Examples with VCDocument org.vcell.util.document.VCDocument used on opensource projects

Example 6 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class ClientRequestManager method runSimulations.

public void runSimulations(final ClientSimManager clientSimManager, final Simulation[] simulations) {
    DocumentWindowManager documentWindowManager = clientSimManager.getDocumentWindowManager();
    /*	run some quick checks to see if we need to do a SaveAs */
    boolean needSaveAs = false;
    if (documentWindowManager.getVCDocument().getVersion() == null) {
        // never saved
        needSaveAs = true;
    } else if (!documentWindowManager.getVCDocument().getVersion().getOwner().compareEqual(getDocumentManager().getUser())) {
        // not the owner
        // keep the user informed this time
        String choice = PopupGenerator.showWarningDialog(documentWindowManager, getUserPreferences(), UserMessage.warn_SaveNotOwner, null);
        if (choice.equals(UserMessage.OPTION_SAVE_AS_NEW)) {
            needSaveAs = true;
        } else {
            // user canceled, just show existing document
            getMdiManager().showWindow(documentWindowManager.getManagerID());
            throw new UserCancelException("user canceled");
        }
    }
    // Before running the simulation, check if all the sizes of structures are set
    if (simulations != null && simulations.length > 0) {
        VCDocument vcd = documentWindowManager.getVCDocument();
        if (vcd instanceof BioModel) {
            String stochChkMsg = null;
            // we want to check when there is stochastic application if the rate laws set in model can be automatically transformed.
            for (int i = 0; i < simulations.length; i++) {
                if (simulations[i].getMathDescription().isNonSpatialStoch() || simulations[i].getMathDescription().isSpatialStoch() || simulations[i].getMathDescription().isSpatialHybrid()) {
                    if (stochChkMsg == null) {
                        stochChkMsg = ((BioModel) vcd).getModel().isValidForStochApp();
                    }
                    if (!(stochChkMsg.equals(""))) {
                        DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem in simulation: " + simulations[i].getName() + ".\n" + stochChkMsg);
                        throw new RuntimeException("Problem in simulation: " + simulations[i].getName() + "\n" + stochChkMsg);
                    }
                }
            }
        }
    }
    // 
    for (int i = 0; simulations != null && i < simulations.length; i++) {
        if (simulations[i].getSimulationVersion() != null && simulations[i].getSimulationVersion().getParentSimulationReference() != null) {
            simulations[i].clearVersion();
        }
    }
    /* now start the dirty work */
    /* block document window */
    JFrame currentDocumentWindow = getMdiManager().blockWindow(documentWindowManager.getManagerID());
    /* prepare hashtable for tasks */
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    hash.put("mdiManager", getMdiManager());
    hash.put(DocumentManager.IDENT, getDocumentManager());
    hash.put(CommonTask.DOCUMENT_WINDOW_MANAGER.name, documentWindowManager);
    hash.put("currentDocumentWindow", currentDocumentWindow);
    hash.put("clientSimManager", clientSimManager);
    hash.put("simulations", simulations);
    hash.put("jobManager", getClientServerManager().getJobManager());
    hash.put("requestManager", this);
    /* create tasks */
    AsynchClientTask[] tasks = null;
    if (needSaveAs) {
        // check document consistency first
        AsynchClientTask documentValid = new DocumentValidTask();
        AsynchClientTask setMathDescription = new SetMathDescription();
        // get a new name
        AsynchClientTask newName = new NewName();
        // save it
        AsynchClientTask saveDocument = new SaveDocument();
        // clean up
        AsynchClientTask finishSave = new FinishSave();
        // run the simulations
        AsynchClientTask runSims = new RunSims();
        // assemble array
        tasks = new AsynchClientTask[] { documentValid, setMathDescription, newName, saveDocument, finishSave, runSims };
    } else {
        // check document consistency first
        AsynchClientTask documentValid = new DocumentValidTask();
        AsynchClientTask setMathDescription = new SetMathDescription();
        // check if unchanged document
        AsynchClientTask checkUnchanged = new CheckUnchanged(true);
        // save it
        AsynchClientTask saveDocument = new SaveDocument();
        // check for lost results
        AsynchClientTask checkBeforeDelete = new CheckBeforeDelete();
        // delete old document
        AsynchClientTask deleteOldDocument = new DeleteOldDocument();
        // clean up
        AsynchClientTask finishSave = new FinishSave();
        // run the simulations
        AsynchClientTask runSims = new RunSims();
        // assemble array
        tasks = new AsynchClientTask[] { documentValid, setMathDescription, checkUnchanged, saveDocument, checkBeforeDelete, deleteOldDocument, finishSave, runSims };
    }
    /* run the tasks */
    ClientTaskDispatcher.dispatch(currentDocumentWindow, hash, tasks, true);
}

