cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistributionImport.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 package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;
  10
  11 import java.sql.ResultSet;
  12 import java.sql.SQLException;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.logging.log4j.LogManager;
  21 import org.apache.logging.log4j.Logger;
  22 import org.springframework.stereotype.Component;
  23 import org.springframework.transaction.TransactionStatus;
  24
  25 import eu.etaxonomy.cdm.io.common.Source;
  26 import eu.etaxonomy.cdm.model.common.CdmBase;
  27 import eu.etaxonomy.cdm.model.description.Distribution;
  28 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  29 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  30 import eu.etaxonomy.cdm.model.location.NamedArea;
  31 import eu.etaxonomy.cdm.model.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33 import eu.etaxonomy.cdm.model.term.TermType;
  34 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  35
  36 /**
  37  * @author a.babadshanjan
  38  * @since 12.05.2009
  39  */
  40 @Component
  41 public class FaunaEuropaeaDistributionImport extends FaunaEuropaeaImportBase {
  42
  43     private static final long serialVersionUID = 746146902707885655L;
  44     private static Logger logger = LogManager.getLogger();
  45
  46         @Override
  47         protected boolean doCheck(FaunaEuropaeaImportState state) {
  48                 boolean result = true;
  49                 logger.warn("Checking for Distributions not yet implemented");
  50                 return result;
  51         }
  52
  53         @Override
  54         protected void doInvoke(FaunaEuropaeaImportState state) {
  55                 /*
  56                 logger.warn("Start distribution doInvoke");
  57                 ProfilerController.memorySnapshot();
  58                 */
  59
  60                 if (!state.getConfig().isDoOccurrence()){
  61                         return;
  62                 }
  63
  64                 int limit = state.getConfig().getLimitSave();
  65                 UUID noDataUuid;
  66                 /* Taxon store for retrieving taxa from and saving taxa to CDM */
  67                 List<TaxonBase> taxonList = null;
  68                 /* UUID store as input for retrieving taxa from CDM */
  69                 Set<UUID> taxonUuids = null;
  70                 /* Store to hold helper objects */
  71                 Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap = null;
  72
  73
  74                 TransactionStatus txStatus = null;
  75
  76                 //txStatus = startTransaction();
  77                 /*PresenceAbsenceTerm noDataStatusTerm = PresenceAbsenceTerm.NewPresenceInstance("no data", "no data", "nod");
  78                 noDataUuid = noDataStatusTerm.getUuid();
  79                 TermVocabulary<PresenceAbsenceTerm> voc = getVocabularyService().find(30);
  80                 HibernateProxyHelper.deproxy(voc, OrderedTermVocabulary.class);
  81                 //voc.addTerm(noDataStatusTerm);
  82         //      getVocabularyService().saveOrUpdate(voc);
  83                 getTermService().save(noDataStatusTerm);*/
  84                 //commitTransaction(txStatus);
  85
  86         //      FaunaEuropaeaTransformer.setUUIDs(noDataUuid);
  87                 logger.info("create termvoc");
  88                 createTermVocabulary(txStatus, state);
  89
  90                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  91                 Source source = fauEuConfig.getSource();
  92
  93         int i = 0;
  94
  95                 String selectCount =
  96                         " SELECT count(*) ";
  97
  98                 String selectColumns =
  99                         " SELECT distribution.*, Area.*, Taxon.UUID ";
 100
 101                 String fromClause =
 102                         " FROM distribution INNER JOIN " +
 103             " Area ON distribution.dis_ara_id = Area.ara_id INNER JOIN " +
 104             " Taxon ON distribution.dis_tax_id = Taxon.TAX_ID ";
 105                 String orderBy = " ORDER BY distribution.dis_tax_id";
 106
 107                 String countQuery =
 108                         selectCount + fromClause;
 109
 110                 String selectQuery =
 111                         selectColumns + fromClause + orderBy;
 112
 113                 if(logger.isInfoEnabled()) { logger.info("Start making distributions..."); }
 114
 115                 try {
 116                         ResultSet rs = source.getResultSet(countQuery);
 117                         rs.next();
 118                         int count = rs.getInt(1);
 119
