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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.Arrays;
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import java.util.List;
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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.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.OrderedTermBase;
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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.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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*
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* This class creates all area vocabularies and all distribution status vocabularies
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* for the German redlists.
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*
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* @author a.oppermann
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* @author a.mueller
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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 BfnXmlImportAddtionalTerms extends BfnXmlImportBase {
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private static final long serialVersionUID = 8997499338798245806L;
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private static final Logger logger = Logger.getLogger(BfnXmlImportAddtionalTerms.class);
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public enum Vocabulary{
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GERMAN_FEDERAL_STATES("Bundesländer"),
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GERMAN_COMBINED_STATES("Kombinierte Bundesländer"),
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GERMAN_MARINE_ALGAE_AREAS("Marine Algen Gebiete"),
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GERMAN_MARINE_INVERTEBRATE_AREAS("Marine Invertebraten Gebiete"),
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GERMAN_PRESENCE_TERMS("Vorkommensstatus"),
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GERMAN_ESTABLISHMENT_TERMS("Etablierungsstatus");
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private final String vocabulary;
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private Vocabulary(final String vocabulary) {
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this.vocabulary = vocabulary;
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}
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@Override
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public String toString() {
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return vocabulary;
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}
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}
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private static final List<String> GERMAN_PRESENCE_ABSENCE_TERMS = Arrays.asList(new String[] {
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"x:" + BfnXmlTransformer.VORHANDEN ,
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"?:" + BfnXmlTransformer.VORHANDEN_UNSICHER,
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"#:" + BfnXmlTransformer.ABWESEND_ABGELEHNT,
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"-:" + BfnXmlTransformer.ABWESEND_KEIN_NACHWEIS,
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"a:" + BfnXmlTransformer.ABWESEND,
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"aa:" + BfnXmlTransformer.ABWESEND_AUSGESTORBEN,
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"an:" + BfnXmlTransformer.ABWESEND_SEIT1980,
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"af:" + BfnXmlTransformer.ABWESEND_FEHLEINGABE,
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"v+:" + BfnXmlTransformer.VORHANDEN_EINBUERGERUNG,
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"ve:" + BfnXmlTransformer.VORHANDEN_ETABLIERT,
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"vk:" + BfnXmlTransformer.VORHANDEN_KULTIVIERT_DOMESTIZIERT,
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"vu:" + BfnXmlTransformer.VORHANDEN_UNBESTAENDIG,
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"v?:" + BfnXmlTransformer.VORHANDEN_VORKOMMEN_UNSICHER,
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});
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private static final List<String> GERMAN_ESTABLISHMENT_STATUS_TERMS = Arrays.asList(new String[] {
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"A:Archaeophyt",
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"I:Indigen",
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"K:Kulturpflanze / domestiziertes Tier",
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"N:Neophyt",
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"KF:Kultuflüchtling"
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});
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private static final List<String> GERMAN_FEDERAL_STATES = Arrays.asList(new String[] {
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"DE:Deutschland",
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"BW:Baden-Württemberg",
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"BY:Bayern",
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"BE:Berlin",
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"BB:Brandenburg",
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"HB:Bremen",
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"HH:Hamburg",
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"HE:Hessen",
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"MV:Mecklenburg-Vorpommern",
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"NI:Niedersachsen",
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"NW:Nordrhein-Westfalen",
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"RP:Rheinland-Pfalz",
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"SL:Saarland",
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"SN:Sachsen",
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"ST:Sachsen-Anhalt",
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"SH:Schleswig-Holstein",
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"TH:Thüringen"
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});
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private static final List<String> GERMAN_COMBINED_STATES = Arrays.asList(new String[] {
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"BB+BE:Brandenburg und Berlin",
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"SH+HH:Schleswig-Holstein und Hamburg"
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});
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private static final List<String> GERMAN_MARINE_ALGAE_AREAS = Arrays.asList(new String[] {
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"HGL:Helgoland",
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"NIW:Niedersächsisches Wattenmeer",
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"SHW:Schleswig-Holsteinisches Wattenmeer",
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"SHO:Schleswig-Holsteinische Ostsee",
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"MVO:Mecklenburg-Vorpommerische Ostsee"
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});
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private static final List<String> GERMAN_MARINE_INVERTEBRATE_AREAS = Arrays.asList(new String[] {
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"ÄWN:Ästuarien und Watt Nordsee",
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"SuN:Sublitoral Nordsee",
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"Hel:Helgoland2", //TODO: the 2 is a workaround to distinguish from Algae Helgoloand, still needs to be discussed with BfN if these are 2 different areas
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"Dog:Doggerbank",
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"Ost:Ostsee"
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});
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/** Hibernate classification vocabulary initialization 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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"synonyms",
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"taxon.*",
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"taxon.sec",
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"taxon.name.*",
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"taxon.synonyms",
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"termVocabulary.*",
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"terms",
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"namedArea"
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});
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public BfnXmlImportAddtionalTerms(){
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super();
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}
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@Override
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public void doInvoke(BfnXmlImportState state){
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logger.info("create german terms ...");
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TransactionStatus tx = startTransaction();
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//areas
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createTerms(GERMAN_FEDERAL_STATES, Vocabulary.GERMAN_FEDERAL_STATES, TermType.NamedArea);
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createTerms(GERMAN_MARINE_ALGAE_AREAS, Vocabulary.GERMAN_MARINE_ALGAE_AREAS, TermType.NamedArea);
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createTerms(GERMAN_MARINE_INVERTEBRATE_AREAS, Vocabulary.GERMAN_MARINE_INVERTEBRATE_AREAS, TermType.NamedArea);
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createTerms(GERMAN_COMBINED_STATES, Vocabulary.GERMAN_COMBINED_STATES, TermType.NamedArea);
