Example usage for java.lang Process getErrorStream

List of usage examples for java.lang Process getErrorStream

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Introduction

In this page you can find the example usage for java.lang Process getErrorStream.

Prototype

public abstract InputStream getErrorStream();

Source Link

Document

Returns the input stream connected to the error output of the process.

Usage

From source file:org.ala.spatial.web.services.GDMWSController.java

private int runGDM(int level, String params) {
    Runtime runtime = Runtime.getRuntime();
    Process proc;
    InputStreamReader isre = null, isr = null;
    BufferedReader bre = null, br = null;
    int exitValue = -1;

    try {//from   ww w  .ja va  2  s. c o  m
        String command = AlaspatialProperties.getAnalysisGdmCmd() + " -g" + level + " " + params;
        System.out.println("Running gdm: " + command);

        //            return 111;

        proc = runtime.exec(command);

        isre = new InputStreamReader(proc.getErrorStream());
        bre = new BufferedReader(isre);
        isr = new InputStreamReader(proc.getInputStream());
        br = new BufferedReader(isr);
        String line;

        while ((line = bre.readLine()) != null) {
            System.out.println(line);
        }

        while ((line = br.readLine()) != null) {
            System.out.println(line);
        }

        int exitVal = proc.waitFor();

        // any error???
        exitValue = exitVal;

    } catch (Exception e) {
        System.out.println("Error executing GDM: ");
        e.printStackTrace(System.out);
    } finally {
        try {
            isre.close();
            bre.close();
            isr.close();
            br.close();
        } catch (IOException ioe) {
            System.out.println("Error closing output and error streams");
        }
    }

    return exitValue;
}

From source file:hu.sztaki.lpds.pgportal.portlets.asm.ClientError.java

private ArrayList<String> getOutputfiles(String resultzipPath, String outputfileMask) {
    String temp_output = resultzipPath;
    String temp_filename = "wf_out.zip";
    String temp_dir = "wf_dir";
    String output_filename = "*.pdbqt";
    //String output_filename="*.*";
    try {//from   www. ja  va2s  .  c  o m
        runSystemcmd();
        Process process;
        process = Runtime.getRuntime().exec("rm -rf  /tmp/" + temp_dir);
        process.waitFor();
        process = Runtime.getRuntime().exec("mkdir -p /tmp/" + temp_dir);
        process.waitFor();
        process = Runtime.getRuntime().exec("cp " + temp_output + " /tmp/" + temp_filename);
        process.waitFor();
        process = Runtime.getRuntime().exec("unzip -o /tmp/" + temp_filename + " -d /tmp/" + temp_dir);
        process.waitFor();
        // get the output_filename location
        // MODIFIED TO SIMULATE MULTIPLE OUTPUT

        Process pr = Runtime.getRuntime()
                .exec(new String[] { "find", "/tmp/" + temp_dir, "-name", output_filename });

        BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
        BufferedReader error = new BufferedReader(new InputStreamReader(pr.getErrorStream()));

        String line = null;
        String string_error = "";
        ArrayList<String> resultPaths = new ArrayList<String>(1);
        while ((line = input.readLine()) != null) {
            resultPaths.add(line);
        }

        string_error = error.readLine();
        // MOVE RESULTS to PDBQT dir

        String pdbqtStorePath = "../webapps/" + request.getContextPath() + "/script/jmol/model/result/";
        ArrayList<String> pdbqtList = new ArrayList<String>(resultPaths.size());

        for (String result : resultPaths) {
            UUID idOne = UUID.randomUUID();
            File resultx = new File(result);
            String pdbqtNewName = idOne + "-" + resultx.getName() + ".pdbqt";
            Runtime.getRuntime().exec("cp -f " + result + " " + pdbqtStorePath + pdbqtNewName);
            pdbqtList.add("" + pdbqtNewName);
        }
    } catch (Exception ex) {
        ;
    }

