Example usage for org.apache.commons.exec DefaultExecutor DefaultExecutor

Introduction

In this page you can find the example usage for org.apache.commons.exec DefaultExecutor DefaultExecutor.

Prototype

public DefaultExecutor() 

Source Link

Document

Default constructor creating a default PumpStreamHandler and sets the working directory of the subprocess to the current working directory.

Usage

From source file:edu.buffalo.fusim.ReadSimulator.java

public void run(String artBinPath, File fusionFile, String outputPrefix, int readLength, int meanFragSize,
        int readCoverage, boolean pairedEnd) {
    // Example art call:
    //   art_illumina -i fusion.txt -o testsim -l 75 -f 10 -p -m 400 -s 10 
    CommandLine cmdLine = new CommandLine(artBinPath);

    // the filename of input DNA reference
    cmdLine.addArgument("-i");
    cmdLine.addArgument("${file}");
    // the prefix of output files
    cmdLine.addArgument("-o");
    cmdLine.addArgument("${outputPrefix}");
    // the length of reads to be simulated
    cmdLine.addArgument("-l");
    cmdLine.addArgument("" + readLength);
    // the fold of read coverage to be simulated
    cmdLine.addArgument("-f");
    cmdLine.addArgument("" + readCoverage);
    if (pairedEnd) {
        // indicate a paired-end read simulation
        cmdLine.addArgument("-p");
        // the mean size of DNA fragments for paired-end simulations
        cmdLine.addArgument("-m");
        cmdLine.addArgument("" + meanFragSize);
        // the standard deviation of DNA fragment size for paired-end simulations.
        cmdLine.addArgument("-s");
        cmdLine.addArgument("10");
    }//from  ww  w  . j  a  v  a2s.c  om
    // quite - turn off end of run summary
    cmdLine.addArgument("-q");

    Map map = new HashMap();
    map.put("file", fusionFile);
    map.put("outputPrefix", outputPrefix);
    cmdLine.setSubstitutionMap(map);

    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValue(0);
    // Timeout after 5 minutes
    ExecuteWatchdog watchdog = new ExecuteWatchdog(300000);
    executor.setWatchdog(watchdog);

    try {
        int exitValue = executor.execute(cmdLine);
    } catch (Exception e) {
        logger.fatal("Failed to execute ART for simulating Illumina reads: " + e.getMessage());
    }
}

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From source file:it.sonarlint.cli.tools.CommandExecutor.java

public int execute(String[] args, @Nullable Path workingDir, Map<String, String> addEnv) throws IOException {
    if (!Files.isExecutable(file)) {
        Set<PosixFilePermission> perms = new HashSet<PosixFilePermission>();
        perms.add(PosixFilePermission.OWNER_READ);
        perms.add(PosixFilePermission.OWNER_EXECUTE);
        Files.setPosixFilePermissions(file, perms);
    }/* w w w. jav  a2s .c o m*/

    ExecuteWatchdog watchdog = new ExecuteWatchdog(TIMEOUT);
    CommandLine cmd = new CommandLine(file.toFile());
    cmd.addArguments(args);
    DefaultExecutor exec = new DefaultExecutor();
    exec.setWatchdog(watchdog);
    exec.setStreamHandler(createStreamHandler());
    exec.setExitValues(null);
    if (workingDir != null) {
        exec.setWorkingDirectory(workingDir.toFile());
    }
    in.close();
    LOG.info("Executing: {}", cmd.toString());
    Map<String, String> env = new HashMap<>(System.getenv());
    env.putAll(addEnv);
    return exec.execute(cmd, env);
}

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From source file:de.simu.decomap.messaging.resultprocessor.impl.helper.RulesExecutor.java

/**
 * Executing a predefined Rule//from www.j av a  2 s.  co  m
 * @param ruleType RuleType
 * @param arg args for Rule
 * @return Success
 */
public boolean executePredefinedRule(byte ruleType, String arg) {
    logger.info("[IPTABLES] -> executing predefined command...");

    // use apache's commons-exec for executing command!
    CommandLine cmdLine = new CommandLine(command);

    // get the predefined rule-parameters
    String[] ruleParams = Rules.getPredefindedRuleParameters(ruleType, arg);

    if (ruleParams != null) {

        // add rule-parameters to CommanLine-Object
        for (int i = 0; i < ruleParams.length; i++) {
            cmdLine.addArgument(ruleParams[i]);
        }

