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

List of usage examples for org.apache.commons.exec DefaultExecutor setStreamHandler

  1. HOME
  2. Java
  3. org.apache.commons
  4. org.apache.commons.exec.*
  5. DefaultExecutor
  6. setStreamHandler

Introduction

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

Prototype

public void setStreamHandler(final ExecuteStreamHandler streamHandler)

Source Link

Usage

From source file:edu.stolaf.cs.wmrserver.testjob.TestJobTask.java

public TestJobResult call() throws IOException {
    // Create the result object
    TestJobResult result = new TestJobResult();

    // Map//from w w  w .  java 2  s . c om

    CappedInputStream mapInput = null;
    try {
        // List the input files and open a stream
        FileSystem fs = _inputPath.getFileSystem(_conf);
        FileStatus[] files = JobServiceHandler.listInputFiles(fs, _inputPath);
        AggregateInputStream aggregateInput = new AggregateInputStream(fs, files);
        mapInput = new CappedInputStream(aggregateInput, _inputCap);

        // Run the mapper
        result.setMapResult(runTransform(_id, _mapperFile, _packageDir, mapInput));
    } finally {
        IOUtils.closeQuietly(mapInput);
    }

    // Return if mapper failed or did not produce output
    if (result.getMapResult().getExitCode() != 0 || result.getMapResult().getOutputFile() == null)
        return result;

    // Sort
    // While this seems (and is) inefficient for computers, this is
    //actually probably the shortest way to write this code since
    // vanilla Java does not provide an equivalent of sort -n.
    // If you want to write it in Java, use java.util.TreeSet.

    File intermediateFile = null;
    FileOutputStream intermediateOutput = null;
    try {
        // Create and open temporary file for sorted intermediate output
        intermediateFile = File.createTempFile("job-" + Long.toString(_id), "-intermediate", _tempDir);
        intermediateOutput = new FileOutputStream(intermediateFile);

        // Run the sort

        CommandLine sortCommand = new CommandLine("sort");
        //sortCommand.addArgument("--field-separator=\t");
        if (_numericSort)
            sortCommand.addArgument("-n");
        sortCommand.addArgument(result.getMapResult().getOutputFile().getCanonicalPath(), false);
        DefaultExecutor exec = new DefaultExecutor();
        ExecuteWatchdog dog = new ExecuteWatchdog(EXECUTABLE_TIMEOUT);
        PumpStreamHandler pump = new PumpStreamHandler(intermediateOutput);
        exec.setWatchdog(dog);
        exec.setStreamHandler(pump);

        try {
            exec.execute(sortCommand);
        } catch (ExecuteException ex) {
            throw new IOException("Sort process failed while running test jobs", ex);
        }
    } finally {
        IOUtils.closeQuietly(intermediateOutput);
    }

    // Reduce

    FileInputStream reduceInput = null;
    try {
        // Open the intermediate file for reading
        reduceInput = new FileInputStream(intermediateFile);

        // Run the reducer
        result.setReduceResult(runTransform(_id, _reducerFile, _packageDir, reduceInput));
    } finally {
        IOUtils.closeQuietly(reduceInput);

        // Delete intermediate file
        intermediateFile.delete();
    }

    return result;
}

From source file:edu.cornell.med.icb.goby.modes.RunParallelMode.java

public void execute() throws IOException {
    final Slice slices[] = new Slice[numParts];
    File file = new File(input);
    if (!(file.isFile() && file.exists() && file.canRead())) {
        System.err.println("Input file cannot be read: " + input);
        System.exit(1);//w w  w. j  a  v a2  s . co  m
    }
    int i = 0;
    for (final Slice slice : slices) {

        slices[i++] = new Slice();
    }
    final long fileLength = file.length();
    final long sliceLength = fileLength / numParts;
    long currentOffset = 0;

    for (final Slice slice : slices) {

        slice.startOffset = currentOffset;
        slice.endOffset = currentOffset + sliceLength;
        currentOffset = slice.endOffset;
    }

    final ObjectOpenHashSet<String> allOutputs = new ObjectOpenHashSet<String>();
    final ObjectOpenHashSet<String> allFastq = new ObjectOpenHashSet<String>();

    final DoInParallel loop = new DoInParallel(numParts) {
        IsDone done = new IsDone();

        @Override
        public void action(final DoInParallel forDataAccess, final String inputBasename, final int loopIndex) {
            try {

