cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelCommonNamesImport.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.berlinModel.in;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.ArrayList;
  15 import java.util.HashMap;
  16 import java.util.HashSet;
  17 import java.util.List;
  18 import java.util.Map;
  19 import java.util.Set;
  20 import java.util.SortedSet;
  21 import java.util.TreeSet;
  22 import java.util.UUID;
  23
  24 import org.apache.commons.lang.StringUtils;
  25 import org.apache.log4j.Logger;
  26 import org.springframework.stereotype.Component;
  27
  28 import eu.etaxonomy.cdm.common.CdmUtils;
  29 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelCommonNamesImportValidator;
  30 import eu.etaxonomy.cdm.io.common.IOValidator;
  31 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  32 import eu.etaxonomy.cdm.io.common.Source;
  33 import eu.etaxonomy.cdm.model.common.Annotation;
  34 import eu.etaxonomy.cdm.model.common.AnnotationType;
  35 import eu.etaxonomy.cdm.model.common.CdmBase;
  36 import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
  37 import eu.etaxonomy.cdm.model.common.Extension;
  38 import eu.etaxonomy.cdm.model.common.ExtensionType;
  39 import eu.etaxonomy.cdm.model.common.Language;
  40 import eu.etaxonomy.cdm.model.common.Representation;
  41 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  42 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  43 import eu.etaxonomy.cdm.model.location.NamedArea;
  44 import eu.etaxonomy.cdm.model.location.TdwgArea;
  45 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47 import eu.etaxonomy.cdm.model.taxon.Taxon;
  48 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  49
  50 /**
  51  *
  52  * @author a.mueller
  53  * @created 20.03.2008
  54  * @version 1.0
  55  */
  56 @Component
  57 public class BerlinModelCommonNamesImport  extends BerlinModelImportBase {
  58         private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);
  59
  60         public static final UUID REFERENCE_LANGUAGE_ISO639_2_UUID = UUID.fromString("40c4f8dd-3d9c-44a4-b77a-76e137a89a5f");
  61         public static final UUID REFERENCE_LANGUAGE_STRING_UUID = UUID.fromString("2a1b678f-c27d-48c1-b43e-98fd0d426305");
  62         public static final UUID STATUS_ANNOTATION_UUID = UUID.fromString("e3f7b80a-1286-458d-812c-5e818f731968");
  63
  64         public static final String NAMESPACE = "common name";
  65
  66
  67         private static int modCount = 10000;
  68         private static final String pluralString = "common names";
  69         private static final String dbTableName = "emCommonName";
  70
  71
  72         //map that stores the regions (named areas) and makes them accessible via the regionFk
  73         private Map<String, NamedArea> regionMap = new HashMap<String, NamedArea>();
  74
  75
  76
  77         public BerlinModelCommonNamesImport(){
  78                 super();
  79         }
  80
  81
  82
  83         @Override
  84         protected String getIdQuery() {
  85                 String result = " SELECT CommonNameId FROM emCommonName ";
  86                 return result;
  87         }
  88
  89
  90
  91         /* (non-Javadoc)
  92          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  93          */
  94         @Override
  95         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  96                 String recordQuery = "";
  97                 recordQuery =
  98                         " SELECT emCommonName.CommonNameId, emCommonName.CommonName, PTaxon.RIdentifier AS taxonId, emCommonName.PTNameFk, emCommonName.RefFk AS refId, emCommonName.Status, " +
  99                                 " emCommonName.RegionFks, emCommonName.MisNameRefFk, emCommonName.NameInSourceFk , emCommonName.Created_When, emCommonName.Updated_When, emCommonName.Created_Who, emCommonName.Updated_Who, emCommonName.Note as Notes," +
 100                         " regionLanguage.Language AS regionLanguage, languageCommonName.Language, languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2, " +
 101                         " emLanguageRegion.Region, emLanguageReference.RefFk as languageRefRefFk, emLanguageReference.ReferenceShort, " +
 102                         " emLanguageReference.ReferenceLong, emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, " +
 103                         " languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2, regionLanguage.ISO639_2 AS regionLanguageIso, " +
 104                         " misappliedTaxon.RIdentifier AS misappliedTaxonId " +
 105                 " FROM emLanguage as regionLanguage RIGHT OUTER JOIN " +
 106                         " emLanguageRegion ON regionLanguage.LanguageId = emLanguageRegion.LanguageFk RIGHT OUTER JOIN " +
 107                         " emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " +
 108                         " emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " +
 109                         " emCommonName INNER JOIN " +
 110                         " PTaxon ON emCommonName.PTNameFk = PTaxon.PTNameFk AND emCommonName.PTRefFk = PTaxon.PTRefFk ON " +
 111                         " emLanguageReference.ReferenceId = emCommonName.LanguageRefFk LEFT OUTER JOIN " +
 112                         " emLanguage AS languageCommonName ON emCommonName.LanguageFk = languageCommonName.LanguageId ON " +
 113                         " emLanguageRegion.RegionId = emCommonName.RegionFks LEFT OUTER JOIN " +
 114                         " PTaxon as misappliedTaxon ON emCommonName.PTNameFk = misappliedTaxon.PTNameFk AND emCommonName.MisNameRefFk = misappliedTaxon.PTRefFk " +
