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

Example 1 with GeoPlatform

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

the class GeoConverterTest method testWithImageNoGenbank.

/*
     * Platform has IMAGE:CCCCC in CLONE_ID column, no genbank accessions anywhere.
     */
@Test
public final void testWithImageNoGenbank() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL222_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.setProcessPlatformsOnly(true);
    parser.parse(is);
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL222");
    Object result = this.gc.convert(platform);
    ArrayDesign ad = (ArrayDesign) result;
    for (CompositeSequence cs : ad.getCompositeSequences()) {
        BioSequence bs = cs.getBiologicalCharacteristic();
        assertTrue(bs.getName().startsWith("IMAGE"));
    }
}

Example 2 with GeoPlatform

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

the class GeoConverterTest method testImageClones.

/*
     * We should not longer use IMAGE:XXXXX as the sequence name.
     */
@Test
public void testImageClones() throws Exception {
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL226_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.parse(is);
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL226");
    Object result = this.gc.convert(platform);
    ArrayDesign ad = (ArrayDesign) result;
    assertNotNull(ad);
    for (CompositeSequence cs : ad.getCompositeSequences()) {
        BioSequence bs = cs.getBiologicalCharacteristic();
        assertTrue("Got: " + bs.getName(), !bs.getName().startsWith("IMAGE") || bs.getSequenceDatabaseEntry() == null);
    }
}

Example 3 with GeoPlatform

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

the class GeoConverterTest method testGPL6096ExonArray.

/*
     * Should result in the rejection of 'irrelevant' probes.
     */
@Test
public void testGPL6096ExonArray() throws Exception {
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.setProcessPlatformsOnly(true);
    try (InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL6096_family.soft.gz"))) {
        parser.parse(is);
    }
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL6096");
    gc.setElementLimitForStrictness(500);
    Object result = this.gc.convert(platform);
    assertNotNull(result);
}

Example 4 with GeoPlatform

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

the class GeoConverterTest method testWithImages.

/*
     * Has image clones.
     */
@Test
public final void testWithImages() throws Exception {
    GeoFamilyParser parser = new GeoFamilyParser();
    parser.setProcessPlatformsOnly(true);
    try (InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL890_family.soft.gz"))) {
        parser.parse(is);
    }
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL890");
    Object result = this.gc.convert(platform);
    ArrayDesign ad = (ArrayDesign) result;
    for (CompositeSequence cs : ad.getCompositeSequences()) {
        BioSequence bs = cs.getBiologicalCharacteristic();
        if (bs != null && bs.getSequence() != null) {
            return;
        }
    }
    fail("No sequences!");
}

Example 5 with GeoPlatform

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

the class GeoConverterTest method testMultipleTaxaIdentifiedBYAbbreviationsOnArrayWithOrganismColumn.

/*
     * Method to test that an array design can have multiple taxa stored against it and that if abbreviations used as
     * probe names mapped to the scientific names correctly if the abbreviation is stored in DB.
     */
@Test
public void testMultipleTaxaIdentifiedBYAbbreviationsOnArrayWithOrganismColumn() throws Exception {
    Taxon rainbowTroat = taxonService.findByAbbreviation("omyk");
    Taxon whiteFish = taxonService.findByAbbreviation("cclu");
    Taxon rainbowSmelt = taxonService.findByAbbreviation("omor");
    Taxon atlanticSalm = taxonService.findByAbbreviation("ssal");
    assertNotNull(atlanticSalm);
    // prototype bean.
    gc = this.getBean(GeoConverter.class);
    InputStream is = new GZIPInputStream(this.getClass().getResourceAsStream("/data/loader/expression/geo/GPL2899_family.soft.gz"));
    GeoFamilyParser parser = new GeoFamilyParser();
    // parse only the plaform
    parser.setProcessPlatformsOnly(true);
    parser.parse(is);
    GeoPlatform platform = ((GeoParseResult) parser.getResults().iterator().next()).getPlatformMap().get("GPL2899");
    Object result = gc.convert(platform);
    ArrayDesign ad = (ArrayDesign) result;
    assertNotNull(ad);
    Set<Taxon> taxa = new HashSet<>();
    BioSequence bs;
    for (CompositeSequence cs : ad.getCompositeSequences()) {
        bs = cs.getBiologicalCharacteristic();
        if (bs != null) {
            assertNotNull(bs.getTaxon());
            taxa.add(bs.getTaxon());
        }
    }
    assertEquals(4, taxa.size());
    // original file has five taxa, test file just kept four.
    assertTrue(taxa.contains(atlanticSalm));
    assertTrue(taxa.contains(rainbowTroat));
    assertTrue(taxa.contains(whiteFish));
    assertTrue(taxa.contains(rainbowSmelt));
}