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

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

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

Prototype

public CommandLine(final CommandLine other)

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Usage

From source file:io.selendroid.standalone.builder.SelendroidServerBuilderTest.java

@Test
public void testShouldBeAbleToCreateASignedSelendroidServerWithCustomKeystore() throws Exception {
    SelendroidServerBuilder builder = getDefaultBuilderWithCustomKeystore();
    builder.init(new DefaultAndroidApp(new File(APK_FILE)));
    builder.cleanUpPrebuildServer();//from  w ww. ja  va 2s . c  o  m
    File file = File.createTempFile("testserver1", "apk");
    builder.signTestServer(builder.createAndAddCustomizedAndroidManifestToSelendroidServer(), file);

    // Verify that apk is signed
    CommandLine cmd = new CommandLine(AndroidSdk.aapt());
    cmd.addArgument("list", false);
    cmd.addArgument(file.getAbsolutePath(), false);

    String output = ShellCommand.exec(cmd);
    String sigFileName = selendroidConfiguration.getKeystoreAlias().toUpperCase();
    if (sigFileName.length() > 8) {
        sigFileName = sigFileName.substring(0, 8);
    }

    assertResultDoesNotContainFile(output, "META-INF/CERT.RSA");
    assertResultDoesNotContainFile(output, "META-INF/CERT.SF");
    assertResultDoesContainFile(output, "META-INF/" + sigFileName + ".SF");
    assertResultDoesContainFile(output, "META-INF/" + sigFileName + ".RSA");
    assertResultDoesContainFile(output, "AndroidManifest.xml");
}

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. j  a  va2s .c  om*/
            .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:com.netflix.genie.web.services.impl.LocalJobKillServiceImpl.java

private void killJobOnUnix(final int pid) throws GenieException {
    try {//from  w w  w . j  av  a 2  s.c o m
        // Ensure this process check can't be timed out
        final Instant tomorrow = Instant.now().plus(1, ChronoUnit.DAYS);
        final ProcessChecker processChecker = new UnixProcessChecker(pid, this.executor, tomorrow);
        processChecker.checkProcess();
    } catch (final ExecuteException ee) {
        // This means the job was done already
        log.debug("Process with pid {} is already done", pid);
        return;
    } catch (final IOException ioe) {
        throw new GenieServerException("Unable to check process status for pid " + pid, ioe);
    }

    // TODO: Do we need retries?
    // This means the job client process is still running
    try {
        final CommandLine killCommand;
        if (this.runAsUser) {
            killCommand = new CommandLine("sudo");
            killCommand.addArgument("kill");
        } else {
            killCommand = new CommandLine("kill");
        }
        killCommand.addArguments(Integer.toString(pid));
        this.executor.execute(killCommand);
    } catch (final IOException ioe) {
        throw new GenieServerException("Unable to kill process " + pid, ioe);
    }
}

From source file:com.tascape.qa.th.android.comm.Adb.java

public List<String> adb(final List<Object> arguments) throws IOException {
    CommandLine cmdLine = new CommandLine(ADB);
    if (!this.serial.isEmpty()) {
        cmdLine.addArgument("-s");
        cmdLine.addArgument(serial);//from  w  w  w  .  j  a v  a2s .c om
    }
    arguments.forEach((arg) -> {
        cmdLine.addArgument(arg + "");
    });
    LOG.debug("[{} {}]", cmdLine.getExecutable(), StringUtils.join(cmdLine.getArguments(), " "));
    List<String> output = new ArrayList<>();
    Executor executor = new DefaultExecutor();
    executor.setStreamHandler(new ESH(output));
    if (executor.execute(cmdLine) != 0) {
        throw new IOException(cmdLine + " failed");
    }
    return output;
}

From source file:com.boundlessgeo.wps.grass.GrassProcesses.java

@DescribeProcess(title = "r.viewshed", description = "Computes the viewshed of a point on an elevation raster map.")
@DescribeResult(description = "area visible from provided location")
public static GridCoverage2D viewshed(
        @DescribeParameter(name = "dem", description = "digitial elevation model") GridCoverage2D dem,
        @DescribeParameter(name = "x", description = "x location in map units") double x,
        @DescribeParameter(name = "y", description = "y location in map units") double y) throws Exception {