 115                         " WHERE emCommonName.CommonNameId IN (" + ID_LIST_TOKEN + ")";
 116                 return recordQuery;
 117         }
 118
 119
 120
 121         @Override
 122         protected boolean doInvoke(BerlinModelImportState state) {
 123                 boolean result = true;
 124                 try {
 125                         result &= makeRegions(state);
 126                 } catch (Exception e) {
 127                         logger.error("Error when creating common name regions:" + e.getMessage());
 128                         result = false;
 129                 }
 130                 result &= super.doInvoke(state);
 131                 return result;
 132         }
 133
 134         /**
 135          * @param state
 136          *
 137          */
 138         private boolean makeRegions(BerlinModelImportState state) {
 139                 boolean result = true;
 140                 try {
 141                         SortedSet<Integer> regionFks = new TreeSet<Integer>();
 142                         Source source = state.getConfig().getSource();
 143
 144                         result = getRegionFks(result, regionFks, source);
 145                         //concat filter string
 146                         String sqlWhere = getSqlWhere(regionFks);
 147
 148                         //get E+M - TDWG Mapping
 149                         Map<String, String> emTdwgMap = getEmTdwgMap(source);
 150                         //fill regionMap
 151                         fillRegionMap(source, sqlWhere, emTdwgMap);
 152
 153                         return result;
 154                 } catch (NumberFormatException e) {
 155                         e.printStackTrace();
 156                         return false;
 157                 } catch (SQLException e) {
 158                         e.printStackTrace();
 159                         return false;
 160                 }
 161         }
 162
 163
 164         /* (non-Javadoc)
 165          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
 166          */
 167         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state)  {
 168                 boolean success = true ;
 169                 BerlinModelImportConfigurator config = state.getConfig();
 170                 Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
 171                 Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
 172                 Map<String, TaxonNameBase> taxonNameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
 173
 174                 Map<String, Reference> biblioRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
 175                 Map<String, Reference> nomRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);
 176
 177                 Map<String, Language> iso6392Map = new HashMap<String, Language>();
 178
 179         //      logger.warn("MisappliedNameRefFk  not yet implemented for Common Names");
 180
 181                 ResultSet rs = partitioner.getResultSet();
 182                 try{
 183                         while (rs.next()){
 184
 185                                 //create TaxonName element
 186                                 Object commonNameId = rs.getObject("CommonNameId");
 187                                 int taxonId = rs.getInt("taxonId");
 188                                 Object refId = rs.getObject("refId");
 189                                 Object ptNameFk = rs.getObject("PTNameFk");
 190                                 String commonNameString = rs.getString("CommonName");
 191                                 String iso639_2 = rs.getString("ISO639_2");
 192                                 String iso639_1 = rs.getString("ISO639_1");
 193                                 String languageString = rs.getString("Language");
 194                                 String originalLanguageString = rs.getString("LanguageOriginal");
 195                                 Object misNameRefFk = rs.getObject("MisNameRefFk");
 196                                 Object languageRefRefFk = rs.getObject("languageRefRefFk");
 197                                 String refLanguage = rs.getString("refLanguage");
 198                                 String refLanguageIso639_2 = rs.getString("refLanguageIso639_2");
 199                                 String status = rs.getString("Status");
 200                                 Object nameInSourceFk = rs.getObject("NameInSourceFk");
 201                                 Object misappliedTaxonId = rs.getObject("misappliedTaxonId");
 202
 203                                 //regions
 204                                 String region = rs.getString("Region");
 205                                 String regionFks  = rs.getString("RegionFks");
 206                                 String[] regionFkSplit = regionFks.split(",");
 207
 208                                 //commonNameString
 209                                 if (CdmUtils.isEmpty(commonNameString)){
 210                                         String message = "CommonName is empty or null. Do not import record for taxon " + taxonId;
 211                                         logger.warn(message);
 212                                         continue;
 213                                 }
 214
 215                                 //taxon
 216                                 Taxon taxon = null;
 217                                 TaxonBase taxonBase = null;
 218                                 taxonBase  = taxonMap.get(String.valueOf(taxonId));
 219                                 if (taxonBase == null){
 220                                         logger.warn("Taxon (" + taxonId + ") could not be found. Common name " + commonNameString + " not imported");
