private List<String> getQueueList() { return Arrays.asList(execution.getAvailableQueues().split(",")); }
private String getDefaultQueue() { return execution.getDefaultQueue(); }
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(); } }
private static String getQueueName(String toolName) throws Exception { String defaultQueue = getDefaultQueue(); logger.debug("SgeManager: default queue: " + defaultQueue); // get all available queues List<String> queueList = getQueueList(); logger.debug("SgeManager: available queues: " + queueList); // search corresponding queue String selectedQueue = defaultQueue; for (String queue : queueList) { if (!queue.equalsIgnoreCase(defaultQueue)) { if (configuration.getExecution().getToolsPerQueue().get(queue) != null) { if (belongsTheToolToQueue(configuration.getExecution().getToolsPerQueue().get(queue), toolName)) { selectedQueue = queue; } } } } logger.info("SgeManager: selected queue for tool '" + toolName + "': " + selectedQueue); return selectedQueue; }
break; case "OPENCGA_EXECUTION_MODE": configuration.getExecution().setMode(envVariables.get(variable)); break; case "OPENCGA_MAIL_HOST":
private static List<String> getQueueList() { if (configuration.getExecution().getAvailableQueues() != null) { String[] queueArray = configuration.getExecution().getAvailableQueues().split(","); return Arrays.asList(queueArray); } else { return new ArrayList<>(); } }
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(); }