EDIT

/**

* Copyright (C) 2015 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.specimen.abcd206.in;

import java.io.InputStream;

import java.net.URI;

import java.util.Date;

import java.util.List;

import javax.xml.parsers.DocumentBuilder;

import javax.xml.parsers.DocumentBuilderFactory;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

import org.w3c.dom.Document;

import org.w3c.dom.Element;

import org.w3c.dom.Node;

import org.w3c.dom.NodeList;

import eu.etaxonomy.cdm.api.application.ICdmRepository;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

/**

 * @author pplitzner

 \* @since 16.06.2015

 *

 */

public class AbcdParseUtility {

    private static final Logger logger = Logger.getLogger(AbcdParseUtility.class);

    public static URI parseFirstUri(NodeList nodeList, SpecimenImportReport report){

        URI uri = null;

        String textContent = parseFirstTextContent(nodeList);

        if(textContent!=null){

            try {

                uri = URI.create(textContent);

            } catch (IllegalArgumentException e) {

                if(report!=null){

                    report.addException("Exception during URI parsing!", e);

                }

            }

        }

        return uri;

    }

    public static String parseFirstTextContent(NodeList nodeList){

        return parseFirstTextContent(nodeList, true);

    }

    public static String parseFirstTextContent(NodeList nodeList, boolean cleanUpWhiteSpaces){

        String string = null;

        if(nodeList!=null && nodeList.getLength()>0){

            string = nodeList.item(0).getTextContent();

            if(cleanUpWhiteSpaces){

                string = string.replace("\n", "").replaceAll("( )+", " ").trim();

            }

        }

        return string;

    }

    public static Double parseFirstDouble(NodeList nodeList, SpecimenImportReport report){

        if(nodeList.getLength()>0){

            return parseDouble(nodeList.item(0), report);

        }

        return null;

    }

    public static Double parseDouble(Node node, SpecimenImportReport report){

        String message = "Could not parse double value for node " + node.getNodeName();

        Double doubleValue = null;

        try{

            String textContent = node.getTextContent();

            //remove 1000 dots

            textContent = textContent.replace(".","");

            //convert commmas

            textContent = textContent.replace(",",".");

            if (!CdmUtils.isBlank(textContent)){

                doubleValue = Double.parseDouble(textContent);

            }

        } catch (NullPointerException npe){

            logger.error(message, npe);

            if(report!=null){

                report.addException(message, npe);

            }

        } catch (NumberFormatException nfe){

            logger.error(message, nfe);

            if(report!=null){

                report.addException(message, nfe);

            }

        }

        return doubleValue;

    }

    public static DateTime parseFirstDateTime(NodeList nodeList) {

        DateTime dateTime = null;

        String textContent = parseFirstTextContent(nodeList);

        if(textContent!=null){

            dateTime = DateTime.parse(textContent);

        }

        return dateTime;

    }

    public static Date parseFirstDate(NodeList nodeList) {

        Date date = null;

        DateTime dateTime = parseFirstDateTime(nodeList);

        if(dateTime!=null){

            date = dateTime.toDate();

        }

        return date;

    }

    public static Reference parseFirstReference(NodeList referenceNodeList, ICdmRepository cdmAppController){

        String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceNodeList);

        //check if reference already exists

        List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitle(Reference.class, referenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();

        Reference reference;

        if(matchingReferences.size()==1){

            reference = matchingReferences.iterator().next();

        }

        else{

            reference = ReferenceFactory.newGeneric();

            reference.setTitle(referenceCitation);

            cdmAppController.getReferenceService().saveOrUpdate(reference);

        }

        return reference;

    }

    /**

     * Return the wrapper with the list of root nodes for an ABCD XML file

     * @param fileName: the file's location

     * @return a wrapper with a list of root nodes ("Unit")

     */

    public static UnitAssociationWrapper parseUnitsNodeList(InputStream inputStream, SpecimenImportReport report) {

        UnitAssociationWrapper unitAssociationWrapper = new UnitAssociationWrapper();

        NodeList unitList = null;

        try {

            DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();

            DocumentBuilder builder = factory.newDocumentBuilder();

            Document document = builder.parse(inputStream);

            Element root = document.getDocumentElement();

            unitList = root.getElementsByTagName("Unit");

            if (unitList.getLength()>0) {

                unitAssociationWrapper.setPrefix("");

                unitAssociationWrapper.setAssociatedUnits(unitList);

                return unitAssociationWrapper;

            }

            unitList = root.getElementsByTagName("abcd:Unit");

            if (unitList.getLength()>0) {

                unitAssociationWrapper.setPrefix("abcd:");

                unitAssociationWrapper.setAssociatedUnits(unitList);

                return unitAssociationWrapper;

            }

            unitList = root.getElementsByTagName("abcd21:Unit");

            if (unitList.getLength()>0) {

                unitAssociationWrapper.setPrefix("abcd21:");

                unitAssociationWrapper.setAssociatedUnits(unitList);

            }

        } catch (Exception e) {

            logger.warn(e);

            if(report!=null){

                report.addException("Exception during parsing of nodeList!", e);

            }

        }

        return unitAssociationWrapper;

    }

}