@Deprecated protected MongoDBAdaptorFactory(List<DataStoreServerAddress> dataStoreServerAddressList, MongoDBConfiguration configuration, String database) throws CatalogDBException { // super(LoggerFactory.getLogger(CatalogMongoDBAdaptor.class)); this.mongoManager = new MongoDataStoreManager(dataStoreServerAddressList); this.configuration = configuration; this.database = database; logger = LoggerFactory.getLogger(this.getClass()); connect(); }
public VariantMongoDBAdaptor(MongoCredentials credentials, String variantsCollectionName, StudyConfigurationManager studyConfigurationManager, StorageConfiguration storageConfiguration) throws UnknownHostException { this(new MongoDataStoreManager(credentials.getDataStoreServerAddresses()), credentials, variantsCollectionName, studyConfigurationManager, storageConfiguration); this.closeConnection = true; }
private synchronized MongoDataStoreManager getMongoDataStoreManager() { if (mongoDataStoreManager == null) { mongoDataStoreManager = new MongoDataStoreManager(getMongoCredentials().getDataStoreServerAddresses()); } return mongoDataStoreManager; }
private void init() { if (mongoDataStoreManager == null) { // String[] hosts = cellBaseConfiguration.getDatabases().get("mongodb").getHost().split(","); String[] hosts = cellBaseConfiguration.getDatabases().getMongodb().getHost().split(","); List<DataStoreServerAddress> dataStoreServerAddresses = new ArrayList<>(hosts.length); for (String host : hosts) { String[] hostPort = host.split(":"); if (hostPort.length == 1) { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort[0], 27017)); } else { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort[0], Integer.parseInt(hostPort[1]))); } } mongoDataStoreManager = new MongoDataStoreManager(dataStoreServerAddresses); logger.debug("MongoDBAdaptorFactory constructor, this should be only be printed once"); } // logger = LoggerFactory.getLogger(this.getClass()); }
private void init() { if (mongoDataStoreManager == null) { // String[] hosts = cellBaseConfiguration.getDatabases().get("mongodb").getHost().split(","); String[] hosts = cellBaseConfiguration.getDatabases().getMongodb().getHost().split(","); List<DataStoreServerAddress> dataStoreServerAddresses = new ArrayList<>(hosts.length); for (String host : hosts) { String[] hostPort = host.split(":"); if (hostPort.length == 1) { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort[0], 27017)); } else { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort[0], Integer.parseInt(hostPort[1]))); } } mongoDataStoreManager = new MongoDataStoreManager(dataStoreServerAddresses); logger.debug("MongoDBAdaptorFactory constructor, this should be only be printed once"); } // logger = LoggerFactory.getLogger(this.getClass()); }
public void clearStorageDB(String storageEngine, String dbName) { if (storageEngine.equalsIgnoreCase("MONGODB")) { logger.info("Cleaning MongoDB {}", dbName); MongoDataStoreManager mongoManager = new MongoDataStoreManager("localhost", 27017); MongoDataStore mongoDataStore = mongoManager.get(dbName); mongoManager.drop(dbName); } else { throw new UnsupportedOperationException(); } }
private void clearCatalog() throws URISyntaxException { List<DataStoreServerAddress> dataStoreServerAddresses = new LinkedList<>(); for (String hostPort : configuration.getCatalog().getDatabase().getHosts()) { if (hostPort.contains(":")) { String[] split = hostPort.split(":"); Integer port = Integer.valueOf(split[1]); dataStoreServerAddresses.add(new DataStoreServerAddress(split[0], port)); } else { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort, 27017)); } } MongoDataStoreManager mongoManager = new MongoDataStoreManager(dataStoreServerAddresses); // MongoDataStore db = mongoManager.get(catalogConfiguration.getDatabase().getDatabase()); MongoDataStore db = mongoManager.get(getCatalogDatabase()); db.getDb().drop(); // mongoManager.close(catalogConfiguration.getDatabase().getDatabase()); mongoManager.close(getCatalogDatabase()); Path rootdir = Paths.get(UriUtils.createDirectoryUri(configuration.getDataDir())); deleteFolderTree(rootdir.toFile()); if (!configuration.getTempJobsDir().isEmpty()) { Path jobsDir = Paths.get(UriUtils.createDirectoryUri(configuration.getTempJobsDir())); if (jobsDir.toFile().exists()) { deleteFolderTree(jobsDir.toFile()); } } }
