cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaTransformer.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.faunaEuropaea;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.Map;
  16
  17 import org.apache.log4j.Logger;
  18 import org.springframework.stereotype.Component;
  19
  20 import eu.etaxonomy.cdm.common.ResultWrapper;
  21 import eu.etaxonomy.cdm.model.description.Feature;
  22 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
  23 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  24 import eu.etaxonomy.cdm.model.location.NamedArea;
  25 import eu.etaxonomy.cdm.model.location.TdwgArea;
  26 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  27 import eu.etaxonomy.cdm.model.name.Rank;
  28 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  29 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  30 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  31
  32 /**
  33  * @author a.babadshanjan
  34  * @created 12.05.2009
  35  * @version 1.0
  36  */
  37
  38 public final class FaunaEuropaeaTransformer {
  39         private static final Logger logger = Logger.getLogger(FaunaEuropaeaTransformer.class);
  40
  41         //TaxonStatus
  42         public static final int T_STATUS_ACCEPTED = 1;
  43         public static final int T_STATUS_NOT_ACCEPTED = 0;
  44
  45         // Rank
  46         public static final int R_KINGDOM = 1;
  47         public static final int R_SUBKINGDOM = 2;
  48         public static final int R_SUPERPHYLUM = 3;
  49         public static final int R_PHYLUM = 4;
  50         public static final int R_SUBPHYLUM = 5;
  51         public static final int R_INFRAPHYLUM = 6;
  52         public static final int R_CLASS = 7;
  53         public static final int R_SUBCLASS = 8;
  54         public static final int R_INFRACLASS = 9;
  55         public static final int R_SUPERORDER = 10;
  56         public static final int R_ORDER = 11;
  57         public static final int R_SUBORDER = 12;
  58         public static final int R_INFRAORDER = 13;
  59         public static final int R_SUPERFAMILY = 14;
  60         public static final int R_FAMILY = 15;
  61         public static final int R_SUBFAMILY = 16;
  62         public static final int R_TRIBE = 17;
  63         public static final int R_SUBTRIBE = 18;
  64         public static final int R_GENUS = 19;
  65         public static final int R_SUBGENUS = 20;
  66         public static final int R_SPECIES = 21;
  67         public static final int R_SUBSPECIES = 22;
  68
  69         private static Map<String, String> tdwgAreas = null;
  70
  71         public static PresenceAbsenceTermBase<?> occStatus2PresenceAbsence (int occStatusId)  throws UnknownCdmTypeException{
  72                 switch (occStatusId){
  73                         case 0: return null;
  74                         case 110: return PresenceTerm.CULTIVATED_REPORTED_IN_ERROR();
  75                         case 120: return PresenceTerm.CULTIVATED();
  76                         case 210: return PresenceTerm.INTRODUCED_REPORTED_IN_ERROR();
  77                         case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
  78                         case 230: return PresenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
  79                         case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
  80                         case 250: return PresenceTerm.INTRODUCED();
  81                         case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
  82                         case 270: return PresenceTerm.INTRODUCED_ADVENTITIOUS();
  83                         case 280: return PresenceTerm.INTRODUCED_NATURALIZED();
  84                         case 310: return PresenceTerm.NATIVE_REPORTED_IN_ERROR();
  85                         case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
  86                         case 330: return PresenceTerm.NATIVE_FORMERLY_NATIVE();
  87                         case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE();
  88                         case 350: return PresenceTerm.NATIVE();
  89                         case 999: {
  90                                         logger.warn("endemic for EM can not be transformed in legal status");
  91                                         //TODO preliminary
  92                                         return PresenceTerm.PRESENT();
  93                                 }
  94                         default: {
  95                                 throw new UnknownCdmTypeException("Unknown occurrence status  (id=" + Integer.valueOf(occStatusId).toString() + ")");
  96                         }
  97                 }
  98         }
  99
 100
 101         public static Rank rankId2Rank (ResultSet rs, boolean useUnknown) throws UnknownCdmTypeException {
 102                 Rank result;
 103                 try {
 104                         int rankId = rs.getInt("rnk_id");
 105                         int parentRankId = rs.getInt("rnk_rnk_id");
 106                         String rankName = rs.getString("rnk_name");
 107                         String rankLatinName = rs.getString("rnk_latinname");
 108                         int rankCategory = rs.getInt("rnk_category");
 109
 110                         if (logger.isDebugEnabled()) {
 111                                 logger.debug(rankId + ", " + parentRankId + ", " + rankName + ", " + rankLatinName + ", " + rankCategory);
 112                         }
 113
 114                         try {
 115                                 result = Rank.getRankByNameOrAbbreviation(rankName);
 116                         } catch (UnknownCdmTypeException e1) {
 117
 118                                 switch (rankId) {
 119                                 case 0: return null;
 120                                 case R_KINGDOM: return Rank.KINGDOM();
 121                                 case R_SUBKINGDOM: return Rank.SUBKINGDOM();
 122                                 case R_SUPERPHYLUM: return Rank.SUPERPHYLUM();
 123                                 case R_PHYLUM: return Rank.PHYLUM();
 124                                 case R_SUBPHYLUM: return Rank.SUBPHYLUM();
 125                                 case R_INFRAPHYLUM: return Rank.INFRAPHYLUM();