                CompactToFastaMode ctfm = new CompactToFastaMode();
                ctfm.setInputFilename(input);
                ctfm.setOutputFormat(CompactToFastaMode.OutputFormat.FASTQ);
                ctfm.setStartPosition(slices[loopIndex].startOffset);
                ctfm.setEndPosition(slices[loopIndex].endOffset);

                String s = FilenameUtils.getBaseName(FilenameUtils.removeExtension(input)) + "-"
                        + Integer.toString(loopIndex);
                String fastqFilename = s + "-input.fq";
                allFastq.add(fastqFilename);
                File tmp1 = new File(s + "-tmp");
                tmp1.deleteOnExit();
                File output = new File(s + "-out");
                output.deleteOnExit();
                ctfm.setOutputFilename(fastqFilename);
                LOG.info(String.format("Extracting FASTQ for slice [%d-%d] loopIndex=%d %n",
                        slices[loopIndex].startOffset, slices[loopIndex].endOffset, loopIndex));
                ctfm.execute();
                if (loopIndex > 0) {
                    while (!done.isDone()) {
                        // wait a bit to give the first thread the time to load the database and establish shared memory pool
                        //   System.out.println("sleep 5 thread "+loopIndex);
                        sleep(5);
                    }
                    System.out.println("Thread " + loopIndex + " can now start.");
                }
                final Map<String, String> replacements = new HashMap<String, String>();

                final String outputFilename = output.getName();

                replacements.put("%read.fastq%", fastqFilename);
                replacements.put("%tmp1%", tmp1.getName());
                replacements.put("%output%", outputFilename);
                final String transformedCommand = transform(processPartCommand, replacements);
                final DefaultExecutor executor = new DefaultExecutor();
                OutputStream logStream = null;
                try {
                    logStream = new LoggingOutputStream(getClass(), Level.INFO, "");
                    executor.setStreamHandler(
                            new PumpStreamHandler(new StreamSignal(done, "scanning", logStream)));

                    final CommandLine parse = CommandLine.parse(transformedCommand, replacements);
                    LOG.info("About to execute: " + parse);
                    final int exitValue = executor.execute(parse);
                    LOG.info("Exit value = " + exitValue);
                    if (new File(outputFilename + ".header").exists()) {
                        // found output alignment:
                        System.out.println("found output file: " + outputFilename);
                        allOutputs.add(outputFilename + ".header");
                    } else {
                        System.out.println("Warning: did not find output alignment: " + outputFilename);
                    }
                } finally {
                    IOUtils.closeQuietly(logStream);
                    // remove the fastq file
                    new File(fastqFilename).delete();
                }

            } catch (IOException e) {
                LOG.error("Error processing index " + loopIndex + ", " + inputBasename, e);
            }
        }
    };
    String[] parts = new String[numParts];

    for (int j = 0; j < numParts; j++) {
        parts[j] = Integer.toString(j);
    }
    try {
        loop.execute(true, parts);
    } catch (Exception e) {
        System.err.println("An error occurred executing a parallel command: ");
        e.printStackTrace();
    }

    System.out.printf("Preparing to concatenate %d outputs..%n", allOutputs.size());
    final ConcatenateAlignmentMode concat = new ConcatenateAlignmentMode();
    concat.setInputFileNames(allOutputs.toArray(new String[allOutputs.size()]));
    concat.setOutputFilename(output);
    concat.setAdjustQueryIndices(false);
    concat.setAdjustSampleIndices(false);
    concat.execute();

}

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

/**
 * https://code.google.com/p/open-source-spin-compiler/wiki/CommandLine
 *
 * @param executable//  w w w.  j  a  v a2s  .  c om
 * @param sourceFile
 * @return
 */
protected boolean compile(String executable, File sourceFile) {
    try {
        File temporaryDestinationFile = File.createTempFile("blocklyapp", ".binary");
        File libDirectory = new File(new File(System.getProperty("user.dir")), "/propeller-lib");
        Map map = new HashMap();
        map.put("sourceFile", sourceFile);
        map.put("destinationFile", temporaryDestinationFile);
        map.put("libDirectory", libDirectory);

        CommandLine cmdLine = new CommandLine(executable);
        cmdLine.addArgument("-o").addArgument("${destinationFile}");
        cmdLine.addArgument("-L").addArgument("${libDirectory}");
        cmdLine.addArgument("${sourceFile}");
        cmdLine.setSubstitutionMap(map);
        DefaultExecutor executor = new DefaultExecutor();
        executor.setExitValues(new int[] { 0, 1 });

