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:fitnesse.maven.io.CommandShell.java

public String execute(File workingDir, String... commands) {
    CommandLine commandLine = CommandLine.parse(commands[0]);
    for (int i = 1; i < commands.length; i++) {
        commandLine.addArgument(commands[i]);
    }/*  w w  w  . jav a 2s.  c o  m*/
    DefaultExecutor executor = new DefaultExecutor();
    try {
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        executor.setStreamHandler(new PumpStreamHandler(baos));
        executor.setWorkingDirectory(workingDir);
        executor.execute(commandLine);
        return new String(baos.toByteArray());
    } catch (ExecuteException e) {
        throw new RuntimeException(e);
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}

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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   www .j av a 2 s .  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:com.adaptris.hpcc.ListLogicalFiles.java

@Override
public AdaptrisMessage request(AdaptrisMessage msg, ProduceDestination destination, long timeoutMs)
        throws ProduceException {
    try {//from ww  w.j a  v  a  2  s . c  om
        String dest = destination.getDestination(msg);
        CommandLine commandLine = retrieveConnection(DfuplusConnection.class).createCommand();
        commandLine.addArgument("action=list");
        commandLine.addArgument(String.format("name=%s", dest));
        log.trace("Executing {}", commandLine);
        try (PrintWriter out = new PrintWriter(msg.getWriter())) {
            // parser is closed as part of the execution
            ListLogicalFilesOutput parser = new ListLogicalFilesOutput(dest, out); // lgtm [java/output-resource-leak]
            executeInternal(commandLine, parser);
        }
    } catch (Exception e) {
        throw ExceptionHelper.wrapProduceException(e);
    }
    return msg;
}

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From source file:de.akquinet.innovation.play.maven.Play2RunMojo.java

public void execute() throws MojoExecutionException {

    String line = getPlay2().getAbsolutePath();

    CommandLine cmdLine = CommandLine.parse(line);
    cmdLine.addArguments(getPlay2SystemPropertiesArguments(), false);
    cmdLine.addArgument("run");
    DefaultExecutor executor = new DefaultExecutor();

    // As where not linked to a project, we can't set the working directory.
    // So it will use the directory where mvn was launched.

    executor.setExitValue(0);/*from   w w w.  j av a 2s. com*/
    try {
        executor.execute(cmdLine, getEnvironment());
    } catch (IOException e) {
        // Ignore.
    }
}

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From source file:com.adaptris.hpcc.SprayToThorImpl.java

protected CommandLine createSprayCommand(AdaptrisMessage msg) throws PasswordException, IOException {
    CommandLine cmdLine = retrieveConnection(DfuplusConnection.class).createCommand();
    cmdLine.addArgument("action=spray");
    cmdLine.addArgument(String.format("dstcluster=%s", msg.resolve(getCluster())));
    cmdLine.addArgument(String.format("overwrite=%d", overwrite() ? 1 : 0));
    cmdLine.addArgument("nowait=1");
    return cmdLine;
}

---

From source file:com.adaptris.hpcc.DeleteFromThor.java

@Override
public AdaptrisMessage request(AdaptrisMessage msg, ProduceDestination destination, long timeoutMs)
        throws ProduceException {
    try {/*from  ww  w. ja v  a  2  s. com*/
        String dest = destination.getDestination(msg);
        CommandLine commandLine = retrieveConnection(DfuplusConnection.class).createCommand();
        commandLine.addArgument("action=remove");
        commandLine.addArgument(String.format("name=%s", dest));
        log.trace("Executing {}", commandLine);
        DeleteOutputParser p = new DeleteOutputParser();
        executeInternal(commandLine, p);
        log.info("Delete on [{}]: {}", dest, p.actualState);
    } catch (AbortJobException e) {
        throw ExceptionHelper.wrapProduceException(generateExceptionMessage(e), e);
    } catch (Exception e) {
        throw ExceptionHelper.wrapProduceException(e);
    }
    return msg;
}

