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

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

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Introduction

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

Prototype

public void setSubstitutionMap(final Map<String, ?> substitutionMap)

Source Link

Document

Set the substitutionMap to expand variables in the command line.

Usage

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

private void runJob(Master.GenerateReport job) {
    TaskEvent taskEvent = job.reportJob.taskEvent;
    CommandLine cmdLine = new CommandLine(agentConfig.getJob().getCommand());
    Map<String, Object> map = new HashMap<>();

    map.put("path", new File(agentConfig.getJob().getJobArtifact(taskEvent.getJobName())));
    cmdLine.addArgument("${path}");

    //parameters come from the task event
    for (Pair<String, String> pair : taskEvent.getParameters()) {
        cmdLine.addArgument(pair.getValue());
    }/*  ww w  . j  av  a  2 s . c om*/
    String dir = agentConfig.getJob().getLogDirectory() + "reports/" + job.reportJob.trackingId + "/";
    cmdLine.addArgument(dir);

    cmdLine.setSubstitutionMap(map);
    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValues(agentConfig.getJob().getExitValues());
    ExecuteWatchdog watchdog = new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT);
    executor.setWatchdog(watchdog);
    executor.setWorkingDirectory(new File(agentConfig.getJob().getPath()));
    FileOutputStream outFile = null;
    FileOutputStream errorFile = null;
    try {
        List<String> resultFiles = new ArrayList<>(job.results.size());
        //download all files adn
        /*int i=0;
        for (Worker.Result result : job.results) {
        String destFile = dir  + i++ + ".log";
        resultFiles.add(destFile);
        DownloadFile.downloadFile(result.metrics,destFile);
        }*/
        AtomicInteger index = new AtomicInteger();
        job.results.parallelStream().forEach(result -> {
            String destFile = dir + index.incrementAndGet() + ".log";
            resultFiles.add(destFile);
            DownloadFile.downloadFile(result.metrics, destFile);
        });
        String outPath = agentConfig.getJob().getOutPath(taskEvent.getJobName(), job.reportJob.trackingId);
        String errPath = agentConfig.getJob().getErrorPath(taskEvent.getJobName(), job.reportJob.trackingId);
        //create the std and err files
        outFile = FileUtils.openOutputStream(new File(outPath));
        errorFile = FileUtils.openOutputStream(new File(errPath));

        PumpStreamHandler psh = new PumpStreamHandler(new ExecLogHandler(outFile),
                new ExecLogHandler(errorFile));

        executor.setStreamHandler(psh);
        System.out.println(cmdLine);
        int exitResult = executor.execute(cmdLine);
        ReportResult result;
        if (executor.isFailure(exitResult)) {
            result = new ReportResult(dir, job.reportJob, false);
            log.info("Report Executor Failed, result: " + job.toString());
        } else {
            result = new ReportResult(job.reportJob.getHtml(), job.reportJob, true);
            log.info("Report Executor Completed, result: " + result.toString());
        }
        for (String resultFile : resultFiles) {
            FileUtils.deleteQuietly(new File(resultFile));
        }
        getSender().tell(result, getSelf());

    } catch (IOException e) {
        e.printStackTrace();
        throw new RuntimeException(e);
    } finally {
        IOUtils.closeQuietly(outFile);
        IOUtils.closeQuietly(errorFile);
    }

}

From source file:be.tarsos.transcoder.ffmpeg.FFMPEGExecutor.java

public String toString() {
    CommandLine cmdLine = new CommandLine(ffmpegExecutablePath);

    int fileNumber = 0;
    Map<String, File> map = new HashMap<String, File>();
    for (int i = 0; i < args.size(); i++) {
        final String arg = args.get(i);
        final Boolean isFile = argIsFile.get(i);
        if (isFile) {
            String key = "file" + fileNumber;
            map.put(key, new File(arg));
            cmdLine.addArgument("${" + key + "}", false);
            fileNumber++;//from  ww w .ja va2s  .c o  m
        } else {
            cmdLine.addArgument(arg);
        }
    }
    cmdLine.setSubstitutionMap(map);
    return cmdLine.toString();
}

