public StorageEngineConfiguration getStorageEngine() { return getStorageEngine(defaultStorageEngineId); }
public static StorageConfiguration load(InputStream configurationInputStream) throws IOException { return load(configurationInputStream, "yaml"); }
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 AbstractStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
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 VariantSearchManager(StudyConfigurationManager studyConfigurationManager, StorageConfiguration storageConfiguration) { this.storageConfiguration = storageConfiguration; this.solrQueryParser = new SolrQueryParser(studyConfigurationManager); this.cellBaseClient = new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration()); this.variantSearchToVariantConverter = new VariantSearchToVariantConverter(); this.solrManager = new SolrManager(storageConfiguration.getSearch().getHosts(), storageConfiguration.getSearch().getMode(), storageConfiguration.getSearch().getTimeout()); // Set internal insert batch size from configuration and default value insertBatchSize = storageConfiguration.getSearch().getInsertBatchSize() > 0 ? storageConfiguration.getSearch().getInsertBatchSize() : DEFAULT_INSERT_BATCH_SIZE; logger = LoggerFactory.getLogger(VariantSearchManager.class); }
@Test public void testDefault() throws Exception { StorageConfiguration storageConfiguration = new StorageConfiguration(); new ServerConfiguration(9090, 9091, "mongodb", Arrays.asList("localhost"), Collections.emptyMap()); storageConfiguration.setDefaultStorageEngineId("mongodb"); storageConfiguration.setCellbase(cellBaseConfiguration); storageConfiguration.setServer(serverConfiguration); storageConfiguration.getStorageEngines().add(storageEngineConfiguration1); storageConfiguration.getStorageEngines().add(storageEngineConfiguration2); storageConfiguration.serialize(os); StorageConfiguration.load(is, "yml");
public void start() throws Exception { StorageConfiguration storageConfiguration = configuration; if (StringUtils.isNotEmpty(restServerCommandOptions.commonOptions.configFile)) { Path path = Paths.get(restServerCommandOptions.commonOptions.configFile); if (Files.exists(path)) { storageConfiguration = StorageConfiguration.load(Files.newInputStream(path)); } } // Setting CLI params in the StorageConfiguration if (restServerCommandOptions.port > 0) { storageConfiguration.getServer().setRest(restServerCommandOptions.port); } if (StringUtils.isNotEmpty(restServerCommandOptions.commonOptions.storageEngine)) { storageConfiguration.setDefaultStorageEngineId(restServerCommandOptions.commonOptions.storageEngine); } if (StringUtils.isNotEmpty(restServerCommandOptions.authManager)) { storageConfiguration.getServer().setAuthManager(restServerCommandOptions.authManager); } // Server crated and started RestStorageServer server = new RestStorageServer(storageConfiguration); server.start(); server.blockUntilShutdown(); logger.info("Shutting down OpenCGA Storage REST server"); }
public StorageEngine(StorageConfiguration configuration) { this(configuration.getDefaultStorageEngineId(), configuration); // this.configuration = configuration; }
if (this.configFile != null) { loadedConfigurationFile = this.configFile; this.configuration = StorageConfiguration.load(new FileInputStream(new File(this.configFile))); } else { if (appHome != null && Files.exists(path)) { loadedConfigurationFile = path.toString(); this.configuration = StorageConfiguration.load(new FileInputStream(path.toFile())); } else { loadedConfigurationFile = StorageConfiguration.class.getClassLoader().getResourceAsStream("storage-configuration.yml") .toString(); this.configuration = StorageConfiguration .load(StorageConfiguration.class.getClassLoader().getResourceAsStream("storage-configuration.yml")); this.logLevel = this.configuration.getLogLevel(); configureDefaultLog(this.logLevel); } else { if (!this.logLevel.equalsIgnoreCase(this.configuration.getLogLevel())) { this.configuration.setLogLevel(this.logLevel); configureDefaultLog(this.logLevel); this.configuration.setLogFile(logFile); if (this.configuration.getLogFile() != null && !this.configuration.getLogFile().isEmpty()) { org.apache.log4j.Logger rootLogger = LogManager.getRootLogger(); + "%m%n"), this.configuration.getLogFile(), true); rollingFileAppender.setThreshold(Level.toLevel(configuration.getLogLevel())); rootLogger.addAppender(rollingFileAppender);
static StorageConfiguration updateStorageConfiguration(StorageConfiguration storageConfiguration, Configuration conf) throws IOException { storageConfiguration.setDefaultStorageEngineId(HadoopVariantStorageEngine.STORAGE_ENGINE_ID); StorageEtlConfiguration variantConfiguration = storageConfiguration.getStorageEngine(HadoopVariantStorageEngine.STORAGE_ENGINE_ID).getVariant(); ObjectMap options = variantConfiguration.getOptions();
protected boolean searchActiveAndAlive() throws StorageEngineException { return configuration.getSearch().isActive() && getVariantSearchManager() != null && getVariantSearchManager().isAlive(dbName); }
private String buildOutputFileName() { return dbName + "." + "benchmark" + "." + storageConfiguration.getBenchmark().getMode(); }
public TieringAnalysis(String opencgaHome, String studyStr, String token, String clinicalAnalysisId, List<String> diseasePanelIds, ObjectMap config) { super(opencgaHome, studyStr, token); this.clinicalAnalysisId = clinicalAnalysisId; this.diseasePanelIds = diseasePanelIds; this.maxCoverage = 20; this.cellBaseClient = new CellBaseClient(storageConfiguration.getCellbase().toClientConfiguration()); this.alignmentStorageManager = new AlignmentStorageManager(catalogManager, StorageEngineFactory.get(storageConfiguration)); }
StorageEngineFactory factory = opencga.getStorageEngineFactory(); StorageConfiguration storageConfiguration = factory.getStorageConfiguration(); storageConfiguration.setDefaultStorageEngineId(STORAGE_ENGINE_DUMMY); storageConfiguration.getStorageEngines().clear(); storageConfiguration.getStorageEngines().add(new StorageEngineConfiguration( STORAGE_ENGINE_DUMMY, new StorageEtlConfiguration(),
public void stop() { int port = configuration.getServer().getRest(); if (restServerCommandOptions.port > 0) { port = restServerCommandOptions.port; } Client client = ClientBuilder.newClient(); WebTarget target = client.target("http://localhost:" + port) .path("opencga") .path("webservices") .path("rest") .path("admin") .path("stop"); Response response = target.request().get(); logger.info(response.toString()); }
public GrpcStorageServer() { this(storageConfiguration.getServer().getGrpc(), storageConfiguration.getDefaultStorageEngineId()); }
Path path = Paths.get(grpcServerCommandOptions.commonOptions.configFile); if (Files.exists(path)) { storageConfiguration = StorageConfiguration.load(Files.newInputStream(path)); storageConfiguration.getServer().setGrpc(grpcServerCommandOptions.port); storageConfiguration.setDefaultStorageEngineId(grpcServerCommandOptions.commonOptions.storageEngine); storageConfiguration.getServer().setAuthManager(grpcServerCommandOptions.authManager);
public VariantBenchmarkRunner(StorageConfiguration storageConfiguration) throws IllegalAccessException, ClassNotFoundException, InstantiationException, StorageEngineException { this(storageConfiguration.getDefaultStorageEngineId(), storageConfiguration); }