        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 {
            temporaryDestinationFile.delete();
            output = outputStream.toString();
        }

        //            System.out.println("output: " + output);
        /*
         Scanner scanner = new Scanner(output);
                
                
         Pattern chipFoundPattern = Pattern.compile(".*?(EVT:505).*?");
         Pattern pattern = Pattern.compile(".*?found on (?<comport>[a-zA-Z0-9]*).$");
         while (scanner.hasNextLine()) {
         String portLine = scanner.nextLine();
         if (chipFoundPattern.matcher(portLine).matches()) {
         Matcher portMatch = pattern.matcher(portLine);
         if (portMatch.find()) {
         //   String port = portMatch.group("comport");
                
         }
         }
         }
         */
        //            System.out.println("output: " + output);
        //            System.out.println("exitValue: " + exitValue);
        success = true;
        return true;
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
        success = false;
        return false;
    }
}

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

protected boolean compileForRam(String executable, File sourceFile, File destinationFile) {
    try {/*from   w w w.  j  a  va2s. c om*/
        File libDirectory = new File(new File(System.getProperty("user.dir")), "/propeller-lib");
        Map map = new HashMap();
        map.put("sourceFile", sourceFile);
        map.put("destinationFile", destinationFile);
        map.put("libDirectory", libDirectory);

        CommandLine cmdLine = new CommandLine(executable);
        cmdLine.addArgument("-b");
        cmdLine.addArgument("-o").addArgument("${destinationFile}");
        cmdLine.addArgument("-L").addArgument("${libDirectory}");
        cmdLine.addArgument("${sourceFile}");
        cmdLine.setSubstitutionMap(map);
        DefaultExecutor executor = new DefaultExecutor();
        //  executor.setExitValues(new int[]{402, 101});

        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();
        }

        //            System.out.println("output: " + output);
        /*
         Scanner scanner = new Scanner(output);
                
                
         Pattern chipFoundPattern = Pattern.compile(".*?(EVT:505).*?");
         Pattern pattern = Pattern.compile(".*?found on (?<comport>[a-zA-Z0-9]*).$");
         while (scanner.hasNextLine()) {
         String portLine = scanner.nextLine();
         if (chipFoundPattern.matcher(portLine).matches()) {
         Matcher portMatch = pattern.matcher(portLine);
         if (portMatch.find()) {
         //   String port = portMatch.group("comport");
                
         }
         }
         }
         */
        //            System.out.println("output: " + output);
        //            System.out.println("exitValue: " + exitValue);
        success = true;
        return true;
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
        success = false;
        return false;
    }
}

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

protected boolean compileForEeprom(String executable, File sourceFile, File destinationFile) {
    try {//from   w  ww  .j a  v a2  s  .  c  o  m
        File libDirectory = new File(new File(System.getProperty("user.dir")), "/propeller-lib");
        Map map = new HashMap();
        map.put("sourceFile", sourceFile);
        map.put("destinationFile", destinationFile);
        map.put("libDirectory", libDirectory);

        CommandLine cmdLine = new CommandLine(executable);
        cmdLine.addArgument("-e");
        cmdLine.addArgument("-o").addArgument("${destinationFile}");
        cmdLine.addArgument("-L").addArgument("${libDirectory}");
        cmdLine.addArgument("${sourceFile}");
        cmdLine.setSubstitutionMap(map);
        DefaultExecutor executor = new DefaultExecutor();
        //  executor.setExitValues(new int[]{402, 101});

        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();
        }

        //            System.out.println("output: " + output);
        /*
         Scanner scanner = new Scanner(output);
                
                
         Pattern chipFoundPattern = Pattern.compile(".*?(EVT:505).*?");
         Pattern pattern = Pattern.compile(".*?found on (?<comport>[a-zA-Z0-9]*).$");
         while (scanner.hasNextLine()) {
         String portLine = scanner.nextLine();
         if (chipFoundPattern.matcher(portLine).matches()) {
         Matcher portMatch = pattern.matcher(portLine);
         if (portMatch.find()) {
         //   String port = portMatch.group("comport");
                
         }
         }
         }
         */
        //            System.out.println("output: " + output);
        //            System.out.println("exitValue: " + exitValue);
        success = true;
        return true;
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
        success = false;
        return false;
    }
}

