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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.in;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.LinkedHashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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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.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.ITaxonService;
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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.redlist.bfnXml.BfnXmlConstants;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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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.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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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.reference.Reference;
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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.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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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("bfnXmlTaxonNameIO")
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@Component
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public class BfnXmlImportTaxonName extends BfnXmlImportBase {
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private static final Logger logger = Logger.getLogger(BfnXmlImportTaxonName.class);
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private static NomenclaturalCode nomenclaturalCode = null;
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private static int parsingProblemCounter = 0;
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private Map<Integer, Taxon> firstList;
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private Map<Integer, Taxon> secondList;
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public BfnXmlImportTaxonName(){
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super();
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}
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@Override
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@SuppressWarnings({"rawtypes" })
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public void doInvoke(BfnXmlImportState state){
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ITaxonService taxonService = getTaxonService();
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BfnXmlImportConfigurator config = state.getConfig();
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nomenclaturalCode = config.getNomenclaturalCode();
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Element elDataSet = getDataSetElement(config);
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//TODO set Namespace
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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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//import taxon lists
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if(currentElement.getName().equalsIgnoreCase(BfnXmlConstants.EL_ROTELISTEDATEN)){
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TransactionStatus tx = startTransaction();
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Map<UUID, TaxonBase> savedTaxonMap = extractTaxonNames(state, taxonService, config, currentElement, bfnNamespace);
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createOrUpdateClassification(config, taxonService, savedTaxonMap, currentElement, state);
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commitTransaction(tx);
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}//import concept relations of taxon lists
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if(config.isHasSecondList()){
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if(currentElement.getName().equalsIgnoreCase(BfnXmlConstants.EL_KONZEPTBEZIEHUNGEN)){
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TransactionStatus tx = startTransaction();
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extractTaxonConceptRelationShips(bfnNamespace,currentElement);
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commitTransaction(tx);
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}
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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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* This method will parse the XML concept relationships and tries to map them into cdm relationship types.
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*
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* @param bfnNamespace
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* @param currentElement
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*/
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private void extractTaxonConceptRelationShips(Namespace bfnNamespace, Element currentElement) {
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String childName;
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String bfnElementName = BfnXmlConstants.EL_KONZEPTBEZIEHUNG;
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ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
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List<Element> elConceptList = currentElement.getChildren(bfnElementName, bfnNamespace);
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List<TaxonBase> updatedTaxonList = new ArrayList<TaxonBase>();
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for(Element element:elConceptList){
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childName = "TAXONYM1";
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Element elTaxon1 = XmlHelp.getSingleChildElement(success, element, childName, bfnNamespace, false);
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String taxNr1 = elTaxon1.getAttributeValue(BfnXmlConstants.ATT_TAXNR);
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int int1 = Integer.parseInt(taxNr1);
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Taxon taxon1 = firstList.get(int1);
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TaxonBase<?> taxonBase1 = getTaxonService().load(taxon1.getUuid());
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taxon1 = (Taxon)taxonBase1;
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childName = "TAXONYM2";
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Element elTaxon2 = XmlHelp.getSingleChildElement(success, element, childName, bfnNamespace, false);
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String taxNr2 = elTaxon2.getAttributeValue(BfnXmlConstants.ATT_TAXNR);
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int int2 = Integer.parseInt(taxNr2);
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Taxon taxon2 = secondList.get(int2);
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TaxonBase<?> taxonBase2 = getTaxonService().load(taxon2.getUuid());
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taxon2 = (Taxon) taxonBase2;
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childName = "STATUS";
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Element elConceptStatus = XmlHelp.getSingleChildElement(success, element, childName, bfnNamespace, false);
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String conceptStatusValue = elConceptStatus.getValue();
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conceptStatusValue = conceptStatusValue.replaceAll("\u00A0", "").trim();
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TaxonRelationshipType taxonRelationType = null;
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/**
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* This if case only exists because it was decided not to have a included_in relationship type.
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*/
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if(conceptStatusValue.equalsIgnoreCase("<")){
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taxon2.addTaxonRelation(taxon1, TaxonRelationshipType.INCLUDES(), null, null);
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}else{
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taxonRelationType = BfnXmlTransformer.getTaxonRelationForConceptCode(conceptStatusValue);
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taxon1.addTaxonRelation(taxon2, taxonRelationType , null, null);
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}
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if(taxonRelationType != null && taxonRelationType.equals(TaxonRelationshipType.ALL_RELATIONSHIPS())){
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List<TaxonRelationship> relationsFromThisTaxon = (List<TaxonRelationship>) taxon1.getRelationsFromThisTaxon();
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TaxonRelationship taxonRelationship = relationsFromThisTaxon.get(0);
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taxonRelationship.setDoubtful(true);
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}
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updatedTaxonList.add(taxon2);
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updatedTaxonList.add(taxon1);
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}
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getTaxonService().saveOrUpdate(updatedTaxonList);
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logger.info("taxon relationships imported...");
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}
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/**
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* This method stores the current imported maps in global variables to make
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* them later available for matching the taxon relationships between these
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* imported lists.
