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(); } }
@Override public void close() { if (mongoManager != null) { mongoManager.close(); } }
public MongoDataStoreManager(DataStoreServerAddress dataStoreServerAddress) { init(); this.addServerAddress(dataStoreServerAddress); }
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(); }
@Override public ObjectMap getDatabaseStatus() { Document dbStatus = mongoManager.get(database, this.configuration).getServerStatus(); try { ObjectMap map = new ObjectMap(getDefaultObjectMapper().writeValueAsString(dbStatus)); return new ObjectMap("ok", map.getInt("ok", 0) > 0); } catch (JsonProcessingException e) { logger.error(e.getMessage(), e); return new ObjectMap(); } }
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 VariantMongoDBAdaptor(MongoCredentials credentials, String variantsCollectionName, StudyConfigurationManager studyConfigurationManager, StorageConfiguration storageConfiguration) throws UnknownHostException { this(new MongoDataStoreManager(credentials.getDataStoreServerAddresses()), credentials, variantsCollectionName, studyConfigurationManager, storageConfiguration); this.closeConnection = true; }
@Override public void deleteCatalogDB() throws CatalogDBException { mongoManager.drop(database); }
@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; } }
@Override public void installCatalogDB(Configuration configuration) throws CatalogException { // TODO: Check META object does not exist. Use {@link isCatalogDBReady} // TODO: Check all collections do not exists, or are empty // TODO: Catch DuplicatedKeyException while inserting META object MongoDataStore mongoDataStore = mongoManager.get(database, this.configuration); if (!mongoDataStore.getCollectionNames().isEmpty()) { throw new CatalogException("Database " + database + " already exists with the following collections: " + StringUtils.join(mongoDataStore.getCollectionNames()) + ".\nPlease, remove the database or choose a different one."); } COLLECTIONS_LIST.forEach(mongoDataStore::createCollection); metaDBAdaptor.createIndexes(); metaDBAdaptor.initializeMetaCollection(configuration); }
MongoDataStoreManager mongoManager = new MongoDataStoreManager(dataStoreServerAddresses); MongoDataStore db = mongoManager.get(catalogManager.getCatalogDatabase()); db.getDb().drop(); mongoManager.close(catalogManager.getCatalogDatabase());
@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(); }
? Integer.parseInt(hostAndPort[1]) : 27017)); mongoDataStoreManager = new MongoDataStoreManager(dataStoreServerAddressList); mongodbCredentials.getUser(), mongodbCredentials.getPassword()); mongoDataStore = mongoDataStoreManager.get(database, mongoDBConfiguration);
public MongoDataStore get(String database) { return get(database, builder().init().build()); }
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()); } }
private synchronized MongoDataStoreManager getMongoDataStoreManager() { if (mongoDataStoreManager == null) { mongoDataStoreManager = new MongoDataStoreManager(getMongoCredentials().getDataStoreServerAddresses()); } return mongoDataStoreManager; }
@Override public void close() { mongoDataStoreManager.close(database); }
public MongoDataStoreManager(String host, int port) { init(); this.addServerAddress(new DataStoreServerAddress(host, port)); }
? Integer.parseInt(hostAndPort[1]) : 27017)); mongoDataStoreManager = new MongoDataStoreManager(dataStoreServerAddressList); mongodbCredentials.getUser(), mongodbCredentials.getPassword()); mongoDataStore = mongoDataStoreManager.get(database, mongoDBConfiguration);
MongoDataStore mongoDatastore = mongoDataStoreManager.get(database, mongoDBConfiguration);