Examples with LibraryLoaderThread cbit.vcell.resource.LibraryLoaderThread used on opensource projects

Example 1 with LibraryLoaderThread

use of cbit.vcell.resource.LibraryLoaderThread in project vcell by virtualcell.

the class VCellClientTest method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    // class ParseVCellUserEvents implements Runnable {
    // AWTEvent event;
    // public ParseVCellUserEvents(AWTEvent event){
    // this.event = event;
    // }
    // @Override
    // public void run() {
    // if(event instanceof MouseEvent){
    // MouseEvent mouseEvent = (MouseEvent)event;
    // Object details = null;
    // if(mouseEvent.getID() == MouseEvent.MOUSE_RELEASED){
    // if(mouseEvent.getComponent() instanceof JTable){
    // JTable comp = (JTable)mouseEvent.getComponent();
    // int[] selRows = comp.getSelectedRows();
    // if(selRows != null && selRows.length > 0){
    // StringBuffer sb = new StringBuffer();
    // for (int i = 0; i < selRows.length; i++) {
    // for (int j = 0; j < comp.getColumnCount(); j++) {
    // try{
    // sb.append((j==0?"":",")+comp.getColumnName(j)+"='"+comp.getModel().getValueAt(selRows[i], j)+"'");
    // }catch(Exception e){
    // e.printStackTrace();
    // }
    // }
    // }
    // details = sb.toString();
    // }
    // }else if(mouseEvent.getComponent() instanceof JTree){
    // JTree comp = (JTree)mouseEvent.getComponent();
    // TreePath treePath = comp.getSelectionPath();
    // if(treePath != null){
    // details = treePath.getLastPathComponent();
    // // BioModel, MathModel, Geometry document tree selections
    // if(details instanceof BioModelNode){
    // //VCellBasicCellRenderer.VCDocumentInfoNode
    // BioModelNode bioModelNode = (BioModelNode)details;
    // boolean isVCDocumentInfo = bioModelNode.getUserObject() instanceof VCDocumentInfo;
    // boolean isBioModelsNetModelInfo = bioModelNode.getUserObject() instanceof BioModelsNetModelInfo;
    // if(!isVCDocumentInfo && bioModelNode.getChildCount() > 0 && bioModelNode.getUserObject() instanceof VCellBasicCellRenderer.VCDocumentInfoNode){
    // TreeNode treeNode = bioModelNode.getFirstChild();
    // if(treeNode instanceof BioModelNode && ((BioModelNode)treeNode).getUserObject() instanceof VCDocumentInfo){
    // details = ((BioModelNode)treeNode).getUserObject();
    // }
    // }else if(isBioModelsNetModelInfo){
    // details = BioModelsNetModelInfo.class.getSimpleName()+" '"+((BioModelsNetModelInfo)bioModelNode.getUserObject()).getName()+"'";
    // }
    // }
    // }
    // }else if(mouseEvent.getComponent() instanceof JTabbedPane){
    // JTabbedPane comp = (JTabbedPane)mouseEvent.getComponent();
    // details = "'"+comp.getTitleAt(comp.getSelectedIndex())+"'";
    // }else if(mouseEvent.getComponent() instanceof JMenuItem){
    // JMenuItem comp = (JMenuItem)mouseEvent.getComponent();
    // details = "'"+comp.getText()+"'";
    // }else if(mouseEvent.getComponent() instanceof AbstractButton){
    // AbstractButton comp = (AbstractButton)mouseEvent.getComponent();
    // Boolean bSelected = (comp instanceof JToggleButton?((JToggleButton)comp).isSelected():null);
    // details = (bSelected != null?"("+(bSelected?"selected":"unselected")+")":"")+"'"+comp.getText()+"'";
    // }else if(mouseEvent.getComponent() instanceof JComboBox<?>){
    // JComboBox<?> comp = (JComboBox<?>)mouseEvent.getComponent();
    // details = "'"+comp.getSelectedItem().toString()+"'";
    // }else if(mouseEvent.getComponent() instanceof JList<?>){
    // JList<?> comp = (JList<?>)mouseEvent.getComponent();
    // details = "'"+comp.getSelectedValue()+"'";
    // }else{
    // details = "TBD "+mouseEvent.getComponent();
    // }
    // Component parentComponent = mouseEvent.getComponent();
    // StringBuffer parentInfo = new StringBuffer();
    // SimpleDateFormat simpleDateFormat = new SimpleDateFormat(BeanUtils.vcDateFormat, Locale.US);
    // do{
    // String title="";
    // if(parentComponent instanceof Dialog){
    // title = ((Dialog)parentComponent).getTitle();
    // }else if(parentComponent instanceof Frame){
    // title = ((Frame)parentComponent).getTitle();
    // }
    // parentInfo.append(parentComponent.getClass().getTypeName()+"("+parentComponent.getName()+(title!=null&& title.length()>0?",title='"+title+"'":"")+")");
    // if(parentComponent instanceof DocumentWindow && ((DocumentWindow)parentComponent).getTopLevelWindowManager() instanceof DocumentWindowManager){
    // VCDocument vcDocument = ((DocumentWindowManager)((DocumentWindow)parentComponent).getTopLevelWindowManager()).getVCDocument();
    // if(vcDocument != null){
    // String date = (vcDocument.getVersion() != null && vcDocument.getVersion().getDate()!=null?simpleDateFormat.format(vcDocument.getVersion().getDate()):"nodate");
    // parentInfo.append("doc="+vcDocument.getDocumentType()+" '"+vcDocument.getName()+"' "+date);
    // }
    // }
    // parentInfo.append(" -> ");
    // }while((parentComponent = parentComponent.getParent()) != null);
    // //try to add event, if full remove an event from the top
    // while(!recordedUserEvents.offer(mouseEvent.getClickCount()+" "+(details==null?"null":details.toString())+BeanUtils.PLAINTEXT_EMAIL_NEWLINE+parentInfo.toString())){
    // recordedUserEvents.poll();
    // }
    // }
    // }
    // }
    // };
    // 
    // 
    // AWTEventListener awtEventListener = new AWTEventListener() {
    // @Override
    // public void eventDispatched(final AWTEvent event) {
    // if(event instanceof MouseEvent){
    // if(((MouseEvent)event).getID() == MouseEvent.MOUSE_RELEASED){
    // new Thread(new ParseVCellUserEvents(event)).start();
    // }
    // }
    // }
    // };
    // Toolkit.getDefaultToolkit().addAWTEventListener(awtEventListener,AWTEvent.MOUSE_EVENT_MASK);
    new Thread(new Runnable() {

