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/**
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* Copyright (C) 2007 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.tcsrdf;
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import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
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import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.XmlHelp;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.reference.Article;
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import eu.etaxonomy.cdm.model.reference.Book;
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import eu.etaxonomy.cdm.model.reference.BookSection;
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import eu.etaxonomy.cdm.model.reference.Generic;
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import eu.etaxonomy.cdm.model.reference.Journal;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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* @created 29.05.2008
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* @version 1.0
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*/
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@Component
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public class TcsRdfReferenceImport extends TcsRdfImportBase implements ICdmIO<IImportConfigurator> {
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private static final Logger logger = Logger.getLogger(TcsRdfReferenceImport.class);
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private static int modCount = 1000;
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public TcsRdfReferenceImport(){
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super();
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}
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@Override
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public boolean doCheck(IImportConfigurator config){
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boolean result = true;
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result &= checkArticlesWithoutJournal(config);
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//result &= checkPartOfJournal(config);
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return result;
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}
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private static boolean checkArticlesWithoutJournal(IImportConfigurator bmiConfig){
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try {
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boolean result = true;
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//TODO
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// result = firstRow = false;
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// }
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//
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return result;
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} catch (Exception e) {
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e.printStackTrace();
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return false;
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}
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}
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protected static CdmIoXmlMapperBase[] standardMappers = new CdmIoXmlMapperBase[]{
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//new CdmTextElementMapper("edition", "edition"),
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new CdmTextElementMapper("volume", "volume"),
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new CdmTextElementMapper("placePublished", "placePublished"),
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new CdmTextElementMapper("publisher", "publisher"),
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//new CdmTextElementMapper("isbn", "isbn"),
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new CdmTextElementMapper("pages", "pages"),
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//new CdmTextElementMapper("series", "series"),
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//new CdmTextElementMapper("issn", "issn"),
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//new CdmTextElementMapper("url", "uri")
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};
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protected static CdmIoXmlMapperBase[] operationalMappers = new CdmIoXmlMapperBase[]{
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new CdmUnclearMapper("year")
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, new CdmUnclearMapper("title")
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, new CdmUnclearMapper("shortTitle")
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, new CdmUnclearMapper("publicationType")
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, new CdmUnclearMapper("parentPublication")
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, new CdmUnclearMapper("authorship")
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};
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// protected static String[] createdAndNotesAttributes = new String[]{
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// "created_When", "updated_When", "created_Who", "updated_Who", "notes"
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// };
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protected static CdmIoXmlMapperBase[] unclearMappers = new CdmIoXmlMapperBase[]{
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};
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private boolean makeStandardMapper(Element parentElement, StrictReferenceBase ref, Set<String> omitAttributes){
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if (omitAttributes == null){
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omitAttributes = new HashSet<String>();
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}
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boolean result = true;
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for (CdmIoXmlMapperBase mapper : standardMappers){
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Object value = getValue(mapper, parentElement);
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//write to destination
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if (value != null){
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String destinationAttribute = mapper.getDestinationAttribute();
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if (! omitAttributes.contains(destinationAttribute)){
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result &= ImportHelper.addValue(value, ref, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
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}
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}
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}
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return true;
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}
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private Object getValue(CdmIoXmlMapperBase mapper, Element parentElement){
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String sourceAttribute = mapper.getSourceAttribute().toLowerCase();
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Namespace sourceNamespace = mapper.getSourceNamespace(parentElement);
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Element child = parentElement.getChild(sourceAttribute, sourceNamespace);
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if (child == null){
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return null;
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}
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if (child.getContentSize() > 1){
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logger.warn("Element is not String");
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}
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Object value = child.getTextTrim();
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return value;
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}
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@Override
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public boolean doInvoke(IImportConfigurator config,
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Map<String, MapWrapper<? extends CdmBase>> stores){
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MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
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MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_STORE);
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TcsRdfImportConfigurator tcsConfig = (TcsRdfImportConfigurator)config;
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Element root = tcsConfig.getSourceRoot();
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logger.info("start makeReferences ...");
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String tcsElementName;
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Namespace tcsNamespace;
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boolean success = true;
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Namespace rdfNamespace = tcsConfig.getRdfNamespace();
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String prefix = "tpub";
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Namespace publicationNamespace = tcsConfig.getPublicationNamespace();
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String idNamespace = "PublicationCitation";
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tcsElementName = "PublicationCitation";
