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

Example 26 with GeoDomainObjectGeneratorLocal

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

the class ProcessedExpressionDataCreateServiceTest method testComputeDevRankForExpressionExperimentB.

@SuppressWarnings("unchecked")
@Test
public void testComputeDevRankForExpressionExperimentB() throws Exception {
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("GSE5949short")));
        Collection<ExpressionExperiment> results = (Collection<ExpressionExperiment>) geoService.fetchAndLoad("GSE5949", false, true, false);
        this.ee = results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        this.ee = ((Collection<ExpressionExperiment>) e.getData()).iterator().next();
    }
    ee = this.eeService.thawLite(ee);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    Collection<ProcessedExpressionDataVector> preferredVectors = this.processedExpressionDataVectorService.getProcessedDataVectors(ee);
    ee = eeService.load(ee.getId());
    ee = this.eeService.thawLite(ee);
    int numQts = ee.getQuantitationTypes().size();
    for (ProcessedExpressionDataVector d : preferredVectors) {
        assertTrue(d.getQuantitationType().getIsMaskedPreferred());
        assertTrue(ee.getQuantitationTypes().contains(d.getQuantitationType()));
        assertNotNull(d.getRankByMean());
        assertNotNull(d.getRankByMax());
    }
    assertNotNull(ee.getNumberOfDataVectors());
    ExpressionExperimentValueObject s = expressionExperimentReportService.generateSummary(ee.getId());
    assertNotNull(s);
    assertEquals(ee.getNumberOfDataVectors(), s.getProcessedExpressionVectorCount());
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    // repeat, make sure deleted old QTs.
    ee = eeService.load(ee.getId());
    ee = this.eeService.thawLite(ee);
    assertEquals(numQts, ee.getQuantitationTypes().size());
}

Example 27 with GeoDomainObjectGeneratorLocal

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

the class VectorMergingServiceTest method test.

@Test
public final void test() throws Exception {
    /*
         * Need a persistent experiment that uses multiple array designs. Then merge the designs, switch the vectors,
         * and merge the vectors. GSE3443
         */
    /*
         * The experiment uses the following GPLs
         *
         * GPL2868, GPL2933, GPL2934, GPL2935, GPL2936, GPL2937, GPL2938
         *
         * Example of a sequence appearing on more than one platform: N57553
         */
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("gse3443merge")));
    Collection<?> results = geoService.fetchAndLoad("GSE3443", false, false, false);
    ee = (ExpressionExperiment) results.iterator().next();
    ee = this.eeService.thawLite(ee);
    Collection<ArrayDesign> aas = eeService.getArrayDesignsUsed(ee);
    assertEquals(7, aas.size());
    /*
         * Check number of sequences across all platforms. This is how many elements we need on the new platform, plus
         * extras for duplicated sequences (e.g. elements that don't have a sequence...)
         */
    Collection<ArrayDesign> taas = new HashSet<>();
    Set<BioSequence> oldbs = new HashSet<>();
    for (ArrayDesign arrayDesign : aas) {
        arrayDesign = arrayDesignService.thaw(arrayDesign);
        taas.add(arrayDesign);
        for (CompositeSequence cs : arrayDesign.getCompositeSequences()) {
            log.info(cs + " " + cs.getBiologicalCharacteristic());
            oldbs.add(cs.getBiologicalCharacteristic());
        }
    }
    assertEquals(63, oldbs.size());
    /*
         * Check total size of elements across all 7 platforms.
         */
    int totalElements = 0;
    for (ArrayDesign arrayDesign : taas) {
        totalElements += arrayDesign.getCompositeSequences().size();
    }
    assertEquals(140, totalElements);
    ArrayDesign firstaa = taas.iterator().next();
    aas.remove(firstaa);
    assertEquals(null, firstaa.getMergedInto());
    mergedAA = arrayDesignMergeService.merge(firstaa, taas, "testMerge" + RandomStringUtils.randomAlphabetic(5), "merged" + RandomStringUtils.randomAlphabetic(5), false);
    assertEquals(72, mergedAA.getCompositeSequences().size());
    Set<BioSequence> seenBs = new HashSet<>();
    for (CompositeSequence cs : mergedAA.getCompositeSequences()) {
        seenBs.add(cs.getBiologicalCharacteristic());
    }
    assertEquals(63, seenBs.size());
    // just to make this explicit. The new array design has to contain all the old sequences.
    assertEquals(oldbs.size(), seenBs.size());
    ee = eeService.thaw(ee);
    assertEquals(1828, ee.getRawExpressionDataVectors().size());
    ee = eePlatformSwitchService.switchExperimentToArrayDesign(ee, mergedAA);
    ee = eeService.thaw(ee);
    // check we actually got switched over.
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(mergedAA, ba.getArrayDesignUsed());
    }
    for (RawExpressionDataVector v : ee.getRawExpressionDataVectors()) {
        assertEquals(mergedAA, v.getDesignElement().getArrayDesign());
    }
    assertEquals(15, ee.getQuantitationTypes().size());
    assertEquals(1828, ee.getRawExpressionDataVectors().size());
    ee = vectorMergingService.mergeVectors(ee);
    // check we got the right processed data
    Collection<ProcessedExpressionDataVector> pvs = processedExpressionDataVectorService.getProcessedDataVectors(ee);
    assertEquals(72, pvs.size());
    ee = eeService.thaw(ee);
    Collection<DoubleVectorValueObject> processedDataArrays = processedExpressionDataVectorService.getProcessedDataArrays(ee, 50);
    assertEquals(50, processedDataArrays.size());
}