    String COMMAND = "viewshed";
    //Stage files in a temporary location
    File geodb = Files.createTempDirectory("grassdata").toFile();
    geodb.deleteOnExit();//from   w w  w .j  a v  a  2s  .co  m
    File location = new File(geodb, COMMAND + Long.toString(random.nextLong()) + "location");

    // stage dem file
    File file = new File(geodb, "dem.tif");
    //The file must exist for FileImageOutputStreamExtImplSpi to create the output stream
    if (!file.exists()) {
        file.getParentFile().mkdirs();
        file.createNewFile();
    }
    final GeoTiffFormat format = new GeoTiffFormat();
    GridCoverageWriter writer = format.getWriter(file);
    writer.write(dem, null);
    LOGGER.info("Staging file:" + file);

    // use file to create location with (returns PERMANENT mapset)
    File mapset = location(location, file);

    DefaultExecutor executor = new DefaultExecutor();
    executor.setWatchdog(new ExecuteWatchdog(60000));
    executor.setStreamHandler(new PumpStreamHandler(System.out));
    executor.setWorkingDirectory(mapset);

    Map<String, String> env = customEnv(geodb, location, mapset);

    // EXPORT IMPORT DEM
    // r.in.gdal input=~/grassdata/viewshed/PERMANENT/dem.tif output=dem --overwrite

    File r_in_gdal = bin("r.in.gdal");
    CommandLine cmd = new CommandLine(r_in_gdal);
    cmd.addArgument("input=${file}");
    cmd.addArgument("output=dem");
    cmd.addArgument("--overwrite");
    cmd.setSubstitutionMap(new KVP("file", file));
    try {
        LOGGER.info(cmd.toString());
        executor.setExitValue(0);
        int exitValue = executor.execute(cmd, env);
    } catch (ExecuteException fail) {
        LOGGER.warning(r_in_gdal.getName() + ":" + fail.getLocalizedMessage());
        throw fail;
    }

    // EXECUTE VIEWSHED
    File r_viewshed = bin("r.viewshed");
    cmd = new CommandLine(r_viewshed);
    cmd.addArgument("input=dem");
    cmd.addArgument("output=viewshed");
    cmd.addArgument("coordinates=${x},${y}");
    cmd.addArgument("--overwrite");
    cmd.setSubstitutionMap(new KVP("x", x, "y", y));

    try {
        LOGGER.info(cmd.toString());
        executor.setExitValue(0);
        int exitValue = executor.execute(cmd, env);
    } catch (ExecuteException fail) {
        LOGGER.warning(r_viewshed.getName() + ":" + fail.getLocalizedMessage());
        throw fail;
    }

    // EXECUTE EXPORT VIEWSHED
    // r.out.gdal --overwrite input=viewshed@PERMANENT output=/Users/jody/grassdata/viewshed/viewshed.tif format=GTiff
    File viewshed = new File(location, "viewshed.tif");

    File r_out_gdal = bin("r.out.gdal");
    cmd = new CommandLine(r_out_gdal);
    cmd.addArgument("input=viewshed");
    cmd.addArgument("output=${viewshed}");
    cmd.addArgument("--overwrite");
    cmd.addArgument("format=GTiff");
    cmd.setSubstitutionMap(new KVP("viewshed", viewshed));

    try {
        LOGGER.info(cmd.toString());
        executor.setExitValue(0);
        int exitValue = executor.execute(cmd, env);
    } catch (ExecuteException fail) {
        LOGGER.warning(r_out_gdal.getName() + ":" + fail.getLocalizedMessage());
        throw fail;
    }

    // STAGE RESULT

    if (!viewshed.exists()) {
        throw new IOException("Generated viweshed.tif not found");
    }
    GeoTiffReader reader = format.getReader(viewshed);
    GridCoverage2D coverage = reader.read(null);
    cleanup(new File(env.get("GISRC")));
    return coverage;
}

From source file:com.netflix.genie.web.services.impl.JobKillServiceV3.java

private void killJobOnUnix(final int pid) throws GenieException {
    try {/*from   w  w w .j a v a  2  s .  c o m*/
        // Ensure this process check can't be timed out
        final Instant tomorrow = Instant.now().plus(1, ChronoUnit.DAYS);
        final ProcessChecker processChecker = this.processCheckerFactory.get(pid, tomorrow);
        processChecker.checkProcess();
    } catch (final ExecuteException ee) {
        // This means the job was done already
        log.debug("Process with pid {} is already done", pid);
        return;
    } catch (final IOException ioe) {
        throw new GenieServerException("Unable to check process status for pid " + pid, ioe);
    }