        // execute command
        DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();
        ExecuteWatchdog watchdog = new ExecuteWatchdog(mTimeout);
        Executor executor = new DefaultExecutor();
        executor.setExitValue(1);
        executor.setWatchdog(watchdog);
        try {
            executor.execute(cmdLine, resultHandler);
        } catch (ExecuteException e) {
            logger.warn("[IPTABLES] -> error while executing predefined command: execute-exception occured!");
            return false;
        } catch (IOException e) {
            logger.warn("[IPTABLES] -> error while executing predefined command: io-exception occured!");
            return false;
        }

        try {
            // some time later the result handler callback was invoked so we
            // can safely request the exit value
            resultHandler.waitFor();
            int exitCode = resultHandler.getExitValue();
            logger.info("[IPTABLES] -> command " + ruleType + " executed, exit-code is: " + exitCode);

            switch (exitCode) {
            case EXIT_CODE_SUCCESS:
                return true;
            case EXIT_CODE_ERROR:
                return false;
            default:
                return false;
            }

        } catch (InterruptedException e) {
            logger.warn(
                    "[IPTABLES] -> error while executing predefined command: interrupted-exception occured!");
            return false;
        }

    } else {
        logger.warn("[IPTABLES] -> error while excuting predefined command: rule-parameters-list is null!");
        return false;
    }
}

---

From source file:com.sonar.scanner.api.it.tools.CommandExecutor.java

public int execute(String[] args, Map<String, String> env, @Nullable Path workingDir) throws IOException {
    if (!Files.isExecutable(file)) {
        Set<PosixFilePermission> perms = new HashSet<PosixFilePermission>();
        perms.add(PosixFilePermission.OWNER_READ);
        perms.add(PosixFilePermission.OWNER_EXECUTE);
        Files.setPosixFilePermissions(file, perms);
    }//  ww w .ja v  a 2  s .c om

    watchdog = new ExecuteWatchdog(TIMEOUT);
    CommandLine cmd = new CommandLine(file.toFile());
    cmd.addArguments(args, false);
    DefaultExecutor exec = new DefaultExecutor();
    exec.setWatchdog(watchdog);
    exec.setStreamHandler(createStreamHandler());
    exec.setExitValues(null);
    if (workingDir != null) {
        exec.setWorkingDirectory(workingDir.toFile());
    }
    in.close();
    LOG.info("Executing: {}", cmd.toString());
    return exec.execute(cmd, env);
}

---

From source file:com.vmware.bdd.usermgmt.job.CfgUserMgmtOnMgmtVMExecutor.java

private void execCommand(CommandLine cmdLine) {
    DefaultExecutor executor = new DefaultExecutor();

    executor.setStreamHandler(new PumpStreamHandler(new ExecOutputLogger(LOGGER, false), //output logger
            new ExecOutputLogger(LOGGER, true)) //error logger
    );/*w  ww .ja v  a2s.com*/

    executor.setWatchdog(new ExecuteWatchdog(1000l * TIMEOUT));

    try {
        int exitVal = executor.execute(cmdLine);
        if (exitVal != 0) {
            throw new UserMgmtExecException("CFG_LDAP_FAIL", null);
        }
    } catch (IOException e) {
        throw new UserMgmtExecException("CFG_LDAP_FAIL", e);
    }
}

---

From source file:its.tools.CommandExecutor.java

public void execute(String[] args, @Nullable Path workingDir) throws IOException {
    if (!Files.isExecutable(file)) {
        Set<PosixFilePermission> perms = new HashSet<PosixFilePermission>();
        perms.add(PosixFilePermission.OWNER_READ);
        perms.add(PosixFilePermission.OWNER_EXECUTE);
        Files.setPosixFilePermissions(file, perms);
    }//from www. ja v a2s  .  c  o  m

    watchdog = new ExecuteWatchdog(TIMEOUT);
    CommandLine cmd = new CommandLine(file.toFile());
    cmd.addArguments(args);
    DefaultExecutor exec = new DefaultExecutor();
    exec.setWatchdog(watchdog);
    exec.setStreamHandler(createStreamHandler());
    exec.setExitValues(null);
    if (workingDir != null) {
        exec.setWorkingDirectory(workingDir.toFile());
    }
    in.close();
    LOG.info("Executing: {}", cmd.toString());
    exec.execute(cmd, new ResultHander());
}

