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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.pesi.faunaEuropaea;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.babadshanjan
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* @since 12.05.2009
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*/
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public final class FaunaEuropaeaTransformer {
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaTransformer.class);
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public static final UUID uuidFauEuArea = UUID.fromString("16325043-e7da-4742-b012-9ce03362a124");
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// Query
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public static final int Q_NO_RESTRICTION = -1;
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// TaxonStatus
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public static final int T_STATUS_ACCEPTED = 1;
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public static final int T_STATUS_NOT_ACCEPTED = 0;
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// Author
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public static final int A_AUCT = 1;
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public static final String A_AUCTNAME = "auct.";
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// Parenthesis
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public static final int P_PARENTHESIS = 1;
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// User
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public static final int U_ACTIVE = 1;
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//new AbsencePresenceTermUUIDs
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// Rank
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public static final int R_KINGDOM = 1;
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public static final int R_SUBKINGDOM = 2;
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public static final int R_SUPERPHYLUM = 3;
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public static final int R_PHYLUM = 4;
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public static final int R_SUBPHYLUM = 5;
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public static final int R_INFRAPHYLUM = 6;
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public static final int R_CLASS = 7;
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public static final int R_SUBCLASS = 8;
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public static final int R_INFRACLASS = 9;
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public static final int R_SUPERORDER = 10;
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public static final int R_ORDER = 11;
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public static final int R_SUBORDER = 12;
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public static final int R_INFRAORDER = 13;
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public static final int R_SUPERFAMILY = 14;
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public static final int R_FAMILY = 15;
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public static final int R_SUBFAMILY = 16;
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public static final int R_TRIBE = 17;
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public static final int R_SUBTRIBE = 18;
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public static final int R_GENUS = 19;
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public static final int R_SUBGENUS = 20;
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public static final int R_SPECIES = 21;
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public static final int R_SUBSPECIES = 22;
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public static PresenceAbsenceTerm occStatus2PresenceAbsence(int occStatusId){
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if (Integer.valueOf(occStatusId) == null) {
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return PresenceAbsenceTerm.PRESENT();
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}
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switch (occStatusId){
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case 0: return PresenceAbsenceTerm.PRESENT();
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case 2: return PresenceAbsenceTerm.ABSENT();
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case 1: return PresenceAbsenceTerm.PRESENT_DOUBTFULLY();
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default: {
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return null;
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}
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}
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}
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public static PresenceAbsenceTerm occStatus2PresenceAbsence_ (int occStatusId) throws UnknownCdmTypeException{
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switch (occStatusId){
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case 0: return null;
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//case 110: return AbsenceTerm.CULTIVATED_REPORTED_IN_ERROR();
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case 120: return PresenceAbsenceTerm.CULTIVATED();
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// case 210: return AbsenceTerm.INTRODUCED_REPORTED_IN_ERROR();
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case 220: return PresenceAbsenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
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case 230: return PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
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case 240: return PresenceAbsenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
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case 250: return PresenceAbsenceTerm.INTRODUCED();
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case 260: return PresenceAbsenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
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case 270: return PresenceAbsenceTerm.CASUAL();
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case 280: return PresenceAbsenceTerm.NATURALISED();
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//case 310: return AbsenceTerm.NATIVE_REPORTED_IN_ERROR();
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case 320: return PresenceAbsenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
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case 330: return PresenceAbsenceTerm.NATIVE_FORMERLY_NATIVE();
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case 340: return PresenceAbsenceTerm.NATIVE_DOUBTFULLY_NATIVE();
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case 350: return PresenceAbsenceTerm.NATIVE();
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case 999: {
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logger.warn("endemic for EM can not be transformed in legal status");
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//TODO preliminary
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return PresenceAbsenceTerm.PRESENT();
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}
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default: {
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throw new UnknownCdmTypeException("Unknown occurrence status (id=" + Integer.valueOf(occStatusId).toString() + ")");
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}
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}
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}
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public static Rank rankId2Rank (ResultSet rs, boolean useUnknown) throws UnknownCdmTypeException {
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Rank result;
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try {
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int rankId = rs.getInt("rnk_id");
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int parentRankId = rs.getInt("rnk_rnk_id");
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String rankName = rs.getString("rnk_name");
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String rankLatinName = rs.getString("rnk_latinname");
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int rankCategory = rs.getInt("rnk_category");
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if (logger.isDebugEnabled()) {
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logger.debug(rankId + ", " + parentRankId + ", " + rankName + ", " + rankCategory);
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}
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try {
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result = Rank.getRankByNameOrIdInVoc(rankName);
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} catch (UnknownCdmTypeException e1) {
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switch (rankId) {
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case 0: return null;
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case R_KINGDOM: return Rank.KINGDOM();
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case R_SUBKINGDOM: return Rank.SUBKINGDOM();
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case R_SUPERPHYLUM: return Rank.SUPERPHYLUM();
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case R_PHYLUM: return Rank.PHYLUM();
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case R_SUBPHYLUM: return Rank.SUBPHYLUM();
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case R_INFRAPHYLUM: return Rank.INFRAPHYLUM();
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case R_CLASS: return Rank.CLASS();
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case R_SUBCLASS: return Rank.SUBCLASS();
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case R_INFRACLASS: return Rank.INFRACLASS();
