Examples with ExportServiceImpl cbit.vcell.export.server.ExportServiceImpl used on opensource projects

Example 1 with ExportServiceImpl

use of cbit.vcell.export.server.ExportServiceImpl in project vcell by virtualcell.

the class ClientSimManager method showSimulationResults0.

private AsynchClientTask[] showSimulationResults0(final boolean isLocal, final ViewerType viewerType) {
    // Create the AsynchClientTasks
    ArrayList<AsynchClientTask> taskList = new ArrayList<AsynchClientTask>();
    taskList.add(new AsynchClientTaskFunction(h -> {
        h.put(H_LOCAL_SIM, isLocal);
        h.put(H_VIEWER_TYPE, viewerType);
    }, "setLocal", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING));
    final DocumentWindowManager documentWindowManager = getDocumentWindowManager();
    AsynchClientTask retrieveResultsTask = new AsynchClientTask("Retrieving results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @SuppressWarnings("unchecked")
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Simulation[] simsToShow = (Simulation[]) hashTable.get("simsArray");
            for (int i = 0; i < simsToShow.length; i++) {
                final Simulation sim = simsToShow[i];
                final VCSimulationIdentifier vcSimulationIdentifier = sim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
                final SimulationWindow simWindow = documentWindowManager.haveSimulationWindow(vcSimulationIdentifier);
                OutputContext outputContext = (OutputContext) hashTable.get("outputContext");
                if (simWindow == null && (viewerType == ViewerType.BothNativeAndPython || viewerType == ViewerType.NativeViewer_only)) {
                    try {
                        // make the manager and wire it up
                        DataViewerController dataViewerController = null;
                        if (!isLocal) {
                            dataViewerController = documentWindowManager.getRequestManager().getDataViewerController(outputContext, sim, 0);
                            // For changes in time or variable
                            documentWindowManager.addDataListener(dataViewerController);
                        } else {
                            // ---- preliminary : construct the localDatasetControllerProvider
                            File primaryDir = ResourceUtil.getLocalRootDir();
                            User usr = sim.getVersion().getOwner();
                            DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
                            ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
                            LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
                            VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
                            File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
                            LocalVCDataIdentifier vcDataId = new LocalVCSimulationDataIdentifier(vcSimulationIdentifier, 0, localSimDir);
                            DataManager dataManager = null;
                            if (sim.isSpatial()) {
                                dataManager = new PDEDataManager(outputContext, vcDataManager, vcDataId);
                            } else {
                                dataManager = new ODEDataManager(outputContext, vcDataManager, vcDataId);
                            }
                            dataViewerController = new SimResultsViewerController(dataManager, sim);
                            dataSetControllerImpl.addDataJobListener(documentWindowManager);
                        }
                        // make the viewer
                        Hashtable<VCSimulationIdentifier, DataViewerController> dataViewerControllers = (Hashtable<VCSimulationIdentifier, DataViewerController>) hashTable.get(H_DATA_VIEWER_CONTROLLERS);
                        if (dataViewerControllers == null) {
                            dataViewerControllers = new Hashtable<VCSimulationIdentifier, DataViewerController>();
                            hashTable.put(H_DATA_VIEWER_CONTROLLERS, dataViewerControllers);
                        }
                        dataViewerControllers.put(vcSimulationIdentifier, dataViewerController);
                    } catch (Throwable exc) {
                        exc.printStackTrace(System.out);
                        saveFailure(hashTable, sim, exc);
                    }
                }
                try {
                    if (viewerType == ViewerType.PythonViewer_only || viewerType == ViewerType.BothNativeAndPython) {
                        VtkManager vtkManager = null;
                        if (!isLocal) {
                            vtkManager = documentWindowManager.getRequestManager().getVtkManager(outputContext, new VCSimulationDataIdentifier(vcSimulationIdentifier, 0));
                        } else {
                            // ---- preliminary : construct the localDatasetControllerProvider
                            File primaryDir = ResourceUtil.getLocalRootDir();
                            User usr = sim.getVersion().getOwner();
                            DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
                            ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
                            LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
                            VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
                            File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
                            VCSimulationDataIdentifier simulationDataIdentifier = new LocalVCSimulationDataIdentifier(vcSimulationIdentifier, 0, localSimDir);
                            vtkManager = new VtkManager(outputContext, vcDataManager, simulationDataIdentifier);
                        }
                        // 
                        // test ability to read data
                        // 
                        VtuVarInfo[] vtuVarInfos = vtkManager.getVtuVarInfos();
                        double[] times = vtkManager.getDataSetTimes();
                        // 
                        // create the SimulationDataSetRef
                        // 
                        VCDocument modelDocument = null;
                        if (documentWindowManager instanceof BioModelWindowManager) {
