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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.redlist.bfnXml;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.UUID;
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import javax.management.ObjectInstance;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.hibernate.id.UUIDGenerator;
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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 org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.IDescriptionService;
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import eu.etaxonomy.cdm.api.service.IFeatureNodeService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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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.ICdmIO;
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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.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.VocabularyEnum;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.persistence.dao.description.IFeatureDao;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
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/**
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*
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* @author a.oppermann
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* @date 04.07.2013
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*
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*/
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@Component
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public class BfnXmlImportFeature extends BfnXmlImportBase implements ICdmIO<BfnXmlImportState> {
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private static final Logger logger = Logger.getLogger(BfnXmlImportFeature.class);
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public BfnXmlImportFeature(){
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super();
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}
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@Override
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public boolean doCheck(BfnXmlImportState state){
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boolean result = true;
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//TODO needs to be implemented
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return result;
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}
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@Override
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@SuppressWarnings({ "unchecked", "rawtypes" })
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public void doInvoke(BfnXmlImportState state){
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IVocabularyService vocabularyService = getVocabularyService();
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logger.warn("start create Features in CDM...");
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ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
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String childName;
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boolean obligatory;
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BfnXmlImportConfigurator config = state.getConfig();
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Element elDataSet = getDataSetElement(config);
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Namespace bfnNamespace = config.getBfnXmlNamespace();
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List contentXML = elDataSet.getContent();
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Element currentElement = null;
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for(Object object:contentXML){
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if(object instanceof Element){
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currentElement = (Element)object;
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if(currentElement.getName().equalsIgnoreCase("ROTELISTEDATEN")){
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TransactionStatus tx = startTransaction();
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childName = "EIGENSCHAFTEN";
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obligatory = false;
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Element elFeatureNames = XmlHelp.getSingleChildElement(success, currentElement, childName, bfnNamespace, obligatory);
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String bfnElementName = "EIGENSCHAFT";
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List<Element> elFeatureList = (List<Element>)elFeatureNames.getChildren(bfnElementName, bfnNamespace);
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List<Feature> featureList = new ArrayList<Feature>();
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//for each taxonName
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for (Element elFeature : elFeatureList){
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if(elFeature.getAttributeValue("standardname", bfnNamespace).equalsIgnoreCase("RL Kat.")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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String featureLabel = "Kat. +/-";
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase(featureLabel)){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("aktuelle Bestandsstituation")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("langfristiger Bestandstrend")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("kurzfristiger Bestandstrend")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Risikofaktoren")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Verantwortlichkeit")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("alte RL- Kat.")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Neobiota")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Eindeutiger Code")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Kommentar zur Taxonomie")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Kommentar zur Gefährdung")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Sonderfälle")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Letzter Nachweis")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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if(elFeature.getAttributeValue("standardname").equalsIgnoreCase("Weitere Kommentare")){
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makeFeature(vocabularyService, featureList,success, obligatory, bfnNamespace,elFeature, state);
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}
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}
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createFeatureTree(featureList);
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commitTransaction(tx);
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logger.info("end create features ...");
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if (!success.getValue()){
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state.setUnsuccessfull();
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}
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return;
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}
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}
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}
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return;
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}
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/**
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* @param featureList
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*/
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private void createFeatureTree(List<Feature> featureList) {
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FeatureTree featureTree = FeatureTree.NewInstance(featureList);
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String featureTreeName = "RedListFeatureTree";
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featureTree.setTitleCache(featureTreeName, true);
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getFeatureTreeService().save(featureTree);
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}
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/**
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*
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* @param vocabularyService
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* @param featureList
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* @param success
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* @param obligatory
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* @param bfnNamespace
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* @param elFeature
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* @param state
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*/
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private void makeFeature(IVocabularyService vocabularyService,
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List<Feature> featureList,
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ResultWrapper<Boolean> success, boolean obligatory,
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Namespace bfnNamespace, Element elFeature, BfnXmlImportState state) {
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String childName;
