Examples with DatabaseServerImpl cbit.vcell.modeldb.DatabaseServerImpl used on opensource projects

Example 6 with DatabaseServerImpl

use of cbit.vcell.modeldb.DatabaseServerImpl in project vcell by virtualcell.

the class DatabaseServer method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    OperatingSystemInfo.getInstance();
    if (args.length != 0) {
        System.out.println("Unexpected arguments: " + DatabaseServer.class.getName());
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties(REQUIRED_SERVICE_PROPERTIES);
        int serviceOrdinal = 99;
        VCMongoMessage.serviceStartup(ServiceName.database, new Integer(serviceOrdinal), args);
        // 
        // JMX registration
        // 
        // MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        // mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        ServiceInstanceStatus serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DB, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
        ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        VCMessagingService vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        String jmshost = PropertyLoader.getRequiredProperty(PropertyLoader.jmsIntHostInternal);
        int jmsport = Integer.parseInt(PropertyLoader.getRequiredProperty(PropertyLoader.jmsIntPortInternal));
        vcMessagingService.setConfiguration(new ServerMessagingDelegate(), jmshost, jmsport);
        DatabaseServer databaseServer = new DatabaseServer(serviceInstanceStatus, databaseServerImpl, vcMessagingService, false);
        databaseServer.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}

Example 7 with DatabaseServerImpl

use of cbit.vcell.modeldb.DatabaseServerImpl 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 8 with DatabaseServerImpl

use of cbit.vcell.modeldb.DatabaseServerImpl 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 9 with DatabaseServerImpl

use of cbit.vcell.modeldb.DatabaseServerImpl 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_int = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        VCMessagingDelegate delegate = new VCMessagingDelegate() {

            @Override
            public void onTraceEvent(String string) {
                if (lg.isTraceEnabled())
                    lg.trace("onTraceEvent(): " + string);
            }

            @Override
            public void onRpcRequestSent(VCRpcRequest vcRpcRequest, UserLoginInfo userLoginInfo, VCMessage vcRpcRequestMessage) {
                if (lg.isTraceEnabled())
                    lg.trace("onRpcRequestSent(): " + vcRpcRequest.getMethodName());
            }

            @Override
            public void onRpcRequestProcessed(VCRpcRequest vcRpcRequest, VCMessage rpcVCMessage) {
                if (lg.isTraceEnabled())
                    lg.trace("onRpcRequestProcessed(): " + vcRpcRequest.getMethodName());
            }

            @Override
            public void onMessageSent(VCMessage message, VCDestination desintation) {
                if (lg.isTraceEnabled())
                    lg.trace("onMessageSent(): " + message);
            }

            @Override
            public void onMessageReceived(VCMessage vcMessage, VCDestination vcDestination) {
                if (lg.isTraceEnabled())
                    lg.trace("onMessageReceived(): " + vcMessage);
            }

            @Override
            public void onException(Exception e) {
                lg.error(e.getMessage(), e);
            }
        };
        String jmshost_int = PropertyLoader.getRequiredProperty(PropertyLoader.jmsIntHostInternal);
        int jmsport_int = Integer.parseInt(PropertyLoader.getRequiredProperty(PropertyLoader.jmsIntPortInternal));
        vcMessagingService_int.setConfiguration(delegate, jmshost_int, jmsport_int);
        lg.trace("rest database service (next)");
        RestDatabaseService restDatabaseService = new RestDatabaseService(databaseServerImpl, localAdminDbServer, vcMessagingService_int);
        lg.trace("rest event service (next)");
        RestEventService restEventService = new RestEventService(vcMessagingService_int);
        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");
        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_int);
        WadlApplication app = new VCellApiApplication(restDatabaseService, userVerifier, 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) {
        lg.error(e.getMessage(), e);
    }
}

Example 10 with DatabaseServerImpl

use of cbit.vcell.modeldb.DatabaseServerImpl in project vcell by virtualcell.

the class SimulationDatabaseDirectTest method test.

@Test
public void test() {
    try (ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory()) {
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, conFactory.getKeyFactory());
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        boolean bCache = false;
        SimulationDatabaseDirect simulationDatabaseDirect = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, bCache);
        SimpleJobStatusQuerySpec querySpec = new SimpleJobStatusQuerySpec();
        querySpec.submitLowMS = null;
        querySpec.submitHighMS = null;
        querySpec.startLowMS = null;
        querySpec.startHighMS = null;
        querySpec.endLowMS = null;
        querySpec.endHighMS = null;
        querySpec.startRow = 0;
        querySpec.maxRows = 100;
        querySpec.serverId = null;
        querySpec.computeHost = null;
        querySpec.userid = null;
        querySpec.simId = null;
        querySpec.jobId = null;
        querySpec.taskId = null;
        querySpec.hasData = null;
        querySpec.waiting = true;
        querySpec.queued = true;
        querySpec.dispatched = true;
        querySpec.running = true;
        querySpec.completed = true;
        querySpec.failed = true;
        querySpec.stopped = true;
        SimulationJobStatus[] resultList = simulationDatabaseDirect.queryJobs(querySpec);
        Gson gson = new Gson();
        for (SimulationJobStatus status : resultList) {
            System.out.println(gson.toJson(status.toRep()));
        }
    // test that there are no repeated jobs
    } catch (Exception e) {
        e.printStackTrace();
        fail("exception: " + e.getMessage());
    }
}