Example 7 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class Translator method translate.

public VCDocument translate(Reader reader, boolean validationOn) throws Exception {
    if (validationOn) {
        this.sRoot = (XmlUtil.readXML(reader, schemaLocation, null, schemaLocationPropName)).getRootElement();
        String errorLog = XmlUtil.getErrorLog();
        if (errorLog.length() > 0) {
            System.err.println(errorLog);
            if (vcLogger != null) {
                vcLogger.sendMessage(VCLogger.Priority.LowPriority, VCLogger.ErrorType.SchemaValidation);
            // vcLogger.sendMessage(VCLogger.LOW_PRIORITY, TranslationMessage.SCHEMA_VALIDATION_ERROR,
            // "The source model has invalid elements/attributes:\n" + errorLog)
            }
        }
    } else {
        this.sRoot = (XmlUtil.readXML(reader, null, null, null)).getRootElement();
    }
    VCDocument vcDoc = translate();
    if (vcLogger != null && vcLogger.hasMessages()) {
        vcLogger.sendAllMessages();
    }
    return vcDoc;
}

Example 8 with VCDocument

use of org.vcell.util.document.VCDocument 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 9 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class PopupGenerator method showErrorDialog.

/**
 * showErrorDialog. If requester is of type DocumentWindowManager, offer to send context information
 * to VCellSupport
 * @param requester
 * @param message to display
 * @param ex may be null
 */
public static void showErrorDialog(TopLevelWindowManager requester, String message, Throwable ex) {
    DialogUtils.ErrorContext errorContext = null;
    if (requester instanceof DocumentWindowManager) {
        DocumentWindowManager dwm = (DocumentWindowManager) requester;
        VCDocument doc = dwm.getVCDocument();
        String contextString = doc.getName();
        Version v = doc.getVersion();
        if (v != null) {
            contextString += " " + v.identificationString();
        }
        errorContext = new DialogUtils.ErrorContext(contextString, requester.getUserPreferences());
    }
    showErrorDialog(requester.getComponent(), message, ex, errorContext);
}

Example 10 with VCDocument

use of org.vcell.util.document.VCDocument in project vcell by virtualcell.

the class IssueTableModel method getComparator.

@Override
protected Comparator<Issue> getComparator(final int col, final boolean ascending) {
    return new Comparator<Issue>() {

        public int compare(Issue o1, Issue o2) {
            VCDocument vcDocument = (issueManager != null) ? (issueManager.getVCDocument()) : null;
            int scale = ascending ? 1 : -1;
            switch(col) {
                case COLUMN_DESCRIPTION:
                    {
                        Severity s1 = o1.getSeverity();
                        Severity s2 = o2.getSeverity();
                        if (s1 == s2) {
                            return scale * o1.getMessage().compareTo(o2.getMessage());
                        } else {
                            return scale * s1.compareTo(s2);
                        }
                    }
                case COLUMN_URL:
                    {
                        String u1 = o1.getHyperlink();
                        String u2 = o2.getHyperlink();
                        return u1 != null ? u1.compareTo(u2) : -1;
                    }
                case COLUMN_SOURCE:
                    return scale * getSourceObjectDescription(vcDocument, o1).compareTo(getSourceObjectDescription(vcDocument, o2));
                case COLUMN_PATH:
                    return scale * getSourceObjectPathDescription(vcDocument, o1).compareTo(getSourceObjectPathDescription(vcDocument, o2));
            }
            return 0;
        }
    };
}