@Override default void clearDB(String dbName) throws Exception { DummyProjectMetadataAdaptor.clear(); DummyStudyConfigurationAdaptor.clear(); }
@After public void tearDown() throws Exception { DummyStudyConfigurationAdaptor.clear(); }
public static synchronized void writeAndClear(Path path) { writeAll(path); clear(); }
@Test public void testExportImport() throws Exception { String export = Paths.get(opencga.createTmpOutdir(studyId, "_EXPORT_", sessionId)).resolve("export.json.gz").toString(); variantManager.exportData(export, VariantOutputFormat.JSON_GZ, studyId, sessionId); DummyStudyConfigurationAdaptor.clear(); variantManager.importData(URI.create(export), studyId2, sessionId); }
@Test public void testExportSomeSamplesImport() throws Exception { String export = Paths.get(opencga.createTmpOutdir(studyId, "_EXPORT_", sessionId)).resolve("export.avro").toString(); List<Sample> samples = catalogManager.getSampleManager().get(studyId, new Query(), new QueryOptions(), sessionId).getResult(); List<String> someSamples = samples.stream().limit(samples.size() / 2).map(Sample::getId).collect(Collectors.toList()); Query query = new Query(VariantQueryParam.INCLUDE_STUDY.key(), studyId) .append(VariantQueryParam.INCLUDE_SAMPLE.key(), someSamples); QueryOptions queryOptions = new QueryOptions(); variantManager.exportData(export, VariantOutputFormat.AVRO, query, queryOptions, sessionId); DummyStudyConfigurationAdaptor.clear(); variantManager.importData(URI.create(export), studyId2, sessionId); } }
@Before public void setUp() throws Exception { DummyStudyConfigurationAdaptor.clear(); scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); parser = new VariantMongoDBQueryParser(scm); scm.updateStudyConfiguration(newStudyConfiguration(1, Arrays.asList(1, 2, 3, 4), false), null); scm.updateStudyConfiguration(newStudyConfiguration(2, Arrays.asList(1, 2, 3, 4), true), null); }
@Before public void setUp() throws Exception { DummyProjectMetadataAdaptor.clear(); DummyStudyConfigurationAdaptor.clear(); scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); }
factory.unregisterVariantStorageEngine(DummyVariantStorageEngine.STORAGE_ENGINE_ID); DummyStudyConfigurationAdaptor.clear();