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*
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* @param config
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* @param taxonMap
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*/
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private void prepareListforConceptImport(BfnXmlImportConfigurator config,Map<Integer, Taxon> taxonMap) {
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if(config.isFillSecondList()){
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secondList = taxonMap;
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}else{
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firstList = taxonMap;
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}
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}
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/**
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*
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* @param state
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* @param taxonService
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* @param config
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* @param elDataSet
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* @param bfnNamespace
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* @return
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*/
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private Map<UUID, TaxonBase> extractTaxonNames(BfnXmlImportState state,
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ITaxonService taxonService, BfnXmlImportConfigurator config,
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Element elDataSet, Namespace bfnNamespace) {
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logger.info("start make TaxonNames...");
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Map<Integer, Taxon> taxonMap = new LinkedHashMap<Integer, Taxon>();
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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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String idNamespace = "TaxonName";
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childName = BfnXmlConstants.EL_TAXONYME;
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obligatory = false;
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Element elTaxonNames = XmlHelp.getSingleChildElement(success, elDataSet, childName, bfnNamespace, obligatory);
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String bfnElementName = BfnXmlConstants.EL_TAXONYM;
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List<Element> elTaxonList = elTaxonNames.getChildren(bfnElementName, bfnNamespace);
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//for each taxonName
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for (Element elTaxon : elTaxonList){
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//create Taxon
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String taxonId = elTaxon.getAttributeValue(BfnXmlConstants.ATT_TAXNR);
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childName = BfnXmlConstants.EL_WISSNAME;
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Element elWissName = XmlHelp.getSingleChildElement(success, elTaxon, childName, bfnNamespace, obligatory);
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String childElementName = BfnXmlConstants.EL_NANTEIL;
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Taxon taxon = createOrUpdateTaxon(success, taxonId, config, bfnNamespace, elWissName, childElementName, state);
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//for each synonym
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childName = "SYNONYME";
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Element elSynonyms = XmlHelp.getSingleChildElement(success, elTaxon, childName, bfnNamespace, obligatory);
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if(elSynonyms != null){
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childElementName = "SYNONYM";
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createOrUpdateSynonym(taxon, success, obligatory, bfnNamespace, childElementName,elSynonyms, taxonId, state);
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}
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//for vernacular name
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childName = BfnXmlConstants.EL_DEUTSCHENAMEN;
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Element elVernacularName = XmlHelp.getSingleChildElement(success, elTaxon, childName, bfnNamespace, obligatory);
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if(elVernacularName != null){
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childElementName = BfnXmlConstants.EL_DNAME;
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createOrUpdateVernacularName(taxon, bfnNamespace, childElementName, elVernacularName, state);
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}
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//for each information concerning the taxon element
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//TODO Information block
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if(config.isDoInformationImport()){
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childName = BfnXmlConstants.EL_INFORMATIONEN;
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Element elInformations = XmlHelp.getSingleChildElement(success, elTaxon, childName, bfnNamespace, obligatory);
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if(elInformations != null){
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childElementName = BfnXmlConstants.EL_BEZUGSRAUM;
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createOrUpdateInformation(taxon, bfnNamespace, childElementName,elInformations, state);
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}
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}
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taxonMap.put(Integer.parseInt(taxonId), taxon);
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}
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//Quick'n'dirty to set concept relationships between two imported list
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prepareListforConceptImport(config, taxonMap);
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Map<UUID, TaxonBase> savedTaxonMap = taxonService.saveOrUpdate((Collection)taxonMap.values());
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//FIXME: after first list don't import metadata yet
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//TODO: import information for second taxon list.
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config.setDoInformationImport(false);
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logger.info("end makeTaxonNames ...");
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if (!success.getValue()){
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state.setUnsuccessfull();
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}
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return savedTaxonMap;
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}
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/**
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* This will put the prior imported list into a classification
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*
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* @param config
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* @param taxonService
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* @param config
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* @param savedTaxonMap
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* @param currentElement
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* @param state
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* @return
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*/
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@SuppressWarnings("rawtypes")
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private boolean createOrUpdateClassification(BfnXmlImportConfigurator config, ITaxonService taxonService, Map<UUID, TaxonBase> savedTaxonMap, Element currentElement, BfnXmlImportState state) {
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boolean isNewClassification = true;
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Classification classification = Classification.NewInstance(currentElement.getAttributeValue("inhalt"), state.getCompleteSourceRef());
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//TODO do we really want toString() or titleCache here?