        @Override
        public void run() {
            BeanUtils.updateDynamicClientProperties();
        }
    }).start();
    // check synchronize Proxy prefs, Proxy Properties
    Preferences prefs = Preferences.userNodeForPackage(RemoteProxyVCellConnectionFactory.class);
    Boolean bHttp = (System.getProperty(NetworkProxyUtils.PROXY_HTTP_HOST) == null && System.getProperty(NetworkProxyUtils.PROXY_SOCKS_HOST) == null ? null : System.getProperty(NetworkProxyUtils.PROXY_HTTP_HOST) != null);
    String currentProxyHost = (bHttp == null ? null : (bHttp ? System.getProperty(NetworkProxyUtils.PROXY_HTTP_HOST) : System.getProperty(NetworkProxyUtils.PROXY_SOCKS_HOST)));
    String currentProxyPort = (bHttp == null ? null : (bHttp ? System.getProperty(NetworkProxyUtils.PROXY_HTTP_PORT) : System.getProperty(NetworkProxyUtils.PROXY_SOCKS_PORT)));
    NetworkProxyUtils.setProxyProperties(false, null, prefs.get(NetworkProxyPreferences.prefProxyType, NetworkProxyPreferences.prefProxyType), currentProxyHost, currentProxyPort, prefs.get(NetworkProxyPreferences.prefProxyType, NetworkProxyPreferences.prefProxyType), prefs.get(NetworkProxyPreferences.prefProxyHost, NetworkProxyPreferences.prefProxyHost), prefs.get(NetworkProxyPreferences.prefProxyPort, NetworkProxyPreferences.prefProxyPort));
    final boolean IS_DEBUG = ManagementFactory.getRuntimeMXBean().getInputArguments().toString().indexOf("-agentlib:jdwp") > 0;
    if (!IS_DEBUG) {
        String siteName = VCellSoftwareVersion.fromSystemProperty().getSite().name().toLowerCase();
        ConsoleCapture.getInstance().captureStandardOutAndError(new File(ResourceUtil.getLogDir(), "vcellrun_" + siteName + ".log"));
    }
    // Logging.init();
    ErrorUtils.setDebug(IS_DEBUG);
    if (args != null && args.length >= 1 && args[0].equals("-console")) {
        // remove install4j parameter
        List<String> newArgs = new ArrayList<String>();
        newArgs.addAll(Arrays.asList(args));
        newArgs.remove(0);
        args = newArgs.toArray(new String[0]);
    }
    StringBuffer stringBuffer = new StringBuffer();
    for (int i = 0; i < args.length; i++) {
        stringBuffer.append("arg" + i + "=\"" + args[i] + "\" ");
    }
    System.out.println("starting with arguments [" + stringBuffer + "]");
    System.out.println("Running under Java major version: ONE point " + ResourceUtil.getJavaVersion().toString() + ".  Specifically: Java " + (System.getProperty("java.version")) + ", published by " + (System.getProperty("java.vendor")) + ", on the " + (System.getProperty("os.arch")) + " architecture running version " + (System.getProperty("os.version")) + " of the " + (System.getProperty("os.name")) + " operating system");
    ClientServerInfo csInfo = null;
    String hoststr = System.getProperty(PropertyLoader.vcellServerHost);
    String[] hosts = null;
    if (hoststr != null) {
        StringTokenizer st = new StringTokenizer(hoststr, " ,;");
        if (st.countTokens() >= 1) {
            hosts = new String[st.countTokens()];
            int count = 0;
            while (st.hasMoreTokens()) {
                hosts[count++] = st.nextToken();
            }
        }
    }
    if (hosts == null) {
        hosts = new String[1];
    }
    String user = null;
    String password = null;
    VCDocument initialDocument = null;
    if (args.length == 3) {
        hosts[0] = args[0];
        user = args[1];
        password = args[2];
    } else if (args.length == 0) {
    // this is ok
    } else if (args.length == 1) {
