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

Example 31 with VCDocument

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

the class DocumentToExport method run.

/**
 * Insert the method's description here. Creation date: (5/31/2004 6:04:14
 * PM)
 *
 * @param hashTable
 *            java.util.Hashtable
 * @param clientWorker
 *            cbit.vcell.desktop.controls.ClientWorker
 */
@Override
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    TopLevelWindowManager topLevelWindowManager = extractRequired(hashTable, TopLevelWindowManager.class, "topLevelWindowManager");
    VCDocument doc = null;
    if (topLevelWindowManager instanceof DocumentWindowManager) {
        doc = ((DocumentWindowManager) topLevelWindowManager).getVCDocument();
    } else if (topLevelWindowManager instanceof DatabaseWindowManager) {
        DocumentManager documentManager = extractRequired(hashTable, DocumentManager.class, CommonTask.DOCUMENT_MANAGER.name);
        VCDocumentInfo documentInfo = ((DatabaseWindowManager) topLevelWindowManager).getPanelSelection();
        if (documentInfo instanceof BioModelInfo) {
            BioModelInfo bmi = (BioModelInfo) documentInfo;
            doc = documentManager.getBioModel(bmi);
        } else if (documentInfo instanceof MathModelInfo) {
            MathModelInfo mmi = (MathModelInfo) documentInfo;
            doc = documentManager.getMathModel(mmi);
        } else if (documentInfo instanceof GeometryInfo) {
            GeometryInfo gmi = (GeometryInfo) documentInfo;
            doc = documentManager.getGeometry(gmi);
        }
        if (doc == null) {
            throw new IllegalStateException("export called on DatabaseWindowManager with selection " + documentInfo);
        }
    }
    if (doc != null) {
        hashTable.put(EXPORT_DOCUMENT, doc);
    } else {
        throw new UnsupportedOperationException("TopLevelWindowManager subclass " + topLevelWindowManager.getClass().getName() + " does not support exporting to document");
    }
}

Example 32 with VCDocument

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

the class FinishSave method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    MDIManager mdiManager = (MDIManager) hashTable.get("mdiManager");
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
        VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
        documentWindowManager.resetDocument(savedDocument);
    }
    mdiManager.unBlockWindow(documentWindowManager.getManagerID());
    mdiManager.showWindow(documentWindowManager.getManagerID());
}

