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

Example 11 with GeoSeries

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

the class GeoConverterTest method testParseGSE44625.

/*
     * bug 3415. The samples do not have the same quantitation types. In some it is "detection pval" and others
     * "raw_value". We would reject "detection pval" but if the qt already has the name "raw_value" we won't. The way
     * the current setup works, we sort of throw up our hands and keep the data, even though it is messed up.
     * <p>
     * This tests that behaviour. If we start rejecting the data, this test will fail (note that rejecting the data is
     * not unreasonable).
     */
@Test
public void testParseGSE44625() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE44625.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoParseResult result = (GeoParseResult) parser.getResults().iterator().next();
    GeoSeries series = result.getSeries().values().iterator().next();
    DatasetCombiner datasetCombiner = new DatasetCombiner(false);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object convert = this.gc.convert(series);
    ExpressionExperiment ee = (ExpressionExperiment) ((Collection<?>) convert).iterator().next();
    assertEquals(2, ee.getQuantitationTypes().size());
}

Example 12 with GeoSeries

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

the class GeoConverterTest method testConvertGSE2122SAGE.

// No SAGE allowed
@SuppressWarnings("unchecked")
@Test
public void testConvertGSE2122SAGE() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse2122shortSage/GSE2122.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE2122");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    // SAGE, rejected
    assertEquals(0, ees.size());
}

Example 13 with GeoSeries

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

the class GeoConverterTest method testConvertGSE2982.

@SuppressWarnings("unchecked")
@Test
public void testConvertGSE2982() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse2982Short/GSE2982_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE2982");
    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();
    boolean ok = false;
    for (RawExpressionDataVector dedv : ee.getRawExpressionDataVectors()) {
        QuantitationType qt = dedv.getQuantitationType();
        if (qt.getIsPreferred()) {
            ok = true;
            assertEquals("VALUE", qt.getName());
            assertEquals(StandardQuantitationType.AMOUNT, qt.getType());
            assertTrue(qt.getIsRatio());
        }
    }
    assertTrue(ok);
}

Example 14 with GeoSeries

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

the class GeoConverterTest method testFetchAndLoadGSE8294.

/*
     * Ends up with too few vectors, because of a problem with the quantitation type guesser.
     */
@Test
public void testFetchAndLoadGSE8294() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE8294_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE8294");
    DatasetCombiner datasetCombiner = new DatasetCombiner(false);
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Set<?> result = (Set<?>) this.gc.convert(series);
    ExpressionExperiment e = (ExpressionExperiment) result.iterator().next();
    assertEquals(66, e.getRawExpressionDataVectors().size());
}

Example 15 with GeoSeries

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

the class GeoConverterTest method testConvertGSE106.

/*
     * caused "GSM3059 had no platform assigned"
     *
     */
@Test
public void testConvertGSE106() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse106Short/GSE106.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE106");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
}