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

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

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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:net.openbyte.gui.WorkFrame.java

private void menuItem1ActionPerformed(ActionEvent e) {
    if (this.api == ModificationAPI.BUKKIT) {
        showBukkitIncompatibleFeature();
        return;//from   w  ww. j  a  va 2s.  c  o m
    }
    System.out.println("Starting client...");
    SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {
        @Override
        protected Void doInBackground() throws Exception {
            GradleConnector.newConnector().forProjectDirectory(workDirectory).connect().newBuild()
                    .forTasks("runClient").run();
            return null;
        }
    };
    if (this.api == ModificationAPI.MCP) {
        worker = new SwingWorker<Void, Void>() {
            @Override
            protected Void doInBackground() throws Exception {
                if (System.getProperty("os.name").startsWith("Windows")) {
                    Runtime.getRuntime().exec("cmd /c startclient.bat", null, workDirectory);
                    return null;
                }
                try {
                    CommandLine startClient = CommandLine.parse("python "
                            + new File(new File(workDirectory, "runtime"), "startclient.py").getAbsolutePath()
                            + " $@");
                    CommandLine authClient = CommandLine.parse("chmod 755 "
                            + new File(new File(workDirectory, "runtime"), "startclient.py").getAbsolutePath());
                    DefaultExecutor executor = new DefaultExecutor();
                    executor.setWorkingDirectory(workDirectory);
                    executor.execute(authClient);
                    executor.execute(startClient);
                } catch (Exception e) {
                    e.printStackTrace();
                }
                return null;
            }
        };
    }
    worker.execute();
}

From source file:com.walmart.gatling.commons.ScriptExecutor.java

private void runCancelJob(Master.Job message) {
    if (getAbortStatus(message.abortUrl, message.trackingId)) {
        CommandLine cmdLine = new CommandLine("/bin/bash");
        cmdLine.addArgument(agentConfig.getJob().getJobArtifact("cancel"));
        cmdLine.addArgument(message.jobId);
        DefaultExecutor killExecutor = new DefaultExecutor();
        ExecuteWatchdog watchdog = new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT);
        killExecutor.setWatchdog(watchdog);
        try {//from w  w  w. j  a v  a2  s  .  c  o m
            log.info("Cancel command: {}", cmdLine);
            killExecutor.execute(cmdLine);
        } catch (IOException e) {
            log.error(e, "Error cancelling job");
        }
    }
}

From source file:modules.NativeProcessMonitoringDaemonModule.java

protected void startNativeMonitor(String command, String options, Path path) throws NativeExecutionException {
    if (command == null || command.equals("")) {
        System.err.println("command null at GeneralNativeCommandModule.extractNative()");
        return;//from w w w .ja v a 2s .  c  om
    }
    CommandLine commandLine = new CommandLine(command);

    if (options != null && !options.equals("")) {
        String[] args = options.split(" ");
        commandLine.addArguments(args);
    }

    if (path != null) {
        commandLine.addArgument(path.toAbsolutePath().toString(), false);
    }
    executor = new DefaultExecutor();
    esh = new MyExecuteStreamHandler();
    executor.setStreamHandler(esh);

    // GeneralExecutableModuleConfig generalExecutableModuleConfig =
    // getConfig();
    executor.setWatchdog(new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT));
    if (getConfig().workingDirectory != null && getConfig().workingDirectory.exists()) {
        executor.setWorkingDirectory(getConfig().workingDirectory);
    }

    try {
        // System.out.println("Now execute: " + commandLine);
        executor.execute(commandLine, this);
    } catch (ExecuteException xs) {
        NativeExecutionException n = new NativeExecutionException();
        n.initCause(xs);
        if (path != null) {
            n.path = path.toAbsolutePath().toString();
        }
        n.exitCode = xs.getExitValue();
        throw n;
    } catch (IOException xs) {
        NativeExecutionException n = new NativeExecutionException();
        n.initCause(xs);
        if (path != null) {
            n.path = path.toAbsolutePath().toString();
        }
        throw n;
    }
    return;
}

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

private static void executeWithInput(final CommandLine commandLine, final InputStream input) {
    try {//w  w  w .j a  v a 2 s  .  com
        PumpStreamHandler handler = new PumpStreamHandler(null, null, input);

        DefaultExecutor executor = new DefaultExecutor();
        executor.setStreamHandler(handler);
        executor.setWatchdog(new ExecuteWatchdog(300000L));
        int returnCode = executor.execute(commandLine);
        if (returnCode != 0) {
            throw new UtilException("Error executing: " + commandLine //NOSONAR
                    + ", return code = " + returnCode); //NOSONAR
        }
    } catch (IOException ioe) {
        throw new UtilException("Error executing: " + commandLine, ioe); //NOSONAR
    }
}

From source file:drat.proteus.DratStartForm.java

private void parseAsVersionControlledRepo(String path, String command, boolean downloadPhase)
        throws IOException {
    if (!downloadPhase) {
        startDrat(path, command);/*  w w w  . ja v a2 s .c om*/
        return;
    }

    String projectName = null;
    boolean git = path.endsWith(".git");
    File tmpDir = new File(System.getProperty("java.io.tmpdir"));
    String tmpDirPath = tmpDir.getCanonicalPath();
    String line = null;
    if (git) {
        projectName = path.substring(path.lastIndexOf("/") + 1, path.lastIndexOf("."));
        line = "git clone --depth 1 --branch master " + path;
    } else {
        projectName = path.substring(path.lastIndexOf("/") + 1);
        line = "svn export " + path;
    }
    String clonePath = tmpDirPath + File.separator + projectName;
    File cloneDir = new File(clonePath);
    if (cloneDir.isDirectory() && cloneDir.exists()) {
        LOG.info("Git / SVN clone: [" + clonePath + "] already exists, removing it.");
        FileUtils.removeDir(cloneDir);
    }
    LOG.info("Cloning Git / SVN project: [" + projectName + "] remote repo: [" + path + "] into " + tmpDirPath);

