de.bund.bfr.knime.pmm.extendedtable.Model2Metadata.java Source code

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Here is the source code for de.bund.bfr.knime.pmm.extendedtable.Model2Metadata.java

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/*******************************************************************************
 * 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.extendedtable;

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 de.bund.bfr.knime.pmm.extendedtable.items.EMLiteratureItem;
import de.bund.bfr.knime.pmm.extendedtable.items.MLiteratureItem;
import de.bund.bfr.knime.pmm.extendedtable.items.Model2AgentXml;
import de.bund.bfr.knime.pmm.extendedtable.items.Model2MatrixXml;

public class Model2Metadata {

    private static final String ELEMENT_PMMDOC = "PmmDoc";

    private Model2AgentXml agentXml;
    private Model2MatrixXml matrixXml;
    private List<MLiteratureItem> modelLiteratureItems;
    private List<EMLiteratureItem> estimatedModelLiteratureItems;
    private String warning;

    public Model2Metadata() {
        agentXml = null;
        matrixXml = null;
        modelLiteratureItems = new ArrayList<>();
        estimatedModelLiteratureItems = new ArrayList<>();
        warning = "";
    }

    public Model2Metadata(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) {

        Element agentElement = rootElement.getChild(Model2AgentXml.ELEMENT_AGENT);
        if (agentElement != null) {
            agentXml = new Model2AgentXml(agentElement);
        }

        Element matrixElement = rootElement.getChild(Model2MatrixXml.ELEMENT_MATRIX);
        if (matrixElement != null) {
            matrixXml = new Model2MatrixXml(matrixElement);
        }

        for (Element literatureElement : rootElement.getChildren(MLiteratureItem.ELEMENT_LITERATURE)) {
            modelLiteratureItems.add(new MLiteratureItem(literatureElement));
        }

        for (Element literatureElement : rootElement.getChildren(EMLiteratureItem.ELEMENT_LITERATURE)) {
            estimatedModelLiteratureItems.add(new EMLiteratureItem(literatureElement));
        }
    }

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

    public String getWarning() {
        return warning;
    }

    public void setAgentXml(Model2AgentXml agentXml) {
        this.agentXml = agentXml;
    }

    public void clearAgentXml() {
        this.agentXml = null;
    }

    public void setMatrixXml(Model2MatrixXml matrixXml) {
        this.matrixXml = matrixXml;
    }

    public void clearMatrixXml() {
        this.matrixXml = null;
    }

    public void addLiteratureItem(MLiteratureItem literatureItem) {
        modelLiteratureItems.add(literatureItem);
    }

    public void removeLiteratureItem(MLiteratureItem literatureItem) {
        modelLiteratureItems.remove(literatureItem);
    }

    public void addLiteratureItem(EMLiteratureItem literatureItem) {
        estimatedModelLiteratureItems.add(literatureItem);
    }

    public void removeLiteratureItem(EMLiteratureItem literatureItem) {
        estimatedModelLiteratureItems.remove(literatureItem);
    }

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

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

        if (agentXml != null) {
            rootElement.addContent(agentXml.toXmlElement());
        }
        if (matrixXml != null) {
            rootElement.addContent(matrixXml.toXmlElement());
        }
        for (MLiteratureItem literatureItem : modelLiteratureItems) {
            rootElement.addContent(literatureItem.toXmlElement());
        }
        for (EMLiteratureItem literatureItem : estimatedModelLiteratureItems) {
            rootElement.addContent(literatureItem.toXmlElement());
        }

        return doc;
    }
}