public MongoDBVariantFileMetadataDBAdaptor(MongoCredentials credentials, String collectionName) throws UnknownHostException { // Mongo configuration mongoManager = new MongoDataStoreManager(credentials.getDataStoreServerAddresses()); MongoDBConfiguration mongoDBConfiguration = credentials.getMongoDBConfiguration(); db = mongoManager.get(credentials.getMongoDbName(), mongoDBConfiguration); this.collectionName = collectionName; variantFileMetadataConverter = new DocumentToVariantFileMetadataConverter(); }
public MongoDBAdaptorFactory(Configuration catalogConfiguration) throws CatalogDBException { MongoDBConfiguration mongoDBConfiguration = MongoDBConfiguration.builder() .setUserPassword( catalogConfiguration.getCatalog().getDatabase().getUser(), catalogConfiguration.getCatalog().getDatabase().getPassword()) .load(catalogConfiguration.getCatalog().getDatabase().getOptions()) .build(); List<DataStoreServerAddress> dataStoreServerAddresses = new LinkedList<>(); for (String hostPort : catalogConfiguration.getCatalog().getDatabase().getHosts()) { if (hostPort.contains(":")) { String[] split = hostPort.split(":"); int port = Integer.valueOf(split[1]); dataStoreServerAddresses.add(new DataStoreServerAddress(split[0], port)); } else { dataStoreServerAddresses.add(new DataStoreServerAddress(hostPort, 27017)); } } this.mongoManager = new MongoDataStoreManager(dataStoreServerAddresses); this.configuration = mongoDBConfiguration; this.database = getCatalogDatabase(catalogConfiguration.getDatabasePrefix()); logger = LoggerFactory.getLogger(this.getClass()); connect(); }
@Override public boolean check() { try (MongoDataStoreManager mongoManager = new MongoDataStoreManager(getDataStoreServerAddresses())) { MongoDataStore db = mongoManager.get(getMongoDbName(), getMongoDBConfiguration()); MongoIterable<String> strings = db.getDb().listCollectionNames(); int count = 0; for (String string : strings) { count++; } return true; } catch (MongoException e) { //FIXME: Throw IllegalOpenCGACredentialsException ?? return false; } }
? Integer.parseInt(hostAndPort[1]) : 27017)); mongoDataStoreManager = new MongoDataStoreManager(dataStoreServerAddressList);
default MongoDataStoreManager getMongoDataStoreManager(String dbName) throws Exception { MongoCredentials credentials = getVariantStorageEngine().getMongoCredentials(); return new MongoDataStoreManager(credentials.getDataStoreServerAddresses()); }
? Integer.parseInt(hostAndPort[1]) : 27017)); mongoDataStoreManager = new MongoDataStoreManager(dataStoreServerAddressList);
MongoDataStoreManager mongoManager = new MongoDataStoreManager(dataStoreServerAddresses);
default void clearDB(String dbName) throws Exception { MongoCredentials credentials = getVariantStorageEngine().getMongoCredentials(); logger.info("Cleaning MongoDB {}", credentials.getMongoDbName()); try (MongoDataStoreManager mongoManager = new MongoDataStoreManager(credentials.getDataStoreServerAddresses())) { mongoManager.get(credentials.getMongoDbName(), credentials.getMongoDBConfiguration()); mongoManager.drop(credentials.getMongoDbName()); } }
MongoDataStoreManager mongoManager = new MongoDataStoreManager(dataStoreServerAddress.getHost(), dataStoreServerAddress.getPort()); MongoDataStore db = mongoManager.get(database); db.getDb().drop();
MongoDataStoreManager mongoManager = new MongoDataStoreManager(dataStoreServerAddress.getHost(), dataStoreServerAddress.getPort()); MongoDataStore db = mongoManager.get(database); db.getDb().drop();