public ObjectMap getOptions() { return configuration.getStorageEngine(storageEngineId).getVariant().getOptions(); }
public GrpcStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
private String buildOutputFileName() { return dbName + "." + "benchmark" + "." + storageConfiguration.getBenchmark().getMode(); }
private void checkParams() { if (configuration.getBenchmark().getDatabaseName() == null || configuration.getBenchmark().getDatabaseName().isEmpty()) { throw new ParameterException("Database name is null or empty. Please provide database name."); } if (configuration.getBenchmark().getTable() == null || configuration.getBenchmark().getTable().isEmpty()) { throw new ParameterException("Table name is null or empty. Please provide table name."); } if (configuration.getBenchmark().getDatabase().getHosts() == null || configuration.getBenchmark().getDatabase().getHosts().isEmpty()) { throw new ParameterException("Database name is null or empty. Please provide Database name."); } }
private void annotationDelete() throws VariantAnnotatorException, StorageEngineException { StorageVariantCommandOptions.AnnotationDeleteCommandOptions cliOptions = variantCommandOptions.annotationDeleteCommandOptions; ObjectMap options = storageConfiguration.getVariant().getOptions(); options.putAll(cliOptions.commonOptions.params); variantStorageEngine.deleteAnnotation(cliOptions.annotationId, options); }
public StorageEngine(StorageConfiguration configuration) { this(configuration.getDefaultStorageEngineId(), configuration); // this.configuration = configuration; }
public static StorageConfiguration load(InputStream configurationInputStream) throws IOException { return load(configurationInputStream, "yaml"); }
public StorageEngineConfiguration getStorageEngine() { return getStorageEngine(defaultStorageEngineId); }
private void init(String storageEngine) throws IllegalAccessException, InstantiationException, ClassNotFoundException, StorageEngineException { StorageEngineFactory storageEngineFactory = StorageEngineFactory.get(storageConfiguration); VariantStorageEngine variantStorageEngine = storageEngineFactory.getVariantStorageEngine(storageEngine, storageConfiguration.getBenchmark().getDatabaseName()); variantDBAdaptor = variantStorageEngine.getDBAdaptor(); }
public StorageConfiguration(String defaultStorageEngineId, List<StorageEngineConfiguration> storageEngines) { this.defaultStorageEngineId = defaultStorageEngineId; this.storageEngines = storageEngines; this.cellbase = new CellBaseConfiguration(); this.server = new ServerConfiguration(); this.cache = new CacheConfiguration(); this.search = new SearchConfiguration(); this.clinical = new SearchConfiguration(); }
public void addStorageEngine(InputStream configurationInputStream) throws IOException { addStorageEngine(configurationInputStream, "yaml"); }
public VariantStoragePipeline(StorageConfiguration configuration, String storageEngineId, VariantDBAdaptor dbAdaptor, VariantReaderUtils variantReaderUtils) { this(configuration, storageEngineId, dbAdaptor, variantReaderUtils, new ObjectMap(configuration.getStorageEngine(storageEngineId).getVariant().getOptions())); }
public AbstractStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
public VariantBenchmarkRunner(StorageConfiguration storageConfiguration) throws IllegalAccessException, ClassNotFoundException, InstantiationException, StorageEngineException { this(storageConfiguration.getDefaultStorageEngineId(), storageConfiguration); }
public RestStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
public String getDefaultStorageEngineId() { return storageConfiguration.getDefaultStorageEngineId(); }
public GrpcStorageServer(StorageConfiguration storageConfiguration) { super(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); GrpcStorageServer.storageConfiguration = storageConfiguration; logger = LoggerFactory.getLogger(this.getClass()); }
public GenericGrpcService(StorageConfiguration storageConfiguration) { this(storageConfiguration, storageConfiguration.getDefaultStorageEngineId()); }
public VariantStorageEngine(StorageConfiguration configuration) { this(configuration.getDefaultStorageEngineId(), configuration); }