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

Example 31 with GeoSeries

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

the class GeoConverterTest method testConvertGenePix.

@Test
public void testConvertGenePix() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/shortGenePix/GSE2221_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE2221");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    Object result = this.gc.convert(series);
    assertNotNull(result);
}

Example 32 with GeoSeries

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

the class GeoConverterTest method testConvertGSE60.

/*
     * Was yielding a 'ArrayDesigns must be converted before datasets'.
     */
@SuppressWarnings("unchecked")
@Test
public void testConvertGSE60() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse60Short/GSE60_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/gse60Short/GDS75.soft.gz"));
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE60");
    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();
    assertEquals(133, ee.getBioAssays().size());
    // used to be more but we reject mote qts now.
    assertEquals(480, ee.getRawExpressionDataVectors().size());
}

Example 33 with GeoSeries

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

the class GeoConverterTest method testConvertMultiTaxonPlatformGSE28843.

@SuppressWarnings("unchecked")
@Test
public void testConvertMultiTaxonPlatformGSE28843() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE28843.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE28843");
    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());
    Taxon primaryTaxon = ees.iterator().next().getBioAssays().iterator().next().getArrayDesignUsed().getPrimaryTaxon();
    assertEquals("salmonid", primaryTaxon.getCommonName());
}

Example 34 with GeoSeries

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

the class GeoConverterTest method testSplitByPlatform.

/*
     * Test splitting
     */
@SuppressWarnings("unchecked")
@Test
public void testSplitByPlatform() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE493Short/GSE493_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE493");
    DatasetCombiner datasetCombiner = new DatasetCombiner();
    GeoSampleCorrespondence correspondence = datasetCombiner.findGSECorrespondence(series);
    series.setSampleCorrespondence(correspondence);
    this.gc.setSplitByPlatform(true);
    Object result = this.gc.convert(series);
    assertNotNull(result);
    Collection<ExpressionExperiment> ees = (Collection<ExpressionExperiment>) result;
    assertEquals(2, ees.size());
    for (ExpressionExperiment ee : ees) {
        // 4 on one platform, 10 on the other. This is a bit sloppy but good enuf for now.
        assertTrue(ee.getBioAssays().size() == 4 || ee.getBioAssays().size() == 10);
    }
}

Example 35 with GeoSeries

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

the class GeoConverterTest method testConvertGSE8134.

/*
     * NPE in converter, not reproduced here.
     */
@SuppressWarnings("unchecked")
@Test
public void testConvertGSE8134() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GSE8134_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoSeries series = ((GeoParseResult) parser.getResults().iterator().next()).getSeriesMap().get("GSE8134");
    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());
}