Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { commandOutput.setExitCode(-1); if (!commandOutput.getStdout().toString().contains("reads were filtered out")) { commandOutput.setExitCode(-1); if (commandOutput != null && commandOutput.getExitCode() == 0) { FileData fileData = new FileData(); fileData.setName(out.getName());
logger.debug("ci.getCommand(): {}", ci.getCommand()); commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) { logger.warn("commandOutput.getStderr(): {}", commandOutput.getStderr());
if (commandOutput != null && commandOutput.getExitCode() == 0) {
String delayedError = null; CommandOutput output = new CommandOutput(); output.setStartDate(new Date()); output.setExitCode(exitCode); output.setExitCode(exitCode); } catch (InterruptedException exp) { delayedError = exp.getMessage(); output.setStdout(stdoutGobbler.getOutput()); output.setStderr(stderrGobbler.getOutput()); output.setEndDate(new Date());
BufferedReader stdout = new BufferedReader(new StringReader(commandOutput.getStdout().toString())); ArrayList<BufferedWriter> fileOutputs = new ArrayList<BufferedWriter>();
try { commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) { logger.warn("commandOutput.getStderr(): {}", commandOutput.getStderr());
if (commandOutput != null && commandOutput.getExitCode() == 0) {
try { commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) { logger.warn("commandOutput.getStderr(): {}", commandOutput.getStderr());
Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { commandOutput.setExitCode(-1); if (!commandOutput.getStdout().toString().contains("reads were filtered out")) { commandOutput.setExitCode(-1); if (commandOutput != null && commandOutput.getExitCode() == 0) { FileData fileData = new FileData(); fileData.setName(out.getName());
prefix)); CommandOutput commandOutput = executor.execute(commandInput, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); } catch (ExecutorException e) { e.printStackTrace();
try { commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) { logger.warn("commandOutput.getStderr(): {}", commandOutput.getStderr());
Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { commandOutput.setExitCode(-1); if (!commandOutput.getStdout().toString().contains("reads were filtered out")) { commandOutput.setExitCode(-1); if (commandOutput != null && commandOutput.getExitCode() == 0) { FileData fileData = new FileData(); fileData.setPath(out.getParentFile().getAbsolutePath());
Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { commandOutput.setExitCode(-1); if (!commandOutput.getStdout().toString().contains("reads were filtered out")) { commandOutput.setExitCode(-1); if (commandOutput != null && commandOutput.getExitCode() == 0) { FileData fileData = new FileData(); fileData.setPath(out.getParentFile().getAbsolutePath());