public StorageEngine(StorageConfiguration configuration) { this(configuration.getDefaultStorageEngineId(), configuration); // this.configuration = configuration; }
public VariantBenchmarkRunner(StorageConfiguration storageConfiguration) throws IllegalAccessException, ClassNotFoundException, InstantiationException, StorageEngineException { this(storageConfiguration.getDefaultStorageEngineId(), storageConfiguration); }
public String getDefaultStorageEngineId() { return storageConfiguration.getDefaultStorageEngineId(); }
public GenericGrpcService(StorageConfiguration storageConfiguration) { this(storageConfiguration, storageConfiguration.getDefaultStorageEngineId()); }
public VariantStorageEngine(StorageConfiguration configuration) { this(configuration.getDefaultStorageEngineId(), configuration); }
public AbstractStorageServer(int port, String defaultStorageEngine) { this.port = port; if (StringUtils.isNotEmpty(defaultStorageEngine)) { this.defaultStorageEngine = defaultStorageEngine; } else { this.defaultStorageEngine = storageConfiguration.getDefaultStorageEngineId(); } }
public GrpcStorageServer(StorageConfiguration storageConfiguration) { super(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); GrpcStorageServer.storageConfiguration = storageConfiguration; logger = LoggerFactory.getLogger(this.getClass()); }
public RestStorageServer(StorageConfiguration storageConfiguration) { super(storageConfiguration.getServer().getRest(), storageConfiguration.getDefaultStorageEngineId()); RestStorageServer.storageConfiguration = storageConfiguration; logger = LoggerFactory.getLogger(this.getClass()); }
public GrpcStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
public AbstractStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
public RestStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
defaultStorageEngine = storageConfiguration.getDefaultStorageEngineId();
private void configure(GeneralCliOptions.CommonOptions commonOptions, String dbName) throws Exception { this.logFile = commonOptions.logFile; /** * Getting VariantStorageEngine * We need to find out the Storage Engine Id to be used * If not storage engine is passed then the default is taken from storage-configuration.yml file **/ this.storageEngine = (storageEngine != null && !storageEngine.isEmpty()) ? storageEngine : configuration.getDefaultStorageEngineId(); logger.debug("Storage Engine set to '{}'", this.storageEngine); this.storageConfiguration = configuration.getStorageEngine(storageEngine); // TODO: Start passing catalogManager StorageEngineFactory storageEngineFactory = StorageEngineFactory.get(configuration); if (storageEngine == null || storageEngine.isEmpty()) { this.variantStorageEngine = storageEngineFactory.getVariantStorageEngine(null, dbName); } else { this.variantStorageEngine = storageEngineFactory.getVariantStorageEngine(storageEngine, dbName); } }
private void configure(ClientCliOptionsParser.CommonOptions commonOptions, String dbName) throws Exception { this.logFile = commonOptions.logFile; /** * Getting VariantStorageEngine * We need to find out the Storage Engine Id to be used * If not storage engine is passed then the default is taken from storage-configuration.yml file **/ this.storageEngine = (storageEngine != null && !storageEngine.isEmpty()) ? storageEngine : configuration.getDefaultStorageEngineId(); logger.debug("Storage Engine set to '{}'", this.storageEngine); this.storageConfiguration = configuration.getStorageEngine(storageEngine); // TODO: Start passing catalogManager StorageEngineFactory storageEngineFactory = StorageEngineFactory.get(configuration); if (storageEngine == null || storageEngine.isEmpty()) { this.alignmentStorageManager = storageEngineFactory.getAlignmentStorageEngine(null, dbName); } else { this.alignmentStorageManager = storageEngineFactory.getAlignmentStorageEngine(storageEngine, dbName); } }