}

From source file:com.twinsoft.convertigo.engine.Engine.java

public static synchronized void start() throws EngineException {
    if (Engine.theApp == null) {
        System.out.println("Starting Convertigo Enterprise Mobility Server");

        // If the engine has been stopped by the admin, we must reload
        // properties
        EnginePropertiesManager.loadProperties();

        boolean bProjectsDataCompatibilityMode = Boolean.parseBoolean(
                EnginePropertiesManager.getProperty(PropertyName.PROJECTS_DATA_COMPATIBILITY_MODE));

        if (bProjectsDataCompatibilityMode) {
            System.out.println("Projects data compatibility mode required");
            try {
                Engine.PROJECTS_PATH = new File(Engine.WEBAPP_PATH + "/projects").getCanonicalPath();
                File projectsDir = new File(Engine.PROJECTS_PATH);
                projectsDir.mkdir();/*  w w  w .  j a  va 2 s.  c o m*/
            } catch (IOException e) {
                throw new EngineException("Unable to update projects path for compatibility mode", e);
            }
        }

        isStarted = false;
        isStartFailed = false;
        RequestableObject.nbCurrentWorkerThreads = 0;

        Engine.startStopDate = System.currentTimeMillis();

        System.out.println("Creating/updating loggers");

        String logFile = EnginePropertiesManager.getProperty(PropertyName.LOG4J_APPENDER_CEMSAPPENDER_FILE);
        System.out.println("Log file: " + logFile);

        // Main loggers
        Engine.logConvertigo = Logger.getLogger("cems");
        Engine.logEngine = Logger.getLogger("cems.Engine");
        Engine.logAdmin = Logger.getLogger("cems.Admin");
        Engine.logBeans = Logger.getLogger("cems.Beans");
        Engine.logBillers = Logger.getLogger("cems.Billers");
        Engine.logEmulators = Logger.getLogger("cems.Emulators");
        Engine.logContext = Logger.getLogger("cems.Context");
        Engine.logUser = Logger.getLogger("cems.Context.User");
        Engine.logUsageMonitor = Logger.getLogger("cems.UsageMonitor");
        Engine.logStatistics = Logger.getLogger("cems.Statistics");
        Engine.logScheduler = Logger.getLogger("cems.Scheduler");
        Engine.logSiteClipper = Logger.getLogger("cems.SiteClipper");
        /** #3437 : Disabled ExternalBrowser feature because it's not terminated
        Engine.logExternalBrowser = Logger.getLogger("cems.ExternalBrowser");
        */
        Engine.logAudit = Logger.getLogger("cems.Context.Audit");

        // Managers
        Engine.logContextManager = Logger.getLogger("cems.ContextManager");
        Engine.logCacheManager = Logger.getLogger("cems.CacheManager");
        Engine.logTracePlayerManager = Logger.getLogger("cems.TracePlayerManager");
        Engine.logJobManager = Logger.getLogger("cems.JobManager");
        Engine.logCertificateManager = Logger.getLogger("cems.CertificateManager");
        Engine.logDatabaseObjectManager = Logger.getLogger("cems.DatabaseObjectManager");
        Engine.logProxyManager = Logger.getLogger("cems.ProxyManager");
        Engine.logDevices = Logger.getLogger("cems.Devices");
        Engine.logCouchDbManager = Logger.getLogger("cems.CouchDbManager");
        Engine.logSecurityTokenManager = Logger.getLogger("cems.SecurityTokenManager");

        // Logger for compatibility issues
        Engine.log = new LogWrapper(Engine.logConvertigo);
        LogWrapper.initWrapper(Engine.logEmulators);

        try {
            Engine.logEngine.info("===========================================================");
            Engine.logEngine.info("Web app home: " + Engine.WEBAPP_PATH);
            Engine.logEngine.info("User workspace: " + Engine.USER_WORKSPACE_PATH);
            Engine.logEngine.info("Configuration path: " + Engine.CONFIGURATION_PATH);