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//distribution status
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createTerms(GERMAN_PRESENCE_ABSENCE_TERMS, Vocabulary.GERMAN_PRESENCE_TERMS, TermType.PresenceAbsenceTerm);
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createTerms(GERMAN_ESTABLISHMENT_STATUS_TERMS, Vocabulary.GERMAN_ESTABLISHMENT_TERMS, TermType.PresenceAbsenceTerm);
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commitTransaction(tx);
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logger.info("end create german terms.");
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return;
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}
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private void createTerms(List<String> termList, Vocabulary vocabulary, TermType termType){
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NamedArea parentGermany = null;
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PresenceAbsenceTerm lastParent = null;
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int id = 0;
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for(String strTerm : termList){
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//Split string into label and abbrevated label
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String[] splittedStrings = StringUtils.splitByWholeSeparator(strTerm, ":");
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String abbrevatedLabel = splittedStrings[0];
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String label = splittedStrings[1];
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//get UUID and load existing term
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UUID termUuuid = null;
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try {
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if(vocabulary == Vocabulary.GERMAN_PRESENCE_TERMS){
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termUuuid = BfnXmlTransformer.getGermanAbsenceTermUUID(label);
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}else if(vocabulary == Vocabulary.GERMAN_ESTABLISHMENT_TERMS){
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termUuuid = BfnXmlTransformer.getGermanEstablishmentTermUUID(label);
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}else if(termType == TermType.NamedArea){
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termUuuid = BfnXmlTransformer.getAreaUUID(label);
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}
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} catch (UnknownCdmTypeException e) {
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logger.warn("Could not match term to uuid: "+e.toString());
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termUuuid = UUID.randomUUID();
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}
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@SuppressWarnings("rawtypes")
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DefinedTermBase term = getTermService().load(termUuuid);
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if(term != null){
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//already in the db, so no need to step through the whole process again.
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return;
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}else{
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if(termType == TermType.NamedArea){
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//Namedareas
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NamedArea namedArea = NamedArea.NewInstance(label, label, abbrevatedLabel);
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term = namedArea;
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term.setIdInVocabulary(Integer.toString(id));
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if (vocabulary == Vocabulary.GERMAN_FEDERAL_STATES){
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namedArea.setType(NamedAreaType.ADMINISTRATION_AREA());
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if(label.equalsIgnoreCase("Deutschland")){
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namedArea.setLevel(NamedAreaLevel.COUNTRY());
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parentGermany = (NamedArea) term;
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}else{
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namedArea.setLevel(NamedAreaLevel.STATE());
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term.setPartOf(parentGermany);
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}
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}else{
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if (vocabulary == Vocabulary.GERMAN_COMBINED_STATES){
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namedArea.setType(NamedAreaType.ADMINISTRATION_AREA());
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}else{
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namedArea.setType(NamedAreaType.NATURAL_AREA());
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}
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}
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}else{
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term = PresenceAbsenceTerm.NewPresenceInstance(label, label, abbrevatedLabel);
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term.setIdInVocabulary(abbrevatedLabel);
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if(vocabulary.equals(Vocabulary.GERMAN_PRESENCE_TERMS)){
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//create hierarchy of terms
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if(abbrevatedLabel.length() >1 ){
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((PresenceAbsenceTerm)term).setPartOf(lastParent);
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}else {
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lastParent = (PresenceAbsenceTerm) term;
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}
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}
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}
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term.setUuid(termUuuid);
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}
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createOrUpdateTermVocabulary(termType, getVocabularyService(), term, vocabulary.toString());
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id++;
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}
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}
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/**
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* @param vocabularyService
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* @param term
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* @param vocUUID
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*/
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@SuppressWarnings({ "unchecked", "rawtypes" })
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private OrderedTermVocabulary createOrUpdateTermVocabulary(TermType termType, IVocabularyService vocabularyService, DefinedTermBase term, String strTermVocabulary) {
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OrderedTermVocabulary termVocabulary = null;
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UUID vocUUID = null;
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try {
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vocUUID=BfnXmlTransformer.getRedlistVocabularyUUID(strTermVocabulary);
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} catch (UnknownCdmTypeException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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if(vocUUID != null){
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termVocabulary = (OrderedTermVocabulary) vocabularyService.load(vocUUID);
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}
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//lookup via String in case uuid lookup does not work
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if(termVocabulary == null && vocUUID == 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 = (OrderedTermVocabulary) tv;
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}
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}
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}
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//create termvocabulary
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if(termVocabulary == null){
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termVocabulary = OrderedTermVocabulary.NewInstance(termType, strTermVocabulary, strTermVocabulary, strTermVocabulary, null);
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if(vocUUID != null){
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termVocabulary.setUuid(vocUUID);
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}
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}
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termVocabulary.addTerm((OrderedTermBase) term);
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vocabularyService.saveOrUpdate(termVocabulary);
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return termVocabulary;
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}
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@Override
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protected boolean isIgnore(BfnXmlImportState state){
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return ! state.getConfig().isDoAdditionalTerms();
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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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}
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