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

Example 36 with XMLSource

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

the class BiomodelDiagramServerResource method get_png.

@Override
@Get("image/png")
public ByteArrayRepresentation get_png() {
    VCellApiApplication application = ((VCellApiApplication) getApplication());
    User vcellUser = application.getVCellUser(getChallengeResponse(), AuthenticationPolicy.ignoreInvalidCredentials);
    String vcml = getBiomodelVCML(vcellUser);
    if (vcml == null) {
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "BioModel not found");
    }
    try {
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(vcml));
        Integer imageWidthInPixels = 1000;
        BufferedImage bufferedImage = ITextWriter.generateDocReactionsImage(bioModel.getModel(), imageWidthInPixels);
        ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
        ImageIO.write(bufferedImage, "png", outputStream);
        byte[] imageBytes = outputStream.toByteArray();
        return new ByteArrayRepresentation(imageBytes, MediaType.IMAGE_PNG, imageBytes.length);
    } catch (Exception e) {
        e.printStackTrace();
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
}

Example 37 with XMLSource

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

the class BiomodelVCMLServerResource method getBiomodelVCML.

private String getBiomodelVCML(User vcellUser) {
    // if (!application.authenticate(getRequest(), getResponse())){
    // // not authenticated
    // return new SimulationTaskRepresentation[0];
    // }else{
    RestDatabaseService restDatabaseService = ((VCellApiApplication) getApplication()).getRestDatabaseService();
    try {
        String cachedVcml = restDatabaseService.query(this, vcellUser);
        BioModel bioModel = XmlHelper.XMLToBioModel(new XMLSource(cachedVcml));
        String latestVcml = XmlHelper.bioModelToXML(bioModel);
        return latestVcml;
    } catch (PermissionException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_UNAUTHORIZED, "permission denied to requested resource");
    } catch (ObjectNotFoundException e) {
        e.printStackTrace();
        throw new ResourceException(Status.CLIENT_ERROR_NOT_FOUND, "biomodel not found");
    } catch (Exception e) {
        throw new ResourceException(Status.SERVER_ERROR_INTERNAL, e.getMessage());
    }
// }
}

Example 38 with XMLSource

use of cbit.vcell.xml.XMLSource 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 39 with XMLSource

use of cbit.vcell.xml.XMLSource 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 40 with XMLSource

use of cbit.vcell.xml.XMLSource 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.");
    }
}