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tcsNamespace = publicationNamespace;
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List<Element> elPublicationCitations = root.getChildren(tcsElementName, tcsNamespace);
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int nomRefCount = 0;
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int biblioRefsCount = 0;
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int i = 0;
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//for each taxonName
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for (Element elPublicationCitation : elPublicationCitations){
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if ((++i % modCount) == 0){ logger.info("references handled: " + (i-1));}
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//create TaxonName element
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String strAbout = elPublicationCitation.getAttributeValue("about", rdfNamespace);
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tcsElementName = "publicationType";
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tcsNamespace = publicationNamespace;
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String strPubType = XmlHelp.getChildAttributeValue(elPublicationCitation, tcsElementName, tcsNamespace, "resource", rdfNamespace);
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try {
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StrictReferenceBase ref = TcsRdfTransformer.pubTypeStr2PubType(strPubType);
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if (ref==null){
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ref = Generic.NewInstance();
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}
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Set<String> omitAttributes = null;
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makeStandardMapper(elPublicationCitation, ref, omitAttributes);
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tcsElementName = "authorship";
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tcsNamespace = publicationNamespace;
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String strAuthorship = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
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//TODO
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TeamOrPersonBase authorTeam = Team.NewInstance();
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authorTeam.setTitleCache(strAuthorship);
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ref.setAuthorTeam(authorTeam);
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tcsElementName = "year";
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tcsNamespace = publicationNamespace;
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String strYear = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
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TimePeriod datePublished = ImportHelper.getDatePublished(strYear);
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ref.setDatePublished(datePublished);
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//Reference
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//TODO
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tcsElementName = "parentPublication";
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tcsNamespace = publicationNamespace;
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String strParent = XmlHelp.getChildAttributeValue(elPublicationCitation, tcsElementName, tcsNamespace, "resource", rdfNamespace);
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ReferenceBase parent = referenceMap.get(strParent);
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if (parent != null){
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if ((ref instanceof Article) && (parent instanceof Journal)){
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((Article)ref).setInJournal((Journal)parent);
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}else if ((ref instanceof BookSection) && (parent instanceof Book)){
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((BookSection)ref).setInBook((Book)parent);
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}else{
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logger.warn("parent type (parent: " + parent.getClass().getSimpleName() +", child("+strAbout+"): " + ref.getClass().getSimpleName() + ")not yet implemented");
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//ref.setParent(parent);
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}
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}
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//FIXME
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//nomRef and reference
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tcsElementName = "shortTitle";
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tcsNamespace = publicationNamespace;
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boolean nomRefExists = false;
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String strShortTitle = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
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if (! CdmUtils.Nz(strShortTitle).trim().equals("")){
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ref.setTitle(strShortTitle);
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ImportHelper.setOriginalSource(ref, config.getSourceReference(), strAbout, idNamespace);
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nomRefMap.put(strAbout, ref);
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nomRefCount++;
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nomRefExists = true;
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}
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tcsElementName = "title";
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tcsNamespace = publicationNamespace;
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String strTitle = elPublicationCitation.getChildText(tcsElementName, tcsNamespace);
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tcsNamespace = publicationNamespace;
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if (! CdmUtils.Nz(strTitle).trim().equals("") || nomRefExists == false){
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//TODO
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StrictReferenceBase biblioRef = (StrictReferenceBase)ref.clone();
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biblioRef.setTitle(strTitle);
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ImportHelper.setOriginalSource(ref, config.getSourceReference(), strAbout, idNamespace);
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referenceMap.put(strAbout, biblioRef);
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biblioRefsCount++;
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}
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checkAdditionalContents(elPublicationCitation, standardMappers, operationalMappers, unclearMappers);
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//ImportHelper.setOriginalSource(nameBase, tcsConfig.getSourceReference(), nameId);
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} catch (UnknownCdmTypeException e) {
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//FIXME
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logger.warn("Name with id " + strAbout + " has unknown type " + strPubType + " and could not be saved.");
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success = false;
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}
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}
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//change conceptRef uuid
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ReferenceBase sec = referenceMap.get(config.getSourceSecId());
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if (sec == null){
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sec = nomRefMap.get(config.getSourceSecId());
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}
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if (sec != null){
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sec.setUuid(config.getSecUuid());
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logger.info("concept reference uuid changed to: " + config.getSecUuid());
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}
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//save and store in map
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logger.info("Save nomenclatural references (" + nomRefCount + ")");
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getReferenceService().saveReferenceAll(nomRefMap.objects());
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logger.info("Save bibliographical references (" + biblioRefsCount +")");
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getReferenceService().saveReferenceAll(referenceMap.objects());
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//referenceService.saveReferenceAll(referenceMap.objects());
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logger.info("end makeReferences ...");
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return success;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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protected boolean isIgnore(IImportConfigurator config){
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return (config.getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
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}
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}
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