From source file:be.tarsos.transcoder.ffmpeg.FFMPEGExecutor.java

/**
 * Executes the ffmpeg process with the previous given arguments.
 * //from w  w w  . ja v  a2s . c  o m
 * @return The standard output of the child process.
 * 
 * @throws IOException
 *             If the process call fails.
 */
public String execute() throws IOException {
    CommandLine cmdLine = new CommandLine(ffmpegExecutablePath);

    int fileNumber = 0;
    Map<String, File> map = new HashMap<String, File>();
    for (int i = 0; i < args.size(); i++) {
        final String arg = args.get(i);
        final Boolean isFile = argIsFile.get(i);
        if (isFile) {
            String key = "file" + fileNumber;
            map.put(key, new File(arg));
            cmdLine.addArgument("'${" + key + "}'", false);
            fileNumber++;
        } else {
            cmdLine.addArgument(arg);
        }
    }
    cmdLine.setSubstitutionMap(map);
    LOG.fine("Execute: " + cmdLine);
    DefaultExecutor executor = new DefaultExecutor();
    //5minutes wait
    ExecuteWatchdog watchdog = new ExecuteWatchdog(60 * 1000 * 5);
    executor.setWatchdog(watchdog);
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    executor.setStreamHandler(new PumpStreamHandler(out));
    int[] exitValues = { 0, 1 };
    executor.setExitValues(exitValues);
    executor.execute(cmdLine);
    return out.toString();
}

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

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

    CommandLine cmdLine = null;

    if (System.getProperty("os.name").equals("Linux")) {
        cmdLine = new CommandLine("convert");
    } else {//from ww w .  j  av  a  2 s.  co m
        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;

}

From source file:de.slackspace.wfail2ban.firewall.impl.DefaultFirewallManager.java

private void addDefaultWindowsFirewallRule(int ruleNumber, String filterName, String ipList) {
    Map<Object, Object> map = new HashMap<Object, Object>();
    map.put("name", createFinalRuleName(ruleNumber, filterName));
    map.put("direction", "in");
    map.put("ipList", ipList);
    CommandLine cmdLine = new CommandLine("cmd.exe");
    cmdLine.addArgument("/C");
    cmdLine.addArgument(System.getenv("WINDIR") + "\\system32\\netsh.exe");
    cmdLine.addArgument("advfirewall");
    cmdLine.addArgument("firewall");
    cmdLine.addArgument("add");
    cmdLine.addArgument("rule");
    cmdLine.addArgument("name=${name}");
    cmdLine.addArgument("dir=${direction}");
    cmdLine.addArgument("action=block");
    cmdLine.addArgument("localip=any");
    cmdLine.addArgument("remoteip=${ipList}");
    cmdLine.addArgument("description=This is a generated rule from wfail2ban. Do not edit!");
    cmdLine.addArgument("profile=any");
    cmdLine.addArgument("interfacetype=any");
    cmdLine.setSubstitutionMap(map);
    DefaultExecutor executor = new DefaultExecutor();
    ExecuteWatchdog watchdog = new ExecuteWatchdog(60000);
    executor.setWatchdog(watchdog);//from   w  ww.j  a va2 s  .  c  om
    try {
        executor.execute(cmdLine);
        if (logger.isDebugEnabled()) {
            logger.debug("Added firewall rule " + createFinalRuleName(ruleNumber, filterName));
        }
    } catch (ExecuteException e) {
        ConsolePrinter.printError("Could not create firewall rule. Continuing with next one...");
        logger.error("", e);
    } catch (IOException e) {
        logger.error("Could not create firewall rule. Error was: ", e);
    }
}

From source file:at.ac.tuwien.ims.latex2mobiformulaconv.converter.latex2html.PandocLatexToHtmlConverter.java

@Override
public Document convert(File tex, String title) {
    logger.debug("Start convert() with file " + tex.toPath().toAbsolutePath().toString() + ", title: " + title);

    CommandLine cmdLine;
    if (execPath != null) {
        // Run the configured pandoc executable
        logger.info("Pandoc will be run from: " + execPath.toString());
        cmdLine = new CommandLine(execPath.toFile());
    } else {//w w w.ja va 2  s  .c o  m
        // Run in system PATH environment
        logger.info("Pandoc will be run within the PATH variable.");
        cmdLine = new CommandLine("pandoc");
    }

    cmdLine.addArgument("--from=latex");
    cmdLine.addArgument("--to=html5");
    cmdLine.addArgument("--asciimathml"); // With this option, pandoc does not render latex formulas

    cmdLine.addArgument("${file}");