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String microRef = state.getCurrentMicroRef() == null ? null : state.getCurrentMicroRef().toString();
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classification.addImportSource(Integer.toString(classification.getId()), classification.getTitleCache(), state.getCompleteSourceRef(), microRef);
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// List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, VOC_CLASSIFICATION_INIT_STRATEGY);
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// for(Classification c : classificationList){
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// if(c.getTitleCache().equalsIgnoreCase(classification.getTitleCache())){
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// classification = c;
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// isNewClassification = false;
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// }
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// }
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// ArrayList<TaxonBase> taxonBaseList = (ArrayList<TaxonBase>) taxonService.list(TaxonBase.class, null, null, null, VOC_CLASSIFICATION_INIT_STRATEGY);
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for(TaxonBase tb:savedTaxonMap.values()){
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if(tb instanceof Taxon){
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TaxonBase tbase = CdmBase.deproxy(tb, TaxonBase.class);
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Taxon taxon = (Taxon)tbase;
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taxon = CdmBase.deproxy(taxon, Taxon.class);
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classification.addChildTaxon(taxon, null, null);
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}
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}
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IClassificationService classificationService = getClassificationService();
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classificationService.saveOrUpdate(classification);
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//set boolean for reference and internal mapping of concept relations
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if(config.isHasSecondList()){
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config.setFillSecondList(true);
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}
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return isNewClassification;
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}
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/**
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* Matches the XML attributes against CDM entities.<BR>
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* Imports Scientific Name, Rank, etc. and creates a taxon.<br>
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* <b>Existing taxon names won't be matched yet</b>
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*
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* @param success
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* @param taxonId
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* @param config
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* @param bfnNamespace
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* @param elTaxonName
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* @param childElementName
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* @param state
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* @return
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*/
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@SuppressWarnings({ "unchecked" })
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334
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private Taxon createOrUpdateTaxon(
|
|
335
|
ResultWrapper<Boolean> success, String taxonId,
|
|
336
|
BfnXmlImportConfigurator config, Namespace bfnNamespace,
|
|
337
|
Element elTaxonName, String childElementName, BfnXmlImportState state) {
|
|
338
|
|
|
339
|
List<Element> elWissNameList = elTaxonName.getChildren(childElementName, bfnNamespace);
|
|
340
|
Rank rank = null;
|
|
341
|
String strAuthor = null;
|
|
342
|
String strSupplement = null;
|
|
343
|
Taxon taxon = null;
|
|
344
|
String uniqueID = null;
|
|
345
|
String uriNameSpace = null;
|
|
346
|
// Long uniqueID = null;
|
|
347
|
for(Element elWissName:elWissNameList){
|
|
348
|
|
|
349
|
if(elWissName.getAttributeValue(BfnXmlConstants.ATT_BEREICH, bfnNamespace).equalsIgnoreCase("Eindeutiger Code")){
|
|
350
|
uriNameSpace = elWissName.getAttributeValue(BfnXmlConstants.ATT_BEREICH);
|
|
351
|
String textNormalize = elWissName.getTextNormalize();
|
|
352
|
if(StringUtils.isBlank(textNormalize)){
|
|
353
|
uniqueID = "";
|
|
354
|
}else{
|
|
355
|
uniqueID = textNormalize;
|
|
356
|
}
|
|
357
|
}
|
|
358
|
if(elWissName.getAttributeValue(BfnXmlConstants.ATT_BEREICH, bfnNamespace).equalsIgnoreCase("Autoren")){
|
|
359
|
strAuthor = elWissName.getTextNormalize();
|
|
360
|
}
|
|
361
|
if(elWissName.getAttributeValue(BfnXmlConstants.ATT_BEREICH, bfnNamespace).equalsIgnoreCase("Rang")){
|
|
362
|
String strRank = elWissName.getTextNormalize();
|
|
363
|
rank = makeRank(strRank);
|
|
364
|
}
|
|
365
|
if(elWissName.getAttributeValue(BfnXmlConstants.ATT_BEREICH, bfnNamespace).equalsIgnoreCase("Zusätze")){
|
|
366
|
strSupplement = elWissName.getTextNormalize();
|
|
367
|
}
|
|
368
|
if(elWissName.getAttributeValue(BfnXmlConstants.ATT_BEREICH, bfnNamespace).equalsIgnoreCase("wissName")){
|
|
369
|
try{
|
|
370
|
TaxonNameBase<?, ?> nameBase = parseNonviralNames(rank,strAuthor,strSupplement,elWissName);
|
|
371
|
if(nameBase.isProtectedTitleCache() == true){
|
|
372
|
logger.warn("Taxon " + nameBase.getTitleCache());
|
|
373
|
}
|
|
374
|
|
|
375
|
//TODO extract to method?
|
|
376
|
if(strSupplement != null){
|
|
377
|
nameBase.setAppendedPhrase(strSupplement);
|
|
378
|
}
|
|
379
|
if(strSupplement != null && strSupplement.equalsIgnoreCase("nom. illeg.")){
|
|
380
|
nameBase.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE()));
|
|
381
|
}
|
|
382
|
/**
|
|
383
|
* BFN does not want any name matching yet
|
|
384
|
*/
|
|
385
|
// TaxonBase<?> taxonBase = null;
|
|
386
|
// //TODO find best matching Taxa
|
|
387
|
// Pager<TaxonNameBase> names = getNameService().findByTitle(null, nameBase.getTitleCache(), null, null, null, null, null, null);
|
|
388
|
// //TODO correct handling for pager
|
|
389
|
// List<TaxonNameBase> nameList = names.getRecords();
|
|
390
|
// if (nameList.isEmpty()){
|
|
391
|
// taxonBase = Taxon.NewInstance(nameBase, config.getSourceReference());
|
|
392
|
// }else{
|
|
393
|
// taxonBase = Taxon.NewInstance(nameList.get(0), config.getSourceReference());
|
|
394
|
// if (nameList.size()>1){
|
|
395
|
// logger.warn("More than 1 matching taxon name found for " + nameBase.getTitleCache());
|
|
396
|
// }
|
|
397
|
// }
|
|
398
|
|
|
399
|
Reference<?> microRef = config.isFillSecondList() ?
