHasAclParent(ba, ee);
        this.checkLacksAces(ba);
        LocalFile rawDataFile = ba.getRawDataFile();
        if (rawDataFile != null) {
            this.checkHasAcl(rawDataFile);
            this.checkHasAclParent(rawDataFile, null);
            this.checkLacksAces(rawDataFile);
        }
        for (LocalFile f : ba.getDerivedDataFiles()) {
            this.checkHasAcl(f);
            this.checkHasAclParent(f, null);
            this.checkLacksAces(f);
        }
        BioMaterial bm = ba.getSampleUsed();
        this.checkHasAcl(bm);
        this.checkHasAclParent(bm, ee);
        this.checkLacksAces(bm);
        ArrayDesign arrayDesign = ba.getArrayDesignUsed();
        this.checkHasAcl(arrayDesign);
        assertTrue(this.getParentAcl(arrayDesign) == null);
        // make sure the localfiles are associated with the array design, not the ee.
        arrayDesign = arrayDesignService.thawLite(arrayDesign);
        for (LocalFile lf : arrayDesign.getLocalFiles()) {
            this.checkHasAcl(lf);
            this.checkLacksAces(lf);
            this.checkHasAclParent(lf, arrayDesign);
        }
    }
}

Example 13 with BioAssay

use of ubic.gemma.model.expression.bioAssay.BioAssay 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 BioAssay

use of ubic.gemma.model.expression.bioAssay.BioAssay in project Gemma by PavlidisLab.

the class ExpressionDataDoubleMatrixTest method testMatrixConversion.

@Test
public void testMatrixConversion() throws Exception {
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("")));
        Collection<?> results = geoService.fetchAndLoad("GSE8294", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
    }
    newee = expressionExperimentService.thaw(newee);
    // make sure we really thawRawAndProcessed them, so we can get the design element sequences.
    Collection<RawExpressionDataVector> vectors = newee.getRawExpressionDataVectors();
    rawExpressionDataVectorService.thaw(vectors);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(vectors);
    ExpressionDataDoubleMatrix matrix = builder.getPreferredData();
    assertTrue(!Double.isNaN(matrix.get(10, 0)));
    assertEquals(66, matrix.rows());
    assertEquals(9, matrix.columns());
    /*
         * Additional tests for files and outlier marking.
         */
    processedDataVectorService.computeProcessedExpressionData(newee);
    File f1 = expressionDataFileService.writeOrLocateDataFile(expressionExperimentService.load(newee.getId()), true, true);
    assertNotNull(f1);
    assertTrue(f1.exists());
    expressionDataFileService.deleteAllFiles(newee);
    assertTrue(!f1.exists());
    /*
         * outlier removal.
         */
    BioAssay tba = newee.getBioAssays().iterator().next();
    Collection<BioAssay> ol = new HashSet<>();
    ol.add(tba);
    sampleRemoveService.markAsMissing(ol);
    assertTrue(tba.getIsOutlier());
    newee = expressionExperimentService.thaw(newee);
    Collection<ProcessedExpressionDataVector> vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    ExpressionDataMatrixBuilder matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    ExpressionDataDoubleMatrix data = matrixBuilder.getProcessedData();
    assertNotNull(data);
    assertTrue(Double.isNaN(data.getColumn(tba)[10]));
    sampleRemoveService.unmarkAsMissing(ol);
    newee = expressionExperimentService.load(newee.getId());
    newee = expressionExperimentService.thaw(newee);
    vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    data = matrixBuilder.getProcessedData();
    assertTrue(!tba.getIsOutlier());
    assertTrue(!Double.isNaN(data.getColumn(tba)[10]));
}

Example 15 with BioAssay

use of ubic.gemma.model.expression.bioAssay.BioAssay 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);
}