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/**
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* Copyright (C) 2015 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.specimen.abcd206.in;
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import java.io.InputStream;
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import java.util.Date;
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import java.util.List;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import org.joda.time.DateTime;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import eu.etaxonomy.cdm.api.application.ICdmRepository;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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/**
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* @author pplitzner
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* @since 16.06.2015
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*/
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public class AbcdParseUtility {
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private static final Logger logger = LogManager.getLogger(AbcdParseUtility.class);
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public static URI parseFirstUri(NodeList nodeList, SpecimenImportReport report){
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URI uri = null;
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String textContent = parseFirstTextContent(nodeList);
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if(textContent!=null){
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try {
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uri = URI.create(textContent);
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} catch (IllegalArgumentException e) {
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if(report!=null){
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report.addException("Exception during URI parsing!", e);
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}
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}
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}
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return uri;
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}
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public static String parseFirstTextContent(NodeList nodeList){
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return parseFirstTextContent(nodeList, true);
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}
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public static String parseFirstTextContent(NodeList nodeList, boolean cleanUpWhiteSpaces){
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String string = null;
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if(nodeList!=null && nodeList.getLength()>0){
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string = nodeList.item(0).getTextContent();
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if(cleanUpWhiteSpaces){
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string = string.replace("\n", "").replaceAll("( )+", " ").trim();
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}
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}
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return string;
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}
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public static Double parseFirstDouble(NodeList nodeList, SpecimenImportReport report){
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if(nodeList.getLength()>0){
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return parseDouble(nodeList.item(0), report);
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}
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return null;
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}
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public static Double parseDouble(Node node, SpecimenImportReport report){
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String message = "Could not parse double value for node " + node.getNodeName();
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Double doubleValue = null;
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try{
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String textContent = node.getTextContent();
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//remove 1000 dots
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textContent = textContent.replace(".","");
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//convert commmas
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textContent = textContent.replace(",",".");
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if (!CdmUtils.isBlank(textContent)){
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doubleValue = Double.parseDouble(textContent);
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}
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} catch (NullPointerException npe){
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logger.error(message, npe);
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if(report!=null){
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report.addException(message, npe);
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}
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} catch (NumberFormatException nfe){
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logger.error(message, nfe);
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if(report!=null){
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report.addException(message, nfe);
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}
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}
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return doubleValue;
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}
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public static DateTime parseFirstDateTime(NodeList nodeList) {
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DateTime dateTime = null;
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String textContent = parseFirstTextContent(nodeList);
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if(textContent!=null){
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dateTime = DateTime.parse(textContent);
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}
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return dateTime;
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}
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public static Date parseFirstDate(NodeList nodeList) {
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Date date = null;
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DateTime dateTime = parseFirstDateTime(nodeList);
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if(dateTime!=null){
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date = dateTime.toDate();
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}
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return date;
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}
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public static Reference parseFirstReference(NodeList referenceNodeList, ICdmRepository cdmAppController){
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String referenceCitation = AbcdParseUtility.parseFirstTextContent(referenceNodeList);
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//check if reference already exists
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List<Reference> matchingReferences = cdmAppController.getReferenceService().findByTitleWithRestrictions(Reference.class, referenceCitation, MatchMode.EXACT, null, null, null, null, null).getRecords();
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Reference reference;
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if(matchingReferences.size()==1){
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reference = matchingReferences.iterator().next();
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}
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else{
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reference = ReferenceFactory.newGeneric();
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reference.setTitle(referenceCitation);
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cdmAppController.getReferenceService().saveOrUpdate(reference);
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}
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return reference;
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}
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/**
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* Return the wrapper with the list of root nodes for an ABCD XML file
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* @param fileName: the file's location
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* @return a wrapper with a list of root nodes ("Unit")
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*/
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public static UnitAssociationWrapper parseUnitsNodeList(InputStream inputStream, SpecimenImportReport report) {
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UnitAssociationWrapper unitAssociationWrapper = new UnitAssociationWrapper();
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NodeList unitList = null;
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try {
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DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
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DocumentBuilder builder = factory.newDocumentBuilder();
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Document document = builder.parse(inputStream);
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Element root = document.getDocumentElement();
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unitList = root.getElementsByTagName("Unit");
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if (unitList.getLength()>0) {
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unitAssociationWrapper.setPrefix("");
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unitAssociationWrapper.setAssociatedUnits(unitList);
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return unitAssociationWrapper;
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}
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unitList = root.getElementsByTagName("abcd:Unit");
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if (unitList.getLength()>0) {
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unitAssociationWrapper.setPrefix("abcd:");
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unitAssociationWrapper.setAssociatedUnits(unitList);
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return unitAssociationWrapper;
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}
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unitList = root.getElementsByTagName("abcd21:Unit");
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if (unitList.getLength()>0) {
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unitAssociationWrapper.setPrefix("abcd21:");
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unitAssociationWrapper.setAssociatedUnits(unitList);
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}
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} catch (Exception e) {
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logger.warn(e);
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if(report!=null){
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report.addException("Exception during parsing of nodeList!", e);
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}
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}
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return unitAssociationWrapper;
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}
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}
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