|
|
400
|
state.getSecondListSecRef():
|
|
401
|
state.getFirstListSecRef();
|
|
402
|
state.setCurrentMicroRef(microRef);
|
|
403
|
taxon = Taxon.NewInstance(nameBase, state.getCurrentMicroRef());
|
|
404
|
//set create and set path of nameSpace
|
|
405
|
Element parentElement = elWissName.getParentElement();
|
|
406
|
Element grandParentElement = parentElement.getParentElement();
|
|
407
|
String namespace = grandParentElement.getName() + ":" + parentElement.getName() + ":"+elWissName.getName() + ":" + uriNameSpace;
|
|
408
|
String microRefStr = microRef == null ? null : microRef.getTitle();
|
|
409
|
taxon.addImportSource(uniqueID, namespace, state.getCompleteSourceRef(), microRefStr);
|
|
410
|
|
|
411
|
taxon.addIdentifier(taxonId, getIdentiferType(state, BfnXmlConstants.UUID_TAX_NR_IDENTIFIER_TYPE, "taxNr", "TaxNr attribute of Bfn Xml file", "taxNr", null));
|
|
412
|
} catch (UnknownCdmTypeException e) {
|
|
413
|
success.setValue(false);
|
|
414
|
}
|
|
415
|
}
|
|
416
|
}
|
|
417
|
return taxon;
|
|
418
|
}
|
|
419
|
|
|
420
|
/**
|
|
421
|
* Matches the XML attributes against CDM entities.<BR>
|
|
422
|
* Imports Scientific Name, Rank etc. and create a synonym.<br>
|
|
423
|
* <b>Existing synonym names won't be matched yet</b>
|
|
424
|
*
|
|
425
|
* @param taxon
|
|
426
|
* @param success
|
|
427
|
* @param obligatory
|
|
428
|
* @param bfnNamespace
|
|
429
|
* @param childElementName
|
|
430
|
* @param elSynonyms
|
|
431
|
* @param taxonId
|
|
432
|
* @param config
|
|
433
|
* @param state
|
|
434
|
*/
|
|
435
|
|
|
436
|
@SuppressWarnings({ "unchecked" })
|
|
437
|
private void createOrUpdateSynonym(Taxon taxon, ResultWrapper<Boolean> success, boolean obligatory, Namespace bfnNamespace,
|
|
438
|
String childElementName, Element elSynonyms, String taxonId, BfnXmlImportState state) {
|
|
439
|
|
|
440
|
String childName;
|
|
441
|
List<Element> elSynonymList = elSynonyms.getChildren(childElementName, bfnNamespace);
|
|
442
|
|
|
443
|
for(Element elSyn:elSynonymList){
|
|
444
|
Rank rank = null;
|
|
445
|
String strAuthor = null;
|
|
446
|
String strSupplement = null;
|
|
447
|
childName = BfnXmlConstants.EL_WISSNAME;
|
|
448
|
Element elSynScientificName = XmlHelp.getSingleChildElement(success, elSyn, childName, bfnNamespace, obligatory);
|
|
449
|
|
|
450
|
childElementName = BfnXmlConstants.EL_NANTEIL;
|
|
451
|
List<Element> elSynDetails = elSynScientificName.getChildren(childElementName, bfnNamespace);
|
|
452
|
|
|
453
|
for(Element elSynDetail:elSynDetails){
|
|
454
|
if(elSynDetail.getAttributeValue(BfnXmlConstants.ATT_BEREICH).equalsIgnoreCase("Rang")){
|
|
455
|
String strRank = elSynDetail.getTextNormalize();
|
|
456
|
rank = makeRank(strRank);
|
|
457
|
}
|
|
458
|
if(elSynDetail.getAttributeValue(BfnXmlConstants.ATT_BEREICH).equalsIgnoreCase("Autoren")){
|
|
459
|
strAuthor = elSynDetail.getTextNormalize();
|
|
460
|
}
|
|
461
|
if(elSynDetail.getAttributeValue(BfnXmlConstants.ATT_BEREICH, bfnNamespace).equalsIgnoreCase("Zusätze")){
|
|
462
|
strSupplement = elSynDetail.getTextNormalize();
|
|
463
|
}
|
|
464
|
if(elSynDetail.getAttributeValue(BfnXmlConstants.ATT_BEREICH).equalsIgnoreCase("wissName")){
|
|
465
|
try{
|
|
466
|
TaxonNameBase<?, ?> nameBase = parseNonviralNames(rank,strAuthor,strSupplement,elSynDetail);
|
|
467
|
|
|
468
|
//TODO find best matching Taxa
|
|
469
|
Synonym synonym = Synonym.NewInstance(nameBase, state.getCurrentMicroRef());
|
|
470
|
taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
|
|
471
|
|
|
472
|
} catch (UnknownCdmTypeException e) {
|
|
473
|
logger.warn("Name with id " + taxonId + " has unknown nomenclatural code.");
|
|
474
|
success.setValue(false);
|
|
475
|
}
|
|
476
|
|
|
477
|
}
|
|
478
|
|
|
479
|
}
|
|
480
|
}
|
|
481
|
}
|
|
482
|
|
|
483
|
|
|
484
|
/**
|
|
485
|
*
|
|
486
|
* @param taxon
|
|
487
|
* @param bfnNamespace
|
|
488
|
* @param childElementName
|
|
489
|
* @param elVernacularName
|
|
490
|
* @param state
|
|
491
|
*/
|
|
492
|
private void createOrUpdateVernacularName(Taxon taxon,
|
|
493
|
Namespace bfnNamespace, String childElementName,
|
|
494
|
Element elVernacularName, BfnXmlImportState state) {
|
|
495
|
|
|
496
|
List<Element> elVernacularNameList = elVernacularName.getChildren(childElementName, bfnNamespace);
|
|
497
|
|
|
498
|
TaxonDescription taxonDescription = getTaxonDescription(taxon, false, true);
|
|
499
|
|
|
500
|
for(Element elVernacular : elVernacularNameList){
|
|
501
|
Element child = elVernacular.getChild("TRIVIALNAME");
|
|
502
|
if(child != null){
|
|
503
|
makeCommonName(taxonDescription, child, state);
|
|
504
|
}
|
|
505
|
}
|
|
506
|
|
|
507
|
}
|
|
508
|
|
|
509
|
/**
|
|
510
|
*
|
|
511
|
* @param taxon
|
|
512
|
* @param bfnNamespace
|
|
513
|
* @param childElementName
|
|
514
|
* @param elInformations
|
|
515
|
* @param state
|
|
516
|
* @throws UnknownCdmTypeException
|
|
517
|
*/
|
|
518
|
|
|
519
|
@SuppressWarnings("unchecked")
|
|
520
|
private void createOrUpdateInformation(Taxon taxon,
|
|
521
|
Namespace bfnNamespace, String childElementName,
|
|
522
|
Element elInformations,
|
|
523
|
BfnXmlImportState state){
|
|
524
|
|
|
525
|