    CommandLine cmdLine = CommandLine.parse(line);
    DefaultExecutor executor = new DefaultExecutor();
    executor.setWorkingDirectory(tmpDir);
    int exitValue = executor.execute(cmdLine);

    if (git) {
        String gitHiddenDirPath = clonePath + File.separator + ".git";
        File gitHiddenDir = new File(gitHiddenDirPath);
        LOG.info("Removing .git directory from " + gitHiddenDirPath);
        FileUtils.removeDir(gitHiddenDir);
    }

    startDrat(clonePath, command);

}

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);/*from w w w.j  a  v  a  2  s  . c  om*/
    }
    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:net.openbyte.gui.CreateProjectFrame.java

public void doOperations() {
    createProjectFolder();/*from w w  w  .j ava 2s  .c  om*/
    monitor.setProgress(20);
    monitor.setNote("Creating solution for project...");
    createSolutionFile();
    monitor.setNote("Creating library solution for project...");
    createLibrarySolution();
    monitor.setProgress(60);
    monitor.setNote("Cloning API...");
    cloneAPI();
    monitor.setProgress(90);
    monitor.setNote("Decompiling Minecraft...");
    if (this.api == ModificationAPI.MCP) {
        if (System.getProperty("os.name").startsWith("Windows")) {
            try {
                Runtime.getRuntime().exec("cmd /c decompile.bat", null, projectFolder);
            } catch (IOException e) {
                e.printStackTrace();
            }
        } else {
            try {
                CommandLine commandLine = CommandLine.parse("python "
                        + new File(new File(projectFolder, "runtime"), "decompile.py").getAbsolutePath()
                        + " $@");
                File runtimePythonDirectory = new File(projectFolder, "runtime");
                File decompilePython = new File(runtimePythonDirectory, "decompile.py");
                CommandLine authPy = CommandLine.parse("chmod 755 " + decompilePython.getAbsolutePath());
                DefaultExecutor executor = new DefaultExecutor();
                executor.setWorkingDirectory(projectFolder);
                executor.execute(authPy);
                executor.execute(commandLine);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    if (this.api == ModificationAPI.MINECRAFT_FORGE) {
        GradleConnector.newConnector().forProjectDirectory(projectFolder).connect().newBuild()
                .setJvmArguments("-XX:-UseGCOverheadLimit").forTasks("setupDecompWorkspace").run();
    }
    monitor.close();
    WelcomeFrame welcomeFrame = new WelcomeFrame();
    welcomeFrame.setVisible(true);
}

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

private void runScriptWithSqlPlus(File file, Map environment)
        throws MojoExecutionException, MojoFailureException {
    checkFileIsReadable(file);//  w w  w .  jav a  2  s.  c o m

    CommandLine commandLine = new CommandLine(sqlplus);
    // logon only once, without this sql*plus would prompt for
    // credentials if given ones are not correct
    commandLine.addArgument("-L");
    StringTokenizer stringTokenizer = new StringTokenizer(getConnectionIdentifier());
    while (stringTokenizer.hasMoreTokens()) {
        commandLine.addArgument(stringTokenizer.nextToken());
    }
    commandLine.addArgument("@" + file.getName());
    if (arguments != null) {
        for (Object argument : arguments) {
            if (argument == null) {
                throw new MojoExecutionException("Misconfigured argument, value is null. "
                        + "Set the argument to an empty value if this is the required behaviour.");
            } else {
                commandLine.addArgument(argument.toString());
            }
        }
    }

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

    Executor exec = new DefaultExecutor();
    exec.setWorkingDirectory(file.getParentFile());
    exec.setStreamHandler(new PumpStreamHandler(System.out, System.err));
    try {
        exec.execute(commandLine, environment);
    } catch (ExecuteException e) {
        throw new MojoExecutionException("program exited with exitCode: " + e.getExitValue());
    } catch (IOException e) {
        throw new MojoExecutionException("Command execution failed.", e);
    }
}

From source file:it.drwolf.ridire.index.sketch.AsyncSketchCreator.java

private void compactLines(List<File> tableFile, File finalTable) throws ExecuteException, IOException {
    Executor executor = new DefaultExecutor();
    File tempTabTot = File.createTempFile("ridireTABTOT", ".tbl");
    File tempSh = File.createTempFile("ridireSH", ".sh");
    StringBuffer stringBuffer = new StringBuffer();
    stringBuffer.append("export LC_ALL=C\n");
    stringBuffer/*from w ww .  ja va  2  s . c  o  m*/
            .append("cat " + StringUtils.join(tableFile, " ") + " > " + tempTabTot.getAbsolutePath() + "\n");
    stringBuffer.append("awk '{a[$2]+= $1; s+=$1}END{for(i in a){print a[i],i;}; print s \"\t\"}' "
            + tempTabTot.getAbsolutePath() + " | sort -k1nr -k2 > " + finalTable.getAbsolutePath());
    FileUtils.writeStringToFile(tempSh, stringBuffer.toString());
    tempSh.setExecutable(true);
    CommandLine commandLine = new CommandLine(tempSh.getAbsolutePath());
    executor.execute(commandLine);
    FileUtils.deleteQuietly(tempTabTot);
    FileUtils.deleteQuietly(tempSh);
}

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 v  a2  s. c o 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;
}