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

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

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Introduction

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

Prototype

public static CommandLine parse(final String line)

Source Link

Document

Create a command line from a string.

Usage

From source file:net.mymam.fileprocessor.VideoFileGenerator.java

private Path generateFile(String cmdLineTemplate, Path in, Path outDir, String outFile, int maxWidth,
        int maxHeight) throws FileProcessingFailedException {
    try {/*from ww w  . j  ava2 s. com*/
        Path out = Paths.get(outDir.toString(), outFile);
        // TODO: Make sure that weired file names cannot be used to inject shell scripts, like '"; rm -r *;'
        String cmdLine = cmdLineTemplate.replace("$INPUT_FILE", "\"" + in.toString() + "\"")
                .replace("$OUTPUT_FILE", "\"" + out.toString() + "\"")
                .replace("$MAX_WIDTH", Integer.toString(maxWidth))
                .replace("$MAX_HEIGHT", Integer.toString(maxHeight));
        CommandLine cmd = CommandLine.parse(cmdLine);
        System.out.println("Executing " + cmd); // TODO: Use logging.
        new DefaultExecutor().execute(cmd);
        return out;
    } catch (Throwable t) {
        throw new FileProcessingFailedException(t);
    }
}

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

public boolean run(String args) {
    String cli = executable.getAbsolutePath() + " " + args;
    System.out.println(">> " + cli);
    CommandLine parse = CommandLine.parse(cli);
    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValue(0);//from   w w w .j av  a 2  s .c  o m
    try {
        return executor.execute(parse) == 0;
    } catch (IOException e) {
        e.printStackTrace();
        return false;
    }
}

From source file:edu.kit.dama.dataworkflow.impl.LocalExecutionHandler.java

/**
 * Execute the user application. This method will start a new process running
 * the prepared user application locally. The method will return as soon as
 * the application has terminated. An asnychronous monitoring task my check
 * whether the process is still running or not via {@link #getTaskStatus(edu.kit.dama.mdm.dataworkflow.DataWorkflowTask)
 * } This method will check the runningIndicator file '.RUNNING', which only
 * exists as long as the application is running.
 *
 * @param pTask The task whose application should be executed.
 *
 * @throws DataWorkflowProcessingException If either the startup or the
 * processing fails for any reason, or if the user application returns an exit
 * code != 0.//from  w w  w.  j ava  2  s . co m
 */
@Override
public void startUserApplication(DataWorkflowTask pTask) throws DataWorkflowProcessingException {
    //simply start the process...monitoring will be connected later
    File runningIndicator = getRunningIndicator(pTask);
    FileOutputStream fout = null;
    FileOutputStream ferr = null;
    File executablePath;

    try {
        executablePath = DataWorkflowHelper.getTaskMainExecutable(pTask);
        File executionBasePath = DataWorkflowHelper.getExecutionBasePath(pTask);
        File workingDirectory = DataWorkflowHelper.getTaskWorkingDirectory(executionBasePath);
        File tempDirectory = DataWorkflowHelper.getTaskTempDirectory(executionBasePath);
        File inputDirectory = DataWorkflowHelper.getTaskInputDirectory(executionBasePath);
        File outputDirectory = DataWorkflowHelper.getTaskOutputDirectory(executionBasePath);

        if (!executablePath.canExecute()) {
            LOGGER.debug("Executable at location {} seems not to be executable. Taking care of this...");
            if (executablePath.setExecutable(true)) {
                LOGGER.debug("Executable was successfully set to be executable.");
            } else {
                LOGGER.warn("Failed to set executable to be executable. Trying to continue.");
            }
        }

        String cmdLineString = executablePath.getAbsolutePath() + " "
                + pTask.getConfiguration().getApplicationArguments() + " " + pTask.getApplicationArguments();
        LOGGER.debug("Building up command array from string '{}'", cmdLineString);

