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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.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.Map;
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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.model.description.AbsenceTerm;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
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import eu.etaxonomy.cdm.model.description.PresenceTerm;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.TdwgArea;
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import eu.etaxonomy.cdm.model.name.Rank;
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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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* @created 12.05.2009
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* @version 1.0
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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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// 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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//new AbsencePresenceTermUUIDs
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public static UUID noData;
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//public static UUID doubtfull_present;
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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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private static Map<String, String> tdwgAreas = null;
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public static PresenceAbsenceTermBase<?> occStatus2PresenceAbsence(int occStatusId) throws UnknownCdmTypeException{
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if (Integer.valueOf(occStatusId) == null) {
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return PresenceTerm.PRESENT();
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}
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switch (occStatusId){
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case 0: return PresenceTerm.PRESENT();
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case 2: return AbsenceTerm.ABSENT();
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case 1: return PresenceTerm.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 void setUUIDs(HashMap<String,UUID> uuids){
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noData = uuids.get("noData");
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//doubtfull_present = uuids.get("doubtfullPresent");
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}
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public static PresenceAbsenceTermBase<?> 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 PresenceTerm.CULTIVATED();
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// case 210: return AbsenceTerm.INTRODUCED_REPORTED_IN_ERROR();
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case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
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case 230: return PresenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
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case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
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case 250: return PresenceTerm.INTRODUCED();
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case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
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case 270: return PresenceTerm.INTRODUCED_ADVENTITIOUS();
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case 280: return PresenceTerm.INTRODUCED_NATURALIZED();
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//case 310: return AbsenceTerm.NATIVE_REPORTED_IN_ERROR();
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case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
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case 330: return PresenceTerm.NATIVE_FORMERLY_NATIVE();
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case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE();
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case 350: return PresenceTerm.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 PresenceTerm.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.getRankByNameOrAbbreviation(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 static NamedArea areaId2TdwgArea (FaunaEuropaeaDistribution fauEuDistribution)
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throws UnknownCdmTypeException {
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NamedArea tdwgArea = null;
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try {
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int areaId = fauEuDistribution.getAreaId();
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String areaName = fauEuDistribution.getAreaName();
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String areaCode = fauEuDistribution.getAreaCode();
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int extraLimital = fauEuDistribution.getExtraLimital();
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//TODO: Verify mappings with comments. Those don't map to TDWG areas.
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if (areaCode.equals("AD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-AN");
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//else if (areaCode.equals("AFR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("24"); // Afro-tropical region - Northeast Tropical Africa
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else if (areaCode.equals("AL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ALB-OO");
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else if (areaCode.equals("AT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-AU");
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//else if (areaCode.equals("AUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("50"); // Australian region - Australia
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else if (areaCode.equals("BA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-BH");
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else if (areaCode.equals("BE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-BE");
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else if (areaCode.equals("BG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BUL-OO");
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else if (areaCode.equals("BY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLR-OO");
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else if (areaCode.equals("CH")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SWI-OO");
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else if (areaCode.equals("CY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CYP-OO");
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else if (areaCode.equals("CZ")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CZE-CZ");
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else if (areaCode.equals("DE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GER-OO");
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else if (areaCode.equals("DK-DEN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("DEN-OO");
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else if (areaCode.equals("DK-FOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FOR-OO");
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else if (areaCode.equals("EE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES");
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//else if (areaCode.equals("EPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("3"); // Palaearctic - Asia-Temperate
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else if (areaCode.equals("ES-BAL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES");
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else if (areaCode.equals("ES-CNY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CNY-OO");
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else if (areaCode.equals("ES-SPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-SP");
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else if (areaCode.equals("FI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FIN-OO");
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else if (areaCode.equals("FR-COR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("COR-OO");
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else if (areaCode.equals("FR-FRA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-FR");
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else if (areaCode.equals("GB-CI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-CI");
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else if (areaCode.equals("GB-GI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-GI");
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else if (areaCode.equals("GB-GRB")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRB-OO");
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else if (areaCode.equals("GB-NI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-NI");
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//else if (areaCode.equals("GR-AEG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // North Aegean Is. - East Aegean Is.
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//else if (areaCode.equals("GR-CYC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO"); // Cyclades Is. - Greece
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//else if (areaCode.equals("GR-DOD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // Dodecanese Is. - East Aegean Is.