 120                         rs = source.getResultSet(selectQuery);
 121
 122                         if (logger.isInfoEnabled()) {
 123                                 logger.info("Number of rows: " + count);
 124                                 logger.info("Count Query: " + countQuery);
 125                                 logger.info("Select Query: " + selectQuery);
 126                         }
 127
 128                         //int taxonId;
 129
 130                         while (rs.next()) {
 131                                 if ((i++ % limit) == 0) {
 132
 133                                         txStatus = startTransaction();
 134                                         taxonUuids = new HashSet<>(limit);
 135                                         fauEuTaxonMap = new HashMap<>(limit);
 136
 137                                         if(logger.isInfoEnabled()) {
 138                                                 logger.info("i = " + i + " - Distribution import transaction started");
 139                                         }
 140                                 }
 141
 142                                 //taxonId = rs.getInt("dis_tax_id");
 143                                 int disId = rs.getInt("dis_id");
 144                                 int occStatusId = rs.getInt("dis_present");
 145                                 int areaId = rs.getInt("ara_id");
 146                                 String areaName = rs.getString("ara_name");
 147                                 String areaCode = rs.getString("ara_code");
 148                                 int extraLimital = rs.getInt("ara_extralimital");
 149                                 UUID currentTaxonUuid = null;
 150                                 if (resultSetHasColumn(rs,"UUID")){
 151                                         currentTaxonUuid = UUID.fromString(rs.getString("UUID"));
 152                                 } else {
 153                                         currentTaxonUuid = UUID.randomUUID();
 154                                 }
 155
 156                                 FaunaEuropaeaDistribution fauEuDistribution = new FaunaEuropaeaDistribution();
 157                                 fauEuDistribution.setDistributionId(disId);
 158                                 fauEuDistribution.setOccurrenceStatusId(occStatusId);
 159                                 fauEuDistribution.setAreaId(areaId);
 160                                 fauEuDistribution.setAreaName(areaName);
 161                                 fauEuDistribution.setAreaCode(areaCode);
 162                                 fauEuDistribution.setExtraLimital(extraLimital);
 163
 164                                 if (!taxonUuids.contains(currentTaxonUuid)) {
 165                                         taxonUuids.add(currentTaxonUuid);
 166                                         FaunaEuropaeaDistributionTaxon fauEuDistributionTaxon =
 167                                                 new FaunaEuropaeaDistributionTaxon(currentTaxonUuid);
 168                                         fauEuTaxonMap.put(currentTaxonUuid, fauEuDistributionTaxon);
 169                                         fauEuDistributionTaxon = null;
 170                                 } else {
 171                                         if (logger.isTraceEnabled()) {
 172                                                 logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
 173                                                 continue;
 174                                         }
 175                                 }
 176
 177                                 fauEuTaxonMap.get(currentTaxonUuid).addDistribution(fauEuDistribution);
 178
 179                                 if (((i % limit) == 0 && i != 1 ) || i == count ) {
 180
 181                                         try {
 182                                                 commitTaxaAndDistribution(state, taxonUuids, fauEuTaxonMap, txStatus);
 183                                                 taxonUuids = null;
 184                                                 taxonList = null;
 185                                                 fauEuTaxonMap = null;
 186
 187                                         } catch (Exception e) {
 188                                                 logger.error("Commit of taxa and distributions failed" + e.getMessage());
 189                                                 e.printStackTrace();
 190                                         }
 191
 192                                         if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}
 193                                 }
 194
 195
 196                         }