        CommandLine cmdLine = CommandLine.parse(cmdLineString);
        DefaultExecutor executor = new DefaultExecutor();
        executor.setExitValue(0);
        Map<String, String> env = new HashMap<>();
        env.put("WORKING_DIR", workingDirectory.getAbsolutePath());
        env.put("TEMP_DIR", tempDirectory.getAbsolutePath());
        env.put("INPUT_DIR", inputDirectory.getAbsolutePath());
        env.put("OUTPUT_DIR", outputDirectory.getAbsolutePath());

        fout = new FileOutputStream(new File(tempDirectory, "stdout.log"));
        ferr = new FileOutputStream(new File(tempDirectory, "stderr.log"));
        LOGGER.debug("Setting stream handler for stdout and stderr.");
        executor.setStreamHandler(new PumpStreamHandler(fout, ferr));
        LOGGER.debug("Creating .RUNNING file for monitoring.");
        FileUtils.touch(runningIndicator);
        LOGGER.debug("Executing process.");
        int exitCode = executor.execute(cmdLine);
        if (exitCode != 0) {
            throw new DataWorkflowProcessingException(
                    "Execution returned exit code " + exitCode + ". See logfiles for details.");
        } else {
            LOGGER.debug("Process successfully finished with exit code {}", exitCode);
        }
    } catch (IOException | UnsupportedOperatingSystemException e) {
        throw new DataWorkflowProcessingException("Failed to start executable for task " + pTask.getId(), e);
    } finally {
        LOGGER.debug("Removing running indicator file {}", runningIndicator);
        FileUtils.deleteQuietly(runningIndicator);
        if (fout != null) {
            try {
                fout.close();
            } catch (IOException ex) {
            }
        }

        if (ferr != null) {
            try {
                ferr.close();
            } catch (IOException ex) {
            }
        }
    }
}

From source file:com.github.seqware.queryengine.tutorial.PosterSGE.java

/**
 * <p>benchmark.</p>/* ww w.j  av a  2 s.  c  om*/
 *
 * @throws java.io.IOException if any.
 */
public void benchmark() throws IOException {
    if (args.length != 3) {
        System.err.println(args.length + " arguments found");
        System.out.println(
                PosterSGE.class.getSimpleName() + " <outputKeyValueFile> <input file dir> <simultaneous jobs>");
        System.exit(-1);
    }

    File outputFile = Utility.checkOutput(args[0]);

    // check if reference has been properly created
    Reference reference = SWQEFactory.getQueryInterface().getLatestAtomByRowKey("hg_19", Reference.class);
    if (reference == null) {
        SGID refID = ReferenceCreator.mainMethod(new String[] { HG_19 });
        reference = SWQEFactory.getQueryInterface().getAtomBySGID(Reference.class, refID);
    }

    // record reference, starting disk space
    keyValues.put("referenceID", reference.getSGID().getRowKey());
    recordSpace("start");
    Utility.writeKeyValueFile(outputFile, keyValues);
    // create new FeatureSet id and pass it onto our children
    CreateUpdateManager manager = SWQEFactory.getModelManager();
    FeatureSet initialFeatureSet = manager.buildFeatureSet().setReference(reference).build();
    manager.flush();

    int count = 0;
    // go through all input files
    File fileDirectory = new File(args[1]);
    File[] listFiles = fileDirectory.listFiles();

    // record start and finish time
    Date startDate = new Date();
    keyValues.put(count + "-start-date-long", Long.toString(startDate.getTime()));
    keyValues.put(count + "-start-date-human", startDate.toString());

    // submit all jobs in parallel via SGE
    StringBuilder jobNames = new StringBuilder();
    for (File inputFile : listFiles) {
        // run without unnecessary parameters
        String cargs = "-w VCFVariantImportWorker -i " + inputFile.getAbsolutePath() + " -b "
                + String.valueOf(BENCHMARKING_BATCH_SIZE) + " -f " + initialFeatureSet.getSGID().getRowKey()
                + " -r " + reference.getSGID().getRowKey();
        String command = "java -Xmx2048m -classpath " + System.getProperty("user.dir")
                + "/seqware-queryengine-0.12.0-full.jar com.github.seqware.queryengine.system.importers.SOFeatureImporter";
        command = command + " " + cargs;
        command = "qsub -q long -l h_vmem=3G -cwd -N dyuen-" + inputFile.getName() + " -b y " + command;

        jobNames.append("dyuen-").append(inputFile.getName()).append(",");
        System.out.println("Running: " + command);
        CommandLine cmdLine = CommandLine.parse(command);
        DefaultExecutor executor = new DefaultExecutor();
        int exitValue = executor.execute(cmdLine);
    }
    String jobs = jobNames.toString().substring(0, jobNames.length() - 1);

    // submit a job that just waits on all the preceding jobs for synchronization
    String command = "java -Xmx1024m -version";
    command = "qsub -cwd -N dyuen-wait -hold_jid " + jobs + " -b y -sync y " + command;
    System.out.println("Running wait: " + command);

