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.AbsenceTerm;
  22 import eu.etaxonomy.cdm.model.description.Feature;
  23 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
  24 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  25 import eu.etaxonomy.cdm.model.location.NamedArea;
  26 import eu.etaxonomy.cdm.model.location.TdwgArea;
  27 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  28 import eu.etaxonomy.cdm.model.name.Rank;
  29 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  30 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  31 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  32
  33 /**
  34  * @author a.babadshanjan
  35  * @created 12.05.2009
  36  * @version 1.0
  37  */
  38
  39 public final class FaunaEuropaeaTransformer {
  40         private static final Logger logger = Logger.getLogger(FaunaEuropaeaTransformer.class);
  41
  42         // Query
  43         public static final int Q_NO_RESTRICTION = -1;
  44
  45         // TaxonStatus
  46         public static final int T_STATUS_ACCEPTED = 1;
  47         public static final int T_STATUS_NOT_ACCEPTED = 0;
  48
  49         // Author
  50         public static final int A_AUCT = 1;
  51         public static final String A_AUCTNAME = "auct.";
  52
  53         // Parenthesis
  54         public static final int P_PARENTHESIS = 1;
  55
  56         // Rank
  57         public static final int R_KINGDOM = 1;
  58         public static final int R_SUBKINGDOM = 2;
  59         public static final int R_SUPERPHYLUM = 3;
  60         public static final int R_PHYLUM = 4;
  61         public static final int R_SUBPHYLUM = 5;
  62         public static final int R_INFRAPHYLUM = 6;
  63         public static final int R_CLASS = 7;
  64         public static final int R_SUBCLASS = 8;
  65         public static final int R_INFRACLASS = 9;
  66         public static final int R_SUPERORDER = 10;
  67         public static final int R_ORDER = 11;
  68         public static final int R_SUBORDER = 12;
  69         public static final int R_INFRAORDER = 13;
  70         public static final int R_SUPERFAMILY = 14;
  71         public static final int R_FAMILY = 15;
  72         public static final int R_SUBFAMILY = 16;
  73         public static final int R_TRIBE = 17;
  74         public static final int R_SUBTRIBE = 18;
  75         public static final int R_GENUS = 19;
  76         public static final int R_SUBGENUS = 20;
  77         public static final int R_SPECIES = 21;
  78         public static final int R_SUBSPECIES = 22;
  79
  80         private static Map<String, String> tdwgAreas = null;
  81
  82         public static PresenceAbsenceTermBase<?> occStatus2PresenceAbsence(int occStatusId)  throws UnknownCdmTypeException{
  83                 switch (occStatusId){
  84                         case 0: return AbsenceTerm.ABSENT();
  85                         case 2: return PresenceTerm.INTRODUCED();
  86                         case 1: return PresenceTerm.NATIVE();
  87                         default: {
  88                                 throw new UnknownCdmTypeException("Unknown presence status (id=" + Integer.valueOf(occStatusId).toString() + ")");
  89                         }
  90                 }
  91         }
  92
  93
  94         public static PresenceAbsenceTermBase<?> occStatus2PresenceAbsence_ (int occStatusId)  throws UnknownCdmTypeException{
  95                 switch (occStatusId){
  96                         case 0: return null;
  97                         case 110: return PresenceTerm.CULTIVATED_REPORTED_IN_ERROR();
  98                         case 120: return PresenceTerm.CULTIVATED();
  99                         case 210: return PresenceTerm.INTRODUCED_REPORTED_IN_ERROR();
 100                         case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
 101                         case 230: return PresenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
 102                         case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
 103                         case 250: return PresenceTerm.INTRODUCED();
 104                         case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
 105                         case 270: return PresenceTerm.INTRODUCED_ADVENTITIOUS();
 106                         case 280: return PresenceTerm.INTRODUCED_NATURALIZED();
 107                         case 310: return PresenceTerm.NATIVE_REPORTED_IN_ERROR();
 108                         case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
 109                         case 330: return PresenceTerm.NATIVE_FORMERLY_NATIVE();
 110                         case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE();
 111                         case 350: return PresenceTerm.NATIVE();
 112                         case 999: {
 113                                         logger.warn("endemic for EM can not be transformed in legal status");
 114                                         //TODO preliminary
 115                                         return PresenceTerm.PRESENT();
 116                                 }
 117                         default: {
 118                                 throw new UnknownCdmTypeException("Unknown occurrence status  (id=" + Integer.valueOf(occStatusId).toString() + ")");
 119                         }
 120                 }
 121         }
 122
 123
 124         public static Rank rankId2Rank (ResultSet rs, boolean useUnknown) throws UnknownCdmTypeException {
 125                 Rank result;
 126                 try {
 127                         int rankId = rs.getInt("rnk_id");
 128                         int parentRankId = rs.getInt("rnk_rnk_id");
 129                         String rankName = rs.getString("rnk_name");
 130                         String rankLatinName = rs.getString("rnk_latinname");
 131                         int rankCategory = rs.getInt("rnk_category");
 132
 133                         if (logger.isDebugEnabled()) {
 134                                 logger.debug(rankId + ", " + parentRankId + ", " + rankName + ", " + rankCategory);
 135                         }
 136
 137                         try {
 138                                 result = Rank.getRankByNameOrAbbreviation(rankName);
 139                         } catch (UnknownCdmTypeException e1) {
 140
 141                                 switch (rankId) {
 142                                 case 0: return null;
 143                                 case R_KINGDOM: return Rank.KINGDOM();
 144                                 case R_SUBKINGDOM: return Rank.SUBKINGDOM();
