Examples with KeyFactory org.vcell.db.KeyFactory used on opensource projects

Example 11 with KeyFactory

use of org.vcell.db.KeyFactory in project vcell by virtualcell.

the class ServerManageConsole method main.

/**
 * main entrypoint - starts the part when it is run as an application
 * @param args java.lang.String[]
 */
public static void main(java.lang.String[] args) {
    try {
        if (args.length == 2 && args[0].equals("-password")) {
            ServerManageConsole.commandLineAdminPassword = args[1];
        }
        PropertyLoader.loadProperties();
        javax.swing.UIManager.setLookAndFeel(javax.swing.UIManager.getSystemLookAndFeelClassName());
        ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        ServerManageConsole aServerManageConsole = new ServerManageConsole(adminDbTopLevel, databaseServerImpl);
        aServerManageConsole.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        java.awt.Insets insets = aServerManageConsole.getInsets();
        aServerManageConsole.setSize(aServerManageConsole.getWidth() + insets.left + insets.right, aServerManageConsole.getHeight() + insets.top + insets.bottom);
        aServerManageConsole.setLocation(200, 200);
        aServerManageConsole.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JFrame");
        exception.printStackTrace(System.out);
    }
}

Example 12 with KeyFactory

use of org.vcell.db.KeyFactory in project vcell by virtualcell.

the class VCellApiMain method main.

/**
 * @param args
 */
public static void main(String[] args) {
    try {
        if (args.length != 2) {
            System.out.println("usage: VCellApiMain javascriptDir port");
            System.exit(1);
        }
        File javascriptDir = new File(args[0]);
        if (!javascriptDir.isDirectory()) {
            throw new RuntimeException("javascriptDir '" + args[0] + "' is not a directory");
        }
        // don't validate
        PropertyLoader.loadProperties();
        lg.debug("properties loaded");
        String portString = args[1];
        // was hard-coded at 8080
        Integer port = null;
        try {
            port = Integer.parseInt(portString);
        } catch (NumberFormatException e) {
            e.printStackTrace();
            throw new RuntimeException("failed to parse port argument '" + portString + "'", e);
        }
        lg.trace("connecting to database");
        lg.trace("oracle factory (next)");
        ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        lg.trace("database impl (next)");
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        lg.trace("local db server (next)");
        LocalAdminDbServer localAdminDbServer = new LocalAdminDbServer(conFactory, keyFactory);
        lg.trace("admin db server (next)");
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        lg.trace("messaging service (next)");
        VCMessagingService vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new VCMessagingDelegate() {

            @Override
            public void onTraceEvent(String string) {
                System.out.println("Trace: " + string);
            }

            @Override
            public void onRpcRequestSent(VCRpcRequest vcRpcRequest, UserLoginInfo userLoginInfo, VCMessage vcRpcRequestMessage) {
                System.out.println("request sent:");
            }

            @Override
            public void onRpcRequestProcessed(VCRpcRequest vcRpcRequest, VCMessage rpcVCMessage) {
                System.out.println("request processed:");
            }

            @Override
            public void onMessageSent(VCMessage message, VCDestination desintation) {
                System.out.println("message sent:");
            }

            @Override
            public void onMessageReceived(VCMessage vcMessage, VCDestination vcDestination) {
                System.out.println("message received");
            }

