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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.reference.endnote.in;
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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.ArrayList;
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import java.util.Arrays;
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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.Content;
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import org.jdom.Element;
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import org.jdom.Namespace;
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import org.jdom.Text;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.ResultWrapper;
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import eu.etaxonomy.cdm.common.XmlHelp;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.CdmIoBase;
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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.io.tcsrdf.CdmSingleAttributeXmlMapperBase;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.reference.IGeneric;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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/**
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* @author a.mueller
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* @created 04.08.2008
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* @version 1.0
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*/
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public abstract class EndNoteImportBase extends CdmImportBase<EndnoteImportConfigurator, EndnoteImportState> {
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private static final Logger logger = Logger.getLogger(EndNoteImportBase.class);
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protected static Namespace nsTcom = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/Common#");
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protected static Namespace nsTn = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonName#");
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protected static Namespace nsTgeo = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/GeographicRegion#");
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protected static Namespace nsTc = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/TaxonConcept#");
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protected static Namespace nsTpub = Namespace.getNamespace("http://rs.tdwg.org/ontology/voc/PublicationCitation#");
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protected static Namespace nsTpalm = Namespace.getNamespace("http://wp5.e-taxonomy.eu/import/palmae/common");
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ReferenceFactory refFactory = ReferenceFactory.newInstance();
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protected abstract boolean doInvoke(EndnoteImportState state);
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// /* (non-Javadoc)
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// * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
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// */
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// @Override
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// protected boolean doInvoke(IImportConfigurator config,
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// Map<String, MapWrapper<? extends CdmBase>> stores){
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// TcsXmlImportState state = ((TcsXmlImportConfigurator)config).getState();
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// state.setConfig((TcsXmlImportConfigurator)config);
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// return doInvoke(state);
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// }
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protected boolean makeStandardMapper(Element parentElement, CdmBase ref, Set<String> omitAttributes, CdmSingleAttributeXmlMapperBase[] classMappers){
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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 (CdmSingleAttributeXmlMapperBase mapper : classMappers){
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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(CdmSingleAttributeXmlMapperBase mapper, Element parentElement){
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String sourceAttribute = mapper.getSourceAttribute();
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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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protected boolean checkAdditionalContents(Element parentElement, CdmSingleAttributeXmlMapperBase[] classMappers, CdmSingleAttributeXmlMapperBase[] operationalMappers, CdmSingleAttributeXmlMapperBase[] unclearMappers){
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List<Content> additionalContentList = new ArrayList<Content>();
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List<Content> contentList = parentElement.getContent();
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List<CdmSingleAttributeXmlMapperBase> mapperList = new ArrayList<CdmSingleAttributeXmlMapperBase>();
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mapperList.addAll(Arrays.asList(classMappers));
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mapperList.addAll(Arrays.asList(operationalMappers));
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mapperList.addAll(Arrays.asList(unclearMappers));
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for(Content content: contentList){
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boolean contentExists = false;
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if (content instanceof Element){
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for (CdmSingleAttributeXmlMapperBase mapper : mapperList){
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if (mapper.mapsSource(content, parentElement)){
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contentExists = true;
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break;
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}
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}
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}else if (content instanceof Text){
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//empty Text
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if (((Text)content).getTextNormalize().equals("")){
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contentExists = true;
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}else{
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//
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}
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}
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if (contentExists == false){
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additionalContentList.add(content);
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}
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}
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for (Content additionalContent : additionalContentList){
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logger.warn("Additional content: " + additionalContent);
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}
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return (additionalContentList.size() == 0);
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}
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protected Element getXmlElement(EndnoteImportConfigurator tcsConfig){
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Element root = tcsConfig.getSourceRoot();
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if (! "xml".equals(root.getName())){
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logger.error("Root element is not 'xml'");
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return null;
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}
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if (tcsConfig.getEndnoteNamespace() == null){
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logger.error("No namespace defined for tcs");
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return null;
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}
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if (! tcsConfig.getEndnoteNamespace().equals(root.getNamespace())){
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logger.error("Wrong namespace for element 'xml'");
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return null;
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}
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//TODO prevent multiple elements
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return root;
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}
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// static public boolean checkFirstTwoFunctionElements(List<Object> objList){
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// if (! (objList.get(0) instanceof TcsXmlImportConfigurator)){