        // Check if arg is drag-n-drop file or a 'hostname'
        try {
            // drag and drop file on install4j VCell launcher will pass filepath as single arg to VCell
            File openThisVCellFile = new File(args[0]);
            if (openThisVCellFile.exists() && openThisVCellFile.isFile()) {
                initialDocument = startupWithOpen(args[0]);
            }
        } catch (Exception e) {
            e.printStackTrace();
        // continue to hostname check
        }
        // If startup file not exist assume arg is a hostname
        if (initialDocument == null) {
            hosts[0] = args[0];
        }
    // If install4j drag-n-drop, hosts[0] stays null and host is assumed to be loaded from a client property
    } else if (args.length == 2 && args[0].equals("-open")) {
        // hosts[0] = "-local";
        initialDocument = startupWithOpen(args[1]);
    } else {
        System.out.println("usage: VCellClientTest ( ((-local|host[:port]) [userid password]) | ([-open] filename) )");
        System.exit(1);
    }
    boolean bLocal = false;
    if (hosts[0] != null && hosts[0].equalsIgnoreCase("-local")) {
        bLocal = true;
    }
    if (bLocal) {
        csInfo = ClientServerInfo.createLocalServerInfo(user, (password == null || password.length() == 0 ? null : new UserLoginInfo.DigestedPassword(password)));
    } else {
        String[] hostParts = hosts[0].split(":");
        String apihost = hostParts[0];
        int apiport = Integer.parseInt(hostParts[1]);
        csInfo = ClientServerInfo.createRemoteServerInfo(apihost, apiport, user, (password == null || password.length() == 0 ? null : new UserLoginInfo.DigestedPassword(password)));
    }
    try {
        if (bLocal) {
            PropertyLoader.loadProperties(ArrayUtils.addAll(REQUIRED_CLIENT_PROPERTIES, REQUIRED_LOCAL_PROPERTIES));
            try {
                VCMongoMessage.enabled = true;
                VCMongoMessage.serviceStartup(ServiceName.client, null, null);
                PropertyLoader.sendErrorsToMongo();
            } catch (Exception e) {
                System.out.println("failed to start Mongo logging");
            }
        } else {
            PropertyLoader.loadProperties(REQUIRED_CLIENT_PROPERTIES);
            VCMongoMessage.enabled = false;
        }
        // call in main thread, since it's quick and not necessarily thread safe
        ResourceUtil.setNativeLibraryDirectory();
        vcellClient = VCellClient.startClient(initialDocument, csInfo);
        // VCellClientDataService vcellClientDataService = new VCellClientDataServiceImpl(vcellClient);
        // VCellProxyServer.startVCellVisitDataServerThread(vcellClientDataService);
        // starting loading libraries
        new LibraryLoaderThread(true).start();
        try {
            PythonSupport.verifyInstallation(PythonPackage.values());
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    // SimulationService.Iface simService = new SimulationServiceImpl();
    // VCellIJServer.startVCellVisitDataServerThread(simService, false);
    } catch (Throwable exception) {
        ErrorUtils.sendRemoteLogMessage(csInfo.getUserLoginInfo(), csInfo.toString() + "\nvcell startup failed\n\n" + exception.getMessage());
        JOptionPane.showMessageDialog(null, exception.getMessage(), "Fatal Error", JOptionPane.OK_OPTION);
        System.err.println("Exception occurred in main() of VCellApplication");
        exception.printStackTrace(System.out);
    }
}

