Examples with AlreadyExistsInSystemException ubic.gemma.core.loader.util.AlreadyExistsInSystemException used on opensource projects

Example 1 with AlreadyExistsInSystemException

use of ubic.gemma.core.loader.util.AlreadyExistsInSystemException in project Gemma by PavlidisLab.

the class BaselineDetectionTest method setUp.

@Before
public void setUp() throws Exception {
    String path = FileTools.resourceToPath("/data/loader/expression/geo/gse18162Short");
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(path));
        Collection<?> results = geoService.fetchAndLoad("GSE18162", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        // OK.
        if (e.getData() instanceof List) {
            ee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
        } else {
            ee = (ExpressionExperiment) e.getData();
        }
    }
    ee = this.eeService.thawLite(ee);
    if (ee.getExperimentalDesign().getExperimentalFactors().isEmpty()) {
        ee = eeService.load(ee.getId());
        ee = this.eeService.thawLite(ee);
        try (InputStream is = this.getClass().getResourceAsStream("/data/loader/expression/geo/gse18162Short/design.txt")) {
            experimentalDesignImporter.importDesign(ee, is);
        }
        ee = eeService.load(ee.getId());
        ee = this.eeService.thawLite(ee);
    }
// end setup
}

Example 2 with AlreadyExistsInSystemException

use of ubic.gemma.core.loader.util.AlreadyExistsInSystemException in project Gemma by PavlidisLab.

the class DiffExMetaAnalyzerServiceTest method loadSet.

private void loadSet(String acc) throws Exception {
    String path = new File(this.getClass().getResource("/data/loader/expression/geo/meta-analysis").toURI()).getAbsolutePath();
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(path));
    try {
        geoService.fetchAndLoad(acc, false, true, false);
    } catch (AlreadyExistsInSystemException ignored) {
        log.info("Set already exists in system.");
    }
}

Example 3 with AlreadyExistsInSystemException

use of ubic.gemma.core.loader.util.AlreadyExistsInSystemException in project Gemma by PavlidisLab.

the class DiffExWithInvalidInteraction2Test method setup.

@Before
public void setup() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(FileTools.resourceToPath("/data/analysis/expression")));
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE37301", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        ee = (ExpressionExperiment) ((Collection<?>) e.getData()).iterator().next();
    }
    ee = expressionExperimentService.thawLite(ee);
    Collection<ExperimentalFactor> toremove = new HashSet<>(ee.getExperimentalDesign().getExperimentalFactors());
    for (ExperimentalFactor ef : toremove) {
        experimentalFactorService.delete(ef);
        ee.getExperimentalDesign().getExperimentalFactors().remove(ef);
    }
    expressionExperimentService.update(ee);
    processedExpressionDataVectorService.computeProcessedExpressionData(ee);
    ee = expressionExperimentService.thaw(ee);
    designImporter.importDesign(ee, this.getClass().getResourceAsStream("/data/analysis/expression/7737_GSE37301_expdesign.data.txt"));
}

Example 4 with AlreadyExistsInSystemException

use of ubic.gemma.core.loader.util.AlreadyExistsInSystemException in project Gemma by PavlidisLab.

the class SVDServiceImplTest method testsvd.

@Test
public void testsvd() throws Exception {
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("shortTest")));
    // also used in the GeoDatasetServiceIntegrationTest.
    try {
        Collection<?> results = geoService.fetchAndLoad("GSE674", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        ee = (ExpressionExperiment) ((Collection<?>) e.getData()).iterator().next();
    }
    assertNotNull(ee);
    ee = eeService.thaw(ee);
    processedExpressionDataVectorService.createProcessedDataVectors(ee);
    ee = eeService.findByShortName("GSE674");
    assertNotNull(ee);
    SVDValueObject svd = svdService.svd(ee.getId());
    assertNotNull(svd);
    assertNotNull(svd.getvMatrix());
    assertEquals(5, svd.getFactorCorrelations().size());
    analysisUtilService.deleteOldAnalyses(ee);
}

Example 5 with AlreadyExistsInSystemException

use of ubic.gemma.core.loader.util.AlreadyExistsInSystemException in project Gemma by PavlidisLab.

the class ExpressionDataDoubleMatrixTest method testMatrixConversion.

@Test
public void testMatrixConversion() throws Exception {
    try {
        geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath("")));
        Collection<?> results = geoService.fetchAndLoad("GSE8294", false, true, false);
        newee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        newee = (ExpressionExperiment) ((List<?>) e.getData()).iterator().next();
    }
    newee = expressionExperimentService.thaw(newee);
    // make sure we really thawRawAndProcessed them, so we can get the design element sequences.
    Collection<RawExpressionDataVector> vectors = newee.getRawExpressionDataVectors();
    rawExpressionDataVectorService.thaw(vectors);
    ExpressionDataMatrixBuilder builder = new ExpressionDataMatrixBuilder(vectors);
    ExpressionDataDoubleMatrix matrix = builder.getPreferredData();
    assertTrue(!Double.isNaN(matrix.get(10, 0)));
    assertEquals(66, matrix.rows());
    assertEquals(9, matrix.columns());
    /*
         * Additional tests for files and outlier marking.
         */
    processedDataVectorService.computeProcessedExpressionData(newee);
    File f1 = expressionDataFileService.writeOrLocateDataFile(expressionExperimentService.load(newee.getId()), true, true);
    assertNotNull(f1);
    assertTrue(f1.exists());
    expressionDataFileService.deleteAllFiles(newee);
    assertTrue(!f1.exists());
    /*
         * outlier removal.
         */
    BioAssay tba = newee.getBioAssays().iterator().next();
    Collection<BioAssay> ol = new HashSet<>();
    ol.add(tba);
    sampleRemoveService.markAsMissing(ol);
    assertTrue(tba.getIsOutlier());
    newee = expressionExperimentService.thaw(newee);
    Collection<ProcessedExpressionDataVector> vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    ExpressionDataMatrixBuilder matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    ExpressionDataDoubleMatrix data = matrixBuilder.getProcessedData();
    assertNotNull(data);
    assertTrue(Double.isNaN(data.getColumn(tba)[10]));
    sampleRemoveService.unmarkAsMissing(ol);
    newee = expressionExperimentService.load(newee.getId());
    newee = expressionExperimentService.thaw(newee);
    vecs = newee.getProcessedExpressionDataVectors();
    this.processedDataVectorService.thaw(vecs);
    assertTrue(!vecs.isEmpty());
    matrixBuilder = new ExpressionDataMatrixBuilder(vecs);
    data = matrixBuilder.getProcessedData();
    assertTrue(!tba.getIsOutlier());
    assertTrue(!Double.isNaN(data.getColumn(tba)[10]));
}