            Engine.logEngine.info("Projects path: " + Engine.PROJECTS_PATH);
            if (bProjectsDataCompatibilityMode) {
                Engine.logEngine.warn("Projects data compatibility mode required");
            }

            Engine.logEngine.info("Log: " + Engine.LOG_PATH);

            if (cloud_customer_name != null) {
                Engine.logEngine.info("Cloud customer: " + cloud_customer_name);
            }

            // Check environment and native dependencies
            if (!isStudioMode()) {
                StartupDiagnostics.run();
            }

            // Initializing the engine
            Engine.theApp = new Engine();

            CachedIntrospector.prefetchDatabaseObjectsAsync();

            try {
                Engine.theApp.usageMonitor = new UsageMonitor();
                Engine.theApp.usageMonitor.init();

                Thread vulture = new Thread(Engine.theApp.usageMonitor);
                vulture.setName("UsageMonitor");
                vulture.setDaemon(true);
                vulture.start();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to launch the usage monitor.", e);
            }

            Engine.theApp.eventManager = new EventManager();
            Engine.theApp.eventManager.init();

            Engine.theApp.databaseObjectsManager = new DatabaseObjectsManager();
            Engine.theApp.databaseObjectsManager.init();

            Engine.theApp.sqlConnectionManager = new JdbcConnectionManager();
            Engine.theApp.sqlConnectionManager.init();

            Engine.theApp.filePropertyManager = new FilePropertyManager();
            Engine.theApp.filePropertyManager.init();

            try {
                Engine.theApp.proxyManager = new ProxyManager();
                Engine.theApp.proxyManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to launch the proxy manager.", e);
            }

            try {
                Engine.theApp.billingManager = new BillingManager();
                Engine.theApp.billingManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to launch the billing manager.", e);
            }

            // Initialization of the trace player
            try {
                Engine.theApp.tracePlayerManager = new TracePlayerManager();
                Engine.theApp.tracePlayerManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to run the trace player.", e);
            }

            try {
                Engine.theApp.minificationManager = new MinificationManager();
                Engine.theApp.minificationManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to run the minification manager.", e);
            }

            try {
                Engine.theApp.couchDbManager = new CouchDbManager();
                Engine.theApp.couchDbManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to run the couchDbProxy manager.", e);
            }

            try {
                Engine.theApp.pluginsManager = new PluginsManager();
                Engine.theApp.pluginsManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to run the plugins manager.", e);
            }

            try {
                Engine.theApp.restApiManager = RestApiManager.getInstance();
                Engine.theApp.restApiManager.init();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to run the rest api manager.", e);
            }

            Engine.logEngine.info("Current working directory is '" + System.getProperty("user.dir") + "'.");

            // Creating the Carioca Authentication objects
            Engine.logEngine.debug("Creating the Carioca Authentication objects");
            String cariocaUserName = EnginePropertiesManager
                    .getProperty(PropertyName.CARIOCA_DEFAULT_USER_NAME);
            String cariocaPassword = EnginePropertiesManager
                    .getProperty(PropertyName.CARIOCA_DEFAULT_USER_PASSWORD);
            Engine.theApp.authentications = new HashMap<String, Authentication>();

            // Initialization of the default TAS properties
            try {
                KeyManager.log = new LogWrapper(Engine.logEngine);
                Authentication auth = Engine.theApp.getAuthenticationObject("", null);
                auth.login(cariocaUserName, cariocaPassword);
            } catch (Exception e) {
                Engine.logEngine.error("The authentication to Carioca has failed (user name: \""
                        + cariocaUserName + "\", user password: \"" + cariocaPassword + "\").", e);
            }

            // TODO : retrieve SOA flag from KeyManager
            isSOA = true;

            // Creation of the session manager
            Engine.theApp.sessionManager = new SessionManager();
            Engine.theApp.sessionManager.setLog(new LogWrapper(Engine.logEngine));
            Engine.theApp.sessionManager.setProductCode(SessionManager.CONVERTIGO);