 126                                 case R_CLASS: return Rank.CLASS();
 127                                 case R_SUBCLASS: return Rank.SUBCLASS();
 128                                 case R_INFRACLASS: return Rank.INFRACLASS();
 129                                 case R_SUPERORDER: return Rank.SUPERORDER();
 130                                 case R_ORDER: return Rank.ORDER();
 131                                 case R_SUBORDER: return Rank.SUBORDER();
 132                                 case R_INFRAORDER: return Rank.INFRAORDER();
 133                                 case R_SUPERFAMILY: return Rank.SUPERFAMILY();
 134                                 case R_FAMILY: return Rank.FAMILY();
 135                                 case R_SUBFAMILY: return Rank.SUBFAMILY();
 136                                 case R_TRIBE: return Rank.TRIBE();
 137                                 case R_SUBTRIBE: return Rank.SUBTRIBE();
 138                                 case R_GENUS: return Rank.GENUS();
 139                                 case R_SUBGENUS: return Rank.SUBGENUS();
 140                                 case R_SPECIES: return Rank.SPECIES();
 141                                 case R_SUBSPECIES: return Rank.SUBSPECIES();
 142
 143                                 default: {
 144                                         if (useUnknown){
 145                                                 logger.error("Rank unknown. Created UNKNOWN_RANK");
 146                                                 return Rank.UNKNOWN_RANK();
 147                                         }
 148                                         throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());
 149                                 }
 150                                 }
 151                         }
 152                         return result;
 153                 } catch (SQLException e) {
 154                         e.printStackTrace();
 155                         logger.warn("Exception occurred. Created UNKNOWN_RANK instead");
 156                         return Rank.UNKNOWN_RANK();
 157                 }
 158         }
 159
 160
 161         public static NamedArea areaId2TdwgArea (ResultSet rs, boolean useUnknown) throws UnknownCdmTypeException {
 162
 163                 NamedArea tdwgArea = null;
 164
 165                 try {
 166                         int areaId = rs.getInt("ara_id");
 167                         String areaName = rs.getString("ara_name");
 168                         String areaCode = rs.getString("ara_code");
 169                         int extraLimital = rs.getInt("ara_extralimital");
 170
 171                         //TODO: Verify mappings with comments. Are those the best matches?
 172
 173                         if (areaCode.equals("AD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-AN");
 174                         else if (areaCode.equals("AFR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("24"); // Afro-tropical region - Northeast Tropical Africa
 175                         else if (areaCode.equals("AL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ALB-OO");
 176                         else if (areaCode.equals("AT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-AU");
 177                         else if (areaCode.equals("AUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("50"); // Australian region - Australia
 178                         else if (areaCode.equals("BA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-BH");
 179                         else if (areaCode.equals("BE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-BE");
 180                         else if (areaCode.equals("BG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BUL-OO");
 181                         else if (areaCode.equals("BY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLR-OO");
 182                         else if (areaCode.equals("CH")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SWI-OO");
 183                         else if (areaCode.equals("CY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CYP-OO");
 184                         else if (areaCode.equals("CZ")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CZE-CZ");
 185                         else if (areaCode.equals("DE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GER-OO");
 186                         else if (areaCode.equals("DK-DEN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("DEN-OO");
 187                         else if (areaCode.equals("DK-FOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FOR-OO");
 188                         else if (areaCode.equals("EE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES");
 189                         else if (areaCode.equals("EPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("Palaearctic");
 190                         else if (areaCode.equals("ES-BAL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES");
 191                         else if (areaCode.equals("ES-CNY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CNY-OO");
 192                         else if (areaCode.equals("ES-SPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-SP");
 193                         else if (areaCode.equals("FI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FIN-OO");
 194                         else if (areaCode.equals("FR-COR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("COR-OO");
 195                         else if (areaCode.equals("FR-FRA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-FR");
 196                         else if (areaCode.equals("GB-CI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-CI");
 197                         else if (areaCode.equals("GB-GI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-GI");
 198                         else if (areaCode.equals("GB-GRB")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRB-OO");
 199                         else if (areaCode.equals("GB-NI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-NI");
 200                         else if (areaCode.equals("GR-AEG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // North Aegean Is. - East Aegean Is.