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else if (areaCode.equals("GR-GRC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO");
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else if (areaCode.equals("GR-KRI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("KRI-OO");
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else if (areaCode.equals("HR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-CR");
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else if (areaCode.equals("HU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("HUN-OO");
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else if (areaCode.equals("IE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-IR");
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else if (areaCode.equals("IS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ICE-OO");
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else if (areaCode.equals("IT-ITA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-IT");
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else if (areaCode.equals("IT-SAR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SAR-OO");
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else if (areaCode.equals("IT-SI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-SI");
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else if (areaCode.equals("LI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-LI");
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else if (areaCode.equals("LT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-LI");
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else if (areaCode.equals("LU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-LU");
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else if (areaCode.equals("LV")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-LA");
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else if (areaCode.equals("MC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-MO");
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else if (areaCode.equals("MD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-MO");
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else if (areaCode.equals("MK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-MA");
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else if (areaCode.equals("MT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-MA");
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//else if (areaCode.equals("NAF")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("20"); // North Africa - Northern Africa
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//else if (areaCode.equals("NEA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("7"); // Nearctic region - Northern America
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//else if (areaCode.equals("NEO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("8"); // Neotropical region - Southern America
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else if (areaCode.equals("NL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NET-OO");
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else if (areaCode.equals("NO-NOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NOR-OO");
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else if (areaCode.equals("NO-SVA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SVA-OO");
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//else if (areaCode.equals("NRE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("34"); // Near East - Western Asia
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//else if (areaCode.equals("ORR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("35"); // Oriental region - Arabian Peninsula
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else if (areaCode.equals("PL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POL-OO");
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else if (areaCode.equals("PT-AZO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AZO-OO");
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else if (areaCode.equals("PT-MDR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("MDR-OO");
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else if (areaCode.equals("PT-POR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POR-OO");
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else if (areaCode.equals("PT-SEL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SEL-OO");
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else if (areaCode.equals("RO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ROM-OO");
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else if (areaCode.equals("RU-FJL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("WSB-OO");
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else if (areaCode.equals("RU-KGD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-KA");
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else if (areaCode.equals("RU-NOZ")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("WSB-OO");
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274
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else if (areaCode.equals("RU-RUC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUC-OO");
|
|
275
|
else if (areaCode.equals("RU-RUE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUE-OO");
|
|
276
|
else if (areaCode.equals("RU-RUN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUN-OO");
|
|
277
|
else if (areaCode.equals("RU-RUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUS-OO");
|
|
278
|
else if (areaCode.equals("RU-RUW")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUW-OO");
|
|
279
|
else if (areaCode.equals("SE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SWE-OO");
|
|
280
|
else if (areaCode.equals("SI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-SL");
|
|
281
|
else if (areaCode.equals("SK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CZE-SK");
|
|
282
|
else if (areaCode.equals("SM")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-SM");
|
|
283
|
else if (areaCode.equals("TR-TUE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("TUE-OO");
|
|
284
|
else if (areaCode.equals("UA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-UK");
|
|
285
|
else if (areaCode.equals("VA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-VC");
|
|
286
|
else if (areaCode.equals("YU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG");
|
|
287
|
else
|
|
288
|
throw new UnknownCdmTypeException("Unknown Area " + areaCode);
|
|
289
|
|
|
290
|
if (logger.isDebugEnabled()) {
|
|
291
|
logger.debug(areaId + ", " + areaName + ", " + areaCode + ", " + extraLimital);
|
|
292
|
}
|
|
293
|
|
|
294
|
} catch (Exception e) {
|
|
295
|
//e.printStackTrace();
|
|
296
|
logger.debug("Exception occurred. Area could not be mapped." + fauEuDistribution.getAreaName());
|
|
297
|
return null;
|
|
298
|
}
|
|
299
|
|
|
300
|
return tdwgArea;
|
|
301
|
}
|
|
302
|
|
|
303
|
public final static HashMap<String, UUID> abbrToUUID = new HashMap<String,UUID>();
|
|
304
|
static
|
|
305
|
{
|
|
306
|
abbrToUUID.put("AUS", UUID.fromString("cf979ca8-8cb6-42df-b2ce-1f432ec7c26b"));
|
|
307
|
abbrToUUID.put("AFR", UUID.fromString("07ac5e75-9fc9-4aa0-938c-1324c9618b97"));
|
|
308
|
abbrToUUID.put("EPA", UUID.fromString("e83446d7-7379-4beb-be05-295f8da6f5ae"));
|
|
309
|
abbrToUUID.put("GR-AEG", UUID.fromString("6bd422aa-9911-4b80-8595-0f6d1ecd5eee"));
|
|
310
|
abbrToUUID.put("GR-CYC", UUID.fromString("8e7d7f1e-3e4d-4f7c-96ec-93ec91e528d6"));
|
|
311
|
abbrToUUID.put("GR-DOD", UUID.fromString("6d6f6842-924e-440b-9e7e-3df1922bf4a6"));
|
|
312
|
abbrToUUID.put("NAF", UUID.fromString("d2c54b1e-5f9f-455d-b308-6859cb153c7b"));
|
|
313
|
abbrToUUID.put("NEA", UUID.fromString("aa87f6b8-110b-44b5-a329-91a08f1a4cc9"));
|
|
314
|
abbrToUUID.put("NEO", UUID.fromString("0e6e0ce9-c6ab-46bc-80b9-aee4a0620e78"));
|
|
315
|
abbrToUUID.put("NRE", UUID.fromString("d51876c2-eaf6-4c7f-963e-337dd3e0d729"));
|
|
316
|
abbrToUUID.put("ORR", UUID.fromString("04cab4f8-b316-4e21-9bcc-236a45e4e83d"));
|
|
317
|
}
|
|
318
|
public static UUID getUUIDByAreaAbbr(String abbr){
|
|
319
|
return abbrToUUID.get(abbr);
|
|
320
|
}
|
|
321
|
|
|
322
|
}
|