Example 2 with LibraryLoaderThread

use of cbit.vcell.resource.LibraryLoaderThread in project vcell by virtualcell.

the class VCellServices 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 != 3 && args.length != 0) {
        System.out.println("Missing arguments: " + VCellServices.class.getName() + " [sshHost sshUser sshKeyFile] ");
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties(REQUIRED_SERVICE_PROPERTIES);
        ResourceUtil.setNativeLibraryDirectory();
        new LibraryLoaderThread(false).start();
        PythonSupport.verifyInstallation(new PythonPackage[] { PythonPackage.VTK, PythonPackage.THRIFT });
        HtcProxy htcProxy = SlurmProxy.creatCommandService(args);
        int serviceOrdinal = 0;
        VCMongoMessage.serviceStartup(ServiceName.dispatch, 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.MASTER, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
        ConnectionFactory conFactory = DatabaseService.getInstance().createConnectionFactory();
        KeyFactory keyFactory = conFactory.getKeyFactory();
        DatabaseServerImpl databaseServerImpl = new DatabaseServerImpl(conFactory, keyFactory);
        AdminDBTopLevel adminDbTopLevel = new AdminDBTopLevel(conFactory);
        SimulationDatabase simulationDatabase = new SimulationDatabaseDirect(adminDbTopLevel, databaseServerImpl, true);
        String cacheSize = PropertyLoader.getRequiredProperty(PropertyLoader.simdataCacheSizeProperty);
        long maxMemSize = Long.parseLong(cacheSize);
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20, maxMemSize);
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty))));
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        // add dataJobListener
        DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
        VCMessagingService vcMessagingService_int = new VCMessagingServiceActiveMQ();
        String jmshost_int = PropertyLoader.getRequiredProperty(PropertyLoader.jmsIntHostInternal);
        int jmsport_int = Integer.parseInt(PropertyLoader.getRequiredProperty(PropertyLoader.jmsIntPortInternal));
        vcMessagingService_int.setConfiguration(new ServerMessagingDelegate(), jmshost_int, jmsport_int);
        VCMessagingService vcMessagingService_sim = new VCMessagingServiceActiveMQ();
        String jmshost_sim = PropertyLoader.getRequiredProperty(PropertyLoader.jmsSimHostInternal);
        int jmsport_sim = Integer.parseInt(PropertyLoader.getRequiredProperty(PropertyLoader.jmsSimPortInternal));
        vcMessagingService_sim.setConfiguration(new ServerMessagingDelegate(), jmshost_sim, jmsport_sim);
        VCellServices vcellServices = new VCellServices(htcProxy, vcMessagingService_int, vcMessagingService_sim, serviceInstanceStatus, databaseServerImpl, dataServerImpl, simulationDatabase);
        dataSetControllerImpl.addDataJobListener(vcellServices);
        exportServiceImpl.addExportListener(vcellServices);
        vcellServices.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}

Example 3 with LibraryLoaderThread

use of cbit.vcell.resource.LibraryLoaderThread in project vcell by virtualcell.

the class SimDataServer 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 != 1) {
        System.out.println("Missing arguments: " + SimDataServer.class.getName() + " (CombinedData | ExportDataOnly | SimDataOnly)");
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties(REQUIRED_SERVICE_PROPERTIES);
        ResourceUtil.setNativeLibraryDirectory();
        new LibraryLoaderThread(false).start();
        PythonSupport.verifyInstallation(new PythonPackage[] { PythonPackage.VTK, PythonPackage.THRIFT });
        int serviceOrdinal = 99;
        SimDataServiceType simDataServiceType = SimDataServiceType.valueOf(args[0]);
        if (simDataServiceType == null) {
            throw new RuntimeException("expecting argument (CombinedData | ExportDataOnly | SimDataOnly)");
        }
        final ServiceInstanceStatus serviceInstanceStatus;
        final ServiceName serviceName;
        switch(simDataServiceType) {
            case ExportDataOnly:
                {
                    serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DATAEXPORT, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
                    serviceName = ServiceName.export;
                    break;
                }
            case SimDataOnly:
                {
                    serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DATA, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
                    serviceName = ServiceName.simData;
                    break;
                }
            case CombinedData:
                {
                    serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.COMBINEDDATA, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
                    serviceName = ServiceName.combinedData;
                    break;
                }
            default:
                {
                    throw new RuntimeException("unexpected SimDataServiceType " + simDataServiceType);
                }
        }
        VCMongoMessage.serviceStartup(serviceName, new Integer(serviceOrdinal), args);
        // //
        // // JMX registration
        // //
        // MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        // mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        String cacheSize = PropertyLoader.getRequiredProperty(PropertyLoader.simdataCacheSizeProperty);
        long maxMemSize = Long.parseLong(cacheSize);
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20, maxMemSize);
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty))));
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
        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);
        SimDataServer simDataServer = new SimDataServer(serviceInstanceStatus, dataServerImpl, vcMessagingService, simDataServiceType, false);
        // add dataJobListener
        dataSetControllerImpl.addDataJobListener(simDataServer);
        // add export listener
        exportServiceImpl.addExportListener(simDataServer);
        simDataServer.init();
    } catch (Throwable e) {
        lg.error("uncaught exception initializing SimDataServer: " + e.getLocalizedMessage(), e);
        System.exit(1);
    }
}