Examples with CompFlatteningConverter org.sbml.jsbml.ext.comp.util.CompFlatteningConverter used on opensource projects

Example 1 with CompFlatteningConverter

use of org.sbml.jsbml.ext.comp.util.CompFlatteningConverter in project vcell by virtualcell.

the class SBMLImporter method getBioModel.

// /**
// * @ TODO: This method doesn't take care of adjusting species in nested
// parameter rules with the species_concetration_factor.
// * @param kinetics
// * @param paramExpr
// * @throws ExpressionException
// */
// private void substituteOtherGlobalParams(Kinetics kinetics, Expression
// paramExpr) throws ExpressionException, PropertyVetoException {
// String[] exprSymbols = paramExpr.getSymbols();
// if (exprSymbols == null || exprSymbols.length == 0) {
// return;
// }
// Model vcModel = vcBioModel.getSimulationContext(0).getModel();
// for (int kk = 0; kk < exprSymbols.length; kk++) {
// ModelParameter mp = vcModel.getModelParameter(exprSymbols[kk]);
// if (mp != null) {
// Expression expr = mp.getExpression();
// if (expr != null) {
// Expression newExpr = new Expression(expr);
// substituteGlobalParamRulesInPlace(newExpr, false);
// // param has constant value, add it as a kinetic parameter if it is not
// already in the kinetics
// kinetics.setParameterValue(exprSymbols[kk], newExpr.infix());
// kinetics.getKineticsParameter(exprSymbols[kk]).setUnitDefinition(getSBMLUnit(sbmlModel.getParameter(exprSymbols[kk]).getUnits(),
// null));
// if (newExpr.getSymbols() != null) {
// substituteOtherGlobalParams(kinetics, newExpr);
// }
// }
// }
// }
// }
/**
 * parse SBML file into biomodel logs errors to log4j if present in source
 * document
 *
 * @return new Biomodel
 * @throws IOException
 * @throws XMLStreamException
 */
public BioModel getBioModel() throws XMLStreamException, IOException {
    if (sbmlFileName == null && sbmlModel == null) {
        throw new IllegalStateException("Expected non-null SBML model");
    }
    SBMLDocument document;
    String defaultErrorPrefix = "Unable to read SBML file";
    if (sbmlFileName != null) {
        try {
            // Read SBML model into libSBML SBMLDocument and create an SBML model
            List<String> readLines = FileUtils.readLines(new File(sbmlFileName), Charset.defaultCharset());
            StringBuffer sb = new StringBuffer();
            // throws NPE when "<sbml ... xmlns:render... " is defined in input document
            for (String line : readLines) {
                String str = "xmlns:render=\"http://www.sbml.org/sbml/level3/version1/render/version1\"";
                int indexOf = line.indexOf(str);
                if (indexOf != -1) {
                    line = line.substring(0, indexOf - 1) + line.substring(indexOf + str.length());
                }
                str = "render:required=\"false\"";
                indexOf = line.indexOf(str);
                if (indexOf != -1) {
                    line = line.substring(0, indexOf - 1) + line.substring(indexOf + str.length());
                }
                sb.append(line + "\n");
            }
            SBMLReader reader = new SBMLReader();
            document = reader.readSBMLFromString(sb.toString());
            // check for VCell origin
            String topNotes = document.getNotesString();
            if (topNotes != null && topNotes.contains("VCell")) {
                isFromVCell = true;
            }
            // document.checkConsistencyOffline();
            // long numProblems = document.getNumErrors();
            // 
            // System.out.println("\n\nSBML Import Error Report");
            // ByteArrayOutputStream os = new ByteArrayOutputStream();
            // PrintStream ps = new PrintStream(os);
            // document.printErrors(ps);
            // String output = os.toString();
            // if (numProblems > 0 && lg.isEnabledFor(Level.WARN)) {
            // lg.warn("Num problems in original SBML document : " + numProblems);
            // lg.warn(output);
            // }
            sbmlModel = document.getModel();
        } catch (Exception e) {
            throw new SBMLImportException(defaultErrorPrefix + ": \n" + sbmlFileName, e);
        }
        if (sbmlModel == null) {
            throw new SBMLImportException(defaultErrorPrefix + ": \n" + sbmlFileName);
        }
    } else {
        // sbmlModel != null
        try {
            document = sbmlModel.getSBMLDocument();
        } catch (Exception e) {
            throw new SBMLImportException(defaultErrorPrefix + ".\n", e);
        }
    }
    if (document == null) {
        throw new SBMLImportException(defaultErrorPrefix + ".\n");
    }
    int numPackages = 0;
    String msgPackages = "";
    try {
        boolean b = document.getPackageRequired("comp");
        if (document.isPackageEnabled("comp")) {
            numPackages++;
            msgPackages += "'comp', ";
            CompSBMLDocumentPlugin cdp = null;
            CompModelPlugin cmp = null;
            CompSBasePlugin csp = null;
            CompFlatteningConverter ccc = null;
        }
        if (document.isPackageEnabled("fbc")) {
            numPackages++;
            msgPackages += "'fbc', ";
        }
        if (document.isPackageEnabled("multi")) {
            numPackages++;
            msgPackages += "'multi', ";
        }
        if (document.isPackageEnabled("qual")) {
            numPackages++;
            msgPackages += "'qual', ";
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to check the SBML file package requirements.");
    }
    String ext = "extension";
    String is = "is";
    String has = "has";
    if (numPackages > 0) {
        if (numPackages > 1) {
            ext += "s";
            is = "are";
        }