---

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

public void run(String bowtiePath, String index, File read1, File read2, File outFile, int threads) {
    // Example bowtie call:
    //   bowtie -t -v 2 -p 12 -m 10 -S
    CommandLine cmdLine = new CommandLine(bowtiePath);

    // print wall-clock time taken by search phases
    cmdLine.addArgument("-t");
    // eport end-to-end hits w/ <=v mismatches; ignore qualities
    cmdLine.addArgument("-v");
    cmdLine.addArgument("2");
    // number of alignment threads to launch
    cmdLine.addArgument("-p");
    cmdLine.addArgument("" + threads);
    // suppress all alignments if > <int> exist
    cmdLine.addArgument("-m");
    cmdLine.addArgument("10");
    // write hits in SAM format
    cmdLine.addArgument("-S");
    // bowtie index
    cmdLine.addArgument("${index}");
    if (read2 != null) {
        // fastq1
        cmdLine.addArgument("-1");
        cmdLine.addArgument("${read1}");
        // fastq2
        cmdLine.addArgument("-2");
        cmdLine.addArgument("${read2}");
    } else {//www .  j a v a  2  s .  c o m
        cmdLine.addArgument("${read1}");
    }
    // output SAM file
    cmdLine.addArgument("${outFile}");

    Map map = new HashMap();
    map.put("index", index);
    map.put("read1", read1);
    if (read2 != null) {
        map.put("read2", read2);
    }
    map.put("outFile", outFile);
    cmdLine.setSubstitutionMap(map);

    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValue(0);
    // Never timeout 
    ExecuteWatchdog watchdog = new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT);
    executor.setWatchdog(watchdog);

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

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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);/*from  ww w  . j a  v a2  s.com*/
    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:de.akquinet.innovation.play.maven.Play2CleanMojo.java

public void execute() throws MojoExecutionException {

    String line = getPlay2().getAbsolutePath();

    CommandLine cmdLine = CommandLine.parse(line);
    cmdLine.addArgument("clean");
    DefaultExecutor executor = new DefaultExecutor();

    if (timeout > 0) {
        ExecuteWatchdog watchdog = new ExecuteWatchdog(timeout);
        executor.setWatchdog(watchdog);//from   w  w w .j a va2 s  .  c o m
    }

    executor.setWorkingDirectory(project.getBasedir());
    executor.setExitValue(0);
    try {
        executor.execute(cmdLine, getEnvironment());
    } catch (IOException e) {
        throw new MojoExecutionException("Error during cleanup", e);
    }

    // Also delete the dist directory
    File dist = new File(project.getBasedir(), "dist");
    if (dist.exists()) {
        getLog().debug("Deleting " + dist.getAbsolutePath());
        try {
            FileUtils.deleteDirectory(dist);
        } catch (IOException e) {
            throw new MojoExecutionException("Can't delete the dist folder", e);
        }
    } else {
        getLog().debug("'dist' directory not found");
    }

    // Delete the log folder
    File logs = new File(project.getBasedir(), "logs");
    if (logs.exists()) {
        getLog().debug("Deleting " + logs.getAbsolutePath());
        try {
            FileUtils.deleteDirectory(logs);
        } catch (IOException e) {
            throw new MojoExecutionException("Can't delete the logs folder", e);
        }
    } else {
        getLog().debug("'logs' directory not found");
    }

    // Also delete the lib directory if set
    if (cleanLibFolder) {
        File lib = new File(project.getBasedir(), "lib");
        if (lib.exists()) {
            getLog().debug("Deleting " + lib.getAbsolutePath());
            try {
                FileUtils.deleteDirectory(lib);
            } catch (IOException e) {
                throw new MojoExecutionException("Can't delete the " + lib + " folder", e);
            }
        } else {
            getLog().debug("'" + lib + "' directory not found");
        }
    }
}

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

/**
 * Starts this server./*from   ww w.ja v  a  2 s .c  om*/
 */
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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