    // TODO: Do we need retries?
    // This means the job client process is still running
    try {
        final CommandLine killCommand;
        if (this.runAsUser) {
            killCommand = new CommandLine("sudo");
            killCommand.addArgument("kill");
        } else {
            killCommand = new CommandLine("kill");
        }
        killCommand.addArguments(Integer.toString(pid));
        this.executor.execute(killCommand);
    } catch (final IOException ioe) {
        throw new GenieServerException("Unable to kill process " + pid, ioe);
    }
}

From source file:com.cip.crane.agent.sheduler.ExecuteTaskThread.java

private void executeJob(ScheduleConf conf, ScheduleStatus status) {
    if (conf == null) {
        LOGGER.error("SchduleConf is empty!");
        status.setStatus(ScheduleStatus.EXECUTE_FAILED);
        status.setFailureInfo("SchduleConf is empty!");
        cs.updateStatus(localIp, taskAttempt, status);
        return;// w  w  w  . java 2s  .  c om
    }
    String attemptID = conf.getAttemptID();
    String taskID = conf.getTaskID();
    String command = conf.getCommand();
    String userName = conf.getUserName();
    String taskType = conf.getTaskType();
    Map<String, String> extendedConfs = conf.getExtendedMap();
    String hadoopName = "hadoop";
    if (extendedConfs != null && extendedConfs.containsKey(HADOOP_NAME)) {
        hadoopName = conf.getExtendedMap().get(HADOOP_NAME);
    }
    if (userName.isEmpty()) {
        userName = "nobody";
    }

    if (attemptID == null || taskID == null || command == null || attemptID.isEmpty() || taskID.isEmpty()
            || command.isEmpty()) {
        LOGGER.error("Configure is not completed!");
        status.setStatus(ScheduleStatus.EXECUTE_FAILED);
        status.setFailureInfo("Configure is not completed!");
        cs.updateStatus(localIp, taskAttempt, status);
        return;
    }

    //create log file stream
    SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
    String date = format.format(new Date());
    String logFilePath = logPath + FILE_SEPRATOR + date + FILE_SEPRATOR + attemptID + ".log";
    String errorFilePath = logPath + FILE_SEPRATOR + date + FILE_SEPRATOR + attemptID + ".error";
    String htmlFileName = attemptID + ".html";
    String htmlFilePath = logPath + FILE_SEPRATOR + date + FILE_SEPRATOR + htmlFileName;
    FileOutputStream logFileStream = null;
    FileOutputStream errorFileStream = null;
    try {
        File logFile = new File(logFilePath);
        File errorFile = new File(errorFilePath);
        logFile.getParentFile().mkdirs();
        logFile.createNewFile();
        errorFile.createNewFile();
        logFileStream = new FileOutputStream(logFilePath);
        errorFileStream = new FileOutputStream(errorFilePath);
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    String path = jobPath + FILE_SEPRATOR + taskID + FILE_SEPRATOR;
    String pidFile = running + FILE_SEPRATOR + '.' + attemptID;
    String returnValueFile = running + FILE_SEPRATOR + "rv." + attemptID;
    int returnCode = 0;
    try {
        LOGGER.debug(taskAttempt + " start execute");

        if (ON_WINDOWS) {
            String escapedCmd = command.replaceAll("\\\\", "\\\\\\\\");
            escapedCmd = escapedCmd.replaceAll("\"", "\\\\\\\"");
            returnCode = executor.execute(attemptID, logFileStream, errorFileStream, escapedCmd);
        } else {
            //hadoop??
            String kdestroyCommand = "";
            String krb5PathCommand = "";
            CommandLine cmdLine;
            if (taskType != null && taskType.equals("hadoop")) {
                krb5PathCommand = String.format(krb5Path, krb5Conf, hadoop, "krb5cc_" + attemptID);
                String kinitCommand = String.format(KINIT_COMMAND_PATTERN, homeDir, hadoopName, hadoopName);
                kinitCommand = String.format(command_pattern, userName, krb5PathCommand, kinitCommand);