            @Override
            public void onException(Exception e) {
                System.out.println("Exception: " + e.getMessage());
                e.printStackTrace();
            }
        });
        lg.trace("rest database service (next)");
        RestDatabaseService restDatabaseService = new RestDatabaseService(databaseServerImpl, localAdminDbServer, vcMessagingService);
        lg.trace("rest event service (next)");
        RestEventService restEventService = new RestEventService(vcMessagingService);
        lg.trace("use verifier (next)");
        UserVerifier userVerifier = new UserVerifier(adminDbTopLevel);
        lg.trace("mongo (next)");
        VCMongoMessage.enabled = true;
        VCMongoMessage.serviceStartup(ServiceName.unknown, port, args);
        System.out.println("setting up server configuration");
        lg.trace("register engine (next)");
        Engine.register(true);
        WadlComponent component = new WadlComponent();
        // Server httpServer = component.getServers().add(Protocol.HTTP, 80);
        // Server httpsServer = component.getServers().add(Protocol.HTTPS, 443);
        // Client httpsClient = component.getClients().add(Protocol.HTTPS);
        // Client httpClient = component.getClients().add(Protocol.HTTP);
        lg.trace("adding FILE protcol");
        @SuppressWarnings("unused") Client httpClient = component.getClients().add(Protocol.FILE);
        lg.trace("adding CLAP protcol");
        @SuppressWarnings("unused") Client clapClient = component.getClients().add(Protocol.CLAP);
        lg.trace("adding CLAP https");
        File keystorePath = new File(PropertyLoader.getRequiredProperty(PropertyLoader.vcellapiKeystoreFile));
        String keystorePassword = PropertyLoader.getSecretValue(PropertyLoader.vcellapiKeystorePswd, PropertyLoader.vcellapiKeystorePswdFile);
        try {
            // 
            // keystorePassword may be encrypted with dbPassword, if it is decypt it.
            // 
            String dbPassword = PropertyLoader.getSecretValue(PropertyLoader.dbPasswordValue, PropertyLoader.dbPasswordFile);
            SecretKeyFactory kf = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
            SecretKey key = kf.generateSecret(new PBEKeySpec(dbPassword.toCharArray()));
            Cipher pbeCipher = Cipher.getInstance("PBEWithMD5AndDES");
            pbeCipher.init(Cipher.DECRYPT_MODE, key, new PBEParameterSpec(new byte[] { 32, 11, 55, 121, 01, 42, 89, 11 }, 20));
            keystorePassword = new String(pbeCipher.doFinal(DatatypeConverter.parseBase64Binary(keystorePassword)));
        } catch (Exception e) {
            System.out.println("password unhashing didn't work - trying clear text password");
            e.printStackTrace();
        }
        Server httpsServer = component.getServers().add(Protocol.HTTPS, port);
        Series<Parameter> parameters = httpsServer.getContext().getParameters();
        parameters.add("keystorePath", keystorePath.toString());
        parameters.add("keystorePassword", keystorePassword);
        parameters.add("keystoreType", "JKS");
        parameters.add("keyPassword", keystorePassword);
        parameters.add("disabledCipherSuites", "SSL_RSA_WITH_3DES_EDE_CBC_SHA " + "SSL_DHE_RSA_WITH_DES_CBC_SHA " + "SSL_DHE_DSS_WITH_DES_CBC_SHA");
        parameters.add("enabledCipherSuites", "TLS_DHE_DSS_WITH_AES_128_CBC_SHA " + "TLS_DHE_RSA_WITH_AES_128_CBC_SHA " + "TLS_RSA_WITH_AES_128_CBC_SHA " + "TLS_DHE_DSS_WITH_AES_256_CBC_SHA " + "TLS_DHE_RSA_WITH_AES_256_CBC_SHA " + "TLS_RSA_WITH_AES_256_CBC_SHA");
        lg.trace("create config");
        Configuration templateConfiguration = new Configuration();
        templateConfiguration.setObjectWrapper(new DefaultObjectWrapper());
        lg.trace("verify python installation");
        PythonSupport.verifyInstallation(new PythonPackage[] { PythonPackage.COPASI, PythonPackage.LIBSBML, PythonPackage.THRIFT });
        lg.trace("start Optimization Service");
        OptServerImpl optServerImpl = new OptServerImpl();
        optServerImpl.start();
        lg.trace("create app");
        boolean bIgnoreHostProblems = true;
        boolean bIgnoreCertProblems = true;
        User testUser = localAdminDbServer.getUser(TEST_USER);
        // lookup hashed auth credentials in database.
        UserInfo testUserInfo = localAdminDbServer.getUserInfo(testUser.getID());
        HealthService healthService = new HealthService(restEventService, "localhost", port, bIgnoreCertProblems, bIgnoreHostProblems, testUserInfo.userid, testUserInfo.digestedPassword0);
        AdminService adminService = new AdminService(adminDbTopLevel, databaseServerImpl);
        RpcService rpcService = new RpcService(vcMessagingService);
        WadlApplication app = new VCellApiApplication(restDatabaseService, userVerifier, optServerImpl, rpcService, restEventService, adminService, templateConfiguration, healthService, javascriptDir);
        lg.trace("attach app");
        component.getDefaultHost().attach(app);
        System.out.println("component start()");
        lg.trace("start component");
        component.start();
        System.out.println("component ended.");
        lg.trace("component started");
        lg.trace("start VCell Health Monitoring service");
        healthService.start();
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 13 with KeyFactory

use of org.vcell.db.KeyFactory in project vcell by virtualcell.

