Example usage for org.apache.commons.exec CommandLine addArgument

Introduction

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

Prototype

public CommandLine addArgument(final String argument) 

Source Link

Document

Add a single argument.

Usage

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qsub command.//from   www  . ja  v  a  2  s.  c  o  m
 * <p>
 * Equivalent to qsub [param]
 *
 * @param input job input file
 * @return job id
 */
public static String qsub(String input) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSUB);
    cmdLine.addArgument(input);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, null, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qsub exit value: " + exitValue);
    LOGGER.fine("qsub output: " + out.toString());

    if (exitValue != 0)
        throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString());

    String jobId = out.toString();
    return jobId.trim();
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * <p>//from w  w w .j  a va2  s . c o m
 * PBS qsub command with arguments resource overrides
 * </p>
 *
 * <p>
 * Equivalent to qsub [param] -l [resource_name=value,resource_name=value]]
 * </p>
 *
 * @param input job input file
 * @param resourceOverrides variable number of resources to override
 * @return job id
 */
public static String qsub(String input, String... resourceOverrides) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSUB);
    cmdLine.addArgument(PARAMETER_RESOURCE_OVERRIDE_STATUS);
    String resourceOverrideArgument = StringUtils.join(resourceOverrides, ",");
    cmdLine.addArgument(resourceOverrideArgument);
    cmdLine.addArgument(input);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qsub exit value: " + exitValue);
    LOGGER.fine("qsub output: " + out.toString());

    if (exitValue != 0)
        throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString());

    String jobId = out.toString();
    return jobId.trim();
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit
 * <p>//  w ww  .  ja  va  2s  .co  m
 * Equivalent to qsub -t 1,2,3 [param]
 *
 * @param input job input file
 * @param pbsArrayIDs list of specified PBS indices
 * @return job id of array job
 */
public static String qsubArrayJob(String input, List<Integer> pbsArrayIDs) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSUB);
    cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS);
    String listArgument = StringUtils.join(pbsArrayIDs, ",");
    cmdLine.addArgument(listArgument);
    cmdLine.addArgument(input);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qsub exit value: " + exitValue);
    LOGGER.fine("qsub output: " + out.toString());

    if (exitValue != 0)
        throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString());

    String jobId = out.toString();
    return jobId.trim();
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit
 * <p>//from w ww  .  ja  v  a 2s  . co m
 * Equivalent to qsub -t 5-20 [param]
 *
 * @param input job input file
 * @param beginIndex beginning of index range
 * @param endIndex end of index range
 * @return job id of array job
 */
public static String qsubArrayJob(String input, int beginIndex, int endIndex) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSUB);
    cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS);
    String rangeArgument = beginIndex + "-" + endIndex;
    cmdLine.addArgument(rangeArgument);
    cmdLine.addArgument(input);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qsub exit value: " + exitValue);
    LOGGER.fine("qsub output: " + out.toString());

    if (exitValue != 0)
        throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString());

    String jobId = out.toString();
    return jobId.trim();
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit AND a range to submit
 * <p>/*from  w w w  .j av a  2s. co m*/
 * Equivalent to qsub -t 1,2,3,5-20 [param]
 *
 * @param input job input file
 * @param pbsArrayIDs list of specified indices
 * @param beginIndex beginning of index range
 * @param endIndex end of index range
 * @return job id of array job
 */
public static String qsubArrayJob(String input, List<Integer> pbsArrayIDs, int beginIndex, int endIndex) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSUB);
    cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS);
    String rangeArgument = beginIndex + "-" + endIndex;
    String listArgument = StringUtils.join(pbsArrayIDs, ",");
    String combinedArgument = listArgument + "," + rangeArgument;
    cmdLine.addArgument(combinedArgument);
    cmdLine.addArgument(input);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qsub exit value: " + exitValue);
    LOGGER.fine("qsub output: " + out.toString());

    if (exitValue != 0)
        throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString());

    String jobId = out.toString();
    return jobId.trim();
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS tracejob command.//from w w  w.j  a v a2 s  .  c om
 * <p>
 * Equivalent to tracejob -n [numberOfDays] [jobId]
 *
 * @param jobId job id
 * @param numberOfDays number of days to look for the job
 * @param quiet quiet mode flag
 * @return tracejob output
 */
public static CommandOutput traceJob(String jobId, int numberOfDays, boolean quiet) {
    final CommandLine cmdLine = new CommandLine(COMMAND_TRACEJOB);
    cmdLine.addArgument(PARAMETER_NUMBER_OF_DAYS);
    cmdLine.addArgument(Integer.toString(numberOfDays));
    if (quiet) {
        cmdLine.addArgument(PARAMETER_QUIET_MODE);
    }
    cmdLine.addArgument(jobId);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, null, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute tracejob command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute tracejob command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute tracejob command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("tracejob exit value: " + exitValue);
    LOGGER.fine("tracejob output: " + out.toString());

    return new CommandOutput(out.toString(), err.toString());
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qstat command.//  w w  w  . ja  va2 s .  c o  m
 * <p>
 * Equivalent to qstat -f [param]
 *
 * @param name job name
 * @return list of jobs
 */
public static List<Job> qstat(String name) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSTAT);
    cmdLine.addArgument(PARAMETER_FULL_STATUS);
    if (StringUtils.isNotBlank(name)) {
        cmdLine.addArgument(name);
    }