---

From source file:io.gatling.mojo.Fork.java

public void run() throws Exception {

    if (propagateSystemProperties) {
        for (Entry<Object, Object> systemProp : System.getProperties().entrySet()) {
            String name = systemProp.getKey().toString();
            String value = systemProp.getValue().toString();
            if (isPropagatableProperty(name)) {
                String escapedValue = StringUtils.escape(value);
                String safeValue = escapedValue.contains(" ") ? '"' + escapedValue + '"' : escapedValue;
                this.jvmArgs.add("-D" + name + "=" + safeValue);
            }/*from  ww w.  j  a v a2 s .co  m*/
        }
    }

    this.jvmArgs.add("-jar");
    this.jvmArgs
            .add(MojoUtils.createBooterJar(classpath, MainWithArgsInFile.class.getName()).getCanonicalPath());

    List<String> command = buildCommand();

    Executor exec = new DefaultExecutor();
    exec.setStreamHandler(new PumpStreamHandler(System.out, System.err, System.in));
    exec.setProcessDestroyer(new ShutdownHookProcessDestroyer());

    CommandLine cl = new CommandLine(javaExecutable);
    for (String arg : command) {
        cl.addArgument(arg, false);
    }

    int exitValue = exec.execute(cl);
    if (exitValue != 0) {
        throw new MojoFailureException("command line returned non-zero value:" + exitValue);
    }
}

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From source file:edu.emory.cci.aiw.neo4jetl.Neo4jHome.java

private void controlServer(String command) throws IOException, InterruptedException, CommandFailedException {
    LOGGER.debug("Executing neo4j command {}...", command);
    CommandLine serverControlCommand = new CommandLine(new File(this.home, SERVER_CONTROL_COMMAND));
    serverControlCommand.addArgument("${command}");
    Map<String, String> map = new HashMap<>();
    map.put("command", command);
    serverControlCommand.setSubstitutionMap(map);

    DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();

    ExecuteWatchdog watchdog = new ExecuteWatchdog(60 * 1000);
    Executor executor = new DefaultExecutor();
    executor.setExitValue(1);/*  w  w  w  .ja va 2 s.  c  om*/
    executor.setWatchdog(watchdog);
    executor.execute(serverControlCommand, resultHandler);
    LOGGER.debug("Neo4j command {} is completed, checking exit value...", command);
    resultHandler.waitFor();
    int exitValue = resultHandler.getExitValue();
    if (exitValue != 0) {
        ExecuteException exception = resultHandler.getException();
        throw new CommandFailedException(exitValue, "Neo4j command '" + command + "' failed", exception);
    }
    LOGGER.debug("Neo4j command {} was successful", command);
}

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From source file:com.github.shyiko.hmp.AbstractHadoopMojo.java

protected void executeCommand(HadoopSettings hadoopSettings, String command, String automaticResponseOnPrompt,
        boolean bindProcessDestroyerToShutdownHook) throws IOException {
    if (getLog().isDebugEnabled()) {
        getLog().debug("Executing " + command);
    }//from  w  ww.  j  a  v  a  2s. c  o  m
    Executor executor = new DefaultExecutor();
    executor.setStreamHandler(new ExecutionStreamHandler(quiet, automaticResponseOnPrompt));
    executor.setWorkingDirectory(hadoopSettings.getHomeDirectory());
    if (bindProcessDestroyerToShutdownHook) {
        executor.setProcessDestroyer(new ShutdownHookProcessDestroyer());
    }
    executor.execute(CommandLine.parse(command), hadoopSettings.getEnvironment());
}

---

From source file:eu.creatingfuture.propeller.blocklyprop.propeller.PropellerLoad.java

protected boolean loadIntoRam(String executable, File ramFile, String comPort) {
    try {//ww  w  .j av  a  2 s  . c  om
        Map map = new HashMap();
        map.put("ramFile", ramFile);

        CommandLine cmdLine = new CommandLine(executable);
        cmdLine.addArgument("-r");
        if (comPort != null) {
            cmdLine.addArgument("-p").addArgument(comPort);
        }
        cmdLine.addArgument("${ramFile}");

        cmdLine.setSubstitutionMap(map);
        DefaultExecutor executor = new DefaultExecutor();
        //executor.setExitValues(new int[]{451, 301});

        ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
        PumpStreamHandler streamHandler = new PumpStreamHandler(outputStream);
        executor.setStreamHandler(streamHandler);

        try {
            exitValue = executor.execute(cmdLine);
        } catch (ExecuteException ee) {
            exitValue = ee.getExitValue();
            logger.log(Level.SEVERE, "Unexpected exit value: {0}", exitValue);
            success = false;
            return false;
        } finally {
            output = outputStream.toString();
        }

        success = true;
        return true;
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
        success = false;
        return false;
    }
}

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