 221                                         continue;
 222                                 }else if (! taxonBase.isInstanceOf(Taxon.class)){
 223                                         logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " +  commonNameId);
 224                                         continue;
 225                                 }else{
 226                                         taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 227                                 }
 228
 229                                 //Language
 230                                 Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString);
 231
 232                                 //CommonTaxonName
 233                                 List<CommonTaxonName> commonTaxonNames = new ArrayList<CommonTaxonName>();
 234                                 for (String regionFk : regionFkSplit){
 235                                         CommonTaxonName commonTaxonName;
 236                                         if (commonTaxonNames.size() == 0){
 237                                                 commonTaxonName = CommonTaxonName.NewInstance(commonNameString, language);
 238                                         }else{
 239                                                 commonTaxonName = (CommonTaxonName)commonTaxonNames.get(0).clone();
 240                                         }
 241                                         commonTaxonNames.add(commonTaxonName);
 242                                         regionFk = regionFk.trim();
 243                                         NamedArea area = regionMap.get(regionFk);
 244                                         if (area == null){
 245                                                 logger.warn("Area for " + regionFk + " not defined.");
 246                                         }else{
 247                                                 commonTaxonName.setArea(area);
 248                                                 TaxonDescription description = getDescription(taxon);
 249                                                 description.addElement(commonTaxonName);
 250                                         }
 251                                 }
 252
 253                                 //Reference/Source
 254                                 String strRefId = String.valueOf(refId);
 255                                 String languageRefFk = String.valueOf(languageRefRefFk);
 256                                 if (! CdmUtils.nullSafeEqual(strRefId, languageRefFk)){
 257                                         logger.warn("CommonName.RefFk (" + CdmUtils.Nz(strRefId) + ") and LanguageReference.RefFk " + CdmUtils.Nz(languageRefFk) + " are not equal. I will import only languageRefFk");
 258                                 }
 259
 260                                 Reference reference = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(languageRefRefFk));
 261                                 String microCitation = null;
 262                                 String originalNameString = null;
 263
 264                                 TaxonNameBase nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));
 265                                 if (nameInSourceFk != null && nameUsedInSource == null){
 266                                         logger.warn("Name used in source (" + nameInSourceFk + ") was not found");
 267                                 }
 268                                 DescriptionElementSource source = DescriptionElementSource.NewInstance(reference, microCitation, nameUsedInSource, originalNameString);
 269                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 270                                         commonTaxonName.addSource(source);
 271                                 }
 272
 273                                 //MisNameRef
 274                                 if (misNameRefFk != null){
 275                                         //Taxon misappliedName = getMisappliedName(biblioRefMap, nomRefMap, misNameRefFk, taxon);
 276                                         Taxon misappliedName = null;
 277                                         if (misappliedTaxonId != null){
 278                                                 misappliedName = taxonMap.get(String.valueOf(misappliedTaxonId));
 279                                         }else{
 280                                                 TaxonNameBase taxonName = taxonNameMap.get(String.valueOf(ptNameFk));
 281                                                 Reference sec = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));
 282                                                 if (taxonName == null || sec == null){
 283                                                         logger.info("Taxon name or misapplied name reference is null for common name " + commonNameId);
 284                                                 }else{
 285                                                         misappliedName = Taxon.NewInstance(taxonName, sec);
 286                                                         taxaToSave.add(misappliedName);
 287                                                 }
 288                                         }
 289                                         if (misappliedName != null){
 290                                                 taxon.addMisappliedName(misappliedName, config.getSourceReference(), null);
 291                                                 TaxonDescription misappliedNameDescription = getDescription(misappliedName);