        msgPackages = msgPackages.substring(0, msgPackages.length() - 1);
        msgPackages = "The model includes elements of SBML " + ext + " " + msgPackages + " which " + is + " required for simulating the model but " + is + " not supported.";
        throw new SBMLImportException("Unable to import the SBML file.\n" + msgPackages);
    }
    try {
        if (document.isPackageEnabled("groups")) {
            numPackages++;
            msgPackages += "'groups', ";
        }
        if (document.isPackageEnabled("layout")) {
            numPackages++;
            msgPackages += "'layout', ";
        }
        if (document.isPackageEnabled("render")) {
            numPackages++;
            msgPackages += "'render', ";
        }
    } catch (Exception e) {
        // we're going to ignore these packages anyway
        e.printStackTrace(System.out);
    }
    if (numPackages > 0) {
        if (numPackages > 1) {
            ext += "s";
            is = "are";
            has = "have";
        }
        msgPackages = "The model includes elements of SBML " + ext + " " + msgPackages + " which " + is + " not required for simulating the model and " + has + " been ignored.";
        localIssueList.add(new Issue(vcBioModel, issueContext, IssueCategory.SBMLImport_UnsupportedFeature, msgPackages, Issue.Severity.WARNING));
    }
    // Convert SBML Model to VCell model
    // An SBML model will correspond to a simcontext - which needs a Model and a Geometry
    // SBML handles only nonspatial geometries at this time, hence creating a non-spatial default geometry
    // get namespace based on SBML model level and version to use in SBMLAnnotationUtil
    this.level = sbmlModel.getLevel();
    // this.version = sbmlModel.getVersion();
    String ns = document.getNamespace();
    // create SBML unit system for the model and create the bioModel.
    ModelUnitSystem modelUnitSystem;
    try {
        modelUnitSystem = createSBMLUnitSystemForVCModel();
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Inconsistent unit system. Cannot import SBML model into VCell.", Category.INCONSISTENT_UNIT, e);
    }
    try {
        Geometry geometry = new Geometry(BioModelChildSummary.COMPARTMENTAL_GEO_STR, 0);
        vcBioModel = new BioModel(null, modelUnitSystem);
        SimulationContext simulationContext = new SimulationContext(vcBioModel.getModel(), geometry, null, null, Application.NETWORK_DETERMINISTIC);
        vcBioModel.addSimulationContext(simulationContext);
        simulationContext.setName(vcBioModel.getSimulationContext(0).getModel().getName());
    // vcBioModel.getSimulationContext(0).setName(vcBioModel.getSimulationContext(0).getModel().getName()+"_"+vcBioModel.getSimulationContext(0).getGeometry().getName());
    } catch (Exception e) {
        // PropertyVetoException
        e.printStackTrace(System.out);
        throw new SBMLImportException("Could not create simulation context corresponding to the input SBML model.\n", e);
    }
    try {
        String biomodelName = sbmlModel.getName();
        if ((biomodelName == null) || biomodelName.trim().equals("")) {
            biomodelName = sbmlModel.getId();
        }
        if ((biomodelName == null) || biomodelName.trim().equals("")) {
            biomodelName = "newBioModel";
        }
        vcBioModel.setName(biomodelName);
        sbmlAnnotationUtil = new SBMLAnnotationUtil(vcBioModel.getVCMetaData(), vcBioModel, ns);
        sbmlAnnotationUtil.readAnnotation(vcBioModel, sbmlModel);
        sbmlAnnotationUtil.readNotes(vcBioModel, sbmlModel);
        // vcBioModel.getVCMetaData().printRdfPretty();
        // vcBioModel.getVCMetaData().printRdfStatements();
        translateSBMLModel();
        vcBioModel.refreshDependencies();
        ReactionStep[] reax = vcBioModel.getModel().getReactionSteps();
        for (int i = 0; i < reax.length; i++) {
            if (reax[i].getKinetics().getKineticsDescription().isLumped()) {
                DistributedKinetics.toDistributedKinetics((LumpedKinetics) reax[i].getKinetics());
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Could not create Biomodel corresponding to the input SBML model.\n", e);
    }
    Issue[] warnings = localIssueList.toArray(new Issue[localIssueList.size()]);
    if (warnings != null && warnings.length > 0) {
        StringBuffer messageBuffer = new StringBuffer("Issues encountered during SBML Import:\n");
        int issueCount = 0;
        for (int i = 0; i < warnings.length; i++) {
            if (warnings[i].getSeverity() == Issue.Severity.WARNING || warnings[i].getSeverity() == Issue.Severity.INFO) {
                // messageBuffer.append("- " + warnings[i].getMessage() + " (" + warnings[i].getCategory() + ", " + warnings[i].getSeverity().name() + ")\n");
                messageBuffer.append("- " + warnings[i].getMessage() + "\n");
                issueCount++;
            }
        }
        if (issueCount > 0) {
            try {
                logger.sendMessage(VCLogger.Priority.MediumPriority, VCLogger.ErrorType.OverallWarning, messageBuffer.toString());
            } catch (Exception e) {
                e.printStackTrace(System.out);
            }
        }
    }
    // if called from GUI application convert if VCell origin, otherwise ask user
    if (isFromVCell) {
        ModelUnitSystem vcUnitSystem = ModelUnitSystem.createDefaultVCModelUnitSystem();
        try {
            BioModel convertedBioModel = ModelUnitConverter.createBioModelWithNewUnitSystem(vcBioModel, vcUnitSystem);
            return convertedBioModel;
        } catch (ExpressionException | XmlParseException e) {
            // TODO maybe alert user? for now fail silently...
            e.printStackTrace();
            return vcBioModel;
        }
    }
    return vcBioModel;
}