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String strRlKat = elFeature.getAttributeValue("standardname");
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UUID featureUUID = null;
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try {
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featureUUID = BfnXmlTransformer.getRedlistFeatureUUID(strRlKat);
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} catch (UnknownCdmTypeException e) {
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e.printStackTrace();
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}
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Feature redListCat = getFeature(state, featureUUID, strRlKat, strRlKat, strRlKat, null);
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featureList.add(redListCat);
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childName = "LISTENWERTE";
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Element elListValues = XmlHelp.getSingleChildElement(success, elFeature, childName, bfnNamespace, obligatory);
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if(elListValues != null && !elListValues.getContent().isEmpty()){
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String childElementName = "LWERT";
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createOrUpdateStates(bfnNamespace, elListValues, childElementName, redListCat, state);
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}
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createOrUpdateTermVocabulary(TermType.Feature, vocabularyService, redListCat, "RedList Feature");
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}
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/**
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* @param vocabularyService
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* @param term
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*/
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@SuppressWarnings({ "unchecked", "rawtypes" })
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private TermVocabulary createOrUpdateTermVocabulary(TermType termType, IVocabularyService vocabularyService, DefinedTermBase term, String strTermVocabulary) {
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TermVocabulary termVocabulary = null;
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List<TermVocabulary> vocList = vocabularyService.list(TermVocabulary.class, null, null, null, VOC_CLASSIFICATION_INIT_STRATEGY);
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for(TermVocabulary tv : vocList){
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if(tv.getTitleCache().equalsIgnoreCase(strTermVocabulary)){
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termVocabulary = tv;
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}
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}
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if(termVocabulary == null){
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termVocabulary = TermVocabulary.NewInstance(termType, strTermVocabulary, strTermVocabulary, strTermVocabulary, null);
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}
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termVocabulary.addTerm(term);
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vocabularyService.saveOrUpdate(termVocabulary);
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return termVocabulary;
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}
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/**
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* @param success
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* @param bfnNamespace
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* @param elListValues
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* @param childElementName
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* @param redListCat
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*/
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@SuppressWarnings({ "unchecked", "rawtypes"})
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private void createOrUpdateStates(Namespace bfnNamespace, Element elListValues, String childElementName,
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Feature redListCat, BfnXmlImportState state) {
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List<Element> elListValueList = (List<Element>)elListValues.getChildren(childElementName, bfnNamespace);
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// List<StateData> stateList = new ArrayList<StateData>();
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OrderedTermVocabulary termVocabulary = null;
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for(Element elListValue:elListValueList){
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String listValue = elListValue.getTextNormalize();
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String matchedListValue;
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UUID stateTermUuid = null;
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UUID vocabularyStateUuid = null;
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try {
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vocabularyStateUuid = BfnXmlTransformer.getRedlistVocabularyUUID(redListCat.toString());
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} catch (UnknownCdmTypeException e1) {
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vocabularyStateUuid = UUID.randomUUID();
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logger.info("Element: " + listValue);
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e1.printStackTrace();
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}
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try {
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matchedListValue = BfnXmlTransformer.redListString2RedListCode(listValue);
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} catch (UnknownCdmTypeException e) {
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matchedListValue = listValue;
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logger.info("no matched red list code nor UUID found. \n" + e);
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}
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try {
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stateTermUuid = BfnXmlTransformer.getRedlistStateTermUUID(matchedListValue, redListCat.getTitleCache());
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} catch (UnknownCdmTypeException e) {
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// stateTermUuid = UUID.randomUUID(); //TODO: needs to be fixed for "eindeutiger Code"
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e.printStackTrace();
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}
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String vocName = redListCat.toString()+" States";
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termVocabulary = (OrderedTermVocabulary) getVocabulary(TermType.State, vocabularyStateUuid, vocName, vocName, vocName, null, true, null);
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State stateTerm = getStateTerm(state, stateTermUuid, matchedListValue, matchedListValue, matchedListValue, termVocabulary);
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}
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if(termVocabulary != null){
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redListCat.addSupportedCategoricalEnumeration(termVocabulary);
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getTermService().saveOrUpdate(redListCat);
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}
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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(BfnXmlImportState state){
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return ! state.getConfig().isDoTaxonNames();
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}
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/** Hibernate classification vocabulary initialisation strategy */
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private static final List<String> VOC_CLASSIFICATION_INIT_STRATEGY = Arrays.asList(new String[] {
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"classification.$",
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"classification.rootNodes",
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"childNodes",
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"childNodes.taxon",
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"childNodes.taxon.name",
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"taxonNodes",
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"taxonNodes.taxon",
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"synonymRelations",
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"taxon.*",
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"taxon.sec",
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"taxon.name.*",
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"taxon.synonymRelations",
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"termVocabulary.*",
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"terms"
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});
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}
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