                            modelDocument = ((BioModelWindowManager) documentWindowManager).getBioModel();
                        } else if (documentWindowManager instanceof MathModelWindowManager) {
                            modelDocument = ((MathModelWindowManager) documentWindowManager).getMathModel();
                        }
                        SimulationDataSetRef simulationDataSetRef = VCellClientDataServiceImpl.createSimulationDataSetRef(sim, modelDocument, 0, isLocal);
                        // Hashtable<VCSimulationIdentifier, SimulationDataSetRef> simDataSetRefs = (Hashtable<VCSimulationIdentifier, SimulationDataSetRef>)hashTable.get(H_SIM_DATASET_REFS);
                        // if (simDataSetRefs == null) {
                        // simDataSetRefs = new Hashtable<VCSimulationIdentifier, SimulationDataSetRef>();
                        // hashTable.put(H_SIM_DATASET_REFS, simDataSetRefs);
                        // }
                        // simDataSetRefs.put(vcSimulationIdentifier, simulationDataSetRef);
                        File visitExe = VCellConfiguration.getFileProperty(PropertyLoader.visitExe);
                        if (visitExe != null) {
                            VisitSupport.launchVisTool(visitExe, simulationDataSetRef);
                        }
                    }
                } catch (Throwable exc) {
                    exc.printStackTrace(System.out);
                    saveFailure(hashTable, sim, exc);
                }
            }
        }
    };
    taskList.add(retrieveResultsTask);
    AsynchClientTask displayResultsTask = new AsynchClientTask("Showing results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @SuppressWarnings("unchecked")
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            boolean isLocal = fetch(hashTable, H_LOCAL_SIM, Boolean.class, true);
            SimulationWindow.LocalState localState = isLocal ? LocalState.LOCAL : LocalState.SERVER;
            Hashtable<Simulation, Throwable> failures = (Hashtable<Simulation, Throwable>) hashTable.get(H_FAILURES);
            Simulation[] simsToShow = (Simulation[]) hashTable.get("simsArray");
            for (int i = 0; i < simsToShow.length; i++) {
                final Simulation sim = simsToShow[i];
                if (failures != null && failures.containsKey(sim)) {
                    continue;
                }
                final VCSimulationIdentifier vcSimulationIdentifier = simsToShow[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
                final SimulationWindow simWindow = documentWindowManager.haveSimulationWindow(vcSimulationIdentifier);
                if (simWindow != null) {
                    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(documentWindowManager.getComponent());
                    ChildWindow childWindow = childWindowManager.getChildWindowFromContext(simWindow);
                    if (childWindow == null) {
                        childWindow = childWindowManager.addChildWindow(simWindow.getDataViewer(), simWindow);
                        childWindow.pack();
                        childWindow.setIsCenteredOnParent();
                        childWindow.show();
                    }
                    setFinalWindow(hashTable, childWindow);
                    simWindow.setLocalState(localState);
                } else {
                    // wire it up the viewer
                    Hashtable<VCSimulationIdentifier, DataViewerController> dataViewerControllers = (Hashtable<VCSimulationIdentifier, DataViewerController>) hashTable.get(H_DATA_VIEWER_CONTROLLERS);
                    DataViewerController viewerController = dataViewerControllers.get(vcSimulationIdentifier);
                    Throwable ex = (failures == null ? null : failures.get(sim));
                    if (viewerController != null && ex == null) {
                        // no failure
                        DataViewer viewer = viewerController.createViewer();
                        getSimWorkspace().getSimulationOwner().getOutputFunctionContext().addPropertyChangeListener(viewerController);
                        documentWindowManager.addExportListener(viewer);
                        // For data related activities such as calculating statistics
                        documentWindowManager.addDataJobListener(viewer);
                        viewer.setSimulationModelInfo(new SimulationWorkspaceModelInfo(getSimWorkspace().getSimulationOwner(), sim.getName()));
                        viewer.setDataViewerManager(documentWindowManager);
                        SimulationWindow newWindow = new SimulationWindow(vcSimulationIdentifier, sim, getSimWorkspace().getSimulationOwner(), viewer);
                        BeanUtils.addCloseWindowKeyboardAction(newWindow.getDataViewer());
                        documentWindowManager.addResultsFrame(newWindow);
                        setFinalWindow(hashTable, viewer);
                        newWindow.setLocalState(localState);
                    }
                }
            }
            StringBuffer failMessage = new StringBuffer();
            if (failures != null) {
                if (!failures.isEmpty()) {
                    failMessage.append("Error, " + failures.size() + " of " + simsToShow.length + " sim results failed to display:\n");
                    Enumeration<Simulation> en = failures.keys();
                    while (en.hasMoreElements()) {
                        Simulation sim = en.nextElement();
                        Throwable exc = (Throwable) failures.get(sim);
                        failMessage.append("'" + sim.getName() + "' - " + exc.getMessage());
                    }
                }
            }
            if (failMessage.length() > 0) {
                PopupGenerator.showErrorDialog(ClientSimManager.this.getDocumentWindowManager(), failMessage.toString());
            }
        }
    };
    if (viewerType == ViewerType.BothNativeAndPython || viewerType == ViewerType.NativeViewer_only) {
        taskList.add(displayResultsTask);
    }
    // Dispatch the tasks using the ClientTaskDispatcher.
    AsynchClientTask[] taskArray = new AsynchClientTask[taskList.size()];
    taskList.toArray(taskArray);
    return taskArray;
}