    CommandLine cmdLine = CommandLine.parse(command);
    DefaultExecutor executor = new DefaultExecutor();
    executor.setExitValues(null);
    int exitValue = executor.execute(cmdLine);

    FeatureSet fSet = SWQEFactory.getQueryInterface().getLatestAtomBySGID(initialFeatureSet.getSGID(),
            FeatureSet.class);
    keyValues.put(count + "-featuresSet-id", fSet.getSGID().getRowKey());
    keyValues.put(count + "-featuresSet-id-timestamp",
            Long.toString(fSet.getSGID().getBackendTimestamp().getTime()));

    //        // runs count query, touches everything but does not write
    //
    //        keyValues.put(count + "-start-count-date-long", Long.toString(System.currentTimeMillis()));
    //        long fsetcount = fSet.getCount();
    //        keyValues.put(count + "-features-loaded", Long.toString(fsetcount));
    //        keyValues.put(count + "-end-count-date-long", Long.toString(System.currentTimeMillis()));

    Date endDate = new Date();
    keyValues.put(count + "-end-date-long", Long.toString(endDate.getTime()));
    keyValues.put(count + "-end-date-human", endDate.toString());
    recordSpace(String.valueOf(count));
    Utility.writeKeyValueFile(outputFile, keyValues);
    count++;

}

From source file:com.blackducksoftware.tools.scmconnector.integrations.teamfoundation.TeamFoundationConnector.java

private int workspaceExists() {
    CommandLine command = CommandLine.parse(executable);

    command.addArgument("workspaces", false);
    command.addArgument("-server:" + server + "/" + collection, false);
    command.addArgument("-login:" + user + "," + password, false);

    int commandReturnStatus = 1;
    String commandOutput = null;//from  w ww.  j a va2s. com

    try {
        CommandResults results = commandLineExecutor.executeCommandForOutput(log, command,
                new File(getFinalSourceDirectory()));
        commandReturnStatus = results.getStatus();
        commandOutput = results.getOutput();

        if (commandOutput.contains(workspace)) {
            workspaceExists = true;
            log.info("The workspace exists");
        } else {
            workspaceExists = false;
            log.info("The workspace does not exist");
        }

    } catch (Exception e) {

        log.error("Failure executing TF Command: " + command.toString() + "; output: " + commandOutput);
        workspaceExists = false;
    }

    return commandReturnStatus;
}

From source file:com.blackducksoftware.tools.scmconnector.integrations.git.GitConnector.java

/**
 * Checkout or update from GIT./* ww  w  .jav a 2  s  .  com*/
 */
@Override
public int sync() {
    int exitStatus = -1;
    try {

        CommandLine command = CommandLine.parse(EXECUTABLE);

        String targetRepoParentPath = getFinalSourceDirectory();
        String targetRepoPath = addPathComponentToPath(targetRepoParentPath,
                getModuleNameFromURLGit(repositoryURL));

        File targetRepoParentDir = new File(targetRepoParentPath);
        File targetRepoDir = new File(targetRepoPath);

        boolean cloneExists = doesGitCloneExist(targetRepoDir);

        if (!cloneExists) {
            command.addArgument(GIT_COMMAND_CLONE);
            command.addArgument(repositoryURL);
            command.addArgument(targetRepoDir.getAbsolutePath());
            exitStatus = commandLineExecutor.executeCommand(log, command, targetRepoParentDir, "yes");
        } else {
            command.addArgument(GIT_COMMAND_PULL);
            exitStatus = commandLineExecutor.executeCommand(log, command, targetRepoDir, "yes");
        }

        if (branch != null) {
            gitCheckoutBranchShaOrPrefixedTag(branch);
        } else if (tag != null) {
            gitCheckoutTag(tag);
        } else if (sha != null) {
            gitCheckoutBranchShaOrPrefixedTag(sha);
        }

    } catch (Exception e) {
        log.error("Unable to perform sync: " + e.getMessage(), e);
        log.info("Cause: " + e.getCause());
        exitStatus = -1;
    }
    return exitStatus;