the class LocalVCellConnectionFactory method createVCellConnection.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.server.VCellConnection
 */
public VCellConnection createVCellConnection() throws AuthenticationException, ConnectionException {
    try {
        if (connectionFactory == null) {
            connectionFactory = DatabaseService.getInstance().createConnectionFactory();
        }
        KeyFactory keyFactory = connectionFactory.getKeyFactory();
        LocalVCellConnection.setDatabaseResources(connectionFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(connectionFactory);
        boolean bEnableRetry = false;
        boolean isLocal = true;
        User user = adminDbTopLevel.getUser(userLoginInfo.getUserName(), userLoginInfo.getDigestedPassword(), bEnableRetry, isLocal);
        if (user != null) {
            userLoginInfo.setUser(user);
        } else {
            throw new AuthenticationException("failed to authenticate as user " + userLoginInfo.getUserName());
        }
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(connectionFactory, keyFactory);
        boolean bCache = false;
        Cachetable cacheTable = null;
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty)));
        SimulationDatabaseDirect simulationDatabase = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, bCache);
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        LocalVCellConnection vcConn = new LocalVCellConnection(userLoginInfo, simulationDatabase, dataSetControllerImpl, exportServiceImpl);
        linkHDFLib();
        return vcConn;
    } catch (Throwable exc) {
        lg.error(exc.getMessage(), exc);
        throw new ConnectionException(exc.getMessage());
    }
}

Example 14 with KeyFactory

use of org.vcell.db.KeyFactory in project vcell by virtualcell.

the class ResultSetCrawler method main.

public static void main(String[] args) {
    ConnectionFactory conFactory = null;
    try {
        boolean SCAN_ONLY = true;
        String singleUsername = null;
        String startingUsername = null;
        String outputDirName = ".";
        String ampliCredName = null;
        String ampliCredPassword = null;
        int count = 0;
        while (count < args.length) {
            if (args[count].equals("-h")) {
                printUsage();
                System.exit(0);
            } else if (args[count].equals("-u")) {
                count++;
                singleUsername = args[count];
            } else if (args[count].equals("-c")) {
                count++;
                startingUsername = args[count];
            } else if (args[count].equals("-o")) {
                count++;
                outputDirName = args[count];
            } else if (args[count].equals("-d")) {
                SCAN_ONLY = false;
            } else if (args[count].equals("-s")) {
                SCAN_ONLY = true;
            } else if (args[count].equals("-y")) {
                count++;
                ampliCredName = args[count];
            } else if (args[count].equals("-z")) {
                count++;
                ampliCredPassword = args[count];
            } else {
                System.out.println("Wrong arguments, see usage below.");
                printUsage();
                System.exit(1);
            }
            count++;
        }
        File outputDir = null;
        if (outputDirName == null) {
            outputDir = new File(".");
        } else {
            outputDir = new File(outputDirName);
            if (!outputDir.exists()) {
                throw new RuntimeException("Outuput directory doesn't exist!");
            }
        }
        PropertyLoader.loadProperties();
        File primaryDataRootDir = new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty));
        File secondaryDataRootDir = new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty));
        if (primaryDataRootDir.equals(secondaryDataRootDir)) {
            secondaryDataRootDir = null;
        }
        // initialize database
        conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        DatabaseServerImpl dbServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        // 
        // determine the list of users to scan
        // 
        UserInfo[] allUserInfos = adminDbTopLevel.getUserInfos(true);
        HashMap<String, User> usersToScan = new HashMap<String, User>();
        for (UserInfo userInfo : allUserInfos) {
            if (singleUsername != null) {
                // accept only the "singleUser"
                if (userInfo.userid.equals(singleUsername)) {
                    usersToScan.put(userInfo.userid, new User(userInfo.userid, userInfo.id));
                    break;
                }
            } else if (startingUsername != null) {
                // accept all users starting with the "startingUser"
                if (userInfo.userid.compareToIgnoreCase(startingUsername) >= 0) {
                    usersToScan.put(userInfo.userid, new User(userInfo.userid, userInfo.id));
                }
            } else {
                // all users
                usersToScan.put(userInfo.userid, new User(userInfo.userid, userInfo.id));
            }
        }
        // 
        // get list of directories to scan (for selected users on both user data directories)
        // 
        List<File> useDirectoriesToScan = getDirectoriesToScan(usersToScan, primaryDataRootDir, secondaryDataRootDir);
        for (File userDir : useDirectoriesToScan) {
            try {
                if (lg.isTraceEnabled())
                    lg.trace("USER: " + userDir.getName());
                User user = usersToScan.get(userDir.getName());
                // find all the user simulations and external data sets (field data)
                SimulationInfo[] simulationInfos = dbServerImpl.getSimulationInfos(user, false);
                ExternalDataIdentifier[] extDataIDArr = adminDbTopLevel.getExternalDataIdentifiers(user, true);
                // scan this user directory
                scanUserDirectory(userDir, extDataIDArr, simulationInfos, outputDir, SCAN_ONLY, (ampliCredName == null || ampliCredPassword == null ? null : new AmplistorUtils.AmplistorCredential(ampliCredName, ampliCredPassword)));
            } catch (Exception ex) {
                lg.error(ex.getMessage(), ex);
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    } finally {
        try {
            if (conFactory != null) {
                conFactory.close();
            }
        } catch (Throwable ex) {
            ex.printStackTrace();
        }
        System.exit(0);
    }
}