SiLeBAT/FSK-Lab

/*******************************************************************************
 * Copyright (c) 2015 Federal Institute for Risk Assessment (BfR), Germany
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Department Biological Safety - BfR
 *******************************************************************************/
package de.bund.bfr.knime.pmm.sbmlwriter;

import java.io.ByteArrayOutputStream;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.xml.stream.XMLStreamException;

import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLReader;
import org.sbml.jsbml.SBMLWriter;
import org.sbml.jsbml.Unit;
import org.sbml.jsbml.UnitDefinition;
import org.sbml.jsbml.xml.XMLAttributes;
import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.XMLTriple;

public class SBMLUtilities {

    public static String toXml(UnitDefinition unit) {
        SBMLDocument doc = new SBMLDocument(unit.getLevel(), unit.getVersion());
        Model model = doc.createModel("ID");

        model.addUnitDefinition(unit);

        ByteArrayOutputStream out = new ByteArrayOutputStream();

        try {
            SBMLWriter.write(doc, out, "test", "1.0", ' ', (short) 0);

            String xml = out.toString(StandardCharsets.UTF_8.name());
            String from = "<listOfUnitDefinitions>";
            String to = "</listOfUnitDefinitions>";

            return xml.substring(xml.indexOf(from) + from.length(),
                    xml.indexOf(to)).replace("\n", "");
        } catch (SBMLException e) {
            e.printStackTrace();
        } catch (XMLStreamException e) {
            e.printStackTrace();
        } catch (UnsupportedEncodingException e) {
            e.printStackTrace();
        }

        return null;
    }

    public static UnitDefinition fromXml(String xml) {
        String preXml = "<?xml version='1.0' encoding='UTF-8' standalone='no'?>"
                + "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" level=\"2\" version=\"4\">"
                + "<model id=\"ID\">" + "<listOfUnitDefinitions>";
        String postXml = "</listOfUnitDefinitions>" + "</model>" + "</sbml>";

        try {
            UnitDefinition def = SBMLReader.read(preXml + xml + postXml)
                    .getModel().getUnitDefinition(0);

            Matcher m = Pattern.compile("name=\"\\w+\"").matcher(xml);

            if (m.find()) {
                String transform = m.group().replace("name=", "")
                        .replace("\"", "");

                def.setAnnotation(createTransformationAnnotation(transform));
            }

            return def;
        } catch (XMLStreamException e) {
            e.printStackTrace();
        }

        return null;
    }

    public static UnitDefinition addUnitToModel(Model model, UnitDefinition unit) {
        UnitDefinition u = model.createUnitDefinition(unit.getId());

        for (int i = 0; i < unit.getNumUnits(); i++) {
            u.addUnit(new Unit(unit.getUnit(i)));
        }

        u.setAnnotation(unit.getAnnotation());

        return u;
    }

    public static Unit.Kind simplify(UnitDefinition unit) {
        unit = unit.clone().simplify();

        if (unit.isUnitKind()) {
            Unit u = unit.getUnit(0);

            if (u.getScale() == 0 && u.getExponent() == 1
                    && u.getMultiplier() == 1) {
                return unit.getUnit(0).getKind();
            }
        }

        return null;
    }

    public static Annotation createTransformationAnnotation(String name) {
        Annotation annotation = new Annotation();
        XMLAttributes attributes = new XMLAttributes();

        attributes.add("name", name);
        attributes
                .add("xmlns",
                        "http://sourceforge.net/projects/microbialmodelingexchange/files/Units");
        annotation.setNonRDFAnnotation(new XMLNode(new XMLTriple(
                "transformation", null, null), attributes));

        return annotation;
    }
}