Examples with XmlParseException cbit.vcell.xml.XmlParseException used on opensource projects

Example 36 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class DataSetControllerImpl method getChomboFiles.

public ChomboFiles getChomboFiles(VCDataIdentifier vcdataID) throws DataAccessException, IOException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getChomboFiles(" + vcdataID.getID() + ")  <<EXIT>>");
    if (lg.isTraceEnabled())
        lg.trace("DataSetControllerImpl.getChomboFiles(" + vcdataID.getOwner().getName() + "," + vcdataID.getID() + ")");
    VCData simData = getVCData(vcdataID);
    try {
        return simData.getChomboFiles();
    } catch (XmlParseException e) {
        e.printStackTrace();
        throw new DataAccessException("failed to getChomboFiles(): " + e.getMessage(), e);
    } catch (ExpressionException e) {
        e.printStackTrace();
        throw new DataAccessException("failed to getChomboFiles(): " + e.getMessage(), e);
    }
}

Example 37 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class ProfileLikelihood method main.

// main
public static void main(String[] args) {
    try {
        File newXML = new File(args[0]);
        XMLSource source = new XMLSource(newXML);
        BioModel biomodel = XmlHelper.XMLToBioModel(source);
        SimulationContext app = biomodel.getSimulationContext("Deterministic");
        AnalysisTask[] task = app.getAnalysisTasks();
        // ParestRun.bFakeOptimization = true;
        final ProfileLikelihoodCallback callback = new ProfileLikelihoodCallback() {

            @Override
            public void report(String msg) {
                System.out.println(msg);
            }
        };
        ProfileLikelihood pl = new ProfileLikelihood(callback);
        pl.run((ParameterEstimationTask) task[0]);
    } catch (XmlParseException e) {
        e.printStackTrace();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 38 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class SBMLStandaloneImporter method attemptImport.

private BioModel attemptImport(File sbmlFile) throws ExecutableException, IOException, ClassNotFoundException, XmlParseException {
    if (subProcess == null || subProcess.getStatus() != LiveProcessStatus.RUNNING) {
        subProcess = createProcess();
    }
    toChildProcess.writeObject(sbmlFile);
    Object back = fromChildProcess.readObject();
    if (back instanceof String) {
        String xml = (String) back;
        if (lg.isDebugEnabled()) {
            try (FileWriter fw = new FileWriter(sbmlFile.getAbsolutePath() + ".dump")) {
                fw.append(xml);
            }
        }
        XMLSource source = new XMLSource(xml);
        return XmlHelper.XMLToBioModel(source);
    }
    if (back instanceof Exception) {
        try {
            throw (Exception) back;
        } catch (SBMLImportException sie) {
            throw sie;
        } catch (Exception e) {
            throw new ExecutableException("child process exception", e);
        }
    }
    throw new ExecutableException("unexpected object from child process:  " + back.getClass().getName() + " " + back.toString());
}

Example 39 with XmlParseException

use of cbit.vcell.xml.XmlParseException in project vcell by virtualcell.

the class SEDMLExporter method main.

public static void main(String[] args) {
    // if (args.length != 1) {
    // System.out.println("Usage:\n\t path_of_vcml_file\n" );
    // System.exit(1);
    // }
    // String pathName = args[0];
    String pathName = "c:\\dan\\SEDML\\SEDML2.vcml";
    try {
        String biomodelXmlStr = XmlUtil.getXMLString(pathName);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(biomodelXmlStr.toString()));
        bioModel.refreshDependencies();
        // invoke the SEDMLEXporter
        SEDMLExporter sedmlExporter = new SEDMLExporter(bioModel, 1, 1);
        String absolutePath = "c:\\dan\\SEDML";
        String sedmlStr = sedmlExporter.getSEDMLFile(absolutePath);
        // String absolutePath = ResourceUtil.getUserHomeDir().getAbsolutePath();
        String outputName = absolutePath + "\\" + TokenMangler.mangleToSName(bioModel.getName()) + ".sedml";
        XmlUtil.writeXMLStringToFile(sedmlStr, outputName, true);
    } catch (IOException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Unable to read VCML file '" + pathName + "' into string.");
    } catch (XmlParseException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Unable to convert VCML file '" + pathName + "' to a biomodel.");
    }
}

Example 40 with XmlParseException

use of cbit.vcell.xml.XmlParseException 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());
    }
}