 197                         if (taxonUuids != null){
 198                                 try {
 199                                         commitTaxaAndDistribution(state, taxonUuids, fauEuTaxonMap, txStatus);
 200                                         taxonUuids = null;
 201                                         taxonList = null;
 202                                         fauEuTaxonMap = null;
 203                                 } catch (Exception e) {
 204                                         logger.error("Commit of taxa and distributions failed");
 205                                         logger.error(e.getMessage());
 206                                         e.printStackTrace();
 207                                 }
 208                         }
 209                         rs = null;
 210                 } catch (SQLException e) {
 211                         logger.error("SQLException:" +  e);
 212                         state.setUnsuccessfull();
 213                 }
 214
 215                 if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
 216
 217
 218                 return;
 219         }
 220
 221         /**
 222      *
 223      */
 224     private void createTermVocabulary(TransactionStatus txStatus, FaunaEuropaeaImportState state) {
 225        TermVocabulary<NamedArea> faunaEuAreaVocabulary = TermVocabulary.NewInstance(TermType.NamedArea,
 226                NamedArea.class, "Areas for Fauna Europaea distribution data", "FE areas", "FE", null);
 227        faunaEuAreaVocabulary.setUuid(FaunaEuropaeaTransformer.uuidFauEuArea);
 228
 229        NamedArea area =NamedArea.NewInstance(null, "Andorra", "AD");
 230        area.setUuid(UUID.randomUUID());
 231        area.setIdInVocabulary("AD");
 232        state.putNamedArea(area);
 233        faunaEuAreaVocabulary.addTerm(area);
 234        area = NamedArea.NewInstance(null, "Albania", "AL");
 235        area.setIdInVocabulary("AL");
 236        area.setUuid(UUID.randomUUID());
 237        state.putNamedArea(area);
 238        faunaEuAreaVocabulary.addTerm(area);
 239        area = NamedArea.NewInstance(null, "Austria", "AT");
 240        area.setIdInVocabulary("AT");
 241        area.setUuid(UUID.randomUUID());
 242        state.putNamedArea(area);
 243        faunaEuAreaVocabulary.addTerm(area);
 244        area = NamedArea.NewInstance(null, "Bosnia and Herzegovina", "BA");
 245        area.setUuid(UUID.randomUUID());
 246        area.setIdInVocabulary("BA");
 247        state.putNamedArea(area);
 248        faunaEuAreaVocabulary.addTerm(area);
 249        area = NamedArea.NewInstance(null, "Belgium", "BE");
 250        area.setUuid(UUID.randomUUID());
 251        area.setIdInVocabulary("BE");
 252        state.putNamedArea(area);
 253        faunaEuAreaVocabulary.addTerm(area);
 254        area = NamedArea.NewInstance(null, "Bulgaria", "BG");
 255        area.setUuid(UUID.randomUUID());
 256        area.setIdInVocabulary("BG");
 257        state.putNamedArea(area);
 258        faunaEuAreaVocabulary.addTerm(area);
 259        area = NamedArea.NewInstance(null, "Belarus", "BY");
 260        area.setUuid(UUID.randomUUID());
 261        area.setIdInVocabulary("BY");
 262        state.putNamedArea(area);
 263        faunaEuAreaVocabulary.addTerm(area);
 264        area = NamedArea.NewInstance(null, "Switzerland", "CH");
 265        area.setUuid(UUID.randomUUID());
 266        area.setIdInVocabulary("CH");
 267        state.putNamedArea(area);
 268        faunaEuAreaVocabulary.addTerm(area);
 269        area = NamedArea.NewInstance(null, "Cyprus", "CY");
 270        area.setUuid(UUID.randomUUID());
 271        area.setIdInVocabulary("CY");
 272        state.putNamedArea(area);
 273        faunaEuAreaVocabulary.addTerm(area);
 274        area = NamedArea.NewInstance(null, "Czech Republic", "CZ");
 275        area.setUuid(UUID.randomUUID());
 276        area.setIdInVocabulary("CZ");
 277        state.putNamedArea(area);
 278        faunaEuAreaVocabulary.addTerm(area);
 279        area = NamedArea.NewInstance(null, "Germany", "DE");
 280        area.setUuid(UUID.randomUUID());
 281        area.setIdInVocabulary("DE");
 282        state.putNamedArea(area);
 283        faunaEuAreaVocabulary.addTerm(area);
 284        area = NamedArea.NewInstance("Incl. Bornholm I.", "Danish mainland", "DK-DEN");
 285        area.setUuid(UUID.randomUUID());
 286        area.setIdInVocabulary("DK-DEN");
 287        state.putNamedArea(area);
 288        faunaEuAreaVocabulary.addTerm(area);
 289        area = NamedArea.NewInstance(null, "Faroe Is.", "DK-FOR");
 290        area.setUuid(UUID.randomUUID());
 291        area.setIdInVocabulary("DK-FOR");
 292        state.putNamedArea(area);
