de.bund.bfr.pmfml.sbml.MetadataAnnotation.java Source code

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Here is the source code for de.bund.bfr.pmfml.sbml.MetadataAnnotation.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.pmfml.sbml;

import de.bund.bfr.pmfml.ModelType;
import org.apache.commons.lang3.StringUtils;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.XMLTriple;

public class MetadataAnnotation {

    private static final String METADATA_TAG = "metadata"; // Metadata tag
    private static final String METADATA_NS = "pmf"; // Metadata namespace

    private final static String CREATOR_NS = "dc";
    private final static String CREATOR_TAG = "creator";

    private final static String CREATED_NS = "dcterms";
    private final static String CREATED_TAG = "created";

    private final static String MODIFIED_NS = "dcterms";
    private final static String MODIFIED_TAG = "modified";

    private final static String TYPE_NS = "dc";
    private final static String TYPE_TAG = "type";

    private final static String RIGHTS_NS = "dc";
    private final static String RIGHTS_TAG = "rights";

    private final static String REFERENCE_NS = "dc";
    private final static String REFERENCE_TAG = "source";

    Metadata metadata;
    Annotation annotation;

    // Builds a MetadataAnntotation from a given metadata object.
    public MetadataAnnotation(final Metadata metadata) {

        final XMLTriple pmfTriple = new XMLTriple(METADATA_TAG, "", METADATA_NS);
        final XMLNode pmfNode = new XMLNode(pmfTriple);

        // Builds creator node
        if (metadata.isSetGivenName() || metadata.isSetFamilyName() || metadata.isSetContact()) {

            final String givenName = metadata.isSetGivenName() ? metadata.getGivenName() : "";
            final String familyName = metadata.isSetFamilyName() ? metadata.getFamilyName() : "";
            final String contact = metadata.isSetContact() ? metadata.getContact() : "";

            String creator = givenName + "." + familyName + "." + contact;
            final XMLNode creatorNode = new XMLNode(new XMLTriple(CREATOR_TAG, null, CREATOR_NS));
            creatorNode.addChild(new XMLNode(creator));

            pmfNode.addChild(creatorNode);
        }

        // Builds created date node
        if (metadata.isSetCreatedDate()) {
            final XMLNode createdNode = new XMLNode(new XMLTriple(CREATED_TAG, "", CREATED_NS));
            createdNode.addChild(new XMLNode(metadata.getCreatedDate()));
            pmfNode.addChild(createdNode);
        }

        // Builds modified date node
        if (metadata.isSetModifiedDate()) {
            final XMLNode modifiedNode = new XMLNode(new XMLTriple(MODIFIED_TAG, "", MODIFIED_NS));
            modifiedNode.addChild(new XMLNode(metadata.getModifiedDate()));
            pmfNode.addChild(modifiedNode);
        }

        // Builds type node
        if (metadata.isSetType()) {
            final XMLNode typeNode = new XMLNode(new XMLTriple(TYPE_TAG, "", TYPE_NS));
            typeNode.addChild(new XMLNode(metadata.getType().name()));
            pmfNode.addChild(typeNode);
        }

        // Builds rights node
        if (metadata.isSetRights()) {
            final XMLNode rightsNode = new XMLNode(new XMLTriple(RIGHTS_TAG, "", RIGHTS_NS));
            rightsNode.addChild(new XMLNode(metadata.getRights()));
            pmfNode.addChild(rightsNode);
        }

        // Builds reference node
        if (metadata.isSetReferenceLink()) {
            final XMLNode refNode = new XMLNode(new XMLTriple(REFERENCE_TAG, "", REFERENCE_NS));
            refNode.addChild(new XMLNode(metadata.getReferenceLink()));
            pmfNode.addChild(refNode);
        }

        // Copies metadata
        this.metadata = metadata;

        // Creates annotation
        annotation = new Annotation();
        annotation.setNonRDFAnnotation(pmfNode);
    }

    public MetadataAnnotation(final Annotation annotation) {
        final XMLNode pmfNode = annotation.getNonRDFannotation().getChildElement(METADATA_TAG, "");

        metadata = SBMLFactory.createMetadata();

        final XMLNode creatorNode = pmfNode.getChildElement(CREATOR_TAG, "");
        if (creatorNode != null) {
            final String[] tempStrings = creatorNode.getChild(0).getCharacters().split("\\.", 3);

            metadata.setGivenName(StringUtils.defaultString(tempStrings[0]));
            metadata.setFamilyName(StringUtils.defaultString(tempStrings[1]));
            metadata.setContact(StringUtils.defaultString(tempStrings[2]));
        }

        final XMLNode createdNode = pmfNode.getChildElement(CREATED_TAG, "");
        if (createdNode != null) {
            metadata.setCreatedDate(createdNode.getChild(0).getCharacters());
        }

        final XMLNode modifiedNode = pmfNode.getChildElement(MODIFIED_TAG, "");
        if (modifiedNode != null) {
            metadata.setModifiedDate(modifiedNode.getChild(0).getCharacters());
        }

        final XMLNode typeNode = pmfNode.getChildElement(TYPE_TAG, "");
        if (typeNode != null) {
            final ModelType modelType = ModelType.valueOf(typeNode.getChild(0).getCharacters());
            metadata.setType(modelType);
        }

        final XMLNode rightsNode = pmfNode.getChildElement(RIGHTS_TAG, "");
        if (rightsNode != null) {
            metadata.setRights(rightsNode.getChild(0).getCharacters());
        }

        final XMLNode refNode = pmfNode.getChildElement(REFERENCE_TAG, "");
        if (refNode != null) {
            metadata.setReferenceLink(refNode.getChild(0).getCharacters());
        }

        // Copies annotation
        this.annotation = annotation;
    }

    // Getters
    public Metadata getMetadata() {
        return metadata;
    }

    public Annotation getAnnotation() {
        return annotation;
    }
}