            String s = EnginePropertiesManager.getProperty(PropertyName.CONNECTORS_MONITORING);
            Engine.theApp.setMonitored(s.equalsIgnoreCase("true"));

            // Create Projects directory if needed
            File projectsDirFile = new File(Engine.PROJECTS_PATH);
            try {
                if (!projectsDirFile.exists())
                    projectsDirFile.mkdirs();
            } catch (Exception e) {
                Engine.logEngine.error("An error occured while creating projects directory.", e);
            }

            // Starts projects migration process
            MigrationManager.performProjectsMigration();

            // Security providers registration
            try {
                File dir = new File(Engine.CERTIFICATES_PATH);
                String[] files = dir.list(new FilenameFilter() {
                    public boolean accept(File dir, String name) {
                        return name.endsWith((".pkcs11"));
                    }
                });

                if (files != null && files.length > 0) {
                    Engine.logEngine.info("Registering security providers...");
                    try {
                        Class<?> sunPKCS11Class = Class.forName("sun.security.pkcs11.SunPKCS11");
                        String file;

                        for (int i = 0; i < files.length; i++) {
                            file = Engine.CERTIFICATES_PATH + "/" + files[i];
                            try {
                                Constructor<?> constructor = sunPKCS11Class
                                        .getConstructor(new Class[] { String.class });
                                Provider provider = (Provider) constructor.newInstance(new Object[] { file });
                                Security.addProvider(provider);
                                Engine.logEngine.info("Provider '" + provider.getName()
                                        + "' has been successfully registered.");
                            } catch (Exception e) {
                                Engine.logEngine.error("Unable to register security provider from file: " + file
                                        + " . Please check that the implementation library is in the Java lib path.");
                            }
                        }
                    } catch (ClassNotFoundException e) {
                        Engine.logEngine.error(
                                "Unable to find sun.security.pkcs11.SunPKCS11 class! PKCS#11 authentication won't be available. You must use JVM 1.5 or higher in order to use PKCS#11 authentication.");
                    }
                }

                Provider[] providers = Security.getProviders();
                String sProviders = "";
                for (int i = 0; i < providers.length; i++) {
                    sProviders += providers[i].getName() + ", ";
                }
                Engine.logEngine.debug("Registered providers: " + sProviders);
            } catch (Exception e) {
                Engine.logEngine.error("Unable to register security providers.", e);
            }

            // Launch the cache manager
            try {
                String cacheManagerClassName = EnginePropertiesManager
                        .getProperty(PropertyName.CACHE_MANAGER_CLASS);
                Engine.logEngine.debug("Cache manager class: " + cacheManagerClassName);
                Engine.theApp.cacheManager = (CacheManager) Class.forName(cacheManagerClassName).newInstance();
                Engine.theApp.cacheManager.init();

                Thread vulture = new Thread(Engine.theApp.cacheManager);
                Engine.theApp.cacheManager.executionThread = vulture;
                vulture.setName("CacheManager");
                vulture.setDaemon(true);
                vulture.start();
            } catch (Exception e) {
                Engine.logEngine.error("Unable to launch the cache manager.", e);
            }

            // Launch the thread manager
            try {
                Engine.theApp.threadManager = new ThreadManager();
                Engine.theApp.threadManager.init();

                Thread vulture = new Thread(Engine.theApp.threadManager);
                Engine.theApp.threadManager.executionThread = vulture;
                vulture.setName("ThreadManager");
                vulture.setDaemon(true);
                vulture.start();
            } catch (Exception e) {
                Engine.theApp.threadManager = null;
                Engine.logEngine.error("Unable to launch the thread manager.", e);
            }

            // Launch the context manager
            try {
                Engine.theApp.contextManager = new ContextManager();
                Engine.theApp.contextManager.init();

