public MongoCredentials(DatabaseCredentials database, String dbName) throws IllegalOpenCGACredentialsException { this(MongoCredentials.parseDataStoreServerAddresses(database.getHosts()), dbName, database.getUser(), database.getPassword(), database.getOptions(), false); }
public CellBaseConfiguration() { this(Arrays.asList(CELLBASE_HOST), CELLBASE_VERSION, new DatabaseCredentials()); }
String user = db.getUser(); String pass = db.getPassword(); List<String> hostList = db.getHosts(); if (hostList != null && hostList.size() > 1) { throw new IllegalStateException("Expect only one server name");
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."); } }
@Test public void transformIsolated() throws Exception { ObjectMap params = new ObjectMap(); URI outputUri = newOutputUri(); VariantStorageEngine variantStorageManager = getVariantStorageEngine(); variantStorageManager.getConfiguration().getStorageEngine(variantStorageManager.getStorageEngineId()).getVariant().getDatabase() .setHosts(Collections.singletonList("1.1.1.1")); StoragePipelineResult etlResult = runETL(variantStorageManager, smallInputUri, outputUri, params, true, true, false); System.out.println("etlResult = " + etlResult); String[] malformedFiles = Paths.get(outputUri).toFile().list((dir, name) -> name.contains(MALFORMED_FILE)); assertEquals(0, malformedFiles.length); }
options.put(VariantStorageEngine.Options.MERGE_MODE.key(), VariantStorageEngine.MergeMode.BASIC); variantConfiguration.getDatabase().setHosts(Collections.singletonList("hbase://" + HadoopVariantStorageTest.configuration.get().get(HConstants.ZOOKEEPER_QUORUM))); return storageConfiguration;
List<String> hosts = storageConfiguration.getCellbase().getDatabase().getHosts(); String hostsString = StringUtils.join(hosts, ","); checkNotNull(hostsString, "cellbase database host"); databaseCredentials.setHost(hostsString); databaseCredentials.setPassword(storageConfiguration.getCellbase().getDatabase().getPassword()); databaseCredentials.setUser(storageConfiguration.getCellbase().getDatabase().getUser()); databaseCredentials.setOptions(storageConfiguration.getCellbase().getDatabase().getOptions()); databases.setMongodb(databaseCredentials); cellBaseConfiguration.setDatabases(databases);
"mongodb", new StorageEtlConfiguration("org.opencb.opencga.storage.mongodb.alignment.MongoDBAlignmentStorageManager", new ObjectMap (), new DatabaseCredentials(Arrays.asList("mongodb-dev:27017"), "user", "password")), new StorageEtlConfiguration("org.opencb.opencga.storage.mongodb.alignment.MongoDBVariantStorageManager", new ObjectMap(), new DatabaseCredentials(Arrays.asList("mongodb-dev:27017"), "user", "password")), options); "hadoop", new StorageEtlConfiguration("org.opencb.opencga.storage.hadoop.alignment.HadoopAlignmentStorageManager", new ObjectMap(), new DatabaseCredentials(Arrays.asList("who-master:60000"), "user", "password")), new StorageEtlConfiguration("org.opencb.opencga.storage.hadoop.alignment.HadoopVariantStorageManager", new ObjectMap(), new DatabaseCredentials(Arrays.asList("who-master:60000"), "user", "password")), options); CellBaseConfiguration cellBaseConfiguration = new CellBaseConfiguration(Arrays.asList("localhost"), "v3", new DatabaseCredentials (Arrays.asList("localhost"), "user", "password")); ServerConfiguration serverConfiguration =
STORAGE_ENGINE_DUMMY, new StorageEtlConfiguration(), new StorageEtlConfiguration(DummyVariantStorageEngine.class.getName(), new ObjectMap(), new DatabaseCredentials()), new ObjectMap() ));