 145                                 case R_SUPERPHYLUM: return Rank.SUPERPHYLUM();
 146                                 case R_PHYLUM: return Rank.PHYLUM();
 147                                 case R_SUBPHYLUM: return Rank.SUBPHYLUM();
 148                                 case R_INFRAPHYLUM: return Rank.INFRAPHYLUM();
 149                                 case R_CLASS: return Rank.CLASS();
 150                                 case R_SUBCLASS: return Rank.SUBCLASS();
 151                                 case R_INFRACLASS: return Rank.INFRACLASS();
 152                                 case R_SUPERORDER: return Rank.SUPERORDER();
 153                                 case R_ORDER: return Rank.ORDER();
 154                                 case R_SUBORDER: return Rank.SUBORDER();
 155                                 case R_INFRAORDER: return Rank.INFRAORDER();
 156                                 case R_SUPERFAMILY: return Rank.SUPERFAMILY();
 157                                 case R_FAMILY: return Rank.FAMILY();
 158                                 case R_SUBFAMILY: return Rank.SUBFAMILY();
 159                                 case R_TRIBE: return Rank.TRIBE();
 160                                 case R_SUBTRIBE: return Rank.SUBTRIBE();
 161                                 case R_GENUS: return Rank.GENUS();
 162                                 case R_SUBGENUS: return Rank.SUBGENUS();
 163                                 case R_SPECIES: return Rank.SPECIES();
 164                                 case R_SUBSPECIES: return Rank.SUBSPECIES();
 165
 166                                 default: {
 167                                         if (useUnknown){
 168                                                 logger.error("Rank unknown. Created UNKNOWN_RANK");
 169                                                 return Rank.UNKNOWN_RANK();
 170                                         }
 171                                         throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());
 172                                 }
 173                                 }
 174                         }
 175                         return result;
 176                 } catch (SQLException e) {
 177                         e.printStackTrace();
 178                         logger.warn("Exception occurred. Created UNKNOWN_RANK instead");
 179                         return Rank.UNKNOWN_RANK();
 180                 }
 181         }
 182
 183
 184         public static NamedArea areaId2TdwgArea (FaunaEuropaeaDistribution fauEuDistribution)
 185         throws UnknownCdmTypeException {
 186
 187                 NamedArea tdwgArea = null;
 188
 189                 try {
 190                         int areaId = fauEuDistribution.getAreaId();
 191                         String areaName = fauEuDistribution.getAreaName();
 192                         String areaCode = fauEuDistribution.getAreaCode();
 193                         int extraLimital = fauEuDistribution.getExtraLimital();
 194
 195                         //TODO: Verify mappings with comments. Those don't map to TDWG areas.
 196
 197                         if (areaCode.equals("AD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-AN");
 198                         else if (areaCode.equals("AFR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("24"); // Afro-tropical region - Northeast Tropical Africa
 199                         else if (areaCode.equals("AL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ALB-OO");
 200                         else if (areaCode.equals("AT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-AU");
 201                         else if (areaCode.equals("AUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("50"); // Australian region - Australia
 202                         else if (areaCode.equals("BA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-BH");
 203                         else if (areaCode.equals("BE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-BE");
 204                         else if (areaCode.equals("BG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BUL-OO");
 205                         else if (areaCode.equals("BY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLR-OO");
 206                         else if (areaCode.equals("CH")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SWI-OO");
 207                         else if (areaCode.equals("CY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CYP-OO");
 208                         else if (areaCode.equals("CZ")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CZE-CZ");
 209                         else if (areaCode.equals("DE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GER-OO");
 210                         else if (areaCode.equals("DK-DEN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("DEN-OO");
 211                         else if (areaCode.equals("DK-FOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FOR-OO");
 212                         else if (areaCode.equals("EE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES");
 213                         else if (areaCode.equals("EPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("3");   // Palaearctic - Asia-Temperate
 214                         else if (areaCode.equals("ES-BAL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-ES");
 215                         else if (areaCode.equals("ES-CNY")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CNY-OO");
 216                         else if (areaCode.equals("ES-SPA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-SP");
 217                         else if (areaCode.equals("FI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FIN-OO");
 218                         else if (areaCode.equals("FR-COR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("COR-OO");
 219                         else if (areaCode.equals("FR-FRA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-FR");
 220                         else if (areaCode.equals("GB-CI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-CI");
 221                         else if (areaCode.equals("GB-GI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SPA-GI");
 222                         else if (areaCode.equals("GB-GRB")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRB-OO");
 223                         else if (areaCode.equals("GB-NI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-NI");
 224                         else if (areaCode.equals("GR-AEG")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // North Aegean Is. - East Aegean Is.
