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

Introduction

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

Prototype

public CommandLine(final CommandLine other) 

Source Link

Document

Copy constructor.

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  .  ja v a 2 s  .com
    // 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:io.werval.maven.MavenDevShellSPI.java

public MavenDevShellSPI(URL[] applicationSources, URL[] applicationClassPath, URL[] runtimeClassPath,
        Set<File> sources, SourceWatcher watcher, File rootDir, String rebuildPhase) {
    super(applicationSources, applicationClassPath, runtimeClassPath, sources, watcher, false);
    pom = new File(rootDir, "pom.xml");
    cmdLine = new CommandLine("mvn");
    cmdLine.addArgument("-f");
    cmdLine.addArgument(pom.getAbsolutePath());
    cmdLine.addArgument(rebuildPhase);//from  w  w w  .ja  v a 2s  .  c  o m
}

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From source file:hu.bme.mit.trainbenchmark.sql.process.MySqlProcess.java

public static void runShell(final String shellCommand) throws ExecuteException, IOException {
    final Executor executor = new DefaultExecutor();
    final CommandLine commandLine = new CommandLine("/bin/bash");
    commandLine.addArgument("-c");
    commandLine.addArgument(shellCommand, false);
    executor.execute(commandLine);/*from  ww  w .ja  v  a 2 s  .  c o m*/
}

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From source file:com.creactiviti.piper.plugin.ffmpeg.Ffmpeg.java

@Override
public Object handle(Task aTask) throws Exception {
    List<String> options = aTask.getList("options", String.class);
    CommandLine cmd = new CommandLine("ffmpeg");
    options.forEach(o -> cmd.addArgument(o));
    log.debug("{}", cmd);
    DefaultExecutor exec = new DefaultExecutor();
    File tempFile = File.createTempFile("log", null);
    try (PrintStream stream = new PrintStream(tempFile);) {
        exec.setStreamHandler(new PumpStreamHandler(stream));
        int exitValue = exec.execute(cmd);
        return exitValue != 0 ? FileUtils.readFileToString(tempFile) : cmd.toString();
    } catch (ExecuteException e) {
        throw new ExecuteException(e.getMessage(), e.getExitValue(),
                new RuntimeException(FileUtils.readFileToString(tempFile)));
    } finally {/*from   ww  w  . jav a 2 s  .com*/
        FileUtils.deleteQuietly(tempFile);
    }
}

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From source file:com.muk.services.util.BarcodeServiceImpl.java

@Override
public File generateBarcode(File path, String giftCardId) {

    CommandLine cmdLine = null;/*from   w  w w . j  a va2  s.  c  om*/

    if (System.getProperty("os.name").equals("Linux")) {
        cmdLine = new CommandLine("convert");
    } else {
        cmdLine = new CommandLine("convert.exe");
    }

    cmdLine.addArgument("-font");
    cmdLine.addArgument("Free-3-of-9-Extended-Regular");
    cmdLine.addArgument("-pointsize");
    cmdLine.addArgument("40");
    cmdLine.addArgument("-bordercolor");
    cmdLine.addArgument("white");
    cmdLine.addArgument("-border");
    cmdLine.addArgument("10x10");
    cmdLine.addArgument("label:${giftCardId}");
    cmdLine.addArgument("${outfile}");

    Map<String, Object> map = new HashMap<String, Object>();
    map.put("giftCardId", giftCardId);
    map.put("outfile", path);

    cmdLine.setSubstitutionMap(map);

    ProcessExecutor executor = new ProcessExecutor();

    try {
        if (0 == executor.runCommandLine(cmdLine, 100000)) {
            return path;
        }
    } catch (IOException ex) {
        LOG.error("Failed to execute imagemagick", ex);
    }

    return null;

}

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From source file:net.robyf.dbpatcher.util.MySqlUtil.java

/**
 * Drops an existing MySQL database.//from w w  w  .  j  a va  2  s  .  com
 * 
 * @param databaseName The name of the database to be dropped
 * @param username Username of the MySQL administration user
 * @param password Password of the MySQL administration user
 */
public static void dropDatabase(final String databaseName, final String username, final String password) {
    CommandLine command = new CommandLine("mysqladmin");
    addCredentials(command, username, password);
    command.addArgument("drop");
    command.addArgument("-f");
    command.addArgument(databaseName);

    execute(command);
}

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From source file:name.martingeisse.webide.nodejs.AbstractNodejsServer.java

/**
 * Starts this server./*from  ww  w .  j av  a 2s . c o m*/
 */
public void start() {

