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

Example 6 with AdminDBTopLevel

use of cbit.vcell.modeldb.AdminDBTopLevel 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 7 with AdminDBTopLevel

use of cbit.vcell.modeldb.AdminDBTopLevel 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());
    }
}