@Override public DummyVariantStoragePipeline newStoragePipeline(boolean connected) throws StorageEngineException { return new DummyVariantStoragePipeline(getConfiguration(), STORAGE_ENGINE_ID, getDBAdaptor(), getVariantReaderUtils()); }
@Override protected VariantImporter newVariantImporter() throws StorageEngineException { return new VariantImporter(getDBAdaptor()) { @Override public void importData(URI input, VariantMetadata metadata, List<StudyConfiguration> scs) throws StorageEngineException, IOException { } }; }
@Before public void setUp() throws Exception { DummyProjectMetadataAdaptor.clear(); DummyStudyConfigurationAdaptor.clear(); scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); }
@Override public StudyConfigurationManager getStudyConfigurationManager() throws StorageEngineException { return new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); } }
protected DummyVariantStoragePipeline mockVariantStorageETL(DummyVariantStorageEngine vsm) throws StorageEngineException { DummyVariantStoragePipeline storageETL = spy(vsm.newStoragePipeline(true)); // doReturn(storageETL).when(vsm).newStoragePipeline(anyBoolean()); Mockito.doAnswer(invocation -> { DummyVariantStoragePipeline etl = (DummyVariantStoragePipeline) invocation.callRealMethod(); storageETL.init(etl.getOptions()); return storageETL; }).when(vsm).newStoragePipeline(anyBoolean()); return storageETL; }
@After public void tearDown() throws Exception { DummyStudyConfigurationAdaptor.writeAndClear(opencga.getOpencgaHome()); DummyVariantFileMetadataDBAdaptor.writeAndClear(opencga.getOpencgaHome()); DummyProjectMetadataAdaptor.writeAndClear(opencga.getOpencgaHome()); }
@After public void tearDown() throws Exception { DummyProjectMetadataAdaptor.writeAndClear(catalogManagerExternalResource.getOpencgaHome()); DummyStudyConfigurationAdaptor.writeAndClear(catalogManagerExternalResource.getOpencgaHome()); }
protected DummyVariantDBAdaptor mockVariantDBAdaptor(DummyVariantStorageEngine vsm) throws StorageEngineException { DummyVariantDBAdaptor dbAdaptor = spy(new DummyVariantDBAdaptor("")); doReturn(dbAdaptor).when(vsm).getDBAdaptor(); return dbAdaptor; }
@Override public void removeFiles(String study, List<String> files) throws StorageEngineException { List<Integer> fileIds = preRemoveFiles(study, files).getFileIds(); try { Thread.sleep(1); } catch (InterruptedException e) { Thread.currentThread().interrupt(); } postRemoveFiles(study, fileIds, false); }
@After public void tearDown() throws Exception { DummyStudyConfigurationAdaptor.clear(); }
@Override default VariantStorageEngine getVariantStorageEngine() throws Exception { try (InputStream is = DummyVariantStorageEngine.class.getClassLoader().getResourceAsStream("storage-configuration.yml")) { StorageConfiguration storageConfiguration = StorageConfiguration.load(is); DummyVariantStorageEngine storageManager = new DummyVariantStorageEngine(); storageManager.setConfiguration(storageConfiguration, DummyVariantStorageEngine.STORAGE_ENGINE_ID); return storageManager; } }
@Override public VariantDBAdaptor getDBAdaptor() throws StorageEngineException { return new DummyVariantDBAdaptor(dbName); }
public void init(ObjectMap options) { getOptions().clear(); getOptions().putAll(options); }
@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); }
@Override public StudyConfigurationManager getStudyConfigurationManager() { return new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); }
@After public void tearDown() throws Exception { DummyProjectMetadataAdaptor.writeAndClear(getTmpRootDir()); DummyStudyConfigurationAdaptor.writeAndClear(getTmpRootDir()); }
@Before public void init() throws StorageEngineException { scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); scm.createStudy(studyName); solrQueryParser = new SolrQueryParser(scm); }