    // determine the path of the associated script
    URL url = getScriptUrl();
    if (!url.getProtocol().equals("file")) {
        throw new RuntimeException("unsupported protocol for associated script URL: " + url);
    }
    File scriptFile = new File(url.getPath());

    // build the command line
    CommandLine commandLine = new CommandLine(Configuration.getBashPath());
    commandLine.addArgument("--login");
    commandLine.addArgument("-c");
    commandLine.addArgument("node " + scriptFile.getName(), false);

    // build I/O streams
    ByteArrayInputStream inputStream = null;
    OutputStream outputStream = System.err;
    OutputStream errorStream = System.err;
    ExecuteStreamHandler streamHandler = new PumpStreamHandler(outputStream, errorStream, inputStream);

    // build an environment map that contains the path to the node_modules
    Map<String, String> environment = new HashMap<String, String>();
    environment.put("NODE_PATH", new File("lib/node_modules").getAbsolutePath());

    // run Node.js
    Executor executor = new DefaultExecutor();
    executor.setProcessDestroyer(new ShutdownHookProcessDestroyer());
    executor.setStreamHandler(streamHandler);
    try {
        executor.setWorkingDirectory(scriptFile.getParentFile());
        executor.execute(commandLine, environment, new ExecuteResultHandler() {

            @Override
            public void onProcessFailed(ExecuteException e) {
            }

            @Override
            public void onProcessComplete(int exitValue) {
            }

        });
    } catch (IOException e) {
        throw new RuntimeException(e);
    }

}

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From source file:de.torstenwalter.maven.plugins.ImpdpMojo.java

public void execute() throws MojoExecutionException, MojoFailureException {
    CommandLine commandLine = new CommandLine(impdp);
    addCommonArguments(commandLine);//  w  w  w.  ja  v a  2 s .co m

    if (StringUtils.isNotEmpty(remap_tablespace)) {
        commandLine.addArgument("REMAP_TABLESPACE=" + remap_tablespace);
    }

    if (StringUtils.isNotEmpty(remap_schema)) {
        commandLine.addArgument("REMAP_SCHEMA=" + remap_schema);
    }

    if (StringUtils.isNotEmpty(table_exists_action)) {
        commandLine.addArgument("TABLE_EXISTS_ACTION=" + table_exists_action);
    }

    getLog().info("Executing command line: " + obfuscateCredentials(commandLine.toString(), getCredentials()));

    Executor exec = new DefaultExecutor();
    exec.setStreamHandler(new PumpStreamHandler(System.out, System.err));
    try {
        exec.execute(commandLine);
    } catch (ExecuteException e) {
        throw new MojoExecutionException("Command execution failed.", e);
    } catch (IOException e) {
        throw new MojoExecutionException("Command execution failed.", e);
    }
}

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From source file:com.creactiviti.piper.plugin.ffmpeg.Ffprobe.java

@Override
public Map<String, Object> handle(Task aTask) throws Exception {
    CommandLine cmd = new CommandLine("ffprobe");
    cmd.addArgument("-v").addArgument("quiet").addArgument("-print_format").addArgument("json")
            .addArgument("-show_error").addArgument("-show_format").addArgument("-show_streams")
            .addArgument(aTask.getRequiredString("input"));
    log.debug("{}", cmd);
    DefaultExecutor exec = new DefaultExecutor();
    File tempFile = File.createTempFile("log", null);
    try (PrintStream stream = new PrintStream(tempFile);) {
        exec.setStreamHandler(new PumpStreamHandler(stream));
        exec.execute(cmd);//from www.  j  av a2s . c  om
        return parse(FileUtils.readFileToString(tempFile));
    } catch (ExecuteException e) {
        throw new ExecuteException(e.getMessage(), e.getExitValue(),
                new RuntimeException(FileUtils.readFileToString(tempFile)));
    } finally {
        FileUtils.deleteQuietly(tempFile);
    }
}

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From source file:com.tribuneqa.utilities.FrameworkUtilities.java

public void appiumStart() throws IOException, InterruptedException {

    // Start command prompt In background.
    CommandLine command = new CommandLine("cmd");

    // Add different arguments In command line which requires to start appium server.
    command.addArgument("/c");

    // Add different arguments In command line which requires to start appium server. 
    command.addArgument("appium");
    command.addArgument("-a");
    command.addArgument("10.20.121.69");
    command.addArgument("-p");
    command.addArgument("8001");
    command.addArgument("-U");
    command.addArgument("4d0081724d5741c7");

    // Execute command line arguments to start appium server. 
    DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();
    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValue(1);//from   w  w w.j av a  2 s  .co m
    executor.execute(command, resultHandler);

    Thread.sleep(15000);

}

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