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, null, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qstat exit value: " + exitValue);

    final List<Job> jobs;
    try {
        jobs = QSTAT_JOBS_PARSER.parse(out.toString());
    } catch (ParseException pe) {
        throw new PBSException("Failed to parse qstat jobs output: " + pe.getMessage(), pe);
    }

    return (jobs == null ? new ArrayList<Job>(0) : jobs);
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qsub command for an Array Job with Specific PBS_ARRAY_IDs to submit, and resource overrides
 * <p>//from w  w  w.  j  a va 2  s  .com
 * Equivalent to qsub -t 1,2,3 -l [resource_name=value,resource_name=value] [param]
 *
 * @param input job input file
 * @param pbsArrayIDs of specified PBS indices
 * @param resourceOverrides list of resource overrides
 * @return job id of array job
 */
public static String qsubArrayJob(String input, List<Integer> pbsArrayIDs, String... resourceOverrides) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSUB);
    cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS);
    String listArgument = StringUtils.join(pbsArrayIDs, ",");
    cmdLine.addArgument(listArgument);
    cmdLine.addArgument(PARAMETER_RESOURCE_OVERRIDE_STATUS);
    String resourceOverrideArgument = StringUtils.join(resourceOverrides, ",");
    cmdLine.addArgument(resourceOverrideArgument);
    cmdLine.addArgument(input);

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qsub command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qsub exit value: " + exitValue);
    LOGGER.fine("qsub output: " + out.toString());

    if (exitValue != 0)
        throw new PBSException("Failed to submit job script " + input + ". Error output: " + err.toString());

    String jobId = out.toString();
    return jobId.trim();
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qstat command.//  ww w  . ja  v a  2 s . c  o m
 * <p>
 * Equivalent to qstat -Q -f [name]
 *
 * @param name queue name
 * @return list of queues
 */
public static List<Queue> qstatQueues(String name) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSTAT);
    cmdLine.addArgument(PARAMETER_FULL_STATUS);
    cmdLine.addArgument(PARAMETER_QUEUE);
    if (StringUtils.isNotBlank(name)) {
        cmdLine.addArgument(name);
    }

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, null, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qstat exit value: " + exitValue);

    final List<Queue> queues;
    try {
        queues = QSTAT_QUEUES_PARSER.parse(out.toString());
    } catch (ParseException pe) {
        throw new PBSException("Failed to parse qstat queues output: " + pe.getMessage(), pe);
    }

    return (queues == null ? new ArrayList<Queue>(0) : queues);
}

---

From source file:com.tupilabs.pbs.PBS.java

/**
 * PBS qstat command for Array Jobs//from   ww  w .j  ava  2s  .co m
 * <p>
 * Equivalent to qstat -f -t [param]
 *
 * @param name job name
 * @return list of jobs
 */
public static List<Job> qstatArrayJob(String name) {
    final CommandLine cmdLine = new CommandLine(COMMAND_QSTAT);
    cmdLine.addArgument(PARAMETER_FULL_STATUS);
    cmdLine.addArgument(PARAMETER_ARRAY_JOB_STATUS);
    if (StringUtils.isNotBlank(name)) {
        cmdLine.addArgument(name);
    }

    final OutputStream out = new ByteArrayOutputStream();
    final OutputStream err = new ByteArrayOutputStream();

    DefaultExecuteResultHandler resultHandler;
    try {
        resultHandler = execute(cmdLine, out, err);
        resultHandler.waitFor(DEFAULT_TIMEOUT);
    } catch (ExecuteException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    } catch (IOException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    } catch (InterruptedException e) {
        throw new PBSException("Failed to execute qstat command: " + e.getMessage(), e);
    }

    final int exitValue = resultHandler.getExitValue();
    LOGGER.info("qstat exit value: " + exitValue);

    final List<Job> jobs;
    try {
        jobs = QSTAT_JOBS_PARSER.parse(out.toString());
    } catch (ParseException pe) {
        throw new PBSException("Failed to parse qstat jobs output: " + pe.getMessage(), pe);
    }

    return (jobs == null ? new ArrayList<Job>(0) : jobs);
}

---

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