From source file:de.jsurf.http.HttpServerHandler.java

@Override
public void messageReceived(ChannelHandlerContext ctx, MessageEvent e) throws Exception {

    HttpRequest request = (HttpRequest) e.getMessage();
    HttpResponse response = new DefaultHttpResponse(HTTP_1_1, OK);
    response.setContent(ChannelBuffers.copiedBuffer(buf.toString(), CharsetUtil.UTF_8));
    response.setHeader(CONTENT_TYPE, "video/mpts");
    /*response.setChunked(true);
    response.setHeader(Names.TRANSFER_ENCODING, Values.CHUNKED);*/

    Channel c = e.getChannel();// www.j a  va  2s .c om

    // create a media reader
    String inputStream = HttpServerConfiguration.getConfiguration().getChannelInput(request.getUri());

    if (inputStream == null) {
        response = new DefaultHttpResponse(HTTP_1_1, NOT_FOUND);
        ChannelFuture future = c.write(response);
        future.addListener(ChannelFutureListener.CLOSE);
        return;
    }

    String path = new java.io.File(".").getCanonicalPath();
    log.debug("Current execution path: " + path);

    String[] parameters = new String[] { "-loglevel", "error", "-i", inputStream, "-vcodec", "copy", "-acodec",
            "copy", "-vbsf", "h264_mp4toannexb", "-f", "mpegts", "pipe:1" };

    CommandLine cmdLine = CommandLine.parse("ffmpeg.exe");
    cmdLine.addArguments(parameters);
    DefaultExecutor executor = new DefaultExecutor();
    final ExecuteWatchdog watchDog = new ExecuteWatchdog(86400000); // One day timeout          
    executor.setWatchdog(watchDog);

    PipedInputStream pin = new PipedInputStream();
    PipedOutputStream pout = new PipedOutputStream(pin);

    PumpStreamHandler streamHandler = new PumpStreamHandler(pout, System.err);
    executor.setStreamHandler(streamHandler);

    DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();
    executor.execute(cmdLine, resultHandler);

    c.write(response);
    InputStream in = new BufferedInputStream(pin);
    ChannelFuture future = c.write(new ChunkedStream(in));

    future.addListener(new ChannelFutureListener() {
        @Override
        public void operationComplete(ChannelFuture future) throws Exception {
            try {
                log.debug("operationComplete: closeChannel");
                future.getChannel().close();
            } catch (Exception e) {

            }
            log.debug("operationComplete: Destroy ffmpeg process");
            watchDog.destroyProcess();
        }
    });
}

From source file:eu.creatingfuture.propeller.webLoader.propeller.OpenSpin.java

/**
 * https://code.google.com/p/open-source-spin-compiler/wiki/CommandLine
 *
 * @param executable//from w w w.  ja va  2 s.  c  om
 * @param sourceFile
 * @return
 */
protected boolean compile(String executable, File sourceFile) {
    try {
        File temporaryDestinationFile = File.createTempFile("blocklyapp", ".binary");
        File libDirectory = new File(new File(System.getProperty("user.dir")), "/propeller-lib");
        Map map = new HashMap();
        map.put("sourceFile", sourceFile);
        map.put("destinationFile", temporaryDestinationFile);
        map.put("libDirectory", libDirectory);

        CommandLine cmdLine = new CommandLine(executable);
        cmdLine.addArgument("-o").addArgument("${destinationFile}");
        cmdLine.addArgument("-L").addArgument("${libDirectory}");
        cmdLine.addArgument("${sourceFile}");
        cmdLine.setSubstitutionMap(map);
        DefaultExecutor executor = new DefaultExecutor();
        //  executor.setExitValues(new int[]{402, 101});

        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 {
            temporaryDestinationFile.delete();
            output = outputStream.toString();
        }

        //            System.out.println("output: " + output);
        /*
         Scanner scanner = new Scanner(output);
                
                
         Pattern chipFoundPattern = Pattern.compile(".*?(EVT:505).*?");
         Pattern pattern = Pattern.compile(".*?found on (?<comport>[a-zA-Z0-9]*).$");
         while (scanner.hasNextLine()) {
         String portLine = scanner.nextLine();
         if (chipFoundPattern.matcher(portLine).matches()) {
         Matcher portMatch = pattern.matcher(portLine);
         if (portMatch.find()) {
         //   String port = portMatch.group("comport");
                