}

From source file:it.drwolf.ridire.utility.RIDIREReTagger.java

public String retagFile(File f) throws ExecuteException, IOException {
    // Map<String, File> map = new HashMap<String, File>();
    String fileIN = f.getAbsolutePath();
    String fileOut = f.getAbsolutePath() + ".iso";
    String posOld = f.getAbsolutePath() + ".iso.pos";
    String posNew = f.getAbsolutePath() + ".pos";
    // first convert from utf8 to iso8859-1
    CommandLine commandLine = CommandLine.parse("iconv");
    commandLine.addArgument("-c").addArgument("-s").addArgument("-f").addArgument("utf8").addArgument("-t")
            .addArgument("iso8859-1//TRANSLIT").addArgument("-o").addArgument(fileOut, false)
            .addArgument(fileIN, false);
    DefaultExecutor executor = new DefaultExecutor();
    ExecuteWatchdog watchdog = new ExecuteWatchdog(RIDIREReTagger.TREETAGGER_TIMEOUT);
    executor.setWatchdog(watchdog);/*from w  ww.  j av  a2s.  c  o m*/
    int exitValue = executor.execute(commandLine);
    if (exitValue == 0) {
        // tag using latin1 and Baroni's tagset
        commandLine = CommandLine.parse(this.treeTaggerBin);
        commandLine.addArgument(fileOut, false);
        executor = new DefaultExecutor();
        executor.setExitValue(0);
        watchdog = new ExecuteWatchdog(RIDIREReTagger.TREETAGGER_TIMEOUT);
        executor.setWatchdog(watchdog);
        TreeTaggerLog treeTaggerLog = new TreeTaggerLog();
        PumpStreamHandler executeStreamHandler = new PumpStreamHandler(treeTaggerLog, null);
        executor.setStreamHandler(executeStreamHandler);
        int exitValue2 = executor.execute(commandLine);
        if (exitValue2 == 0) {
            // FileUtils.deleteQuietly(new File(fileOut));
            File posTagFile = new File(posOld);
            FileUtils.writeLines(posTagFile, treeTaggerLog.getLines());
        }
        // reconvert to utf8
        commandLine = CommandLine.parse("iconv");
        commandLine.addArgument("-s").addArgument("-f").addArgument("iso8859-1").addArgument("-t")
                .addArgument("utf8//TRANSLIT").addArgument("-o").addArgument(posNew, false)
                .addArgument(posOld, false);
        executor = new DefaultExecutor();
        watchdog = new ExecuteWatchdog(RIDIREReTagger.TREETAGGER_TIMEOUT);
        executor.setWatchdog(watchdog);
        int exitValue3 = executor.execute(commandLine);
        if (exitValue3 == 0) {
            // FileUtils.deleteQuietly(new File(f.getPath() + ".iso.pos"));
            return new File(posNew).getCanonicalPath();
        }
    }
    return null;
}

From source file:com.k42b3.sacmis.Sacmis.java

private void executeCommand() {
    out.setText("");

    try {/*from www.jav  a  2s.com*/
        // save file
        saveFile();

        CommandLine commandLine = CommandLine.parse(this.path + " " + this.args.getText());

        // set timeout
        ExecuteWatchdog watchdog = new ExecuteWatchdog(timeout);

        // create executor
        DefaultExecutor executor = new DefaultExecutor();

        executor.setExitValue(this.exitCode);

        this.baos = new ByteArrayOutputStream();

        this.baosErr = new ByteArrayOutputStream();

        if (this.writerStdIn) {
            this.bais = new ByteArrayInputStream(in.getText().getBytes());

            executor.setStreamHandler(new PumpStreamHandler(this.baos, this.baosErr, this.bais));
        } else {
            executor.setStreamHandler(new PumpStreamHandler(this.baos, this.baosErr));
        }

        executor.setWatchdog(watchdog);

        executor.execute(commandLine, new ExecuteResultHandler() {

            public void onProcessComplete(int e) {
                out.setText(baos.toString());
            }

            public void onProcessFailed(ExecuteException e) {
                out.setText(baosErr.toString());
            }

        });
    } catch (Exception e) {
        out.setText(e.getMessage());
    }
}

From source file:net.openbyte.gui.WorkFrame.java

private void menuItem1ActionPerformed(ActionEvent e) {
    if (this.api == ModificationAPI.BUKKIT) {
        showBukkitIncompatibleFeature();
        return;//from  w w w. ja  v  a  2 s. 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:net.openbyte.gui.CreateProjectFrame.java

public void doOperations() {
    createProjectFolder();//from   w  w w  .  ja v  a2s  . c  o m
    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);
}