public AuthenticationOrigin(String id, String type, String host, Map<String, Object> options) { this.id = id; this.type = AuthenticationType.valueOf(type); this.host = host; this.options = options; }
AuthenticationOrigin getAuthenticationOrigin(String authOrigin) { if (configuration.getAuthentication().getAuthenticationOrigins() != null) { for (AuthenticationOrigin authenticationOrigin : configuration.getAuthentication().getAuthenticationOrigins()) { if (authOrigin.equals(authenticationOrigin.getId())) { return authenticationOrigin; } } } return null; }
JwtManager(Configuration configuration) { this.configuration = configuration; this.secretKey = this.configuration.getAdmin().getSecretKey(); this.expiration = this.configuration.getAuthentication().getExpiration(); logger = LoggerFactory.getLogger(JwtManager.class); }
public CatalogSolrManager(CatalogManager catalogManager) { this.catalogManager = catalogManager; SearchConfiguration searchConfiguration = catalogManager.getConfiguration().getCatalog().getSearch(); this.solrManager = new SolrManager(searchConfiguration.getHosts(), searchConfiguration.getMode(), searchConfiguration.getTimeout()); insertBatchSize = searchConfiguration.getInsertBatchSize() > 0 ? searchConfiguration.getInsertBatchSize() : DEFAULT_INSERT_BATCH_SIZE; DATABASE_PREFIX = catalogManager.getConfiguration().getDatabasePrefix() + "_"; populateConfigCollectionMap(); logger = LoggerFactory.getLogger(CatalogSolrManager.class); }
public void createSolrCollections() { if (catalogManager.getConfiguration().getCatalog().getSearch().getMode().equals("cloud")) { createCatalogSolrCollections(); } else { createCatalogSolrCores(); } }
public void initializeMetaCollection(Configuration configuration) throws CatalogException { Admin admin = configuration.getAdmin(); admin.setPassword(CatalogAuthenticationManager.cypherPassword(admin.getPassword())); Metadata metadata = new Metadata().setIdCounter(configuration.getCatalog().getOffset()).setVersion(VERSION); Document metadataObject = getMongoDBDocument(metadata, "Metadata"); metadataObject.put(PRIVATE_ID, MongoDBAdaptorFactory.METADATA_OBJECT_ID); Document adminDocument = getMongoDBDocument(admin, "Admin"); metadataObject.put("admin", adminDocument); metaCollection.insert(metadataObject, null); }
private void initializeAdmin() throws CatalogDBException { if (StringUtils.isEmpty(this.configuration.getAdmin().getSecretKey())) { this.configuration.getAdmin().setSecretKey(this.catalogDBAdaptorFactory.getCatalogMetaDBAdaptor().readSecretKey()); } this.configuration.getAdmin().setAlgorithm("HS256"); // if (StringUtils.isEmpty(this.configuration.getAdmin().getAlgorithm())) { // this.configuration.getAdmin().setAlgorithm(this.catalogDBAdaptorFactory.getCatalogMetaDBAdaptor().readAlgorithm()); // } }
public static Configuration load(InputStream configurationInputStream) throws IOException { return load(configurationInputStream, DEFAULT_CONFIGURATION_FORMAT); }
private static String getDefaultQueue() throws Exception { if (StringUtils.isEmpty(configuration.getExecution().getDefaultQueue())) { throw new Exception("Execution default queue is not defined!"); } return configuration.getExecution().getDefaultQueue(); }
private static List<String> getQueueList() { if (configuration.getExecution().getAvailableQueues() != null) { String[] queueArray = configuration.getExecution().getAvailableQueues().split(","); return Arrays.asList(queueArray); } else { return new ArrayList<>(); } }
public String getCatalogDatabase() { return catalogDBAdaptorFactory.getCatalogDatabase(configuration.getDatabasePrefix()); }
String getSecretKey() { if (StringUtils.isEmpty(secretKey)) { secretKey = configuration.getAdmin().getSecretKey(); } return secretKey; }
@Deprecated public String getHost() { return String.join(",", getHosts()); }
public ExecutorManager(Configuration configuration) { if (configuration != null) { if (configuration.getExecution().getMode().equalsIgnoreCase("local")) { this.executor = new LocalExecutor(); } else if (configuration.getExecution().getMode().equalsIgnoreCase("sge")) { // init sge executor this.executor = new SGEExecutor(configuration); System.out.println("SGE not ready"); } } if (executor == null) { // Load default executor this.executor = new LocalExecutor(); } }
public void deleteCatalogDB(boolean force) throws CatalogException, URISyntaxException { if (!force) { userManager.validatePassword("admin", configuration.getAdmin().getPassword(), true); } catalogDBAdaptorFactory.deleteCatalogDB(); clearCatalog(); }
private String getDefaultQueue() { return execution.getDefaultQueue(); }
private List<String> getQueueList() { return Arrays.asList(execution.getAvailableQueues().split(",")); }
public SGEExecutor(Configuration configuration) { logger = LoggerFactory.getLogger(SGEExecutor.class); sgeManager = new SGEManager(configuration.getExecution()); }
public AuthenticationOrigin() { this("internal", AuthenticationType.OPENCGA.name(), "localhost", Collections.emptyMap()); }
public static Configuration load(Path configurationPath) throws IOException { InputStream inputStream = FileUtils.newInputStream(configurationPath); return load(inputStream, DEFAULT_CONFIGURATION_FORMAT); }