FeatureIndexManagerTest.java 文件源码

@Test
@Transactional(propagation = Propagation.REQUIRES_NEW)
public void testCreateUnmappedGeneIndex() throws IOException, InterruptedException, FeatureIndexException,
        NoSuchAlgorithmException {
    Chromosome chr1 = EntityHelper.createNewChromosome("chr1");
    chr1.setSize(TEST_CHROMOSOME_SIZE);
    Reference testHumanReference = EntityHelper.createNewReference(chr1,
            referenceGenomeManager.createReferenceId());

    referenceGenomeManager.register(testHumanReference);
    Long humanReferenceId = testHumanReference.getId();

    Resource resource = context.getResource("classpath:templates/mrna.sorted.chunk.gtf");

    FeatureIndexedFileRegistrationRequest request = new FeatureIndexedFileRegistrationRequest();
    request.setReferenceId(humanReferenceId);
    request.setPath(resource.getFile().getAbsolutePath());

    GeneFile geneFile = gffManager.registerGeneFile(request);
    Assert.assertNotNull(geneFile);
    Assert.assertNotNull(geneFile.getId());

    Project project = new Project();
    project.setName(TEST_PROJECT_NAME + 1);

    project.setItems(Arrays.asList(
            new ProjectItem(new BiologicalDataItem(geneFile.getBioDataItemId())),
            new ProjectItem(new BiologicalDataItem(testHumanReference.getBioDataItemId()))));
    projectManager.saveProject(project);

    List<FeatureIndexEntry> entryList = (List<FeatureIndexEntry>)
            featureIndexManager.searchFeaturesInProject("", project.getId()).getEntries();
    Assert.assertTrue(entryList.isEmpty());

    entryList = (List<FeatureIndexEntry>) featureIndexManager.searchFeaturesInProject("AM992871",
                                                                                      project.getId()).getEntries();
    Assert.assertTrue(entryList.isEmpty()); // we don't search for exons
}