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

Example 21 with GeoSeries

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

the class DatasetCombinerTest method testFindGSE3193.

/*
     * Has multiple platforms, but no GES's are defined
     */
@Test
public void testFindGSE3193() throws Exception {
    GeoFamilyParser parser = new GeoFamilyParser();
    try (InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE3193Short/GSE3193_family.soft.gz"))) {
        parser.parse(is);
    }
    GeoParseResult parseResult = ((GeoParseResult) parser.getResults().iterator().next());
    // GeoDataset gd = parseResult.getDatasets().values().iterator().next();
    GeoSeries gse = parseResult.getSeries().values().iterator().next();
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence result = datasetCombiner.findGSECorrespondence(gse);
    DatasetCombinerTest.log.debug(result);
    Iterator<Set<String>> it = result.iterator();
    int numBioMaterials = 0;
    while (it.hasNext()) {
        it.next();
        // assertTrue( c.size() == 1 );
        numBioMaterials++;
    }
    // note, i'm not at all sure these are right! this used to be 60.
    assertEquals(57, numBioMaterials);
}

Example 22 with GeoSeries

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

the class DatasetCombinerTest method testFindGSE88.

@Test
public void testFindGSE88() throws Exception {
    GeoFamilyParser parser = new GeoFamilyParser();
    try (InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE88Short/GDS184.soft.gz"))) {
        parser.parse(is);
    }
    try (InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE88Short/GSE88_family.soft.gz"))) {
        parser.parse(is);
    }
    GeoParseResult parseResult = ((GeoParseResult) parser.getResults().iterator().next());
    GeoDataset gd = parseResult.getDatasets().values().iterator().next();
    GeoSeries gse = parseResult.getSeries().values().iterator().next();
    gd.getSeries().add(gse);
    gds = new HashSet<>();
    gds.add(gd);
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence result = datasetCombiner.findGSECorrespondence(gds);
    DatasetCombinerTest.log.debug(result);
    Iterator<Set<String>> it = result.iterator();
    int numBioMaterials = 0;
    while (it.hasNext()) {
        Collection<String> c = it.next();
        assertTrue(c.size() == 1);
        numBioMaterials++;
    }
    assertEquals(31, numBioMaterials);
}

Example 23 with GeoSeries

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

the class GeoConverterTest method testConvertGSE3791.

/*
     * Has two species.
     */
@SuppressWarnings("unchecked")
@Test
public void testConvertGSE3791() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse3791Short/GSE3791_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE3791");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    assertEquals(2, ees.size());
}

Example 24 with GeoSeries

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

the class GeoConverterTest method testConvertWithLotsOfPlatforms.

@Test
public void testConvertWithLotsOfPlatforms() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse3500Short/GSE3500_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE3500");
    DatasetCombiner datasetCombiner = new DatasetCombiner(false);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
}

Example 25 with GeoSeries

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

the class GeoConverterTest method test5091.

/*
     * quantitation type problem. See bug 1760
     */
@SuppressWarnings("unchecked")
@Test
public void test5091() throws Exception {
    GeoFamilyParser parser = new GeoFamilyParser();
    try (InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE5091Short/GSE5091_family.soft.gz"))) {
        parser.parse(is);
    }
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE5091");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    assertEquals(1, ees.size());
    ExpressionExperiment ee = ees.iterator().next();
    for (QuantitationType qt : ee.getQuantitationTypes()) {
        if (qt.getName().equals("VALUE")) {
            assertEquals(PrimitiveType.DOUBLE, qt.getRepresentation());
            return;
        }
    }
    fail("Didn't find the 'value' quantitation type");
}