SiLeBAT/FSK-Lab

package de.bund.bfr.knime.pmm.common.writer;

import java.util.LinkedList;
import java.util.List;

import javax.xml.stream.XMLStreamException;

import org.sbml.jsbml.Model;
import org.sbml.jsbml.Parameter;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.ext.comp.CompConstants;

import de.bund.bfr.knime.pmm.common.CatalogModelXml;
import de.bund.bfr.knime.pmm.common.DepXml;
import de.bund.bfr.knime.pmm.common.EstModelXml;
import de.bund.bfr.knime.pmm.common.IndepXml;
import de.bund.bfr.knime.pmm.common.LiteratureItem;
import de.bund.bfr.knime.pmm.common.ParamXml;
import de.bund.bfr.knime.pmm.common.PmmXmlDoc;
import de.bund.bfr.knime.pmm.common.PmmXmlElementConvertable;
import de.bund.bfr.knime.pmm.common.generictablemodel.KnimeTuple;
import de.bund.bfr.knime.pmm.common.pmmtablemodel.Model2Schema;
import de.bund.bfr.pmfml.sbml.LimitsConstraint;
import de.bund.bfr.pmfml.sbml.Metadata;
import de.bund.bfr.pmfml.sbml.MetadataAnnotation;
import de.bund.bfr.pmfml.sbml.Model2Annotation;
import de.bund.bfr.pmfml.sbml.ModelRule;
import de.bund.bfr.pmfml.sbml.PMFCoefficient;
import de.bund.bfr.pmfml.sbml.Reference;
import de.bund.bfr.pmfml.sbml.SecDep;
import de.bund.bfr.pmfml.sbml.SecIndep;
import de.bund.bfr.pmfml.sbml.Uncertainties;

public class Model2Parser {

    SBMLDocument sbmlDocument;

    public Model2Parser(KnimeTuple tuple, Metadata metadata, String notes) {

        TableReader.replaceCelsiusAndFahrenheit(tuple);
        TableReader.renameLog(tuple);

        // Retrieve Model2Schema cells
        CatalogModelXml catModel = (CatalogModelXml) tuple.getPmmXml(Model2Schema.ATT_MODELCATALOG).get(0);
        EstModelXml estModel = (EstModelXml) tuple.getPmmXml(Model2Schema.ATT_ESTMODEL).get(0);
        DepXml dep = (DepXml) tuple.getPmmXml(Model2Schema.ATT_DEPENDENT).get(0);
        PmmXmlDoc indepDoc = tuple.getPmmXml(Model2Schema.ATT_INDEPENDENT);
        PmmXmlDoc paramsDoc = tuple.getPmmXml(Model2Schema.ATT_PARAMETER);
        PmmXmlDoc mLitDoc = tuple.getPmmXml(Model2Schema.ATT_MLIT);
        PmmXmlDoc emLitDoc = tuple.getPmmXml(Model2Schema.ATT_EMLIT);
        int globalModelID = tuple.getInt(Model2Schema.ATT_GLOBAL_MODEL_ID);

        // Creates SBMLDocument for the secondary model
        sbmlDocument = new SBMLDocument(TableReader.LEVEL, TableReader.VERSION);

        // Enables Hierarchical Composition package and adds namespaces
        sbmlDocument.enablePackage(CompConstants.shortLabel);
        TableReader.addNamespaces(sbmlDocument);

        // Adds document annotation
        sbmlDocument.setAnnotation(new MetadataAnnotation(metadata).getAnnotation());
        if (notes != null) {
            try {
                sbmlDocument.setNotes(notes);
            } catch (XMLStreamException e) {
                e.printStackTrace();
            }
        }

        // Creates model and names it
        Model model = sbmlDocument.createModel("model_" + dep.name);
        if (estModel.name != null) {
            model.setName(estModel.name);
        }

        // Gets model references
        Reference[] mLits = new Reference[mLitDoc.size()];
        for (int i = 0; i < mLitDoc.size(); i++) {
            mLits[i] = WriterUtils.literatureItem2Reference((LiteratureItem) mLitDoc.get(i));
        }

        // Gets estimated model references
        Reference[] emLits = new Reference[emLitDoc.size()];
        for (int i = 0; i < emLitDoc.size(); i++) {
            emLits[i] = WriterUtils.literatureItem2Reference((LiteratureItem) emLitDoc.get(i));
        }

        // Adds model annotation
        Uncertainties uncertainties = WriterUtils.estModel2Uncertainties(estModel);
        model.setAnnotation(new Model2Annotation(globalModelID, uncertainties, emLits).getAnnotation());

        // Gets independent parameters
        List<IndepXml> indepXmls = new LinkedList<>();
        for (PmmXmlElementConvertable item : indepDoc.getElementSet()) {
            indepXmls.add((IndepXml) item);
        }

        // Gets constant parameters
        List<ParamXml> constXmls = new LinkedList<>();
        for (PmmXmlElementConvertable item : paramsDoc.getElementSet()) {
            constXmls.add((ParamXml) item);
        }

        // Adds dep
        Parameter depParam = new SecDep(dep.name, dep.description, dep.unit).getParam();
        // Adds dep constraint
        LimitsConstraint depLc = new LimitsConstraint(dep.name, dep.min, dep.max);
        if (depLc.getConstraint() != null) {
            model.addConstraint(depLc.getConstraint());
        }
        model.addParameter(depParam);

        // Adds independent parameters
        for (IndepXml indepXml : indepXmls) {
            // Creates SBML parameter
            SecIndep secIndep = new SecIndep(indepXml.name, indepXml.description, indepXml.unit);
            model.addParameter(secIndep.getParam());
            // Adds constraint
            LimitsConstraint lc = new LimitsConstraint(indepXml.name, indepXml.min, indepXml.max);
            if (lc.getConstraint() != null) {
                model.addConstraint(lc.getConstraint());
            }
        }

        // Adds constant parameters
        for (ParamXml paramXml : constXmls) {
            // Creates SBML parameter
            PMFCoefficient coefficient = WriterUtils.paramXml2Coefficient(paramXml);
            model.addParameter(coefficient.getParameter());

            // Adds constraint
            LimitsConstraint lc = new LimitsConstraint(paramXml.name, paramXml.min, paramXml.max);
            if (lc.getConstraint() != null) {
                model.addConstraint(lc.getConstraint());
            }
        }

        // Adds unit definitions
        try {
            TableReader.addUnitDefinitions(model, dep, indepXmls, constXmls);
        } catch (XMLStreamException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }

        // Creates rule of the model and adds it to the rest of rules
        ModelRule rule = WriterUtils.createM2Rule(catModel, mLits);
        model.addRule(rule.getRule());
    }

    public SBMLDocument getDocument() {
        return sbmlDocument;
    }
}