 293        faunaEuAreaVocabulary.addTerm(area);
 294        area = NamedArea.NewInstance(null, "Estonia", "EE");
 295        area.setUuid(UUID.randomUUID());
 296        area.setIdInVocabulary("EE");
 297        state.putNamedArea(area);
 298        faunaEuAreaVocabulary.addTerm(area);
 299        area = NamedArea.NewInstance("Incl. Mallorca I., Menorca I., and Pityuses Is.(=Ibiza I. + Formentera I.)", "Balearic Is.", "ES-BAL");
 300        area.setUuid(UUID.randomUUID());
 301        area.setIdInVocabulary("ES-BAL");
 302        state.putNamedArea(area);
 303        faunaEuAreaVocabulary.addTerm(area);
 304        area = NamedArea.NewInstance(null, "Canary Is.", "ES-CNY");
 305        area.setUuid(UUID.randomUUID());
 306        area.setIdInVocabulary("ES-CNY");
 307        state.putNamedArea(area);
 308        faunaEuAreaVocabulary.addTerm(area);
 309        area = NamedArea.NewInstance("Incl. Alboran I.", "Spanish mainland", "ES-SPA");
 310        area.setUuid(UUID.randomUUID());
 311        area.setIdInVocabulary("ES-SPA");
 312        state.putNamedArea(area);
 313        faunaEuAreaVocabulary.addTerm(area);
 314        area = NamedArea.NewInstance(null, "Finland", "FI");
 315        area.setUuid(UUID.randomUUID());
 316        area.setIdInVocabulary("FI");
 317        state.putNamedArea(area);
 318        faunaEuAreaVocabulary.addTerm(area);
 319        area = NamedArea.NewInstance(null, "Corsica", "FR-COR");
 320        area.setUuid(UUID.randomUUID());
 321        area.setIdInVocabulary("FR-COR");
 322        state.putNamedArea(area);
 323        faunaEuAreaVocabulary.addTerm(area);
 324        area = NamedArea.NewInstance(null, "French mainland", "FR-FRA");
 325        area.setUuid(UUID.randomUUID());
 326        area.setIdInVocabulary("FR-FRA");
 327        state.putNamedArea(area);
 328        faunaEuAreaVocabulary.addTerm(area);
 329        area = NamedArea.NewInstance("Incl. Jersey, Guernsey, Alderney", "Channel Is.", "GB-CI");
 330        area.setUuid(UUID.randomUUID());
 331        area.setIdInVocabulary("GB-CI");
 332        state.putNamedArea(area);
 333        faunaEuAreaVocabulary.addTerm(area);
 334        area = NamedArea.NewInstance(null, "Gibraltar", "GB-GI");
 335        area.setUuid(UUID.randomUUID());
 336        area.setIdInVocabulary("GB-GI");
 337        state.putNamedArea(area);
 338        faunaEuAreaVocabulary.addTerm(area);
 339        area = NamedArea.NewInstance("Incl. Shetlands, Orkneys, Hebrides and Man Is.", "Britain I.", "GB-GRB");
 340        area.setUuid(UUID.randomUUID());
 341        area.setIdInVocabulary("GB-GRB");
 342        state.putNamedArea(area);
 343        faunaEuAreaVocabulary.addTerm(area);
 344        area = NamedArea.NewInstance(null, "Northern Ireland", "GB-NI");
 345        area.setUuid(UUID.randomUUID());
 346        area.setIdInVocabulary("GB-NI");
 347        state.putNamedArea(area);
 348        faunaEuAreaVocabulary.addTerm(area);
 349        area = NamedArea.NewInstance("Incl. Andípsara, Áyios Evstrátios, Foúrnoi,Ikaría, Khíos, "
 350                + "Lésvos, Límnos, Oinoúsa, Psará, Sámos, Skópelos Kaloyeroi and other smaller"
 351                + " islands","Vóreion Aiyáion (North Aegean Is.)", "GR-AEG");
 352        area.setUuid(UUID.randomUUID());
 353        area.setIdInVocabulary("GR-AEG");
 354        state.putNamedArea(area);
 355        faunaEuAreaVocabulary.addTerm(area);
 356        area = NamedArea.NewInstance("Incl. Amorgós, Anáfi, Ánidros, Ándros, Andíparos, Denoúsa, Folégandros, "
 357                + "Íos, Iráklia, Káros, Kímolos, Kéa, Kýthnos, Mílos, Mýkonos, Náxos, Páros, Políaigos, Sérifos, "
 358                + "Sífnos, Síkinos, Sýros, Thíra, Tínos, Yiarós and other smaller islands", "Kikládes (Cyclades Is.)", "GR-CYC");
 359        area.setUuid(UUID.randomUUID());
 360        area.setIdInVocabulary("GR-CYC");
 361        state.putNamedArea(area);
 362        faunaEuAreaVocabulary.addTerm(area);
 363        area = NamedArea.NewInstance("Incl. Alimniá, Árkoi, Astipálaia, Avgonísi, Ankathonísi, Farmakonísi, Ioinianísia,"
 364                + " Kálimnos, Kalolímnos, Kandelioúsa, Kárpathos, Kásos, Khálki, Khamilí, Kínaros, Kos, Léros, Levítha, "
 365                + "Lipsói, Meyísti, Nísiros, Ofidoúsa, Pátmos, Ródhos, Saría, Sími, Sírina, Tílos, Tría Nisiá, Yialí "
 366                + "and other smaller islands", "Dodekánisos (Dodecanese Is.) ", "GR-DOD");
 367        area.setUuid(UUID.randomUUID());
 368        area.setIdInVocabulary("GR-DOD");
 369        state.putNamedArea(area);
 370        faunaEuAreaVocabulary.addTerm(area);
 371        area = NamedArea.NewInstance(" Incl. Andikíthira I., Evvia I., Ionian Is., Samothráki I., Northern Sporades Is., Thásos I.",