                Thread vulture = new Thread(Engine.theApp.contextManager);
                Engine.theApp.contextManager.executionThread = vulture;
                vulture.setName("ContextManager");
                vulture.setDaemon(true);
                vulture.start();
            } catch (Exception e) {
                Engine.theApp.contextManager = null;
                Engine.logEngine.error("Unable to launch the context manager.", e);
            }

            // Launch the security token manager
            Engine.theApp.securityTokenManager = new SecurityTokenManager();
            Engine.theApp.securityTokenManager.init();

            // Initialize the HttpClient
            try {
                Engine.logEngine.debug("HttpClient initializing...");

                Engine.theApp.httpClient = HttpUtils.makeHttpClient3(true);
                Engine.theApp.httpClient4 = HttpUtils.makeHttpClient4(true);

                Engine.logEngine.debug("HttpClient initialized!");
            } catch (Exception e) {
                Engine.logEngine.error("Unable to initialize the HttpClient.", e);
            }

            // Initialization of the schedule manager
            Engine.theApp.schedulerManager = new SchedulerManager(true);

            // Initialization of the RSA manager
            Engine.theApp.rsaManager = new RsaManager();
            Engine.theApp.rsaManager.init();

            // Initialization of the External Browser manager
            /** #3437 : Disabled ExternalBrowser feature because it's not terminated
            Engine.theApp.externalBrowserManager = new ExternalBrowserManager();
            Engine.theApp.externalBrowserManager.init();
            */

            // Initialization of the Schema manager
            Engine.theApp.schemaManager = new SchemaManager();
            Engine.theApp.schemaManager.init();

            // XUL initialization
            String xulrunner_url = System.getProperty("org.eclipse.swt.browser.XULRunnerPath");
            if (xulrunner_url == null || xulrunner_url.equals("")) {
                xulrunner_url = EnginePropertiesManager.getProperty(PropertyName.XULRUNNER_URL);
            }

            File f = new File(xulrunner_url);
            if (f.exists()) {
                xulrunner_url = f.getAbsolutePath();
                Engine.logEngine
                        .debug("initMozillaSWT: org.eclipse.swt.browser.XULRunnerPath=" + xulrunner_url);
                System.setProperty("org.eclipse.swt.browser.XULRunnerPath", xulrunner_url);
            } else {
                Engine.logEngine.error("Error in initMozillaSWT: " + xulrunner_url
                        + " doesn't exist, fix it with xulrunner.url");
            }

            if (Engine.isEngineMode() && Engine.isLinux()
                    && "true".equals(EnginePropertiesManager.getProperty(PropertyName.LINUX_LAUNCH_XVNC))) {

                Engine.logEngine
                        .debug("initMozillaSWT: org.eclipse.swt.browser.XULRunnerPath=" + xulrunner_url);
                final String display = System.getenv("DISPLAY");
                if (display != null) {
                    try {
                        String port = System.getProperty("xvnc.port");
                        if (port == null) {
                            port = "" + (Integer.parseInt(display.replaceAll(".*:(\\d*)", "$1")) + 5900);
                            System.setProperty("xvnc.port", port);
                        }
                        Engine.logEngine.debug("Xvnc should listen on " + port + " port");
                    } catch (Exception e) {
                    }
                    try {
                        File vncDir = new File(Engine.WEBAPP_PATH + "/WEB-INF/xvnc");
                        File Xvnc = new File(vncDir, "/Xvnc");
                        File fonts = new File(vncDir, "/fonts");
                        File wm = new File(vncDir, "/matchbox-window-manager");
                        if (vncDir.exists() && Xvnc.exists() && fonts.exists() && wm.exists()) {
                            for (File file : GenericUtils.<File>asList(Xvnc, wm)) {
                                new ProcessBuilder("/bin/chmod", "u+x", file.getAbsolutePath()).start()
                                        .waitFor();
                            }
                            String depth = EnginePropertiesManager.getProperty(PropertyName.LINUX_XVNC_DEPTH);
                            String geometry = EnginePropertiesManager
                                    .getProperty(PropertyName.LINUX_XVNC_GEOMETRY);
                            Engine.logEngine
                                    .debug("Xvnc will use depth " + depth + " and geometry " + geometry);
                            Process pr_xvnc = new ProcessBuilder(Xvnc.getAbsolutePath(), display, "-fp",
                                    fonts.getAbsolutePath(), "-depth", depth, "-geometry", geometry).start();
                            Thread.sleep(500);
                            try {
                                int exit = pr_xvnc.exitValue();
                                InputStream err = pr_xvnc.getErrorStream();
                                byte[] buf = new byte[err.available()];
                                err.read(buf);
                                Engine.logEngine.debug("Xvnc failed to run with exit code " + exit
                                        + " and this error : <<" + new String(buf, "UTF-8") + ">>");
                            } catch (Exception e) {
                                new ProcessBuilder(wm.getAbsolutePath()).start();
                                Engine.logEngine.debug("Xvnc successfully started !");
                            }
                        } else {
                            Engine.logEngine.info(
                                    vncDir.getAbsolutePath() + " not found or incomplet, cannot start Xvnc");
                        }
                    } catch (Exception e) {
                        Engine.logEngine.info("failed to launch Xvnc (maybe already launched", e);
                    }
                } else
                    Engine.logEngine
                            .warn("Trying to start Xvnc on Linux without DISPLAY environment variable !");
            }