Example 33 with VCDocument

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

the class RunSims method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    ClientSimManager clientSimManager = (ClientSimManager) hashTable.get("clientSimManager");
    // DocumentManager documentManager = (DocumentManager)hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    JobManager jobManager = (JobManager) hashTable.get("jobManager");
    Simulation[] simulations = (Simulation[]) hashTable.get("simulations");
    Hashtable<Simulation, Throwable> failures = new Hashtable<Simulation, Throwable>();
    if (simulations != null && simulations.length > 0) {
        // we need to get the new ones if a save occurred...
        if (hashTable.containsKey(SaveDocument.DOC_KEY)) {
            VCDocument savedDocument = (VCDocument) hashTable.get(SaveDocument.DOC_KEY);
            Simulation[] allSims = null;
            if (savedDocument instanceof BioModel) {
                allSims = ((BioModel) savedDocument).getSimulations();
            } else if (savedDocument instanceof MathModel) {
                allSims = ((MathModel) savedDocument).getSimulations();
            }
            Vector<Simulation> v = new Vector<Simulation>();
            for (int i = 0; i < simulations.length; i++) {
                for (int j = 0; j < allSims.length; j++) {
                    if (simulations[i].getName().equals(allSims[j].getName())) {
                        v.add(allSims[j]);
                        break;
                    }
                }
            }
            simulations = (Simulation[]) BeanUtils.getArray(v, Simulation.class);
        }
        for (Simulation sim : simulations) {
            try {
                int dimension = sim.getMathDescription().getGeometry().getDimension();
                if (clientSimManager.getSimulationStatus(sim).isCompleted()) {
                    // completed
                    String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_1, sim.getName());
                    String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                    if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                        continue;
                    }
                }
                DataProcessingInstructions dataProcessingInstructions = sim.getDataProcessingInstructions();
                try {
                    if (dataProcessingInstructions != null) {
                        dataProcessingInstructions.getSampleImageFieldData(sim.getVersion().getOwner());
                    }
                } catch (Exception ex) {
                    DialogUtils.showErrorDialog(documentWindowManager.getComponent(), "Problem found in simulation '" + sim.getName() + "':\n" + ex.getMessage());
                    continue;
                }
                if (dimension > 0) {
                    MeshSpecification meshSpecification = sim.getMeshSpecification();
                    boolean bCellCentered = sim.hasCellCenteredMesh();
                    if (meshSpecification != null && !meshSpecification.isAspectRatioOK(bCellCentered)) {
                        String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_2, sim.getName(), "\u0394x=" + meshSpecification.getDx(bCellCentered) + "\n" + "\u0394y=" + meshSpecification.getDy(bCellCentered) + (dimension < 3 ? "" : "\n\u0394z=" + meshSpecification.getDz(bCellCentered)));
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                    if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.Smoldyn)) {
                        if (!isSmoldynTimeStepOK(sim)) {
                            double s = smoldynTimestepVars.getSpatialResolution();
                            double dMax = smoldynTimestepVars.getMaxDiffusion();
                            double condn = (s * s) / (2.0 * dMax);
                            String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_3, Double.toString(s), Double.toString(dMax), Double.toString(condn));
                            DialogUtils.showErrorDialog(documentWindowManager.getComponent(), warningMessage);
                            continue;
                        }
                    }
                    // check the number of regions if the simulation mesh is coarser.
                    Geometry mathGeometry = sim.getMathDescription().getGeometry();
                    ISize newSize = meshSpecification.getSamplingSize();
                    ISize defaultSize = mathGeometry.getGeometrySpec().getDefaultSampledImageSize();
                    if (!sim.getSolverTaskDescription().getSolverDescription().isChomboSolver()) {
                        int defaultTotalVolumeElements = mathGeometry.getGeometrySurfaceDescription().getVolumeSampleSize().getXYZ();
                        int newTotalVolumeElements = meshSpecification.getSamplingSize().getXYZ();
                        if (defaultTotalVolumeElements > newTotalVolumeElements) {
                            // coarser