 201                         else if (areaCode.equals("GR-CYC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO"); // Cyclades Is. - Greece
 202                         else if (areaCode.equals("GR-DOD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // Dodecanese Is. - East Aegean Is.
 203                         else if (areaCode.equals("GR-GRC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO");
 204                         else if (areaCode.equals("GR-KRI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("KRI-OO");
 205                         else if (areaCode.equals("HR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-CR");
 206                         else if (areaCode.equals("HU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("HUN-OO");
 207                         else if (areaCode.equals("IE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-IR");
 208                         else if (areaCode.equals("IS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ICE-OO");
 209                         else if (areaCode.equals("IT-ITA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-IT");
 210                         else if (areaCode.equals("IT-SAR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SAR-OO");
 211                         else if (areaCode.equals("IT-SI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-SI");
 212                         else if (areaCode.equals("LI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-LI");
 213                         else if (areaCode.equals("LT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-LI");
 214                         else if (areaCode.equals("LU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-LU");
 215                         else if (areaCode.equals("LV")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-LA");
 216                         else if (areaCode.equals("MC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-MO");
 217                         else if (areaCode.equals("MD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-MO");
 218                         else if (areaCode.equals("MK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-MA");
 219                         else if (areaCode.equals("MT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-MA");
 220                         else if (areaCode.equals("NAF")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("20"); // North Africa - Northern Africa
 221                         else if (areaCode.equals("NEA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("7");    // Nearctic region - Northern America
 222                         else if (areaCode.equals("NEO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("8"); // Neotropical region - Southern America
 223 else if (areaCode.equals("NL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NET-OO");
 224                         else if (areaCode.equals("NO-NOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NOR-OO");
 225                         else if (areaCode.equals("NO-SVA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SVA-OO");
 226                         else if (areaCode.equals("NRE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("34"); // Near East - Western Asia
 227                         else if (areaCode.equals("ORR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("35");   // Oriental region - Arabian Peninsula
 228                         else if (areaCode.equals("PL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POL-OO");
 229                         else if (areaCode.equals("PT-AZO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AZO-OO");
 230                         else if (areaCode.equals("PT-MDR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("MDR-OO");
 231                         else if (areaCode.equals("PT-POR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POR-OO");
 232                         else if (areaCode.equals("PT-SEL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SEL-OO");
 233                         else if (areaCode.equals("RO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ROM-OO");
 234                         else if (areaCode.equals("RU-FJL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("WSB-OO");
 235                         else if (areaCode.equals("RU-KGD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-KA");
 236                         else if (areaCode.equals("RU-NOZ")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("WSB-OO");
 237                         else if (areaCode.equals("RU-RUC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUC-OO");
 238                         else if (areaCode.equals("RU-RUE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUE-OO");
 239                         else if (areaCode.equals("RU-RUN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUN-OO");
 240                         else if (areaCode.equals("RU-RUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUS-OO");
 241                         else if (areaCode.equals("RU-RUW")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUW-OO");
 242                         else if (areaCode.equals("SE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SWE-OO");
 243                         else if (areaCode.equals("SI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-SL");
 244                         else if (areaCode.equals("SK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CZE-SL");
 245                         else if (areaCode.equals("SM")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-SM");
 246                         else if (areaCode.equals("TR-TUE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("TUE-OO");
 247                         else if (areaCode.equals("UA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-UK");
 248                         else if (areaCode.equals("VA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-VC");
 249                         else if (areaCode.equals("YU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG");
 250                         else
 251                                 throw new UnknownCdmTypeException("Unknown Area " + areaCode);
 252
 253
 254                         if (logger.isDebugEnabled()) {
 255                                 logger.debug(areaId + ", " + areaName + ", " + areaCode + ", " + extraLimital);
 256                         }
 257
 258                 } catch (SQLException e) {
 259                         e.printStackTrace();
 260                         logger.warn("Exception occurred. Area could not be mapped.");
 261                         return null;
 262                 }
 263
 264                 return tdwgArea;
 265         }
 266
 267 }