 225                         else if (areaCode.equals("GR-CYC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO"); // Cyclades Is. - Greece
 226                         else if (areaCode.equals("GR-DOD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("EAI-OO"); // Dodecanese Is. - East Aegean Is.
 227                         else if (areaCode.equals("GR-GRC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("GRC-OO");
 228                         else if (areaCode.equals("GR-KRI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("KRI-OO");
 229                         else if (areaCode.equals("HR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-CR");
 230                         else if (areaCode.equals("HU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("HUN-OO");
 231                         else if (areaCode.equals("IE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("IRE-IR");
 232                         else if (areaCode.equals("IS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ICE-OO");
 233                         else if (areaCode.equals("IT-ITA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-IT");
 234                         else if (areaCode.equals("IT-SAR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SAR-OO");
 235                         else if (areaCode.equals("IT-SI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-SI");
 236                         else if (areaCode.equals("LI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AUT-LI");
 237                         else if (areaCode.equals("LT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-LI");
 238                         else if (areaCode.equals("LU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BGM-LU");
 239                         else if (areaCode.equals("LV")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-LA");
 240                         else if (areaCode.equals("MC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("FRA-MO");
 241                         else if (areaCode.equals("MD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-MO");
 242                         else if (areaCode.equals("MK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-MA");
 243                         else if (areaCode.equals("MT")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SIC-MA");
 244                         else if (areaCode.equals("NAF")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("20");   // North Africa - Northern Africa
 245                         else if (areaCode.equals("NEA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("7");    // Nearctic region - Northern America
 246                         else if (areaCode.equals("NEO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("8");    // Neotropical region - Southern America
 247                         else if (areaCode.equals("NL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NET-OO");
 248                         else if (areaCode.equals("NO-NOR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("NOR-OO");
 249                         else if (areaCode.equals("NO-SVA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SVA-OO");
 250                         else if (areaCode.equals("NRE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("34");   // Near East - Western Asia
 251                         else if (areaCode.equals("ORR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("35");   // Oriental region - Arabian Peninsula
 252                         else if (areaCode.equals("PL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POL-OO");
 253                         else if (areaCode.equals("PT-AZO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("AZO-OO");
 254                         else if (areaCode.equals("PT-MDR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("MDR-OO");
 255                         else if (areaCode.equals("PT-POR")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("POR-OO");
 256                         else if (areaCode.equals("PT-SEL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SEL-OO");
 257                         else if (areaCode.equals("RO")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ROM-OO");
 258                         else if (areaCode.equals("RU-FJL")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("WSB-OO");
 259                         else if (areaCode.equals("RU-KGD")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("BLT-KA");
 260                         else if (areaCode.equals("RU-NOZ")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("WSB-OO");
 261                         else if (areaCode.equals("RU-RUC")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUC-OO");
 262                         else if (areaCode.equals("RU-RUE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUE-OO");
 263                         else if (areaCode.equals("RU-RUN")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUN-OO");
 264                         else if (areaCode.equals("RU-RUS")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUS-OO");
 265                         else if (areaCode.equals("RU-RUW")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("RUW-OO");
 266                         else if (areaCode.equals("SE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("SWE-OO");
 267                         else if (areaCode.equals("SI")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG-SL");
 268                         else if (areaCode.equals("SK")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("CZE-SK");
 269                         else if (areaCode.equals("SM")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-SM");
 270                         else if (areaCode.equals("TR-TUE")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("TUE-OO");
 271                         else if (areaCode.equals("UA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("UKR-UK");
 272                         else if (areaCode.equals("VA")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("ITA-VC");
 273                         else if (areaCode.equals("YU")) tdwgArea = TdwgArea.getAreaByTdwgAbbreviation("YUG");
 274                         else
 275                                 throw new UnknownCdmTypeException("Unknown Area " + areaCode);
 276
 277                         if (logger.isDebugEnabled()) {
 278                                 logger.debug(areaId + ", " + areaName + ", " + areaCode + ", " + extraLimital);
 279                         }
 280
 281                 } catch (Exception e) {
 282                         e.printStackTrace();
 283                         logger.warn("Exception occurred. Area could not be mapped.");
 284                         return null;
 285                 }
 286
 287                 return tdwgArea;
 288         }
 289
 290 }