Examples with SimulationDataSetRef cbit.vcell.client.pyvcellproxy.SimulationDataSetRef used on opensource projects

Example 1 with SimulationDataSetRef

use of cbit.vcell.client.pyvcellproxy.SimulationDataSetRef in project vcell by virtualcell.

the class VCellClientDataServiceImpl method createSimulationDataSetRef.

public static SimulationDataSetRef createSimulationDataSetRef(Simulation simulation, VCDocument modelDocument, int jobIndex, boolean isLocal) {
    SimulationDataSetRef simulationDataSetReference = new SimulationDataSetRef();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    SimulationInfo simInfo = simulation.getSimulationInfo();
    simulationDataSetReference.setSimName(simInfo.getName());
    // String simName = simInfo.getName();
    // if (jobIndex!=0){
    // simName = simName + " job#"+String.valueOf(jobIndex);
    // }
    final String modelId;
    final boolean isMathModel;
    final String modelName;
    final String simContextName;
    if (modelDocument != null) {
        modelId = modelDocument.getVersion().getVersionKey().toString();
        isMathModel = (modelDocument instanceof MathModel);
        modelName = modelDocument.getName();
        if (modelDocument instanceof BioModel && simulation.getSimulationOwner() != null) {
            simContextName = simulation.getSimulationOwner().getName();
        } else {
            simContextName = null;
        }
    } else {
        modelId = "no id";
        isMathModel = false;
        modelName = "no model";
        simContextName = null;
    }
    simulationDataSetReference.setSimId(simInfo.getAuthoritativeVCSimulationIdentifier().getSimulationKey().toString());
    simulationDataSetReference.setModelId(modelId);
    simulationDataSetReference.setUsername(simInfo.getVersion().getOwner().getName());
    simulationDataSetReference.setUserkey(simInfo.getVersion().getOwner().getID().toString());
    simulationDataSetReference.setIsMathModel(isMathModel);
    simulationDataSetReference.setJobIndex(jobIndex);
    simulationDataSetReference.setModelName(modelName);
    simulationDataSetReference.setOriginXYZ(Arrays.asList(new Double[] { origin.getX(), origin.getY(), origin.getZ() }));
    simulationDataSetReference.setExtentXYZ(Arrays.asList(new Double[] { extent.getX(), extent.getY(), extent.getZ() }));
    if (simContextName != null) {
        simulationDataSetReference.setSimulationContextName(simContextName);
    }
    simulationDataSetReference.setSimName(simInfo.getName());
    boolean movingBoundarySolver = simulation.getSolverTaskDescription().getSolverDescription().isMovingBoundarySolver();
    simulationDataSetReference.setIsTimeVaryingMesh(movingBoundarySolver);
    simulationDataSetReference.setIsLocal(isLocal);
    return simulationDataSetReference;
}

Example 2 with SimulationDataSetRef

use of cbit.vcell.client.pyvcellproxy.SimulationDataSetRef in project vcell by virtualcell.

the class VCellClientDataServiceImpl method getSimsFromOpenModels.

@Override
public List<SimulationDataSetRef> getSimsFromOpenModels() {
    ArrayList<SimulationDataSetRef> simulationDataSetRefs = new ArrayList<SimulationDataSetRef>();
    for (TopLevelWindowManager windowManager : vcellClient.getMdiManager().getWindowManagers()) {
        Simulation[] simulations = null;
        VCDocument modelDocument = null;
        if (windowManager instanceof BioModelWindowManager) {
            BioModelWindowManager selectedBioWindowManager = (BioModelWindowManager) windowManager;
            BioModel bioModel = selectedBioWindowManager.getBioModel();
            simulations = bioModel.getSimulations();
            modelDocument = bioModel;
        // simOwnerCount = bioModel.getNumSimulationContexts();
        } else if (windowManager instanceof MathModelWindowManager) {
            MathModelWindowManager selectedMathWindowManager = (MathModelWindowManager) windowManager;
            MathModel mathModel = selectedMathWindowManager.getMathModel();
            simulations = mathModel.getSimulations();
            modelDocument = mathModel;
        // simOwnerCount = 1;
        }
        if (simulations != null) {
            for (Simulation simulation : simulations) {
                if (!isVtkSupported(simulation)) {
                    continue;
                }
                Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
                Extent extent = simulation.getMathDescription().getGeometry().getExtent();
                SimulationInfo simInfo = simulation.getSimulationInfo();
                SimulationStatus simStatus = vcellClient.getRequestManager().getServerSimulationStatus(simInfo);
                for (int jobIndex = 0; jobIndex < simulation.getScanCount(); jobIndex++) {
                    if (simStatus != null && simStatus.getHasData()) {
                        SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simulation, modelDocument, jobIndex, false);
                        simulationDataSetRefs.add(simulationDataSetReference);
                    }
                }
            }
        }
    }
    File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    String[] simtaskFilenames = localSimDir.list((dir, name) -> (name.endsWith(".simtask.xml")));
    for (String simtaskFilename : simtaskFilenames) {
        try {
            SimulationTask simTask = XmlHelper.XMLToSimTask(org.apache.commons.io.FileUtils.readFileToString(new File(localSimDir, simtaskFilename)));
            VCDocument modelDocument = null;
            SimulationDataSetRef simulationDataSetReference = VCellClientDataServiceImpl.createSimulationDataSetRef(simTask.getSimulation(), modelDocument, simTask.getSimulationJob().getJobIndex(), true);
            simulationDataSetRefs.add(simulationDataSetReference);
        } catch (ExpressionException | XmlParseException | IOException e) {
            e.printStackTrace();
        }
    }
    return simulationDataSetRefs;
}