    HashMap<String, Path> map = new HashMap<String, Path>();
    map.put("file", Paths.get(tex.toURI()));

    cmdLine.setSubstitutionMap(map);

    DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();

    ExecuteWatchdog watchdog = new ExecuteWatchdog(60 * 1000); // max execution time 1 minute
    Executor executor = new DefaultExecutor();
    executor.setExitValue(1);
    executor.setWatchdog(watchdog);
    StringWriter writer = new StringWriter();
    WriterOutputStream writerOutputStream = new WriterOutputStream(writer, Charset.forName("UTF-8"));

    ExecuteStreamHandler pandocStreamHandler = new PumpStreamHandler(writerOutputStream, System.err);
    executor.setStreamHandler(pandocStreamHandler);

    logger.debug("Launching pandoc:");
    logger.debug(cmdLine.toString());

    try {
        executor.execute(cmdLine, resultHandler);
    } catch (IOException e) {
        logger.error("Pandoc's execution failed, exiting...");
        logger.error(e.getMessage(), e);
        System.exit(-1);
    }

    try {
        resultHandler.waitFor();
        int exitValue = resultHandler.getExitValue();

        logger.debug("Pandoc execution's exit value: " + exitValue);
        ExecuteException executeException = resultHandler.getException();
        if (executeException != null && executeException.getCause() != null) {

            String exceptionKlass = executeException.getCause().getClass().getCanonicalName();
            String exceptionMessage = executeException.getCause().getMessage();

            if (exceptionKlass.endsWith("IOException")
                    || exceptionMessage.contains("Cannot run program \"pandoc\"")) {
                logger.error("Pandoc could not be found! Exiting...");
                logger.debug(executeException);
                System.exit(1);
            }
            logger.debug(exceptionKlass + ": " + exceptionMessage);
        }

    } catch (InterruptedException e) {
        logger.error("pandoc conversion thread got interrupted, exiting...");
        logger.error(e.getMessage(), e);
        System.exit(1);
    }

    // add html document structure to output
    // pandoc returns no document markup (html, head, body)
    // therefore we have to use a template
    String htmlOutput = "<!DOCTYPE html>\n" + "<html>\n" + "<head>\n" +
    // set title
            "<title>" + title + "</title>\n" +
            // include css
            "<link rel=\"stylesheet\" type=\"text/css\" href=\"main.css\"></link>\n" + "</head>\n" + "<body>";
    try {
        htmlOutput += writer.getBuffer().toString();
        writer.close();

    } catch (IOException e) {
        logger.error("Error reading html result from StringBuffer...");
        logger.error(e.getMessage(), e);
        System.exit(1);
    }

    // Close tags in template
    htmlOutput += "</body>\n" + "</html>";

    // output loading as JDOM Document
    SAXBuilder sax = new SAXBuilder();
    Document document = null;
    try {
        document = sax.build(new StringReader(htmlOutput));
    } catch (JDOMException e) {
        logger.error("JDOM Parsing error");
        logger.error(e.getMessage(), e);
        System.exit(1);
    } catch (IOException e) {
        logger.error("Error reading from String...");
        logger.error(e.getMessage(), e);
        System.exit(1);
    }
    return document;
}

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

private Object runJob(Object message) {
    Master.Job job = (Master.Job) message;
    TaskEvent taskEvent = (TaskEvent) job.taskEvent;

    CommandLine cmdLine = new CommandLine(agentConfig.getJob().getCommand());
    log.info("Verified Script worker received task: {}", message);
    Map<String, Object> map = new HashMap<>();

    if (StringUtils.isNotEmpty(agentConfig.getJob().getMainClass()))
        cmdLine.addArgument(agentConfig.getJob().getCpOrJar());

    map.put("path", new File(agentConfig.getJob().getJobArtifact(taskEvent.getJobName())));
    cmdLine.addArgument("${path}");

    if (!StringUtils.isEmpty(agentConfig.getJob().getMainClass())) {
        cmdLine.addArgument(agentConfig.getJob().getMainClass());
    }/*  www . j a v  a2s  .c o  m*/
    //parameters come from the task event
    for (Pair<String, String> pair : taskEvent.getParameters()) {
        cmdLine.addArgument(pair.getValue());
    }
    cmdLine.addArgument("-rf").addArgument(agentConfig.getJob().getResultPath(job.roleId, job.jobId));