 372                "Greek mainland", "GR-GRC");
 373        area.setUuid(UUID.randomUUID());
 374        area.setIdInVocabulary("GR-GRC");
 375        state.putNamedArea(area);
 376        faunaEuAreaVocabulary.addTerm(area);
 377        area = NamedArea.NewInstance("Incl. small adjacent islands like Gávdhos. Note that Andikíthira I. although being "
 378                + "closer to Kriti than to mainland, belongs to a mainland province", "Kriti (Crete)", "GR-KRI");
 379        area.setUuid(UUID.randomUUID());
 380        area.setIdInVocabulary("GR-KRI");
 381        state.putNamedArea(area);
 382        faunaEuAreaVocabulary.addTerm(area);
 383        area = NamedArea.NewInstance(null, "Croatia", "HR");
 384        area.setUuid(UUID.randomUUID());
 385        area.setIdInVocabulary("HR");
 386        state.putNamedArea(area);
 387        faunaEuAreaVocabulary.addTerm(area);
 388        area = NamedArea.NewInstance(null, "Hungary", "HU");
 389        area.setUuid(UUID.randomUUID());
 390        area.setIdInVocabulary("HU");
 391        state.putNamedArea(area);
 392        faunaEuAreaVocabulary.addTerm(area);
 393        area = NamedArea.NewInstance(null, "Ireland", "IE");
 394        area.setUuid(UUID.randomUUID());
 395        area.setIdInVocabulary("IE");
 396        state.putNamedArea(area);
 397        faunaEuAreaVocabulary.addTerm(area);
 398        area = NamedArea.NewInstance(null, "Iceland", "IS");
 399        area.setUuid(UUID.randomUUID());
 400        area.setIdInVocabulary("IS");
 401        state.putNamedArea(area);
 402        faunaEuAreaVocabulary.addTerm(area);
 403        area = NamedArea.NewInstance(null, "Italian mainland", "IT-ITA");
 404        area.setUuid(UUID.randomUUID());
 405        area.setIdInVocabulary("IT-ITA");
 406        state.putNamedArea(area);
 407        faunaEuAreaVocabulary.addTerm(area);
 408        area = NamedArea.NewInstance(null, "Sardinia", "IT-SAR");
 409        area.setUuid(UUID.randomUUID());
 410        area.setIdInVocabulary("IT-SAR");
 411        state.putNamedArea(area);
 412        faunaEuAreaVocabulary.addTerm(area);
 413        area = NamedArea.NewInstance(" Incl. adjacent Italian islands (Lipari Is., Ustica I., Egadi Is., "
 414                + "Pantelleria I., Pelagie Is.) ", "Sicily", "IT-SI");
 415        area.setUuid(UUID.randomUUID());
 416        area.setIdInVocabulary("IT-SI");
 417        state.putNamedArea(area);
 418        faunaEuAreaVocabulary.addTerm(area);
 419        area = NamedArea.NewInstance(null, "Liechtenstein", "LI");
 420        area.setUuid(UUID.randomUUID());
 421        area.setIdInVocabulary("LI");
 422        state.putNamedArea(area);
 423        faunaEuAreaVocabulary.addTerm(area);
 424        area = NamedArea.NewInstance(null, "Lithuania", "LT");
 425        area.setUuid(UUID.randomUUID());
 426        area.setIdInVocabulary("LT");
 427        state.putNamedArea(area);
 428        faunaEuAreaVocabulary.addTerm(area);
 429        area = NamedArea.NewInstance(null, "Luxembourg", "LU");
 430        area.setUuid(UUID.randomUUID());
 431        area.setIdInVocabulary("LU");
 432        state.putNamedArea(area);
 433        faunaEuAreaVocabulary.addTerm(area);
 434        area = NamedArea.NewInstance(null, "Latvia", "LV");
 435        area.setUuid(UUID.randomUUID());
 436        area.setIdInVocabulary("LV");
 437        state.putNamedArea(area);
 438        faunaEuAreaVocabulary.addTerm(area);
 439        area = NamedArea.NewInstance(null, "Monaco", "MC");
 440        area.setUuid(UUID.randomUUID());
 441        area.setIdInVocabulary("MC");
 442        state.putNamedArea(area);
 443        faunaEuAreaVocabulary.addTerm(area);
 444        area = NamedArea.NewInstance(null, "Moldova, Republic of", "MD");
 445        area.setUuid(UUID.randomUUID());
 446        area.setIdInVocabulary("MD");
 447        state.putNamedArea(area);
 448        faunaEuAreaVocabulary.addTerm(area);
 449        area = NamedArea.NewInstance(null, "Macedonia, the former Yugoslav Republic of", "MK");
 450        area.setUuid(UUID.randomUUID());
 451        area.setIdInVocabulary("MK");
 452        state.putNamedArea(area);
 453        faunaEuAreaVocabulary.addTerm(area);
 454        area = NamedArea.NewInstance(null, "Malta", "MT");
 455        area.setUuid(UUID.randomUUID());
 456        area.setIdInVocabulary("MT");
 457        state.putNamedArea(area);
 458        faunaEuAreaVocabulary.addTerm(area);
 459        area = NamedArea.NewInstance(null, "The Netherlands", "NL");
 460        area.setUuid(UUID.randomUUID());
 461        area.setIdInVocabulary("NL");
 462        state.putNamedArea(area);
 463        faunaEuAreaVocabulary.addTerm(area);
