Examples with ThriftDataAccessException org.vcell.vcellij.api.ThriftDataAccessException used on opensource projects

Example 1 with ThriftDataAccessException

use of org.vcell.vcellij.api.ThriftDataAccessException in project vcell by virtualcell.

the class SimulationServiceImpl method getTimePoints.

public List<Double> getTimePoints(SimulationInfo simInfo) throws ThriftDataAccessException, TException {
    SimulationServiceContext simServiceContext = sims.get(simInfo.id);
    if (simServiceContext == null) {
        throw new ThriftDataAccessException("simulation results not found");
    }
    try {
        DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
        ArrayList<Double> times = new ArrayList<Double>();
        double[] timeArray;
        timeArray = datasetController.getDataSetTimes(simServiceContext.vcDataIdentifier);
        for (double t : timeArray) {
            times.add(t);
        }
        return times;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to retrieve times for simulation: " + e.getMessage());
    }
}

Example 2 with ThriftDataAccessException

use of org.vcell.vcellij.api.ThriftDataAccessException in project vcell by virtualcell.

the class SimulationServiceImpl method computeModel.

public SimulationInfo computeModel(SBMLModel model, SimulationSpec simSpec) throws ThriftDataAccessException, TException {
    try {
        SBMLImporter importer = new SBMLImporter(model.getFilepath(), vcLogger(), true);
        BioModel bioModel = importer.getBioModel();
        return computeModel(bioModel, simSpec, null);
    } catch (Exception exc) {
        exc.printStackTrace(System.out);
        return null;
    }
}

Example 3 with ThriftDataAccessException

use of org.vcell.vcellij.api.ThriftDataAccessException in project vcell by virtualcell.

the class SimulationServiceImpl method getSBML.

public String getSBML(String vcml, String applicationName) throws ThriftDataAccessException, TException {
    try {
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml));
        SimulationContext simContext = bioModel.getSimulationContext(applicationName);
        SBMLExporter exporter = new SBMLExporter(simContext, 3, 1, simContext.getGeometry().getDimension() > 0);
        VCellSBMLDoc sbmlDoc = exporter.convertToSBML();
        return sbmlDoc.xmlString;
    } catch (SBMLException | XmlParseException | SbmlException | XMLStreamException e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to generate SBML document: " + e.getMessage());
    }
}

Example 4 with ThriftDataAccessException

use of org.vcell.vcellij.api.ThriftDataAccessException in project vcell by virtualcell.

the class SimulationServiceImpl method getData.

public List<Double> getData(SimulationInfo simInfo, VariableInfo varInfo, int timeIndex) throws ThriftDataAccessException, TException {
    SimulationServiceContext simServiceContext = sims.get(simInfo.id);
    if (simServiceContext == null) {
        throw new RuntimeException("simulation results not found");
    }
    DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
    try {
        double[] times = datasetController.getDataSetTimes(simServiceContext.vcDataIdentifier);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        SimDataBlock simDataBlock = datasetController.getSimDataBlock(outputContext, simServiceContext.vcDataIdentifier, varInfo.getVariableVtuName(), times[timeIndex]);
        double[] dataArray = simDataBlock.getData();
        ArrayList<Double> dataList = new ArrayList<Double>();
        for (double d : dataArray) {
            dataList.add(d);
        }
        return dataList;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to retrieve data for variable " + varInfo.getVariableVtuName() + ": " + e.getMessage());
    }
}

Example 5 with ThriftDataAccessException

use of org.vcell.vcellij.api.ThriftDataAccessException in project vcell by virtualcell.

the class SimulationServiceImpl method getVariableList.

public List<VariableInfo> getVariableList(SimulationInfo simInfo) throws ThriftDataAccessException, TException {
    SimulationServiceContext simServiceContext = sims.get(simInfo.id);
    if (simServiceContext == null) {
        throw new ThriftDataAccessException("simulation results not found");
    }
    try {
        DataSetControllerImpl datasetController = getDataSetController(simServiceContext);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final DataIdentifier[] dataIdentifiers;
        try {
            dataIdentifiers = datasetController.getDataIdentifiers(outputContext, simServiceContext.vcDataIdentifier);
        } catch (IOException | DataAccessException e) {
            e.printStackTrace();
            throw new RuntimeException("failed to retrieve variable information: " + e.getMessage(), e);
        }
        ArrayList<VariableInfo> varInfos = new ArrayList<VariableInfo>();
        for (DataIdentifier dataIdentifier : dataIdentifiers) {
            final DomainType domainType;
            if (dataIdentifier.getVariableType().equals(VariableType.VOLUME)) {
                domainType = DomainType.VOLUME;
            } else if (dataIdentifier.getVariableType().equals(VariableType.MEMBRANE)) {
                domainType = DomainType.MEMBRANE;
            } else {
                continue;
            }
            String domainName = "";
            if (dataIdentifier.getDomain() != null) {
                domainName = dataIdentifier.getDomain().getName();
            }
            VariableInfo varInfo = new VariableInfo(dataIdentifier.getName(), dataIdentifier.getDisplayName(), domainName, domainType);
            varInfos.add(varInfo);
        }
        return varInfos;
    } catch (Exception e) {
        e.printStackTrace();
        throw new ThriftDataAccessException("failed to retrieve variable list: " + e.getMessage());
    }
}