    cmdLine.setSubstitutionMap(map);
    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValues(agentConfig.getJob().getExitValues());
    ExecuteWatchdog watchdog = new ExecuteWatchdog(ExecuteWatchdog.INFINITE_TIMEOUT);
    executor.setWatchdog(watchdog);
    executor.setWorkingDirectory(new File(agentConfig.getJob().getPath()));
    FileOutputStream outFile = null;
    FileOutputStream errorFile = null;
    String outPath = "", errPath = "";
    try {
        outPath = agentConfig.getJob().getOutPath(taskEvent.getJobName(), job.jobId);
        errPath = agentConfig.getJob().getErrorPath(taskEvent.getJobName(), job.jobId);
        //create the std and err files
        outFile = FileUtils.openOutputStream(new File(outPath));
        errorFile = FileUtils.openOutputStream(new File(errPath));

        PumpStreamHandler psh = new PumpStreamHandler(new ExecLogHandler(outFile),
                new ExecLogHandler(errorFile));
        executor.setStreamHandler(psh);
        log.info("command: {}", cmdLine);
        int exitResult = executor.execute(cmdLine);
        //executor.getWatchdog().destroyProcess().
        Worker.Result result = new Worker.Result(exitResult, agentConfig.getUrl(errPath),
                agentConfig.getUrl(outPath), null, job);
        log.info("Exit code: {}", exitResult);
        if (executor.isFailure(exitResult) || exitResult == 1) {
            log.info("Script Executor Failed, job: " + job.jobId);
            //getSender().tell(new Worker.WorkFailed(result), getSelf());
            return new Worker.WorkFailed(result);
        } else {
            result = new Worker.Result(exitResult, agentConfig.getUrl(errPath), agentConfig.getUrl(outPath),
                    agentConfig.getUrl(getMetricsPath(job)), job);
            log.info("Script Executor Completed, job: " + result);
            //getSender().tell(new Worker.WorkComplete(result), getSelf());
            return new Worker.WorkComplete(result);
        }

    } catch (IOException e) {
        log.error(e.toString());
        Worker.Result result = new Worker.Result(-1, agentConfig.getUrl(errPath), agentConfig.getUrl(outPath),
                null, job);
        log.info("Executor Encountered run time exception, result: " + result.toString());
        //getSender().tell(new Worker.WorkFailed(result), getSelf());
        return new Worker.WorkFailed(result);
    } finally {
        IOUtils.closeQuietly(outFile);
        IOUtils.closeQuietly(errorFile);
    }
}

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 w w w.  ja  v  a  2 s .c o  m*/
    // 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());
    }
}

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("${read2}");
    } else {/*  w ww  . ja  v a 2 s .co  m*/
        cmdLine.addArgument("${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());
    }
}

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

protected boolean compileForEeprom(String executable, File sourceFile, File destinationFile) {
    try {/*from w  ww .  java2 s  .c  om*/
        List<CLib> libs = new ArrayList<>();
        libs.add(cLibs.get("simpletools"));
        libs.add(cLibs.get("simpletext"));
        libs.add(cLibs.get("simplei2c"));

        File libDirectory = new File(new File(System.getProperty("user.dir")), "/propeller-c-lib");
        Map map = new HashMap();
        map.put("sourceFile", sourceFile);
        map.put("destinationFile", destinationFile);
        CommandLine cmdLine = new CommandLine(executable);
        for (CLib lib : libs) {
            cmdLine.addArgument("-I").addArgument("${libdir" + lib.getName() + "}");
            cmdLine.addArgument("-L").addArgument("${memorymodel" + lib.getName() + "}");
            cmdLine.addArgument("-l" + lib.getName());

            map.put("libdir" + lib.getName(), new File(libDirectory, lib.getLibdir()));
            map.put("memorymodel" + lib.getName(), new File(libDirectory, lib.getMemoryModel().get("cmm")));
        }
        cmdLine.addArgument("-Os");
        cmdLine.addArgument("-mcmm");
        cmdLine.addArgument("-m32bit-doubles");
        cmdLine.addArgument("-std=c99");
        cmdLine.addArgument("-o").addArgument("${destinationFile}");
        cmdLine.addArgument("${sourceFile}");
        cmdLine.addArgument("-lm");
        for (CLib lib : libs) {
            cmdLine.addArgument("-l" + lib.getName());
        }
        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;
    }
}