 464        area = NamedArea.NewInstance(null, "Norwegian mainland", "NO-NOR");
 465        area.setUuid(UUID.randomUUID());
 466        area.setIdInVocabulary("NO-NOR");
 467        state.putNamedArea(area);
 468        faunaEuAreaVocabulary.addTerm(area);
 469        area = NamedArea.NewInstance("Incl. Bear I.", "Svalbard & Jan Mayen", "NO-SVA");
 470        area.setUuid(UUID.randomUUID());
 471        area.setIdInVocabulary("NO-SVA");
 472        state.putNamedArea(area);
 473        faunaEuAreaVocabulary.addTerm(area);
 474        area = NamedArea.NewInstance(null, "Poland", "PL");
 475        area.setUuid(UUID.randomUUID());
 476        area.setIdInVocabulary("PL");
 477        state.putNamedArea(area);
 478        faunaEuAreaVocabulary.addTerm(area);
 479        area = NamedArea.NewInstance(null, "Azores Is.", "PT-AZO");
 480        area.setUuid(UUID.randomUUID());
 481        area.setIdInVocabulary("PT-AZO");
 482        state.putNamedArea(area);
 483        faunaEuAreaVocabulary.addTerm(area);
 484        area = NamedArea.NewInstance(null, "Madeira Is.", "PT-MDR");
 485        area.setUuid(UUID.randomUUID());
 486        area.setIdInVocabulary("PT-MDR");
 487        state.putNamedArea(area);
 488        faunaEuAreaVocabulary.addTerm(area);
 489        area = NamedArea.NewInstance(null, "Portuguese mainland", "PT-POR");
 490        area.setUuid(UUID.randomUUID());
 491        area.setIdInVocabulary("PT-POR");
 492        state.putNamedArea(area);
 493        faunaEuAreaVocabulary.addTerm(area);
 494        area = NamedArea.NewInstance(null, "Selvagens Is.", "PT-SEL");
 495        area.setUuid(UUID.randomUUID());
 496        area.setIdInVocabulary("PT-SEL");
 497        state.putNamedArea(area);
 498        faunaEuAreaVocabulary.addTerm(area);
 499        area = NamedArea.NewInstance(null, "Romania", "RO");
 500        area.setUuid(UUID.randomUUID());
 501        area.setIdInVocabulary("RO");
 502        state.putNamedArea(area);
 503        faunaEuAreaVocabulary.addTerm(area);
 504        area = NamedArea.NewInstance("Excl. Ushakova I. and Vize I.", "Franz Josef Land", "RU-FJL");
 505        area.setUuid(UUID.randomUUID());
 506        area.setIdInVocabulary("RU-FJL");
 507        state.putNamedArea(area);
 508        faunaEuAreaVocabulary.addTerm(area);
 509        area = NamedArea.NewInstance(null, "Kaliningrad Region", "RU-KGD");
 510        area.setUuid(UUID.randomUUID());
 511        area.setIdInVocabulary("RU-KGD");
 512        state.putNamedArea(area);
 513        faunaEuAreaVocabulary.addTerm(area);
 514        area = NamedArea.NewInstance(null, "Novaya Zemlya", "RU-NOZ");
 515        area.setUuid(UUID.randomUUID());
 516        area.setIdInVocabulary("RU-NOZ");
 517        state.putNamedArea(area);
 518        faunaEuAreaVocabulary.addTerm(area);
 519        area = NamedArea.NewInstance(null, "Central European Russia", "RU-RUC");
 520        area.setUuid(UUID.randomUUID());
 521        area.setIdInVocabulary("RU-RUC");
 522        state.putNamedArea(area);
 523        faunaEuAreaVocabulary.addTerm(area);
 524        area = NamedArea.NewInstance(null, "East European Russia", "RU-RUE");
 525        area.setUuid(UUID.randomUUID());
 526        area.setIdInVocabulary("RU-RUE");
 527        state.putNamedArea(area);
 528
 529        faunaEuAreaVocabulary.addTerm(area);
 530        area = NamedArea.NewInstance(null, "North European Russia", "RU-RUN");
 531        area.setUuid(UUID.randomUUID());
 532        area.setIdInVocabulary("RU-RUN");
 533        state.putNamedArea(area);
 534        faunaEuAreaVocabulary.addTerm(area);
 535        area = NamedArea.NewInstance(null, "South European Russia", "RU-RUS");
 536        area.setUuid(UUID.randomUUID());
 537        area.setIdInVocabulary("RU-RUS");
 538        state.putNamedArea(area);
 539        faunaEuAreaVocabulary.addTerm(area);
 540        area = NamedArea.NewInstance(null, "Northwest European Russia", "RU-RUW");
 541        area.setUuid(UUID.randomUUID());
 542        area.setIdInVocabulary("RU-RUW");
 543        state.putNamedArea(area);
 544        faunaEuAreaVocabulary.addTerm(area);
 545        area = NamedArea.NewInstance("Incl. Gotland I.", "Sweden", "SE");
 546        area.setUuid(UUID.randomUUID());
 547        area.setIdInVocabulary("SE");
 548        state.putNamedArea(area);
 549        faunaEuAreaVocabulary.addTerm(area);
 550        area = NamedArea.NewInstance(null, "Slovenia", "SI");
 551        area.setUuid(UUID.randomUUID());
 552        area.setIdInVocabulary("SI");
 553        state.putNamedArea(area);
 554        faunaEuAreaVocabulary.addTerm(area);
 555        area = NamedArea.NewInstance(null, "Slovakia", "SK");
 556        area.setUuid(UUID.randomUUID());