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case R_SUPERORDER: return Rank.SUPERORDER();
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case R_ORDER: return Rank.ORDER();
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case R_SUBORDER: return Rank.SUBORDER();
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case R_INFRAORDER: return Rank.INFRAORDER();
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case R_SUPERFAMILY: return Rank.SUPERFAMILY();
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case R_FAMILY: return Rank.FAMILY();
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case R_SUBFAMILY: return Rank.SUBFAMILY();
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case R_TRIBE: return Rank.TRIBE();
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case R_SUBTRIBE: return Rank.SUBTRIBE();
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case R_GENUS: return Rank.GENUS();
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case R_SUBGENUS: return Rank.SUBGENUS();
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case R_SPECIES: return Rank.SPECIES();
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case R_SUBSPECIES: return Rank.SUBSPECIES();
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default: {
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if (useUnknown){
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logger.error("Rank unknown. Created UNKNOWN_RANK");
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return Rank.UNKNOWN_RANK();
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}
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throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());
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}
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}
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}
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return result;
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} catch (SQLException e) {
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e.printStackTrace();
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logger.warn("Exception occurred. Created UNKNOWN_RANK instead");
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return Rank.UNKNOWN_RANK();
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}
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}
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public final static HashMap<Integer, Language> languageFK2Language = new HashMap<>();
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static
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{
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languageFK2Language.put(1, Language.ALBANIAN());
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languageFK2Language.put(4, Language.AZERBAIJANI());
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languageFK2Language.put(6, Language.BULGARIAN());
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languageFK2Language.put(10, Language.DANISH());
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languageFK2Language.put(11, Language.DUTCH_MIDDLE());
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languageFK2Language.put(12, Language.ENGLISH());
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languageFK2Language.put(16, Language.FRENCH());
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languageFK2Language.put(18, Language.GERMAN());
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languageFK2Language.put(19, Language.GREEK_MODERN());
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languageFK2Language.put(23, Language.HEBREW());
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languageFK2Language.put(24, Language.ITALIAN());
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languageFK2Language.put(26, Language.LITHUANIAN());
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languageFK2Language.put(30, Language.NORWEGIAN());
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languageFK2Language.put(31, Language.POLISH());
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languageFK2Language.put(34, Language.RUSSIAN());
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languageFK2Language.put(54, Language.SLOVAK());
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languageFK2Language.put(55, Language.SLOVENIAN());
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languageFK2Language.put(57, Language.SWEDISH());
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languageFK2Language.put(58, Language.TURKISH());
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languageFK2Language.put(59, Language.UKRAINIAN());
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languageFK2Language.put(60, Language.WELSH());
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languageFK2Language.put(62, Language.GALICIAN());
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//languageFK2Language.put(83, getEnglishUS());
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languageFK2Language.put(97, Language.IRISH());
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220
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languageFK2Language.put(100, Language.NORWEGIAN_BOKMOL());
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languageFK2Language.put(101, Language.NORWEGIAN_NYNORSK());
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languageFK2Language.put(102, Language.ARABIC());
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languageFK2Language.put(103, Language.ARMENIAN());
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languageFK2Language.put(104, Language.CATALAN_VALENCIAN());
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languageFK2Language.put(105, Language.CHINESE());
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languageFK2Language.put(106, Language.ESTONIAN());
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languageFK2Language.put(107, Language.FINNISH());
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languageFK2Language.put(108, Language.GAELIC_SCOTTISH_GAELIC());
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languageFK2Language.put(109, Language.JAPANESE());
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languageFK2Language.put(110, Language.KOREAN());
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languageFK2Language.put(111, Language.LATIN());
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languageFK2Language.put(112, Language.LATVIAN());
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languageFK2Language.put(113, Language.PERSIAN());
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languageFK2Language.put(114, Language.PORTUGUESE());
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languageFK2Language.put(115, Language.ROMANIAN());
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240
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languageFK2Language.put(116, Language.GAELIC_SCOTTISH_GAELIC());
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241
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languageFK2Language.put(117, Language.SWAHILI());
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languageFK2Language.put(118, Language.SPANISH_CASTILIAN());
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}
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244
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245
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static NomenclaturalStatusType nomStatusTempNamed;
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246
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247
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private static DefinedTerm taxonomicSpecialistType;
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248
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249
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private static UUID uuidTaxonomicSpecialistType = UUID.fromString("006879e4-cf99-405a-a720-2e81d9cbc34c");
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250
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251
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private static DefinedTerm groupCoordinatorType;
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252
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253
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private static UUID uuidGroupCoordinatorType = UUID.fromString("3a827ebe-4410-40e5-a241-941b17028e11");
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254
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255
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private static DefinedTerm associateSpecialistType;
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256
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257
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private static UUID uuidAssociateSpecialistType = UUID.fromString("8258f73c-e0ad-4f87-a88c-53c58c08bba9");
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258
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259
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private static Language langEnglishUS;
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260
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261
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private static UUID uuidEnglishUS;
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262
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263
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public static NomenclaturalStatusType getNomStatusTempNamed(ITermService termService){
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264
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if (nomStatusTempNamed == null){
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265
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nomStatusTempNamed = (NomenclaturalStatusType)termService.find(PesiTransformer.uuidNomStatusTemporaryName);