Example 2 with ExportServiceImpl

use of cbit.vcell.export.server.ExportServiceImpl in project vcell by virtualcell.

the class VirtualFrapWindowManager method startExport.

public void startExport(Component requester, OutputContext outContext, ExportSpecs exportSpecs) {
    try {
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        DataServerImpl dataServerImpl = new DataServerImpl(localWorkSpace.getDataSetControllerImpl(), exportServiceImpl);
        exportServiceImpl.addExportListener(new ExportListener() {

            public void exportMessage(ExportEvent event) {
                System.out.println(event.toString());
            }
        });
        exportServiceImpl.makeRemoteFile(null, LocalWorkspace.getDefaultOwner(), dataServerImpl, exportSpecs);
    } catch (DataAccessException e) {
        e.printStackTrace(System.out);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 3 with ExportServiceImpl

use of cbit.vcell.export.server.ExportServiceImpl in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getVtkManager.

@Override
public VtkManager getVtkManager(SimulationDataSetRef simulationDataSetRef) throws FileNotFoundException, DataAccessException {
    VCSimulationDataIdentifier vcSimulationDataIdentifier = getVCSimulationDataIdentifier(simulationDataSetRef);
    VtkManager vtkManager = null;
    if (!simulationDataSetRef.isLocal) {
        vtkManager = vcellClient.getRequestManager().getVtkManager(null, vcSimulationDataIdentifier);
    } else {
        // ---- preliminary : construct the localDatasetControllerProvider
        File primaryDir = ResourceUtil.getLocalRootDir();
        User usr = User.tempUser;
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
        ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
        LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
        VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
        vtkManager = new VtkManager(null, vcDataManager, vcSimulationDataIdentifier);
    }
    return vtkManager;
}