List<Element> elInformationList = elInformations.getChildren(childElementName, bfnNamespace);
|
|
526
|
|
|
527
|
for(Element elInfo:elInformationList){
|
|
528
|
//check if geographical scope is Bund and import only these information for now
|
|
529
|
//TODO create several taxon descriptions for different geographical scope
|
|
530
|
if(elInfo.getName().equalsIgnoreCase(BfnXmlConstants.EL_BEZUGSRAUM) && elInfo.getAttributeValue("name").equalsIgnoreCase("Bund")){
|
|
531
|
childElementName = BfnXmlConstants.EL_IWERT;
|
|
532
|
TaxonDescription taxonDescription = getTaxonDescription(taxon, false, true);
|
|
533
|
UUID germanStateUUID;
|
|
534
|
try {
|
|
535
|
germanStateUUID = BfnXmlTransformer.getGermanStateUUID("Deutschland");
|
|
536
|
NamedArea area = (NamedArea)getTermService().load(germanStateUUID);
|
|
537
|
//FIXME GEOSCOPE_ID CANNOT BE NULL Exception
|
|
538
|
// taxonDescription.addGeoScope(area);
|
|
539
|
} catch (UnknownCdmTypeException e) {
|
|
540
|
// TODO Auto-generated catch block
|
|
541
|
e.printStackTrace();
|
|
542
|
}
|
|
543
|
List<Element> elInfoDetailList = elInfo.getChildren(childElementName, bfnNamespace);
|
|
544
|
|
|
545
|
for(Element elInfoDetail : elInfoDetailList){
|
|
546
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("RL Kat.")){
|
|
547
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
548
|
}
|
|
549
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Kat. +/-")){
|
|
550
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
551
|
}
|
|
552
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("aktuelle Bestandsstituation")){
|
|
553
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
554
|
}
|
|
555
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("langfristiger Bestandstrend")){
|
|
556
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
557
|
}
|
|
558
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("kurzfristiger Bestandstrend")){
|
|
559
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
560
|
}
|
|
561
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Risikofaktoren")){
|
|
562
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
563
|
}
|
|
564
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Verantwortlichkeit")){
|
|
565
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
566
|
}
|
|
567
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("alte RL- Kat.")){
|
|
568
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
569
|
}
|
|
570
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Neobiota")){
|
|
571
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
572
|
}
|
|
573
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Eindeutiger Code")){
|
|
574
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
575
|
}
|
|
576
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Kommentar zur Taxonomie")){
|
|
577
|
makeFeatures(taxonDescription, elInfoDetail, state, true);
|
|
578
|
}
|
|
579
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Kommentar zur Gefährdung")){
|
|
580
|
makeFeatures(taxonDescription, elInfoDetail, state, true);
|
|
581
|
}
|
|
582
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Sonderfälle")){
|
|
583
|
makeFeatures(taxonDescription, elInfoDetail, state, false);
|
|
584
|
}
|
|
585
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Letzter Nachweis")){
|
|
586
|
makeFeatures(taxonDescription, elInfoDetail, state, true);
|
|
587
|
}
|
|
588
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("Weitere Kommentare")){
|
|
589
|
makeFeatures(taxonDescription, elInfoDetail, state, true);
|
|
590
|
}
|
|
591
|
//create german federal states distribution status
|
|
592
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("BW")){
|
|
593
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
594
|
}
|
|
595
|
//create german federal states distribution status
|
|
596
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("BY")){
|
|
597
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
598
|
}
|
|
599
|
//create german federal states distribution status
|
|
600
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("BE")){
|
|
601
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
602
|
}
|
|
603
|
//create german federal states distribution status
|
|
604
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("BB")){
|
|
605
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
606
|
}
|
|
607
|
//create german federal states distribution status
|
|
608
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("HB")){
|
|
609
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
610
|
}
|
|
611
|
//create german federal states distribution status
|
|
612
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("HH")){
|
|
613
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
614
|
}
|
|
615
|
//create german federal states distribution status
|
|
616
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("HE")){
|
|
617
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
618
|
}
|
|
619
|
//create german federal states distribution status
|
|
620
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("MV")){
|
|
621
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