 557        area.setIdInVocabulary("SK");
 558        state.putNamedArea(area);
 559        faunaEuAreaVocabulary.addTerm(area);
 560        area = NamedArea.NewInstance(null, "San Marino", "SM");
 561        area.setUuid(UUID.randomUUID());
 562        area.setIdInVocabulary("SM");
 563        state.putNamedArea(area);
 564        faunaEuAreaVocabulary.addTerm(area);
 565        area = NamedArea.NewInstance("Incl. Imroz I. - Gökçeada, but not those in the Sea of Marmara",
 566                "European Turkey", "TR-TUE");
 567        area.setUuid(UUID.randomUUID());
 568        area.setIdInVocabulary("TR-TUE");
 569        state.putNamedArea(area);
 570        faunaEuAreaVocabulary.addTerm(area);
 571        area = NamedArea.NewInstance(null, "Ukraine", "UA");
 572        area.setUuid(UUID.randomUUID());
 573        area.setIdInVocabulary("UA");
 574        state.putNamedArea(area);
 575        faunaEuAreaVocabulary.addTerm(area);
 576        area = NamedArea.NewInstance(null, "Vatican City", "VA");
 577        area.setUuid(UUID.randomUUID());
 578        area.setIdInVocabulary("VA");
 579        state.putNamedArea(area);
 580        faunaEuAreaVocabulary.addTerm(area);
 581        area = NamedArea.NewInstance("Incl. Serbia, Kosovo, Voivodina, Montenegro", "Yugoslavia", "YU");
 582        area.setUuid(UUID.randomUUID());
 583        area.setIdInVocabulary("YU");
 584        state.putNamedArea(area);
 585        faunaEuAreaVocabulary.addTerm(area);
 586        area = NamedArea.NewInstance(null, "Afro-tropical region", "AFR");
 587        area.setUuid(UUID.randomUUID());
 588        area.setIdInVocabulary("AFR");
 589        state.putNamedArea(area);
 590        faunaEuAreaVocabulary.addTerm(area);
 591        area = NamedArea.NewInstance(null, "Australian region", "AUS");
 592        area.setUuid(UUID.randomUUID());
 593        area.setIdInVocabulary("AUS");
 594        state.putNamedArea(area);
 595        faunaEuAreaVocabulary.addTerm(area);
 596        area = NamedArea.NewInstance("East of the border line here defined", "East Palaearctic", "EPA");
 597        area.setUuid(UUID.randomUUID());
 598        area.setIdInVocabulary("EPA");
 599        state.putNamedArea(area);
 600        faunaEuAreaVocabulary.addTerm(area);
 601        area = NamedArea.NewInstance("Not including Sinai Peninsula", "North Africa", "NAF");
 602        area.setUuid(UUID.randomUUID());
 603        area.setIdInVocabulary("NAF");
 604        state.putNamedArea(area);
 605        faunaEuAreaVocabulary.addTerm(area);
 606        area = NamedArea.NewInstance(null, "Nearctic region", "NEA");
 607        area.setUuid(UUID.randomUUID());
 608        area.setIdInVocabulary("NEA");
 609        state.putNamedArea(area);
 610        faunaEuAreaVocabulary.addTerm(area);
 611        area = NamedArea.NewInstance(null, "Neotropical region", "NEO");
 612        area.setUuid(UUID.randomUUID());
 613        area.setIdInVocabulary("NEO");
 614        state.putNamedArea(area);
 615        faunaEuAreaVocabulary.addTerm(area);
 616        area = NamedArea.NewInstance("Asian Turkey, Caucasian Russian republics, Georgia, Armenia, Azerbaijan, "
 617                + "Lebanon, Syria, Israel, Jordan, Sinai Peninsula (Egypt), Arabian peninsula, Iran, Iraq",
 618                "Near East", "NRE");
 619        area.setUuid(UUID.randomUUID());
 620        area.setIdInVocabulary("NRE");
 621        state.putNamedArea(area);
 622        faunaEuAreaVocabulary.addTerm(area);
 623        area = NamedArea.NewInstance(null, "Oriental region", "ORR");
 624        area.setUuid(UUID.randomUUID());
 625        area.setIdInVocabulary("ORR");
 626        state.putNamedArea(area);
 627        faunaEuAreaVocabulary.addTerm(area);
 628        if (txStatus == null){
 629            txStatus = startTransaction();
 630        }
 631        //txStatus = startTransaction();
 632        faunaEuAreaVocabulary = getVocabularyService().save(faunaEuAreaVocabulary);
 633        logger.info("save voc");
 634        commitTransaction(txStatus);
 635        state.setAreaVoc(faunaEuAreaVocabulary);
 636     }
 637
 638     private void commitTaxaAndDistribution(
 639                         FaunaEuropaeaImportState state,
 640                         Set<UUID> taxonUuids,
 641                         Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap,
 642                         TransactionStatus txStatus) throws Exception {
 643
 644         List<TaxonBase> taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
 645
 646                 getTaxonService().save(taxonList);
 647                 taxonList = null;
 648                 taxonUuids = null;
 649                 fauEuTaxonMap = null;
 650                 commitTransaction(txStatus);