                kdestroyCommand = KDESTROY_COMMAND;
                cmdLine = new CommandLine("bash");
                cmdLine.addArgument("-c");
                cmdLine.addArgument(kinitCommand, false);
                int kinitRV = 0;
                try {
                    kinitRV = executor.execute(attemptID, 0, null, cmdLine, logFileStream, errorFileStream);
                } catch (Exception e) {
                    LOGGER.error(e, e);
                    setFailResult(status);
                    return;
                }
                returnCode = kinitRV;
            }
            if (returnCode == 0) {
                //execute cmd
                String escapedCmd = command.replaceAll("\\\\", "\\\\\\\\");
                escapedCmd = escapedCmd.replaceAll("\"", "\\\\\\\"");
                cmdLine = new CommandLine("bash");
                cmdLine.addArgument("-c");
                String mainCmd = String.format(MAIN_COMMAND_PATTERN, pidFile, path, path, env, env, escapedCmd);
                String sotreRvCmd = String.format(STORE_RETURN_VALUE_PATTERN, returnValueFile);
                mainCmd = String.format(command_pattern, userName, krb5PathCommand, mainCmd);
                if (!kdestroyCommand.isEmpty()) {
                    kdestroyCommand = String.format(command_pattern, userName, krb5PathCommand,
                            kdestroyCommand);
                }
                String postCmd = String.format(CLEAN_FILES_PATTERN, pidFile, kdestroyCommand);

                cmdLine.addArgument(mainCmd + " ;" + sotreRvCmd + postCmd, false);

                executor.execute(attemptID, 0, null, cmdLine, logFileStream, errorFileStream);

                try {
                    BufferedReader br = new BufferedReader(new FileReader((new File(returnValueFile))));
                    String returnValStr = br.readLine();
                    br.close();
                    returnCode = Integer.parseInt(returnValStr);
                    new File(returnValueFile).delete();
                } catch (NumberFormatException e) {
                    LOGGER.error(e, e);
                    returnCode = 1;
                } catch (IOException e) {
                    LOGGER.error(e, e);
                    returnCode = 1;
                }
            }
        }
        setResult(returnCode, status);
    } catch (Exception e) {
        LOGGER.error(e, e);
        setFailResult(status);
    }

    try {
        taskHelper.uploadLog(returnCode, errorFilePath, logFilePath, htmlFilePath, htmlFileName);
    } catch (IOException e) {
        LOGGER.error(e, e);
    }

}

From source file:com.dp.bigdata.taurus.agent.sheduler.ExecuteTaskThread.java

private void executeJob(ScheduleConf conf, ScheduleStatus status) {
    if (conf == null) {
        LOGGER.error("SchduleConf is empty!");
        status.setStatus(ScheduleStatus.EXECUTE_FAILED);
        status.setFailureInfo("SchduleConf is empty!");
        cs.updateStatus(localIp, taskAttempt, status);
        return;/*  ww  w.  ja va 2  s .  co  m*/
    }
    String attemptID = conf.getAttemptID();
    String taskID = conf.getTaskID();
    String command = conf.getCommand();
    String userName = conf.getUserName();
    String taskType = conf.getTaskType();
    Map<String, String> extendedConfs = conf.getExtendedMap();
    String hadoopName = "hadoop";
    if (extendedConfs != null && extendedConfs.containsKey(HADOOP_NAME)) {
        hadoopName = conf.getExtendedMap().get(HADOOP_NAME);
    }
    if (userName.isEmpty()) {
        userName = "nobody";
    }

    if (attemptID == null || taskID == null || command == null || attemptID.isEmpty() || taskID.isEmpty()
            || command.isEmpty()) {
        LOGGER.error("Configure is not completed!");
        status.setStatus(ScheduleStatus.EXECUTE_FAILED);
        status.setFailureInfo("Configure is not completed!");
        cs.updateStatus(localIp, taskAttempt, status);
        return;
    }

