public static StorageConfiguration load(InputStream configurationInputStream) throws IOException { return load(configurationInputStream, "yaml"); }
/** * This method attempts to load storage configuration from OpenCGA installation folder, if not exists then loads JAR storage-configuration.yml. * * @throws IOException If any IO problem occurs */ public void loadStorageConfiguration() throws IOException { FileUtils.checkDirectory(Paths.get(this.opencgaHome)); // We load configuration file either from app home folder or from the JAR Path path = Paths.get(this.opencgaHome).resolve("conf").resolve("storage-configuration.yml"); if (Files.exists(path)) { logger.debug("Loading storage configuration from '{}'", path.toAbsolutePath()); this.storageConfiguration = StorageConfiguration.load(new FileInputStream(path.toFile())); } else { logger.debug("Loading storage configuration from JAR file"); this.storageConfiguration = StorageConfiguration .load(StorageConfiguration.class.getClassLoader().getResourceAsStream("storage-configuration.yml")); } }
static StorageConfiguration getStorageConfiguration(Configuration conf) throws IOException { StorageConfiguration storageConfiguration; try (InputStream is = HadoopVariantStorageTest.class.getClassLoader().getResourceAsStream("storage-configuration.yml")) { storageConfiguration = StorageConfiguration.load(is); } return updateStorageConfiguration(storageConfiguration, conf); }
@Test public void testLoad() throws Exception { StorageConfiguration storageConfiguration = StorageConfiguration.load(getClass().getResource("/storage-configuration-test.yml") .openStream()); System.out.println("storageConfiguration = " + storageConfiguration); }
default MongoDBVariantStorageEngine newVariantStorageEngine() throws Exception { synchronized (managers) { MongoDBVariantStorageEngine storageManager = new MongoDBVariantStorageEngine(); InputStream is = MongoDBVariantStorageTest.class.getClassLoader().getResourceAsStream("storage-configuration.yml"); StorageConfiguration storageConfiguration = StorageConfiguration.load(is); storageManager.setConfiguration(storageConfiguration, MongoDBVariantStorageEngine.STORAGE_ENGINE_ID, DB_NAME); managers.add(storageManager); return storageManager; } }
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"));
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"); }
default MongoDBVariantStorageEngine getVariantStorageEngine() throws Exception { synchronized (manager) { MongoDBVariantStorageEngine storageManager = manager.get(); if (storageManager == null) { storageManager = new MongoDBVariantStorageEngine(); manager.set(storageManager); } InputStream is = MongoDBVariantStorageTest.class.getClassLoader().getResourceAsStream("storage-configuration.yml"); StorageConfiguration storageConfiguration = StorageConfiguration.load(is); storageManager.setConfiguration(storageConfiguration, MongoDBVariantStorageEngine.STORAGE_ENGINE_ID, DB_NAME); return storageManager; } }
@Before public void setUp() throws Exception { storageConfiguration = StorageConfiguration.load(StorageManager.class.getClassLoader().getResourceAsStream("storage-configuration.yml"), "yml"); projectMetadata = new ProjectMetadata("hsapiens", "grch38", 1); }
@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; } }
Path path = Paths.get(grpcServerCommandOptions.commonOptions.configFile); if (Files.exists(path)) { storageConfiguration = StorageConfiguration.load(Files.newInputStream(path));
@Override protected void setup(Context context) throws IOException, InterruptedException { super.setup(context); this.forceAnnotation = context.getConfiguration().getBoolean(CONFIG_VARIANT_TABLE_ANNOTATE_FORCE, false); /* Annotation -> Phoenix converter */ annotationConverter = new VariantAnnotationToPhoenixConverter(getHelper().getColumnFamily()); columnsOrdered = VariantPhoenixHelper.VariantColumn.values(); /* Annotator config */ String configFile = "storage-configuration.yml"; String storageEngine = "hadoop"; // ObjectMap options = new ObjectMap(); // empty ProjectMetadata projectMetadata; try (StudyConfigurationManager scm = new StudyConfigurationManager(new HBaseVariantStorageMetadataDBAdaptorFactory(getHelper()))) { projectMetadata = scm.getProjectMetadata().first(); } try { // FIXME! This is WRONG. Should read StorageConfigurationFile from client StorageConfiguration storageConfiguration = StorageConfiguration.load( StorageConfiguration.class.getClassLoader().getResourceAsStream(configFile)); this.variantAnnotator = VariantAnnotatorFactory.buildVariantAnnotator(storageConfiguration, storageEngine, projectMetadata, options); } catch (Exception e) { throw new IllegalStateException("Problems loading storage configuration from " + configFile, e); } } private final CopyOnWriteArrayList<Variant> variantsToAnnotate = new CopyOnWriteArrayList<>();
InputStream inputStream = StorageManager.class.getClassLoader().getResourceAsStream("storage-configuration.yml"); storageConfiguration = StorageConfiguration.load(inputStream, "yml");
StorageConfiguration.load(is, "yml");