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266
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if (nomStatusTempNamed == null){
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267
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nomStatusTempNamed = NomenclaturalStatusType.NewInstance("temporary named", "temporary named", "temp. named", Language.ENGLISH());
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268
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Representation repLatin = Representation.NewInstance("", "", "", Language.LATIN());
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269
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nomStatusTempNamed.addRepresentation(repLatin);
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270
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nomStatusTempNamed.setUuid(PesiTransformer.uuidNomStatusTemporaryName);
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271
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NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusTempNamed);
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272
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termService.save(nomStatusTempNamed);
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273
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}
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274
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}
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275
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return nomStatusTempNamed;
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276
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}
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277
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278
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public static Language getEnglishUS(ITermService termService){
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279
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if (langEnglishUS == null){
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280
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langEnglishUS = (Language)termService.find(uuidEnglishUS);
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281
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if (langEnglishUS == null){
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282
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logger.info("create language english-us");
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283
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langEnglishUS = Language.NewInstance("english-United States", "english-US", "eng-US");
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284
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langEnglishUS.setUuid(uuidEnglishUS);
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285
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286
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langEnglishUS = (Language)termService.save(langEnglishUS);
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287
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languageFK2Language.put(83, langEnglishUS);
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288
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}
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289
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}
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290
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return langEnglishUS;
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291
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}
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292
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293
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public static DefinedTerm getTaxonomicSpecialistType(ITermService termService) {
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294
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if (taxonomicSpecialistType == null){
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295
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taxonomicSpecialistType = (DefinedTerm)termService.find(uuidTaxonomicSpecialistType);
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296
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if (taxonomicSpecialistType == null){
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297
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logger.info("create taxonomic specialist type");
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298
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taxonomicSpecialistType = DefinedTerm.NewInstance(TermType.TaxonNodeAgentRelationType, "taxonomic specialist", "taxonomic specialist", "TS");
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299
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300
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taxonomicSpecialistType.setUuid(uuidTaxonomicSpecialistType);
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301
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302
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termService.save(taxonomicSpecialistType);
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303
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}
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304
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}
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305
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return taxonomicSpecialistType;
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306
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}
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|
307
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308
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public static DefinedTerm getGroupCoordinatorType(ITermService termService) {
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309
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if (groupCoordinatorType == null){
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310
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groupCoordinatorType = (DefinedTerm)termService.find(uuidGroupCoordinatorType);
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311
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if (groupCoordinatorType == null){
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312
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groupCoordinatorType = DefinedTerm.NewInstance(TermType.TaxonNodeAgentRelationType, "group coordinator", "group coordinator", "GC");
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313
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314
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groupCoordinatorType.setUuid(uuidGroupCoordinatorType);
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315
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316
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termService.save(groupCoordinatorType);
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317
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}
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318
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}
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319
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return groupCoordinatorType;
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320
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}
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321
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322
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public static DefinedTerm getAssociateSpecialistType(ITermService termService) {
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323
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if (associateSpecialistType == null){
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324
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associateSpecialistType = (DefinedTerm)termService.find(uuidAssociateSpecialistType);
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325
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if (associateSpecialistType == null){
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326
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associateSpecialistType = DefinedTerm.NewInstance(TermType.TaxonNodeAgentRelationType, "associate specialist", "associate specialist", "AS");
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327
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328
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associateSpecialistType.setUuid(uuidAssociateSpecialistType);
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329
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330
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termService.save(associateSpecialistType);
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331
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}
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332
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}
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333
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return associateSpecialistType;
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334
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}
|
|
335
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336
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public static Language langFK2Language(Integer languageFk) {
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337
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Language result = languageFK2Language.get(languageFk);
|
|
338
|
return result;
|
|
339
|
}
|
|
340
|
}
|