    //create log file stream
    SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
    String date = format.format(new Date());
    String logFilePath = logPath + FILE_SEPRATOR + date + FILE_SEPRATOR + attemptID + ".log";
    String errorFilePath = logPath + FILE_SEPRATOR + date + FILE_SEPRATOR + attemptID + ".error";
    String htmlFileName = attemptID + ".html";
    String htmlFilePath = logPath + FILE_SEPRATOR + date + FILE_SEPRATOR + htmlFileName;
    FileOutputStream logFileStream = null;
    FileOutputStream errorFileStream = null;
    try {
        File logFile = new File(logFilePath);
        File errorFile = new File(errorFilePath);
        logFile.getParentFile().mkdirs();
        logFile.createNewFile();
        errorFile.createNewFile();
        logFileStream = new FileOutputStream(logFilePath);
        errorFileStream = new FileOutputStream(errorFilePath);
    } catch (IOException e) {
        LOGGER.error(e.getMessage(), e);
    }

    String path = jobPath + FILE_SEPRATOR + taskID + FILE_SEPRATOR;
    String pidFile = running + FILE_SEPRATOR + '.' + attemptID;
    String returnValueFile = running + FILE_SEPRATOR + "rv." + attemptID;
    int returnCode = 0;
    try {
        LOGGER.debug(taskAttempt + " start execute");

        if (ON_WINDOWS) {
            String escapedCmd = command.replaceAll("\\\\", "\\\\\\\\");
            escapedCmd = escapedCmd.replaceAll("\"", "\\\\\\\"");
            returnCode = executor.execute(attemptID, logFileStream, errorFileStream, escapedCmd);
        } else {
            //hadoop??
            String kdestroyCommand = "";
            String krb5PathCommand = "";
            CommandLine cmdLine;
            if (taskType != null && taskType.equals("hadoop")) {
                krb5PathCommand = String.format(krb5Path, hadoop, "krb5cc_" + attemptID);
                String kinitCommand = String.format(KINIT_COMMAND_PATTERN, homeDir, hadoopName, hadoopName);
                kinitCommand = String.format(command_pattern, userName, krb5PathCommand, kinitCommand);

                kdestroyCommand = KDESTROY_COMMAND;
                cmdLine = new CommandLine("bash");
                cmdLine.addArgument("-c");
                cmdLine.addArgument(kinitCommand, false);
                int kinitRV = 0;
                try {
                    kinitRV = executor.execute(attemptID, 0, null, cmdLine, logFileStream, errorFileStream);
                } catch (Exception e) {
                    LOGGER.error(e, e);
                    setFailResult(status);
                    return;
                }
                returnCode = kinitRV;
            }
            if (returnCode == 0) {
                //execute cmd
                String escapedCmd = command.replaceAll("\\\\", "\\\\\\\\");
                escapedCmd = escapedCmd.replaceAll("\"", "\\\\\\\"");
                cmdLine = new CommandLine("bash");
                cmdLine.addArgument("-c");
                String mainCmd = String.format(MAIN_COMMAND_PATTERN, pidFile, path, path, env, env, escapedCmd);
                String sotreRvCmd = String.format(STORE_RETURN_VALUE_PATTERN, returnValueFile);
                mainCmd = String.format(command_pattern, userName, krb5PathCommand, mainCmd);
                if (!kdestroyCommand.isEmpty()) {
                    kdestroyCommand = String.format(command_pattern, userName, krb5PathCommand,
                            kdestroyCommand);
                }
                String postCmd = String.format(CLEAN_FILES_PATTERN, pidFile, kdestroyCommand);

                cmdLine.addArgument(mainCmd + ";" + sotreRvCmd + postCmd, false);

                executor.execute(attemptID, 0, null, cmdLine, logFileStream, errorFileStream);

                try {
                    BufferedReader br = new BufferedReader(new FileReader((new File(returnValueFile))));
                    String returnValStr = br.readLine();
                    br.close();
                    returnCode = Integer.parseInt(returnValStr);
                    new File(returnValueFile).delete();
                } catch (NumberFormatException e) {
                    LOGGER.error(e, e);
                    returnCode = 1;
                } catch (IOException e) {
                    LOGGER.error(e, e);
                    returnCode = 1;
                }
            }
        }
        setResult(returnCode, status);
    } catch (Exception e) {
        LOGGER.error(e, e);
        setFailResult(status);
    }

    try {
        taskHelper.uploadLog(returnCode, errorFilePath, logFilePath, htmlFilePath, htmlFileName);
    } catch (IOException e) {
        LOGGER.error(e, e);
    }