            // SAP provider registration
            try {
                SapJcoDestinationDataProvider.init();
                Engine.logEngine.debug("SAP destination provider successfully registered");
            } catch (Throwable e) {
                Engine.logEngine.error("Error while registering SAP destination provider", e);
            }

            isStarted = true;

            Engine.logEngine.info("Convertigo engine started");
        } catch (Throwable e) {
            isStartFailed = true;
            Engine.logEngine.error("Unable to successfully start the engine.", e);
        }
    } else {
        Engine.logEngine.info("Convertigo engine already started");
    }
}

From source file:mitm.common.security.smime.SMIMEBuilderImplTest.java

private static void verifyMessage(File messageFile, X509Certificate rootCertificate, File outputFile)
        throws IOException {
    OpenSSLWrapper wrapper = new OpenSSLWrapper();

    wrapper.setCertificateAuthorities(rootCertificate);

    Process p = wrapper.verify(messageFile);

    InputStream result = p.getInputStream();

    FileOutputStream output = new FileOutputStream(outputFile);

    IOUtils.copy(result, output);/*from  w  w  w . j  a  v a2 s . co m*/

    output.close();

    String error = IOUtils.toString(p.getErrorStream(), "US-ASCII");

    assertTrue("Error message: " + error, error.startsWith("Verification successful"));
}

From source file:mitm.common.security.smime.SMIMEBuilderImplTest.java

private static void decryptMessage(File messageFile, PrivateKey privateKey, File outputFile)
        throws IOException {
    OpenSSLWrapper wrapper = new OpenSSLWrapper();

    wrapper.setPrivateKey(privateKey);//from   www .  j a  v a2 s.c  o  m

    Process p = wrapper.decrypt(messageFile);

    InputStream result = p.getInputStream();

    FileOutputStream output = new FileOutputStream(outputFile);

    IOUtils.copy(result, output);

    output.close();

    String error = IOUtils.toString(p.getErrorStream(), "US-ASCII");

    assertEquals("", error.trim());
}

From source file:hu.sztaki.lpds.pgportal.portlets.asm.ClientError.java

@SuppressWarnings("empty-statement")
public void doCheckStatus(ActionRequest request, ActionResponse response)
        throws PortletException, MalformedURLException, IOException {
    try {//from   w ww  .  ja  v a 2 s . c  o m
        String selected_job = "collector.sh";
        String selected_port = "0";
        String userId = request.getRemoteUser();

        String status_code = "";
        String status = "";
        String jobid = "wtf";
        String output_port = "0";