622
|
}
|
|
623
|
//create german federal states distribution status
|
|
624
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("NI")){
|
|
625
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
626
|
}
|
|
627
|
//create german federal states distribution status
|
|
628
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("NW")){
|
|
629
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
630
|
}
|
|
631
|
//create german federal states distribution status
|
|
632
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("RP")){
|
|
633
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
634
|
}
|
|
635
|
//create german federal states distribution status
|
|
636
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("SL")){
|
|
637
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
638
|
}
|
|
639
|
//create german federal states distribution status
|
|
640
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("SN")){
|
|
641
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
642
|
}
|
|
643
|
//create german federal states distribution status
|
|
644
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("ST")){
|
|
645
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
646
|
}
|
|
647
|
//create german federal states distribution status
|
|
648
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("SH")){
|
|
649
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
650
|
}
|
|
651
|
//create german federal states distribution status
|
|
652
|
if(elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME).equalsIgnoreCase("TH")){
|
|
653
|
createGermanDistributionStatus(taxon, elInfoDetail, state, taxonDescription);
|
|
654
|
}
|
|
655
|
}
|
|
656
|
}
|
|
657
|
}
|
|
658
|
}
|
|
659
|
|
|
660
|
|
|
661
|
private void makeCommonName(TaxonDescription taxonDescription,
|
|
662
|
Element child, BfnXmlImportState state) {
|
|
663
|
String commonNameValue = child.getValue();
|
|
664
|
NamedArea area = getTermService().getAreaByTdwgAbbreviation("GER");
|
|
665
|
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameValue, Language.GERMAN(), area);
|
|
666
|
taxonDescription.addElement(commonName);
|
|
667
|
}
|
|
668
|
|
|
669
|
|
|
670
|
/**
|
|
671
|
*
|
|
672
|
* @param taxonDescription
|
|
673
|
* @param elInfoDetail
|
|
674
|
* @param state
|
|
675
|
* @param isTextData
|
|
676
|
*/
|
|
677
|
private void makeFeatures(
|
|
678
|
TaxonDescription taxonDescription,
|
|
679
|
Element elInfoDetail,
|
|
680
|
BfnXmlImportState state,
|
|
681
|
boolean isTextData) {
|
|
682
|
|
|
683
|
String transformedRlKatValue = null;
|
|
684
|
UUID featureUUID = null;
|
|
685
|
UUID stateTermUUID = null;
|
|
686
|
String strRlKatValue = elInfoDetail.getChild(BfnXmlConstants.EL_WERT).getValue();
|
|
687
|
String strRlKat = elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME);
|
|
688
|
boolean randomStateUUID = false;
|
|
689
|
try {
|
|
690
|
featureUUID = BfnXmlTransformer.getRedlistFeatureUUID(strRlKat);
|
|
691
|
transformedRlKatValue = BfnXmlTransformer.redListString2RedListCode(strRlKatValue);
|
|
692
|
} catch (UnknownCdmTypeException e) {
|
|
693
|
transformedRlKatValue = strRlKatValue;
|
|
694
|
}
|
|
695
|
Feature redListFeature = getFeature(state, featureUUID);
|
|
696
|
State rlState = null;
|
|
697
|
//if is text data a state is not needed
|
|
698
|
if(!isTextData){
|
|
699
|
try {
|
|
700
|
stateTermUUID = BfnXmlTransformer.getRedlistStateTermUUID(transformedRlKatValue, strRlKat);
|
|
701
|
} catch (UnknownCdmTypeException e) {
|
|
702
|
stateTermUUID = UUID.randomUUID();
|
|
703
|
randomStateUUID = true;
|
|
704
|
}
|
|
705
|
if(randomStateUUID || stateTermUUID == BfnXmlConstants.stateTermEmpty){
|
|
706
|
if(stateTermUUID == BfnXmlConstants.stateTermEmpty) {
|
|
707
|
transformedRlKatValue = "keine Angabe";
|
|
708
|
}
|
|
709
|
rlState = getStateTerm(state, stateTermUUID, transformedRlKatValue, transformedRlKatValue, transformedRlKatValue, null);
|
|
710
|
}else{
|
|
711
|
rlState = getStateTerm(state, stateTermUUID);
|
|
712
|
}
|
|
713
|
}
|
|
714
|
if(isTextData){
|
|
715
|
TextData textData = TextData.NewInstance(redListFeature);
|
|
716
|
textData.putText(Language.GERMAN(), strRlKatValue);
|
|
717
|
DescriptionElementBase descriptionElement = textData;
|
|
718
|
taxonDescription.addElement(descriptionElement);
|
|
719
|
}else{
|
|
720
|
CategoricalData catData = CategoricalData.NewInstance(rlState, redListFeature);
|
|
721
|
DescriptionElementBase descriptionElement = catData;
|
|
722
|
taxonDescription.addElement(descriptionElement);
|
|
723
|
}
|
|
724
|
}
|
|
725
|
|
|
726
|
/**
|
|
727
|
* Returns the rank represented by the rank element.<br>
|
|
728
|
* Returns <code>null</code> if the element is null.<br>
|
|
729
|
* Returns <code>null</code> if the code and the text are both either empty or do not exists.<br>
|
|
730
|
* Returns the rank represented by the code attribute, if the code attribute is not empty and could be resolved.<br>
|
|
731
|
* If the code could not be resolved it returns the rank represented most likely by the elements text.<br>
|
|
732
|
* Returns UNKNOWN_RANK if code attribute and element text could not be resolved.