                            Geometry resampledGeometry = (Geometry) BeanUtils.cloneSerializable(mathGeometry);
                            GeometrySurfaceDescription geoSurfaceDesc = resampledGeometry.getGeometrySurfaceDescription();
                            geoSurfaceDesc.setVolumeSampleSize(newSize);
                            geoSurfaceDesc.updateAll();
                            if (mathGeometry.getGeometrySurfaceDescription().getGeometricRegions() == null) {
                                mathGeometry.getGeometrySurfaceDescription().updateAll();
                            }
                            int defaultNumGeometricRegions = mathGeometry.getGeometrySurfaceDescription().getGeometricRegions().length;
                            int numGeometricRegions = geoSurfaceDesc.getGeometricRegions().length;
                            if (numGeometricRegions != defaultNumGeometricRegions) {
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_4, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), numGeometricRegions, defaultNumGeometricRegions);
                                String result = PopupGenerator.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                        if (mathGeometry.getGeometrySpec().hasImage()) {
                            // if it's an image.
                            if (defaultSize.getX() + 1 < newSize.getX() || defaultSize.getY() + 1 < newSize.getY() || defaultSize.getZ() + 1 < newSize.getZ()) {
                                // finer
                                String defaultSizeString = (defaultSize.getX() + 1) + (dimension > 1 ? " x " + (defaultSize.getY() + 1) : "") + (dimension > 2 ? " x " + (defaultSize.getZ() + 1) : "");
                                String warningMessage = VCellErrorMessages.getErrorMessage(VCellErrorMessages.RunSims_5, newSize.getX() + (dimension > 1 ? " x " + newSize.getY() : "") + (dimension > 2 ? " x " + newSize.getZ() : ""), sim.getName(), defaultSizeString, defaultSizeString);
                                String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                                if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                                    continue;
                                }
                            }
                        }
                    }
                    boolean bGiveWarning = false;
                    for (int i = 0; i < sim.getScanCount(); i++) {
                        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE)) {
                            SimulationJob simJob = new SimulationJob(sim, i, null);
                            if (simJob.getSimulationSymbolTable().hasTimeVaryingDiffusionOrAdvection()) {
                                bGiveWarning = true;
                                break;
                            }
                        }
                    }
                    if (bGiveWarning) {
                        String warningMessage = VCellErrorMessages.RunSims_6;
                        String result = DialogUtils.showWarningDialog(documentWindowManager.getComponent(), warningMessage, new String[] { UserMessage.OPTION_OK, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_OK);
                        if (result == null || !result.equals(UserMessage.OPTION_OK)) {
                            continue;
                        }
                    }
                }
                SimulationInfo simInfo = sim.getSimulationInfo();
                if (simInfo != null) {
                    // 
                    // translate to common ancestral simulation (oldest mathematically equivalent simulation)
                    // 
                    SimulationStatus simulationStatus = jobManager.startSimulation(simInfo.getAuthoritativeVCSimulationIdentifier(), sim.getScanCount());
                    // updateStatus
                    clientSimManager.updateStatusFromStartRequest(sim, simulationStatus);
                } else {
                    // this should really not happen...
                    throw new RuntimeException(">>>>>>>>>> trying to run an unsaved simulation...");
                }
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                failures.put(sim, exc);
            }
        }
    }
    // we deal with individual request failures here, passing down only other things (that break the whole thing down) to dispatcher
    if (!failures.isEmpty()) {
        Enumeration<Simulation> en = failures.keys();
        while (en.hasMoreElements()) {
            Simulation sim = en.nextElement();
            Throwable exc = (Throwable) failures.get(sim);
            // // updateStatus
            // SimulationStatus simulationStatus = clientSimManager.updateStatusFromStartRequest(sim, true, exc.getMessage());
            // notify user
            PopupGenerator.showErrorDialog(documentWindowManager, "Failed to start simulation'" + sim.getName() + "'\n" + exc.getMessage());
        }
    }
}