        String status_str = "";
        try {
            status_str = asm_service.getWorkflowStatus(userId, selected_wf).getStatus();
        } catch (Exception ex) {
            ;
        }
        if (status_str.equals("FINISHED")) {
            String temp_output = asm_service.getFiletoPortalServer(userId, selected_wf, selected_job,
                    output_port);

            // EXTRACT THE OUTPUTVALUE FROM RESULTZIP FILE
            String temp_filename = "wf_out.zip";
            String temp_dir = "wf_dir";
            String output_filename = "*.pdbqt";
            //String output_filename="*.*";
            Process process;
            process = Runtime.getRuntime().exec("rm -rf  /tmp/" + temp_dir);
            process.waitFor();
            process = Runtime.getRuntime().exec("mkdir -p /tmp/" + temp_dir);
            process.waitFor();
            process = Runtime.getRuntime().exec("cp " + temp_output + " /tmp/" + temp_filename);
            process.waitFor();
            process = Runtime.getRuntime().exec("unzip -o /tmp/" + temp_filename + " -d /tmp/" + temp_dir);
            process.waitFor();
            // get the output_filename location
            // MODIFIED TO SIMULATE MULTIPLE OUTPUT

            Process pr = Runtime.getRuntime()
                    .exec(new String[] { "find", "/tmp/" + temp_dir, "-name", output_filename });

            BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
            BufferedReader error = new BufferedReader(new InputStreamReader(pr.getErrorStream()));

            String line = null;
            String string_error = "";
            ArrayList<String> resultPaths = new ArrayList<String>(1);
            while ((line = input.readLine()) != null) {
                resultPaths.add(line);
            }

            string_error = error.readLine();
            // MOVE RESULTS to PDBQT dir

            String pdbqtStorePath = "../webapps/" + request.getContextPath() + "/script/jmol/model/result/";
            ArrayList<String> pdbqtList = new ArrayList<String>(resultPaths.size());

            for (String result : resultPaths) {
                UUID idOne = UUID.randomUUID();
                File resultx = new File(result);
                String pdbqtNewName = idOne + "-" + resultx.getName() + ".pdbqt";
                Runtime.getRuntime().exec("cp -f " + result + " " + pdbqtStorePath + pdbqtNewName);
                pdbqtList.add("" + pdbqtNewName);
            }

            /*
                            String result =temp_output;
                            UUID idOne = UUID.randomUUID();
                            File resultx=new File(result);
                            String pdbqtNewName=idOne +"-"+resultx.getName()+".pdbqt";
                            Runtime.getRuntime().exec("cp -f "+result+" "+pdbqtStorePath+pdbqtNewName);
                            pdbqtList.add(""+pdbqtNewName);
                    
             */
            throwError("found results: " + resultPaths.size() + " e:" + string_error, 10);
            request.setAttribute("resultpdbqts", pdbqtList);
        } else {
            request.setAttribute("resultpdbqts", "");
        }
        //
    } catch (Exception ex) {
        throwError(ex.getMessage(), 10);
    }
    request.setAttribute("layerMoleculaVisualizeEnableVar", "1");
    request.setAttribute("nextJSP", DISPLAY_PAGE);
    String nextJSP = DISPLAY_PAGE;
    PortletRequestDispatcher dispatcher;
    dispatcher = getPortletContext().getRequestDispatcher(nextJSP);
    dispatcher.include(request, response);
}

From source file:vmTools.java

private String runCommand(String command) {
    String result = "";
    String error = "";
    String s = null;/*w ww. j a  va2 s  .c  o m*/
    try {

        Process p = Runtime.getRuntime().exec(command);
        //p.waitFor();
        BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream()));

        BufferedReader stdError = new BufferedReader(new InputStreamReader(p.getErrorStream()));
        // read the output from the command
        while ((s = stdInput.readLine()) != null) {
            result = result + s;
        }

        // read any errors from the attempted command
        while ((s = stdError.readLine()) != null) {
            error = error + s;
        }
        if (error != "") {
            return error;
        } else {
            return result;
        }
    } catch (IOException e) {
        return "unknown error";
    }
}

