edu.northwestern.bioinformatics.studycalendar.xml.AbstractStudyCalendarXmlSerializer.java Source code

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Here is the source code for edu.northwestern.bioinformatics.studycalendar.xml.AbstractStudyCalendarXmlSerializer.java

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/*L
 * Copyright Northwestern University.
 *
 * Distributed under the OSI-approved BSD 3-Clause License.
 * See http://ncip.github.io/psc/LICENSE.txt for details.
 */

package edu.northwestern.bioinformatics.studycalendar.xml;

import edu.northwestern.bioinformatics.studycalendar.StudyCalendarSystemException;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.DocumentHelper;
import org.dom4j.Element;
import org.dom4j.Namespace;
import org.dom4j.QName;
import org.dom4j.io.OutputFormat;
import org.dom4j.io.SAXReader;
import org.dom4j.io.XMLWriter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.io.InputStream;
import java.io.StringWriter;

/**
 * @author Rhett Sutphin
 * @author John Dzak
 */
public abstract class AbstractStudyCalendarXmlSerializer<R> implements StudyCalendarXmlSerializer<R> {
    protected final Logger log = LoggerFactory.getLogger(getClass());

    public static final String XML_NS = "http://www.w3.org/2000/xmlns/";
    public static final String XSI_NS = "http://www.w3.org/2001/XMLSchema-instance";
    public static final String PSC_NS = "http://bioinformatics.northwestern.edu/ns/psc";
    public static final String SCHEMA_LOCATION = "http://bioinformatics.northwestern.edu/ns/psc/psc.xsd";

    public static final Namespace DEFAULT_NAMESPACE = DocumentHelper.createNamespace("", PSC_NS);
    protected static final OutputFormat OUTPUT_FORMAT = new OutputFormat("  ", true);

    public static final String SCHEMA_NAMESPACE_ATTRIBUTE = "xmlns";
    public static final String SCHEMA_LOCATION_ATTRIBUTE = "schemaLocation";
    public static final String XML_SCHEMA_ATTRIBUTE = "xsi";

    // Attributes
    public static final String ID = "id";
    public static final String NAME = "name";

    public Document createDocument(R root) {
        Document document = DocumentHelper.createDocument();
        Element element = createElement(root);

        configureRootElement(element);

        document.add(element);

        return document;
    }

    protected void configureRootElement(Element element) {
        element.add(DEFAULT_NAMESPACE);
        element.addNamespace(XML_SCHEMA_ATTRIBUTE, XSI_NS).addAttribute("xsi:" + SCHEMA_LOCATION_ATTRIBUTE,
                PSC_NS + ' ' + SCHEMA_LOCATION);
    }

    public String createDocumentString(R root) {
        return createDocumentString(createDocument(root));
    }

    protected String createDocumentString(Document doc) {
        StringWriter capture = new StringWriter();
        try {
            new XMLWriter(capture, OUTPUT_FORMAT).write(doc);
        } catch (IOException e) {
            throw new StudyCalendarSystemException("Unexpected error when serializing XML", e);
        }
        return capture.toString();
    }

    public R readDocument(Document document) {
        return readElement(document.getRootElement());
    }

    public R readDocument(InputStream in) {
        Document document = deserializeDocument(in);
        return readElement(document.getRootElement());
    }

    public abstract Element createElement(R object);

    public abstract R readElement(Element element);

    //// Helper Methods

    protected Document deserializeDocument(InputStream in) {
        Document document;
        try {
            SAXReader saxReader = new SAXReader();
            document = saxReader.read(in);
        } catch (DocumentException de) {
            throw new StudyCalendarXmlParsingException(de);
        }
        return document;
    }

    protected Element element(String elementName) {
        // Using QName is the only way to attach the namespace to the element
        QName qNode = DocumentHelper.createQName(elementName, DEFAULT_NAMESPACE);
        return DocumentHelper.createElement(qNode);
    }
}