Example 34 with VCDocument

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

the class SaveDocument method run.

/**
 * Insert the method's description here.
 * Creation date: (5/31/2004 6:04:14 PM)
 * @param hashTable java.util.Hashtable
 * @param clientWorker cbit.vcell.desktop.controls.ClientWorker
 */
public void run(Hashtable<String, Object> hashTable) throws java.lang.Exception {
    long l1 = System.currentTimeMillis();
    DocumentWindowManager documentWindowManager = (DocumentWindowManager) hashTable.get(CommonTask.DOCUMENT_WINDOW_MANAGER.name);
    VCDocument currentDocument = documentWindowManager.getVCDocument();
    DocumentManager documentManager = (DocumentManager) hashTable.get(CommonTask.DOCUMENT_MANAGER.name);
    RequestManager requestManager = (RequestManager) hashTable.get("requestManager");
    boolean bAsNew = hashTable.containsKey("newName");
    String newName = bAsNew ? (String) hashTable.get("newName") : null;
    Simulation[] simulationsToRun = (Simulation[]) hashTable.get("simulations");
    String[] independentSims = null;
    if (simulationsToRun != null && simulationsToRun.length > 0) {
        independentSims = new String[simulationsToRun.length];
        for (int i = 0; i < simulationsToRun.length; i++) {
            independentSims[i] = simulationsToRun[i].getName();
        }
    }
    VCDocument savedDocument = null;
    switch(currentDocument.getDocumentType()) {
        case BIOMODEL_DOC:
            {
                if (bAsNew) {
                    // Substitute Field Func Names-----
                    VersionableTypeVersion originalVersionableTypeVersion = null;
                    if (currentDocument.getVersion() != null) {
                        // From Opened...
                        originalVersionableTypeVersion = new VersionableTypeVersion(VersionableType.BioModelMetaData, currentDocument.getVersion());
                    }
                    documentManager.substituteFieldFuncNames((BioModel) currentDocument, originalVersionableTypeVersion);
                    // --------------------------------
                    savedDocument = documentManager.saveAsNew((BioModel) currentDocument, newName, independentSims);
                } else {
                    savedDocument = documentManager.save((BioModel) currentDocument, independentSims);
                }
                break;
            }
        case MATHMODEL_DOC:
            {
                if (bAsNew) {
                    // Substitute Field Func Names-----
                    VersionableTypeVersion originalVersionableTypeVersion = ((MathModelWindowManager) documentWindowManager).getCopyFromBioModelAppVersionableTypeVersion();
                    if (originalVersionableTypeVersion == null && currentDocument.getVersion() != null) {
                        // From Opened...
                        originalVersionableTypeVersion = new VersionableTypeVersion(VersionableType.MathModelMetaData, currentDocument.getVersion());
                    }
                    documentManager.substituteFieldFuncNames((MathModel) currentDocument, originalVersionableTypeVersion);
                    // --------------------------------
                    savedDocument = documentManager.saveAsNew((MathModel) currentDocument, newName, independentSims);
                } else {
                    savedDocument = documentManager.save((MathModel) currentDocument, independentSims);
                }
                break;
            }
        case GEOMETRY_DOC:
            {
                if (bAsNew) {
                    savedDocument = documentManager.saveAsNew((Geometry) currentDocument, newName);
                } else {
                    savedDocument = documentManager.save((Geometry) currentDocument);
                }
                break;
            }
        default:
            {
                throw new RuntimeException("unexpected document type " + currentDocument.getDocumentType().name());
            }
    }
    documentWindowManager.prepareDocumentToLoad(savedDocument, false);
    hashTable.put(SaveDocument.DOC_KEY, savedDocument);
    // generate PerformanceMonitorEvent
    long l2 = System.currentTimeMillis();
    double duration = ((double) (l2 - l1)) / 1000;
// requestManager.getAsynchMessageManager().reportPerformanceMonitorEvent(
// new PerformanceMonitorEvent(
// this, documentManager.getUser(), new PerformanceData(
// "SaveDocument.run()",
// MessageEvent.SAVING_STAT,
// new PerformanceDataEntry[] {
// new PerformanceDataEntry("document saved", savedDocument.getName()),
// new PerformanceDataEntry("remote call duration", Double.toString(duration))
// }
// )
// )
// );
}

Example 35 with VCDocument

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

the class ClientRequestManager method isDifferentFromBlank.

/**
 * Insert the method's description here.
 * Creation date: (5/10/2004 3:48:16 PM)
 */
public boolean isDifferentFromBlank(VCDocumentType documentType, VCDocument vcDocument) {
    if (documentType != vcDocument.getDocumentType()) {
        // we have to open the doc in a new window, hence return true;
        return true;
    }
    VCDocument blank = null;
    if (vcDocument.getDocumentType() != VCDocumentType.GEOMETRY_DOC) {
        // BioModel/MathModel
        blank = createDefaultDocument(vcDocument.getDocumentType());
        try {
            blank.setName(vcDocument.getName());
        }// ignore. doesn't happen
         catch (PropertyVetoException e) {
        }
        return !blank.compareEqual(vcDocument);
    } else {
        // Geometry
        blank = new Geometry(vcDocument.getName(), 1);
        if (blank.compareEqual(vcDocument)) {
            return false;
        }
        blank = new Geometry(vcDocument.getName(), 2);
        if (blank.compareEqual(vcDocument)) {
            return false;
        }
        blank = new Geometry(vcDocument.getName(), 3);
        if (blank.compareEqual(vcDocument)) {
            return false;
        }
        return true;
    }
}