Example 4 with ExportServiceImpl

use of cbit.vcell.export.server.ExportServiceImpl 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 });
        CommandService commandService = null;
        if (args.length == 3) {
            String sshHost = args[0];
            String sshUser = args[1];
            File sshKeyFile = new File(args[2]);
            try {
                commandService = new CommandServiceSshNative(sshHost, sshUser, sshKeyFile);
                commandService.command(new String[] { "/usr/bin/env bash -c ls | head -5" });
                lg.trace("SSH Connection test passed with installed keyfile, running ls as user " + sshUser + " on " + sshHost);
            } catch (Exception e) {
                e.printStackTrace();
                try {
                    commandService = new CommandServiceSshNative(sshHost, sshUser, sshKeyFile, new File("/root"));
                    commandService.command(new String[] { "/usr/bin/env bash -c ls | head -5" });
                    lg.trace("SSH Connection test passed after installing keyfile, running ls as user " + sshUser + " on " + sshHost);
                } catch (Exception e2) {
                    e.printStackTrace();
                    throw new RuntimeException("failed to establish an ssh command connection to " + sshHost + " as user '" + sshUser + "' using key '" + sshKeyFile + "'", e);
                }
            }
            // can't make user directories, they are remote.
            AbstractSolver.bMakeUserDirs = false;
        } else {
            commandService = new CommandServiceLocal();
        }
        BatchSystemType batchSystemType = BatchSystemType.SLURM;
        HtcProxy htcProxy = null;
        switch(batchSystemType) {
            case SLURM:
                {
                    htcProxy = new SlurmProxy(commandService, PropertyLoader.getRequiredProperty(PropertyLoader.htcUser));
                    break;
                }
            default:
                {
                    throw new RuntimeException("unrecognized batch scheduling option :" + batchSystemType);
                }
        }
        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);
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20);
        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 = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        VCellServices vcellServices = new VCellServices(htcProxy, vcMessagingService, serviceInstanceStatus, databaseServerImpl, dataServerImpl, simulationDatabase);
        dataSetControllerImpl.addDataJobListener(vcellServices);
        exportServiceImpl.addExportListener(vcellServices);
        vcellServices.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}

Example 5 with ExportServiceImpl

use of cbit.vcell.export.server.ExportServiceImpl 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) {
    if (args.length < 1) {
        System.out.println("Missing arguments: " + SimDataServer.class.getName() + " serviceOrdinal [EXPORTONLY] [logdir]");
        System.exit(1);
    }
    try {
        PropertyLoader.loadProperties();
        int serviceOrdinal = Integer.parseInt(args[0]);
        String logdir = null;
        boolean bExportOnly = false;
        if (args.length > 1) {
            if (args[1].equalsIgnoreCase("EXPORTONLY")) {
                bExportOnly = true;
                VCMongoMessage.serviceStartup(ServiceName.export, new Integer(serviceOrdinal), args);
                if (args.length > 2) {
                    logdir = args[2];
                }
            } else {
                VCMongoMessage.serviceStartup(ServiceName.simData, new Integer(serviceOrdinal), args);
                logdir = args[1];
            }
        }
        ServiceInstanceStatus serviceInstanceStatus = null;
        ServiceName serviceName = null;
        if (bExportOnly) {
            serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DATAEXPORT, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
            serviceName = ServiceName.export;
        } else {
            serviceInstanceStatus = new ServiceInstanceStatus(VCellServerID.getSystemServerID(), ServiceType.DATA, serviceOrdinal, ManageUtils.getHostName(), new Date(), true);
            serviceName = ServiceName.simData;
        }
        VCMongoMessage.serviceStartup(serviceName, new Integer(serviceOrdinal), args);
        // 
        // JMX registration
        // 
        MBeanServer mbs = ManagementFactory.getPlatformMBeanServer();
        mbs.registerMBean(new VCellServiceMXBeanImpl(), new ObjectName(VCellServiceMXBean.jmxObjectName));
        Cachetable cacheTable = new Cachetable(MessageConstants.MINUTE_IN_MS * 20);
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(cacheTable, new File(PropertyLoader.getRequiredProperty(PropertyLoader.primarySimDataDirInternalProperty)), new File(PropertyLoader.getRequiredProperty(PropertyLoader.secondarySimDataDirInternalProperty)));
        ExportServiceImpl exportServiceImpl = new ExportServiceImpl();
        DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, exportServiceImpl);
        VCMessagingService vcMessagingService = VCellServiceHelper.getInstance().loadService(VCMessagingService.class);
        vcMessagingService.setDelegate(new ServerMessagingDelegate());
        SimDataServer simDataServer = new SimDataServer(serviceInstanceStatus, dataServerImpl, vcMessagingService, false);
        // add dataJobListener
        dataSetControllerImpl.addDataJobListener(simDataServer);
        // add export listener
        exportServiceImpl.addExportListener(simDataServer);
        simDataServer.init();
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
}