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.common;

import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;

import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;
import org.jdom2.output.DOMOutputter;
import org.jdom2.output.XMLOutputter;

public class PmmXmlDoc {

    private static final String ELEMENT_PMMDOC = "PmmDoc";

    private List<PmmXmlElementConvertable> elementSet;
    private String warning = "";

    public PmmXmlDoc() {
        elementSet = new ArrayList<>();
    }

    public PmmXmlDoc(PmmXmlElementConvertable rootElement) {
        elementSet = new ArrayList<>();
        elementSet.add(rootElement);
    }

    public PmmXmlDoc(String xmlString) throws IOException, JDOMException {
        this();
        SAXBuilder builder = new SAXBuilder();
        Document doc = builder.build(new StringReader(xmlString));

        Element rootElement = doc.getRootElement();
        parseElement(rootElement);
    }

    private void parseElement(Element rootElement) {
        for (Element el : rootElement.getChildren()) {
            /*
             * if (el instanceof PmmXmlElementConvertable) { elementSet.add(new
             * ParametricModel(el)); }
             */
            switch (el.getName()) {
            case ParametricModel.ELEMENT_PARAMETRICMODEL:
                elementSet.add(new ParametricModel(el));
                break;
            case MiscXml.ELEMENT_MISC:
                elementSet.add(new MiscXml(el));
                break;
            case ParamXml.ELEMENT_PARAM:
                elementSet.add(new ParamXml(el));
                break;
            case IndepXml.ELEMENT_INDEP:
                elementSet.add(new IndepXml(el));
                break;
            case DepXml.ELEMENT_DEPENDENT:
                elementSet.add(new DepXml(el));
                break;
            case TimeSeriesXml.ELEMENT_TIMESERIES:
                elementSet.add(new TimeSeriesXml(el));
                break;
            case MdInfoXml.ELEMENT_MDINFO:
                elementSet.add(new MdInfoXml(el));
                break;
            case LiteratureItem.ELEMENT_LITERATURE:
                elementSet.add(new LiteratureItem(el));
                break;
            case "MLiteratureItem":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.LiteratureItem(el));
                break;
            case "MDLiteratureItem":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.LiteratureItem(el));
                break;
            case "EstimatedModelLiterature":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.LiteratureItem(el));
                break;
            case CatalogModelXml.ELEMENT_CATALOGMODEL:
                elementSet.add(new CatalogModelXml(el));
                break;
            case EstModelXml.ELEMENT_ESTMODEL:
                elementSet.add(new EstModelXml(el));
                break;
            case AgentXml.ELEMENT_AGENT:
                elementSet.add(new AgentXml(el));
                break;
            case "mdAgent":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.AgentXml(el));
                break;
            case "model1Agent":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.AgentXml(el));
                break;
            case "model2Agent":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.AgentXml(el));
                break;
            case MatrixXml.ELEMENT_MATRIX:
                elementSet.add(new MatrixXml(el));
                break;
            case "mdMatrix":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.MatrixXml(el));
                break;
            case "model1Matrix":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.MatrixXml(el));
                break;
            case "model2Matrix":
                elementSet.add(new de.bund.bfr.knime.pmm.extendedtable.items.MatrixXml(el));
                break;
            case PmmTimeSeries.ELEMENT_TIMESERIES:
                elementSet.add(new PmmTimeSeries(el));
                break;
            }
        }
    }

    public void addWarning(String warning) {
        this.warning += warning;
    }

    public String getWarning() {
        return warning;
    }

    public void add(PmmXmlElementConvertable el) {
        elementSet.add(el);
    }

    public void remove(PmmXmlElementConvertable el) {
        elementSet.remove(el);
    }

    public org.w3c.dom.Document getW3C() {
        try {
            Document doc = toXmlDocument();
            return new DOMOutputter().output(doc);
        } catch (JDOMException e) {
            e.printStackTrace();
        }
        return null;
    }

    public Document toXmlDocument() {
        Document doc = new Document();
        Element rootElement = new Element(ELEMENT_PMMDOC);
        doc.setRootElement(rootElement);

        for (PmmXmlElementConvertable element : elementSet) {
            rootElement.addContent(element.toXmlElement());
        }
        return doc;
    }

    public String toXmlString() {
        Document doc = toXmlDocument();
        XMLOutputter xmlo = new XMLOutputter();
        return xmlo.outputString(doc);
    }

    public int size() {
        return elementSet.size();
    }

    public PmmXmlElementConvertable get(int i) {
        if (elementSet.size() > 0)
            return elementSet.get(i);
        else
            return null;
    }

    public void set(int i, PmmXmlElementConvertable el) {
        elementSet.set(i, el);
    }

    public List<PmmXmlElementConvertable> getElementSet() {
        return elementSet;
    }

    public PmmXmlDoc clonePMs() {
        PmmXmlDoc doc = new PmmXmlDoc();
        for (PmmXmlElementConvertable el : this.getElementSet()) {
            if (el instanceof ParametricModel) {
                ParametricModel model = (ParametricModel) el;
                doc.add(model.clone());
            } else
                doc.add(el);
        }
        return doc;
    }

}