Examples with BeforeClass org.testng.annotations.BeforeClass used on opensource projects

Example 61 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk-protected by broadinstitute.

the class TargetCoverageSexGenotypeCalculatorUnitTest method initSexGenotyper.

@BeforeClass
public static void initSexGenotyper() {
    final List<ContigGermlinePloidyAnnotation> contigPloidyAnnotsList;
    final ReadCountCollection readCounts;
    try {
        contigPloidyAnnotsList = ContigGermlinePloidyAnnotationTableReader.readContigGermlinePloidyAnnotationsFromFile(TEST_CONTIG_PLOIDY_ANNOTS_FILE);
        readCounts = ReadCountCollectionUtils.parse(TEST_RCC_FILE);
    } catch (final IOException ex) {
        throw new UserException.CouldNotReadInputFile("Could not read test resource files");
    }
    genotyper = new TargetCoverageSexGenotypeCalculator(readCounts, readCounts.targets(), contigPloidyAnnotsList, DEFAULT_MAPPING_ERROR_PROBABILITY);
}

Example 62 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk-protected by broadinstitute.

the class BayesianHetPulldownCalculatorUnitTest method initHeaders.

@BeforeClass
public void initHeaders() throws IOException {
    try (final SamReader normalBamReader = SamReaderFactory.makeDefault().open(NORMAL_BAM_FILE);
        final SamReader tumorBamReader = SamReaderFactory.makeDefault().open(TUMOR_BAM_FILE)) {
        normalHeader = normalBamReader.getFileHeader();
        tumorHeader = tumorBamReader.getFileHeader();
    }
}

Example 63 with BeforeClass

use of org.testng.annotations.BeforeClass in project midpoint by Evolveum.

the class SearchTest method beforeClass.

@BeforeClass
public void beforeClass() throws Exception {
    super.beforeClass();
    PrismTestUtil.resetPrismContext(MidPointPrismContextFactory.FACTORY);
    FullTextSearchConfigurationType fullTextConfig = new FullTextSearchConfigurationType();
    FullTextSearchIndexedItemsConfigurationType entry = new FullTextSearchIndexedItemsConfigurationType();
    entry.getItem().add(new ItemPath(ObjectType.F_NAME).asItemPathType());
    entry.getItem().add(new ItemPath(ObjectType.F_DESCRIPTION).asItemPathType());
    fullTextConfig.getIndexed().add(entry);
    repositoryService.applyFullTextSearchConfiguration(fullTextConfig);
    LOGGER.info("Applying full text search configuration: {}", fullTextConfig);
    List<PrismObject<? extends Objectable>> objects = prismContext.parserFor(new File(FOLDER_BASIC, "objects.xml")).parseObjects();
    objects.addAll(prismContext.parserFor(new File(FOLDER_BASIC, "objects-2.xml")).parseObjects());
    OperationResult result = new OperationResult("add objects");
    for (PrismObject object : objects) {
        repositoryService.addObject(object, null, result);
    }
    result.recomputeStatus();
    assertTrue(result.isSuccess());
}

Example 64 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk by broadinstitute.

the class TargetCoverageSexGenotypeCalculatorUnitTest method initSexGenotyper.

@BeforeClass
public static void initSexGenotyper() {
    final List<ContigGermlinePloidyAnnotation> contigPloidyAnnotsList;
    final ReadCountCollection readCounts;
    try {
        contigPloidyAnnotsList = ContigGermlinePloidyAnnotationTableReader.readContigGermlinePloidyAnnotationsFromFile(TEST_CONTIG_PLOIDY_ANNOTS_FILE);
        readCounts = ReadCountCollectionUtils.parse(TEST_RCC_FILE);
    } catch (final IOException ex) {
        throw new UserException.CouldNotReadInputFile("Could not read test resource files");
    }
    genotyper = new TargetCoverageSexGenotypeCalculator(readCounts, readCounts.targets(), contigPloidyAnnotsList, DEFAULT_MAPPING_ERROR_PROBABILITY);
}

Example 65 with BeforeClass

use of org.testng.annotations.BeforeClass in project gatk by broadinstitute.

the class ContextCovariateUnitTest method init.

@BeforeClass
public void init() {
    RAC = new RecalibrationArgumentCollection();
    covariate = new ContextCovariate(RAC);
}