public BenchmarkRunner(StorageConfiguration storageConfiguration, Path jmeterHome, Path outdir) throws IOException { StorageEngineFactory.configure(storageConfiguration); this.storageConfiguration = storageConfiguration; storageEngine = storageConfiguration.getDefaultStorageEngineId(); dbName = storageConfiguration.getBenchmark().getDatabaseName(); this.jmeterHome = jmeterHome; this.outdir = outdir; init(); }
public void clearStorageDB(String dbName) { clearStorageDB(getStorageConfiguration().getDefaultStorageEngineId(), dbName); }
@Test public void testSkipVariant() throws VariantAnnotatorException { ObjectMap options = new ObjectMap(VariantAnnotationManager.ANNOTATOR, VariantAnnotatorFactory.AnnotationSource.OTHER.toString()) .append(VariantAnnotationManager.VARIANT_ANNOTATOR_CLASSNAME, TestCellBaseRestVariantAnnotator.class.getName()); VariantAnnotator variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(TestCellBaseRestVariantAnnotator.class))); TestCellBaseRestVariantAnnotator testAnnotator = (TestCellBaseRestVariantAnnotator) variantAnnotator; testAnnotator.skip("10:1000:A:C"); List<VariantAnnotation> annotate = testAnnotator.annotate(Arrays.asList(new Variant("10:999:A:C"), new Variant("10:1000:A:C"), new Variant("10:1001:A:C"))); assertEquals(2, annotate.size()); }
@Test public void testErrorVariant() throws VariantAnnotatorException { ObjectMap options = new ObjectMap(VariantAnnotationManager.ANNOTATOR, VariantAnnotatorFactory.AnnotationSource.OTHER.toString()) .append(VariantAnnotationManager.VARIANT_ANNOTATOR_CLASSNAME, TestCellBaseRestVariantAnnotator.class.getName()); VariantAnnotator variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(TestCellBaseRestVariantAnnotator.class))); TestCellBaseRestVariantAnnotator testAnnotator = (TestCellBaseRestVariantAnnotator) variantAnnotator; testAnnotator.remove("10:1000:A:C"); Exception exception = AbstractCellBaseVariantAnnotator.unexpectedVariantOrderException("10:1000:A:C", "10:1001:A:C"); thrown.expect(exception.getClass()); thrown.expectMessage(exception.getMessage()); testAnnotator.annotate(Arrays.asList(new Variant("10:999:A:C"), new Variant("10:1000:A:C"), new Variant("10:1001:A:C"))); }
@Test public void testVariantFactory() throws Exception { ObjectMap options = new ObjectMap(VariantAnnotationManager.ANNOTATOR, VariantAnnotatorFactory.AnnotationSource.CELLBASE_DB_ADAPTOR); VariantAnnotator variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(CellBaseDirectVariantAnnotator.class))); storageConfiguration.getStorageEngine().getVariant().getOptions().put(VariantAnnotationManager.ANNOTATOR, VariantAnnotatorFactory.AnnotationSource.CELLBASE_DB_ADAPTOR.toString()); options = new ObjectMap(); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(CellBaseDirectVariantAnnotator.class))); options = new ObjectMap(VariantAnnotationManager.ANNOTATOR, null); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(CellBaseDirectVariantAnnotator.class))); storageConfiguration.getStorageEngine().getVariant().getOptions().put(VariantAnnotationManager.ANNOTATOR, VariantAnnotatorFactory.AnnotationSource.CELLBASE_REST); options = new ObjectMap(VariantAnnotationManager.ANNOTATOR, null); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(CellBaseRestVariantAnnotator.class))); storageConfiguration.getStorageEngine().getVariant().getOptions().remove(VariantAnnotationManager.ANNOTATOR); options = new ObjectMap(); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(CellBaseRestVariantAnnotator.class))); options = new ObjectMap(VariantAnnotationManager.ANNOTATOR, VariantAnnotatorFactory.AnnotationSource.OTHER.toString()) .append(VariantAnnotationManager.VARIANT_ANNOTATOR_CLASSNAME, TestCellBaseRestVariantAnnotator.class.getName()); variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageConfiguration.getDefaultStorageEngineId(), projectMetadata, options); assertThat(variantAnnotator, is(instanceOf(TestCellBaseRestVariantAnnotator.class))); }