Example 28 with GeoDomainObjectGeneratorLocal

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

the class ExpressionExperimentBatchCorrectionServiceTest method testComBatOnEE.

@Test
public void testComBatOnEE() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("gse18162Short")));
    ExpressionExperiment newee;
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE18162", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
    }
    assertNotNull(newee);
    newee = expressionExperimentService.thawLite(newee);
    processedExpressionDataVectorService.computeProcessedExpressionData(newee);
    try (InputStream deis = this.getClass().getResourceAsStream("/data/loader/expression/geo/gse18162Short/design.txt")) {
        experimentalDesignImporter.importDesign(newee, deis);
    }
    ExpressionDataDoubleMatrix comBat = correctionService.comBat(newee);
    assertNotNull(comBat);
}

Example 29 with GeoDomainObjectGeneratorLocal

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

the class SVDServiceImplTest method testsvdGapped.

/*
     * See bug 2139; two different sets of bioassays in the data.
     */
@Test
public void testsvdGapped() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("gse482short")));
    // also used in the GeoDatasetServiceIntegrationTest.
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE482", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        if (e.getData() instanceof List) {
            ee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
        } else {
            ee = (ExpressionExperiment) e.getData();
        }
    }
    assertNotNull(ee);
    ee = eeService.thaw(ee);
    processedExpressionDataVectorService.createProcessedDataVectors(ee);
    ee = eeService.findByShortName("GSE482");
    assertNotNull(ee);
    SVDValueObject svd = svdService.svd(ee.getId());
    assertNotNull(svd);
    assertNotNull(svd.getvMatrix());
    assertEquals(10, svd.getBioMaterialIds().length);
}

Example 30 with GeoDomainObjectGeneratorLocal

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

the class ArrayDesignSequenceProcessorTest method testFetchAndLoadWithSequences.

@Test
public void testFetchAndLoadWithSequences() throws Exception {
    GeoService geoService = this.getBean(GeoService.class);
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
    @SuppressWarnings("unchecked") final Collection<ArrayDesign> ads = (Collection<ArrayDesign>) geoService.fetchAndLoad("GPL226", true, true, false);
    result = ads.iterator().next();
    result = arrayDesignService.thaw(result);
    try {
        Collection<BioSequence> res = app.processArrayDesign(result, new String[] { "testblastdb", "testblastdbPartTwo" }, FileTools.resourceToPath("/data/loader/genome/blast"), false);
        assertNotNull(res);
        for (BioSequence sequence : res) {
            assertNotNull(sequence.getSequence());
        }
    } catch (Exception e) {
        if (StringUtils.isNotBlank(e.getMessage()) && e.getMessage().contains("not found")) {
            log.error("fastacmd is not installed or is misconfigured.  Test skipped");
            return;
        }
        throw e;
    }
}