}

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

/**
 * PBS qstat command for Array Jobs/*from   w ww.j  a  va  2 s .  c  om*/
 * <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);
}

From source file:io.selendroid.builder.SelendroidServerBuilder.java

File createAndAddCustomizedAndroidManifestToSelendroidServer()
        throws IOException, ShellCommandException, AndroidSdkException {
    String targetPackageName = applicationUnderTest.getBasePackage();
    File tempdir = new File(FileUtils.getTempDirectoryPath() + File.separatorChar + targetPackageName
            + System.currentTimeMillis());

    if (!tempdir.exists()) {
        tempdir.mkdirs();//from  w ww  . j  a  va 2 s .co m
    }

    File customizedManifest = new File(tempdir, "AndroidManifest.xml");
    log.info("Adding target package '" + targetPackageName + "' to " + customizedManifest.getAbsolutePath());

    // add target package
    InputStream inputStream = getResourceAsStream(selendroidApplicationXmlTemplate);
    if (inputStream == null) {
        throw new SelendroidException("AndroidApplication.xml template file was not found.");
    }
    String content = IOUtils.toString(inputStream, Charset.defaultCharset().displayName());

    // find the first occurance of "package" and appending the targetpackagename to begining
    int i = content.toLowerCase().indexOf("package");
    int cnt = 0;
    for (; i < content.length(); i++) {
        if (content.charAt(i) == '\"') {
            cnt++;
        }
        if (cnt == 2) {
            break;
        }
    }
    content = content.substring(0, i) + "." + targetPackageName + content.substring(i);
    log.info("Final Manifest File:\n" + content);
    content = content.replaceAll(SELENDROID_TEST_APP_PACKAGE, targetPackageName);
    // Seems like this needs to be done
    if (content.contains(ICON)) {
        content = content.replaceAll(ICON, "");
    }

    OutputStream outputStream = new FileOutputStream(customizedManifest);
    IOUtils.write(content, outputStream, Charset.defaultCharset().displayName());
    IOUtils.closeQuietly(inputStream);
    IOUtils.closeQuietly(outputStream);

    // adding the xml to an empty apk
    CommandLine createManifestApk = new CommandLine(AndroidSdk.aapt());

    createManifestApk.addArgument("package", false);
    createManifestApk.addArgument("-M", false);
    createManifestApk.addArgument(customizedManifest.getAbsolutePath(), false);
    createManifestApk.addArgument("-I", false);
    createManifestApk.addArgument(AndroidSdk.androidJar(), false);
    createManifestApk.addArgument("-F", false);
    createManifestApk.addArgument(tempdir.getAbsolutePath() + File.separatorChar + "manifest.apk", false);
    createManifestApk.addArgument("-f", false);
    log.info(ShellCommand.exec(createManifestApk, 20000L));

    ZipFile manifestApk = new ZipFile(
            new File(tempdir.getAbsolutePath() + File.separatorChar + "manifest.apk"));
    ZipArchiveEntry binaryManifestXml = manifestApk.getEntry("AndroidManifest.xml");

    File finalSelendroidServerFile = new File(tempdir.getAbsolutePath() + "selendroid-server.apk");
    ZipArchiveOutputStream finalSelendroidServer = new ZipArchiveOutputStream(finalSelendroidServerFile);
    finalSelendroidServer.putArchiveEntry(binaryManifestXml);
    IOUtils.copy(manifestApk.getInputStream(binaryManifestXml), finalSelendroidServer);

    ZipFile selendroidPrebuildApk = new ZipFile(selendroidServer.getAbsolutePath());
    Enumeration<ZipArchiveEntry> entries = selendroidPrebuildApk.getEntries();
    for (; entries.hasMoreElements();) {
        ZipArchiveEntry dd = entries.nextElement();
        finalSelendroidServer.putArchiveEntry(dd);

        IOUtils.copy(selendroidPrebuildApk.getInputStream(dd), finalSelendroidServer);
    }

    finalSelendroidServer.closeArchiveEntry();
    finalSelendroidServer.close();
    manifestApk.close();
    log.info("file: " + finalSelendroidServerFile.getAbsolutePath());
    return finalSelendroidServerFile;
}