|
|
733
|
* @param strRank bfn rank element
|
|
734
|
* @return
|
|
735
|
*/
|
|
736
|
protected static Rank makeRank(String strRank){
|
|
737
|
Rank result;
|
|
738
|
if (strRank == null){
|
|
739
|
return null;
|
|
740
|
}
|
|
741
|
Rank codeRank = BfnXmlTransformer.getRankForRankCode(strRank);
|
|
742
|
if(codeRank==null){
|
|
743
|
codeRank = Rank.UNKNOWN_RANK();
|
|
744
|
}
|
|
745
|
//codeRank exists
|
|
746
|
if ( (codeRank != null) && !codeRank.equals(Rank.UNKNOWN_RANK())){
|
|
747
|
result = codeRank;
|
|
748
|
}
|
|
749
|
//codeRank does not exist
|
|
750
|
else{
|
|
751
|
result = codeRank;
|
|
752
|
logger.warn("string rank used, because code rank does not exist or was not recognized: " + codeRank.getTitleCache()+" "+strRank);
|
|
753
|
}
|
|
754
|
return result;
|
|
755
|
}
|
|
756
|
|
|
757
|
/**
|
|
758
|
* @param rank
|
|
759
|
* @param strAuthor
|
|
760
|
* @param strSupplement
|
|
761
|
* @param elWissName
|
|
762
|
* @return
|
|
763
|
* @throws UnknownCdmTypeException
|
|
764
|
*/
|
|
765
|
private TaxonNameBase<?, ?> parseNonviralNames(Rank rank, String strAuthor, String strSupplement, Element elWissName)
|
|
766
|
throws UnknownCdmTypeException {
|
|
767
|
TaxonNameBase<?,?> taxonNameBase = null;
|
|
768
|
|
|
769
|
String strScientificName = elWissName.getTextNormalize();
|
|
770
|
/**
|
|
771
|
*
|
|
772
|
* trim strScienctificName because sometimes
|
|
773
|
* getTextNormalize() does not removes all the
|
|
774
|
* whitespaces
|
|
775
|
*
|
|
776
|
**/
|
|
777
|
strScientificName = StringUtils.trim(strScientificName);
|
|
778
|
strScientificName = StringUtils.remove(strScientificName, "\u00a0");
|
|
779
|
strScientificName = StringUtils.remove(strScientificName, "\uc281");
|
|
780
|
|
|
781
|
if(strSupplement != null && !strSupplement.isEmpty()){
|
|
782
|
strScientificName = StringUtils.remove(strScientificName, strSupplement);
|
|
783
|
}
|
|
784
|
NonViralName<?> nonViralName = null;
|
|
785
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
|
786
|
nonViralName = parser.parseFullName(strScientificName, nomenclaturalCode, rank);
|
|
787
|
if(nonViralName.hasProblem()){
|
|
788
|
for(ParserProblem p:nonViralName.getParsingProblems()){
|
|
789
|
logger.warn(++parsingProblemCounter + " " +nonViralName.getTitleCache() +" "+p.toString());
|
|
790
|
}
|
|
791
|
}
|
|
792
|
//check for parsed rank
|
|
793
|
Rank parsedRank = nonViralName.getRank();
|
|
794
|
if(parsedRank != rank){
|
|
795
|
nonViralName.setRank(rank);
|
|
796
|
}
|
|
797
|
//check for parsed author
|
|
798
|
String parsedAuthor = nonViralName.getAuthorshipCache();
|
|
799
|
strAuthor = StringUtils.trim(strAuthor);
|
|
800
|
parsedAuthor = StringUtils.trim(parsedAuthor);
|
|
801
|
if(parsedAuthor.equalsIgnoreCase(strAuthor)){
|
|
802
|
logger.info("Taxon " + nonViralName.getTitleCache() +":"
|
|
803
|
+"\t Author field: " + strAuthor +" and parsed AuthorshipCache: "+nonViralName.getAuthorshipCache());
|
|
804
|
}
|
|
805
|
taxonNameBase = nonViralName;
|
|
806
|
return taxonNameBase;
|
|
807
|
}
|
|
808
|
|
|
809
|
/**
|
|
810
|
* This method will match the BFN XML status to a distribution status
|
|
811
|
* and map it to the german federal state area. The vocabulary needs to be
|
|
812
|
* created first by the Importer, in order to map the terms correctly. Have a look
|
|
813
|
* for further details at the file BfnXmlImportAdditionalTerms.