From source file:dk.clarin.tools.create.java

public boolean PDFhasNoFonts(File pdfFile) {
    String lastline = "";
    String lasterrline = "";
    try {//from w  w  w  .  j  ava2s  .  co  m
        String line;
        OutputStream stdin = null;
        InputStream stderr = null;
        InputStream stdout = null;

        String command = "/usr/bin/pdffonts " + pdfFile.getAbsolutePath();

        final Process process = Runtime.getRuntime().exec(command);
        stdin = process.getOutputStream();
        stderr = process.getErrorStream();
        stdout = process.getInputStream();
        stdin.close();

        // clean up if any output in stdout
        BufferedReader brCleanUp = new BufferedReader(new InputStreamReader(stdout));
        while ((line = brCleanUp.readLine()) != null) {
            lastline = line;
        }
        brCleanUp.close();

        // clean up if any output in stderr
        brCleanUp = new BufferedReader(new InputStreamReader(stderr));
        while ((line = brCleanUp.readLine()) != null) {
            lasterrline = line;
        }
        brCleanUp.close();
    } catch (Exception e) {
        logger.error("cannot analyse: " + pdfFile.getName() + ", error is: " + e.getMessage());
    }
    logger.debug("lasterrline [" + lasterrline + "] lastline [" + lastline + "]");
    return lasterrline.equals("") && (lastline.endsWith("---------"));
}

From source file:com.taobao.adfs.util.Utilities.java

public static String runCommand(String command, Integer expectedExitCode, String extraPath, String libPath,
        boolean destory) throws IOException {
    BufferedReader stdOutputReader = null;
    StringBuilder output = new StringBuilder();
    Process process = runCommand(command, extraPath, libPath);
    ;// w w  w.j  a va  2s  .  com
    try {
        stdOutputReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
        String line;
        while ((line = stdOutputReader.readLine()) != null) {
            output.append(line).append('\n');
        }
        if (output.length() > 0)
            output.deleteCharAt(output.length() - 1);
        if (expectedExitCode != null && process.waitFor() != expectedExitCode)
            throw new IOException(
                    "exit code=" + process.exitValue() + ", expected exit code=" + expectedExitCode);
    } catch (Throwable t) {
        destory = true;
        throw new IOException("fail to exceute " + command + ", output=" + output
                + (extraPath == null ? "" : ", extraPath=" + extraPath)
                + (libPath == null ? "" : ", libPath=" + libPath), t);
    } finally {
        if (stdOutputReader != null)
            stdOutputReader.close();
        process.getOutputStream().close();
        process.getInputStream().close();
        process.getErrorStream().close();
        if (destory)
            process.destroy();
    }
    return output.toString();
}

From source file:mrcg.MRCGInstance.java

private void createSQL() throws Exception {
    String databaseType = getString("database.type");
    DBScripter dbScripter = DB_SCRIPTER.get(databaseType);
    String script = dbScripter.buildScript(getString("database.name"), types);
    File file = new File(projectPath + "database/" + databaseType + "/01-create-generated.sql");
    boolean changed = content(file, script, true);
    if (isSkipDatabaseEnabled())
        return;/* w  w w . java 2  s  . co m*/
    if (isDesignAlwaysModeEnabled() || (changed && isDesignModeEnabled())) {
        System.out.print("Running SQL Script...");

        Process process = Runtime.getRuntime().exec("bash runall.sh", null,
                new File(projectPath + "database/" + databaseType));
        BufferedReader in = new BufferedReader(new InputStreamReader(process.getInputStream()));
        BufferedReader err = new BufferedReader(new InputStreamReader(process.getErrorStream()));
        System.out.println(process.waitFor());
        while (in.ready() || err.ready()) {
            if (in.ready()) {
                System.out.println(in.readLine());
            } else if (err.ready()) {
                System.err.println(err.readLine());
            }
        }
    }
}