         }
         }
         }
         */
        //            System.out.println("output: " + output);
        //            System.out.println("exitValue: " + exitValue);
        success = true;
        return true;
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
        success = false;
        return false;
    }
}

From source file:edu.stolaf.cs.wmrserver.testjob.TestJobTask.java

protected TestJobResult.TransformResult runTransform(long id, File executable, File workingDir,
        InputStream input) throws IOException {
    // Create the result object
    TestJobResult.TransformResult result = new TestJobResult.TransformResult();

    CountingOutputStream output = null;//from  w w  w  . j a va  2  s .  co  m
    CountingOutputStream error = null;
    try {
        // Create and open temporary file for standard output
        File outputFile = File.createTempFile("job-" + Long.toString(_id), "-output", _tempDir);
        output = new CountingOutputStream(new FileOutputStream(outputFile));

        // Create and open temporary file for standard error
        File errorFile = File.createTempFile("job-" + Long.toString(_id), "-error", _tempDir);
        error = new CountingOutputStream(new FileOutputStream(errorFile));

        // If executable is relative, try to resolve in working directory
        // (This emulates the behavior of Streaming)
        if (!executable.isAbsolute()) {
            File resolvedExecutable = new File(workingDir, executable.toString());
            if (resolvedExecutable.isFile()) {
                resolvedExecutable.setExecutable(true);
                executable = resolvedExecutable.getAbsoluteFile();
            }
        }

        // Run the transform

        CommandLine command;
        if (_switchUserCommand == null)
            command = new CommandLine(executable);
        else {
            command = CommandLine.parse(_switchUserCommand);
            HashMap<String, String> substitutionMap = new HashMap<String, String>();
            substitutionMap.put("cmd", executable.toString());
            command.setSubstitutionMap(substitutionMap);
        }

        DefaultExecutor executor = new DefaultExecutor();
        ExecuteWatchdog dog = new ExecuteWatchdog(EXECUTABLE_TIMEOUT);
        PumpStreamHandler pump = new PumpStreamHandler(output, error, input);
        executor.setWorkingDirectory(workingDir);
        executor.setWatchdog(dog);
        executor.setStreamHandler(pump);
        executor.setExitValues(null);

        int exitCode = executor.execute(command);

        result.setExitCode(exitCode);

        // Check whether it produced any output
        if (output.getByteCount() == 0) {
            output.close();
            outputFile.delete();
        } else
            result.setOutputFile(outputFile);

        // Check whether it produced any error output
        if (error.getByteCount() == 0) {
            error.close();
            errorFile.delete();
        } else
            result.setErrorFile(errorFile);
    } finally {
        IOUtils.closeQuietly(output);
        IOUtils.closeQuietly(error);
    }

    return result;
}

From source file:io.vertx.config.vault.utils.VaultProcess.java

public void runAndProcess(String command, Consumer<String> processor) {
    String cli = executable.getAbsolutePath() + " " + command;
    System.out.println(">> " + cli);
    CommandLine parse = CommandLine.parse(cli);
    DefaultExecutor executor = new DefaultExecutor();
    PumpStreamHandler pump = new PumpStreamHandler(new VaultOutputStream().addExtractor(processor), System.err);

    ExecuteWatchdog watchDog = new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT);
    executor.setWatchdog(watchDog);//ww w . j av  a 2s.c  o m
    executor.setStreamHandler(pump);
    try {
        executor.execute(parse);
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}

From source file:io.rhiot.utils.process.ExecProcessManager.java

@Override
public List<String> executeAndJoinOutput(String... command) {

    CommandLine cmdLine = CommandLine.parse(String.join(" ", command));
    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValue(0);/*  w ww  . j  ava 2s  .c o  m*/
    ExecResultHandler resultHandler = null;

    if (getTimeout() > 0) {
        ExecuteWatchdog watchdog = new ExecuteWatchdog(getTimeout());
        executor.setWatchdog(watchdog);
        resultHandler = new ExecResultHandler(watchdog);
    }
    try {
        CollectingLogOutputStream outAndErr = new CollectingLogOutputStream();
        executor.setStreamHandler(new PumpStreamHandler(outAndErr));
        if (resultHandler != null) {
            executor.execute(cmdLine, resultHandler);
        } else {
            executor.execute(cmdLine);
        }
        resultHandler.waitFor();
        return outAndErr.getLines();

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