|
|
814
|
*
|
|
815
|
*
|
|
816
|
* @param taxon, for saving the distribution and its status
|
|
817
|
* @param elInfoDetail, keeps the details from the import, in this case the distribution detail
|
|
818
|
* @param state, import state
|
|
819
|
* @param germanState, the abbreviated label for the German state
|
|
820
|
*
|
|
821
|
*/
|
|
822
|
private void createGermanDistributionStatus(Taxon taxon, Element elInfoDetail, BfnXmlImportState state,
|
|
823
|
TaxonDescription taxonDescription){
|
|
824
|
|
|
825
|
String strDistributionValue = elInfoDetail.getChild(BfnXmlConstants.EL_WERT).getValue();
|
|
826
|
String strGermanState = elInfoDetail.getAttributeValue(BfnXmlConstants.ATT_STANDARDNAME);
|
|
827
|
//match DistributionValue
|
|
828
|
UUID matchedDistributionUUID = null;
|
|
829
|
PresenceAbsenceTerm status = null;
|
|
830
|
try {
|
|
831
|
matchedDistributionUUID = BfnXmlTransformer.matchDistributionValue(strDistributionValue);
|
|
832
|
DefinedTermBase load = getTermService().load(matchedDistributionUUID);
|
|
833
|
if(load.isInstanceOf(PresenceAbsenceTerm.class)) {
|
|
834
|
status = CdmBase.deproxy(load, PresenceAbsenceTerm.class);
|
|
835
|
}else{
|
|
836
|
logger.warn(strDistributionValue + " is not PresenceAbsence Term " + load.getTitleCache() + " " + load.getTermType().toString());
|
|
837
|
return;
|
|
838
|
}
|
|
839
|
} catch (UnknownCdmTypeException e1) {
|
|
840
|
logger.warn("could not match xml value "+ strDistributionValue +" to distribution status for "+strGermanState);
|
|
841
|
e1.printStackTrace();
|
|
842
|
return;
|
|
843
|
}
|
|
844
|
//load vocabulary and german state
|
|
845
|
UUID vocabularyUUID = null;
|
|
846
|
TermVocabulary vocabulary = null;
|
|
847
|
UUID stateUUID = null;
|
|
848
|
|
|
849
|
try {
|
|
850
|
stateUUID = BfnXmlTransformer.getGermanStateUUID(strGermanState);
|
|
851
|
} catch (UnknownCdmTypeException e1) {
|
|
852
|
logger.warn("could not match state" + strGermanState + " to UUID");
|
|
853
|
e1.printStackTrace();
|
|
854
|
return;
|
|
855
|
}
|
|
856
|
NamedArea area = (NamedArea)getTermService().load(stateUUID);
|
|
857
|
|
|
858
|
// try {
|
|
859
|
// vocabularyUUID = BfnXmlTransformer.getRedlistVocabularyUUID("Bundesländer");
|
|
860
|
// vocabulary = getVocabularyService().load(vocabularyUUID);
|
|
861
|
// } catch (UnknownCdmTypeException e) {
|
|
862
|
// logger.warn("could not load vocabulary");
|
|
863
|
// e.printStackTrace();
|
|
864
|
// return;
|
|
865
|
// }
|
|
866
|
// NamedArea area = null;
|
|
867
|
// for(Object term: vocabulary){
|
|
868
|
// //TODO match german state
|
|
869
|
// NamedArea narea = (NamedArea) term;
|
|
870
|
// Set<Representation> representations = narea.getRepresentations();
|
|
871
|
// for(Representation r:representations){
|
|
872
|
// if(r.getAbbreviatedLabel().equalsIgnoreCase(strGermanState)){
|
|
873
|
// area = narea;
|
|
874
|
// }
|
|
875
|
// }
|
|
876
|
//
|
|
877
|
// }
|
|
878
|
//create new taxon description
|
|
879
|
DescriptionElementBase descriptionElement = Distribution.NewInstance(area, status);
|
|
880
|
taxonDescription.addElement(descriptionElement);
|
|
881
|
}
|
|
882
|
|
|
883
|
|
|
884
|
@Override
|
|
885
|
public boolean doCheck(BfnXmlImportState state){
|
|
886
|
boolean result = true;
|
|
887
|
return result;
|
|
888
|
}
|
|
889
|
|
|
890
|
@Override
|
|
891
|
protected boolean isIgnore(BfnXmlImportState state){
|
|
892
|
return ! state.getConfig().isDoTaxonNames();
|
|
893
|
}
|
|
894
|
}
|