Examples with GeoDomainObjectGeneratorLocal ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal used on opensource projects

Example 41 with GeoDomainObjectGeneratorLocal

use of ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal in project Gemma by PavlidisLab.

the class ContinuousVariableDiffExTest method setup.

@Before
public void setup() throws Exception {
    /*
         * this is an exon array data set that has the data present. It's an annoying choice for a test in that it
         * exposes issues with our attempts to ignore the data from exon arrays until we get it from the raw CEL files.
         */
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(FileTools.resourceToPath("/data/analysis/expression/gse13949short")));
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE13949", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        ee = (ExpressionExperiment) ((Collection<?>) e.getData()).iterator().next();
    }
    ee = expressionExperimentService.thawLite(ee);
    Collection<ExperimentalFactor> toremove = new HashSet<>(ee.getExperimentalDesign().getExperimentalFactors());
    for (ExperimentalFactor ef : toremove) {
        experimentalFactorService.delete(ef);
        ee.getExperimentalDesign().getExperimentalFactors().remove(ef);
    }
    expressionExperimentService.update(ee);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    ee = expressionExperimentService.thaw(ee);
    designImporter.importDesign(ee, this.getClass().getResourceAsStream("/data/analysis/expression/gse13949short/1151_GSE13949_expdesign.data.txt"));
}

Example 42 with GeoDomainObjectGeneratorLocal

use of ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal in project Gemma by PavlidisLab.

the class DiffExTest method testGSE35930.

/**
 * Test where probes have constant values. See bug 3177.
 */
@Test
public void testGSE35930() throws Exception {
    ExpressionExperiment ee;
    // eeService.remove( eeService.findByShortName( "GSE35930" ) );
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("GSE35930")));
        Collection<?> results = geoService.fetchAndLoad("GSE35930", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        // OK.
        if (e.getData() instanceof List) {
            ee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
        } else {
            ee = (ExpressionExperiment) e.getData();
        }
    }
    ee = this.eeService.thawLite(ee);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    if (ee.getExperimentalDesign().getExperimentalFactors().isEmpty()) {
        ee = eeService.load(ee.getId());
        ee = this.eeService.thawLite(ee);
        try (InputStream is = this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE35930/design.txt")) {
            experimentalDesignImporter.importDesign(ee, is);
        }
        ee = eeService.load(ee.getId());
        ee = this.eeService.thawLite(ee);
    }
    DifferentialExpressionAnalysisConfig config = new DifferentialExpressionAnalysisConfig();
    config.setFactorsToInclude(ee.getExperimentalDesign().getExperimentalFactors());
    Collection<DifferentialExpressionAnalysis> analyses = analyzer.run(ee, config);
    assertNotNull(analyses);
    assertEquals(1, analyses.size());
    DifferentialExpressionAnalysis results = analyses.iterator().next();
    boolean found = false;
    ExpressionAnalysisResultSet resultSet = results.getResultSets().iterator().next();
    for (DifferentialExpressionAnalysisResult r : resultSet.getResults()) {
        // this probe has a constant value
        if (r.getProbe().getName().equals("1622910_at")) {
            fail("Should not have found a result for constant probe");
        // found = true;
        // assertTrue( "Got: " + pvalue, pvalue == null || pvalue.equals( Double.NaN ) );
        } else {
            // got to have something...
            found = true;
        }
    }
    assertTrue(found);
}

Example 43 with GeoDomainObjectGeneratorLocal

use of ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal in project Gemma by PavlidisLab.

the class ExperimentalDesignWriterTest method setup.

@Before
public void setup() throws Exception {
    ee = eeService.findByShortName(shortName);
    if (ee == null) {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("gds994Medium")));
        Collection<?> results = geoService.fetchAndLoad(shortName, false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    }
    ee = eeService.thaw(ee);
}

Example 44 with GeoDomainObjectGeneratorLocal

use of ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal in project Gemma by PavlidisLab.

the class ExonArrayDataAddIntegrationTest method testAddAffyExonArrayDataExpressionExperiment.

@Test
public void testAddAffyExonArrayDataExpressionExperiment() throws Exception {
    if (!hasApt) {
        log.warn("Test skipped due to lack of Affy Power Tools executable");
        return;
    }
    ExpressionExperiment ee;
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
        Collection<?> results = geoService.fetchAndLoad("GSE12135", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        ee = (ExpressionExperiment) ((List<?>) e.getData()).get(0);
    }
    /*
         * Add the raw data.
         */
    dataUpdater.addAffyExonArrayData(ee);
    experimentService.load(ee.getId());
}

Example 45 with GeoDomainObjectGeneratorLocal

use of ubic.gemma.core.loader.expression.geo.GeoDomainObjectGeneratorLocal in project Gemma by PavlidisLab.

the class DesignElementDataVectorServiceTest method testFindByQt.

@Test
public void testFindByQt() throws Exception {
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("gse432Short")));
        Collection<?> results = geoService.fetchAndLoad("GSE432", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) e.getData();
    }
    newee.setShortName(RandomStringUtils.randomAlphabetic(12));
    expressionExperimentService.update(newee);
    newee = this.expressionExperimentService.thawLite(newee);
    RawExpressionDataVectorService rawService = this.getBean(RawExpressionDataVectorService.class);
    QuantitationType qt = null;
    for (QuantitationType q : newee.getQuantitationTypes()) {
        if (q.getIsPreferred()) {
            qt = q;
            break;
        }
    }
    assertNotNull("QT is null", qt);
    Collection<? extends DesignElementDataVector> preferredVectors = rawService.findRawAndProcessed(qt);
    assertNotNull(preferredVectors);
    assertEquals(40, preferredVectors.size());
}