 651
 652         }
 653
 654         private List<TaxonBase> prepareTaxaAndDistribution(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap,  FaunaEuropaeaImportState state) throws Exception{
 655
 656                 Distribution newDistribution = null;
 657                 NamedArea namedArea;
 658                 PresenceAbsenceTerm presenceAbsenceStatus;
 659                 FaunaEuropaeaDistributionTaxon fauEuHelperTaxon;
 660                 UUID taxonUuid;
 661                 TaxonDescription taxonDescription;
 662                 Taxon taxon;
 663                 for (TaxonBase<?> taxonBase : taxonList) {
 664
 665                         if (taxonBase != null) {
 666
 667                                 if (taxonBase instanceof Taxon) {
 668                                         taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 669                                 } else {
 670                                         logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
 671                                                         + taxonBase.getClass().getSimpleName());
 672                                         continue;
 673                                 }
 674
 675                                 Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
 676                                 if (descriptionSet.size() > 0) {
 677                                         taxonDescription = descriptionSet.iterator().next();
 678                                 } else {
 679                                         taxonDescription = TaxonDescription.NewInstance();
 680                                         taxon.addDescription(taxonDescription);
 681                                         taxonDescription.setDefault(true);
 682                                         //addOriginalSource(taxonDescription, null, "Default Import", state.getConfig().getSourceReference());
 683                                 }
 684
 685                                 taxonUuid = taxonBase.getUuid();
 686                                 fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);
 687
 688                                 for (FaunaEuropaeaDistribution fauEuHelperDistribution : fauEuHelperTaxon.getDistributions()) {
 689                                         namedArea = null;
 690                                         newDistribution = null;
 691                                         presenceAbsenceStatus = null;
 692
 693                                         presenceAbsenceStatus = FaunaEuropaeaTransformer.occStatus2PresenceAbsence(fauEuHelperDistribution.getOccurrenceStatusId());
 694
 695
 696                                         namedArea = state.areaId2NamedArea(fauEuHelperDistribution, state);
 697                                         if (namedArea == null){
 698                         logger.warn("Area " + fauEuHelperDistribution.getAreaCode() + "not found in FE transformer");
 699                     }
 700                                         if (namedArea == null){
 701                                                 //UUID areaUuid= FaunaEuropaeaTransformer.getUUIDByAreaAbbr(fauEuHelperDistribution.getAreaCode());
 702                                                 //if (areaUuid == null){
 703                                                         //logger.warn("Area " + fauEuHelperDistribution.getAreaCode() + "not found in FE transformer");
 704                                         //      }
 705 //                                              namedArea = getNamedArea(state, areaUuid, fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaCode(), null, null, state.getAreaVoc(), TermMatchMode.UUID_ABBREVLABEL);
 706 //                                              namedArea.setIdInVocabulary(fauEuHelperDistribution.getAreaCode());
 707 //                                          state.putNamedArea(namedArea);
 708                                         }
 709
 710                                         newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
 711                                         newDistribution.setCreated(null);
 712
 713                                         taxonDescription.addElement(newDistribution);
 714
 715                                 }
 716                         }
 717                 }
 718
 719                 taxonDescription= null;
 720                 newDistribution = null;
 721                 namedArea= null;
 722                 return taxonList;
 723         }
 724
 725     @Override
 726     protected boolean isIgnore(FaunaEuropaeaImportState state){
 727                 return !state.getConfig().isDoOccurrence();
 728         }
 729 }