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// logger.error("first method object has wrong type. Must be " + TcsXmlImportConfigurator.class.getSimpleName() + " but is " + (objList.get(0) == null ? "null": objList.get(0).getClass().getSimpleName()));
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// return false;
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// }
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// if (! (objList.get(1) == null) && ! (objList.get(1) instanceof Element)){
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// logger.error("first method object has wrong type. Must be " + Element.class.getSimpleName() + " but is " + (objList.get(1) == null ? "null": objList.get(1).getClass().getSimpleName()));
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// return false;
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// }
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// return true;
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// }
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protected boolean testAdditionalElements(Element parentElement, List<String> excludeList){
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boolean result = true;
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List<Element> list = parentElement.getChildren();
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for (Element element : list){
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if (! excludeList.contains(element.getName())){
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logger.warn("Unknown element (" + element.getName() + ") in parent element (" + parentElement.getName() + ")");
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result = false;
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}
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}
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return result;
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}
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protected <T extends IdentifiableEntity> T makeReferenceType(Element element, ReferenceType refType, MapWrapper<? extends T> objectMap, ResultWrapper<Boolean> success){
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T result = null;
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String linkType = element.getAttributeValue("linkType");
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String ref = element.getAttributeValue("ref");
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if(ref == null && linkType == null){
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result = (T) refFactory.newReference(refType);
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if (result != null){
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String title = element.getTextNormalize();
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result.setTitleCache(title, true);
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}
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}else if (linkType == null || linkType.equals("local")){
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//TODO
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result = objectMap.get(ref);
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if (result == null){
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logger.warn("Object (ref = " + ref + ")could not be found in WrapperMap");
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}
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}else if(linkType.equals("external")){
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logger.warn("External link types not yet implemented");
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}else if(linkType.equals("other")){
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logger.warn("Other link types not yet implemented");
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}else{
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logger.warn("Unknown link type or missing ref");
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}
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if (result == null){
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success.setValue(false);
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}
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return result;
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}
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protected ReferenceBase makeAccordingTo(Element elAccordingTo, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
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ReferenceBase result = null;
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if (elAccordingTo != null){
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String childName = "AccordingToDetailed";
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boolean obligatory = false;
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Element elAccordingToDetailed = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
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childName = "Simple";
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obligatory = true;
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Element elSimple = XmlHelp.getSingleChildElement(success, elAccordingTo, childName, elAccordingTo.getNamespace(), obligatory);
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if (elAccordingToDetailed != null){
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result = makeAccordingToDetailed(elAccordingToDetailed, referenceMap, success);
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}else{
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result = refFactory.newGeneric();
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String title = elSimple.getTextNormalize();
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result.setTitleCache(title, true);
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}
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}
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return result;
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}
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private ReferenceBase makeAccordingToDetailed(Element elAccordingToDetailed, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
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ReferenceBase result = null;
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Namespace tcsNamespace = elAccordingToDetailed.getNamespace();
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if (elAccordingToDetailed != null){
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//AuthorTeam
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String childName = "AuthorTeam";
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boolean obligatory = false;
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Element elAuthorTeam = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
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makeAccordingToAuthorTeam(elAuthorTeam, success);
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//PublishedIn
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childName = "PublishedIn";
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obligatory = false;
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Element elPublishedIn = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
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result = makeReferenceType(elPublishedIn, ReferenceType.Generic, referenceMap, success);
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//MicroReference
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childName = "MicroReference";
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obligatory = false;
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Element elMicroReference = XmlHelp.getSingleChildElement(success, elAccordingToDetailed, childName, tcsNamespace, obligatory);
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String microReference = elMicroReference.getTextNormalize();
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if (CdmUtils.Nz(microReference).equals("")){
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//TODO
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logger.warn("MicroReference not yet implemented for AccordingToDetailed");
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}
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}
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return result;
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}
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private Team makeAccordingToAuthorTeam(Element elAuthorTeam, ResultWrapper<Boolean> succes){
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Team result = null;
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if (elAuthorTeam != null){
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//TODO
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logger.warn("AuthorTeam not yet implemented for AccordingToDetailed");
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}
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return result;
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}
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}
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