 292                                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 293                                                         CommonTaxonName commonNameClone = (CommonTaxonName)commonTaxonName.clone();
 294                                                         misappliedNameDescription.addElement(commonNameClone);
 295                                                 }
 296                                         }else{
 297                                                 logger.warn("Misapplied name is null for common name " + commonNameId);
 298                                         }
 299
 300                                 }
 301
 302
 303                                 //reference extensions
 304                                 if (reference != null){
 305                                         if (CdmUtils.isNotEmpty(refLanguage)){
 306                                                 ExtensionType refLanguageExtensionType = getExtensionType( state, REFERENCE_LANGUAGE_STRING_UUID, "reference language","The language of the reference","ref. lang.");
 307                                                 Extension.NewInstance(reference, refLanguage, refLanguageExtensionType);
 308                                         }
 309
 310                                         if (CdmUtils.isNotEmpty(refLanguageIso639_2)){
 311                                                 ExtensionType refLanguageIsoExtensionType = getExtensionType( state, REFERENCE_LANGUAGE_ISO639_2_UUID, "reference language iso 639-2","The iso 639-2 code of the references language","ref. lang. 639-2");
 312                                                 Extension.NewInstance(reference, refLanguageIso639_2, refLanguageIsoExtensionType);
 313                                         }
 314                                 }else if (CdmUtils.isNotEmpty(refLanguage) || CdmUtils.isNotEmpty(refLanguageIso639_2)){
 315                                         logger.warn("Reference is null (" + languageRefRefFk + ") but refLanguage (" + CdmUtils.Nz(refLanguage) + ") or iso639_2 (" + CdmUtils.Nz(refLanguageIso639_2) + ") was not null");
 316                                 }
 317
 318                                 //status
 319                                 if (CdmUtils.isNotEmpty(status)){
 320                                         AnnotationType statusAnnotationType = getAnnotationType( state, STATUS_ANNOTATION_UUID, "status","The status of this object","status");
 321                                         Annotation annotation = Annotation.NewInstance(status, statusAnnotationType, Language.DEFAULT());
 322                                         for (CommonTaxonName commonTaxonName : commonTaxonNames){
 323                                                 commonTaxonName.addAnnotation(annotation);
 324                                         }
 325
 326                                 }
 327
 328                                 //Notes
 329                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 330                                         doIdCreatedUpdatedNotes(state, commonTaxonName, rs, String.valueOf(commonNameId), NAMESPACE);
 331                                 }
 332                                 partitioner.startDoSave();
 333                                 taxaToSave.add(taxon);
 334
 335                         }
 336                 } catch (SQLException e) {
 337                         logger.error("SQLException:" +  e);
 338                         return false;
 339                 } catch (ClassCastException e) {
 340                         e.printStackTrace();
 341                 }
 342
 343                 //      logger.info( i + " names handled");
 344                 getTaxonService().save(taxaToSave);
 345                 return success;
 346
 347         }
 348
 349
 350
 351         /**
 352          * Not used anymore. Use MisappliedName RIdentifier instead
 353          * @param biblioRefMap
 354          * @param nomRefMap
 355          * @param misNameRefFk
 356          * @param taxon
 357          */
 358         private boolean isFirstMisappliedName = true;
 359         private Taxon getMisappliedName(Map<String, Reference> biblioRefMap, Map<String, Reference> nomRefMap,
 360                         Object misNameRefFk, Taxon taxon) {
 361                 Taxon misappliedTaxon = null;
 362                 Reference misNameRef = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));
 363                 misappliedTaxon = Taxon.NewInstance(taxon.getName(), misNameRef);
 364                 Set<String> includeProperty = new HashSet<String>();
 365                 try {
 366 //                      //IMatchStrategy matchStrategy = DefaultMatchStrategy.NewInstance(TaxonBase.class);
 367 //                      //List<TaxonBase> misappliedList1 = getCommonService().findMatching(misappliedTaxon, matchStrategy);
 368                         List<TaxonBase> misappliedList = getTaxonService().list(misappliedTaxon, includeProperty, null, null, null, null);
 369                         if (misappliedList.size() > 0){
 370                                 misappliedTaxon = CdmBase.deproxy(misappliedList.get(0), Taxon.class);
 371                         }
 372                 } catch (ClassCastException e) {
 373                         logger.error(e.getMessage());
 374                         if (isFirstMisappliedName){
 375                                 e.printStackTrace();
 376                                 isFirstMisappliedName = false;
 377                         }
 378                 }
 379                 return misappliedTaxon;
 380         }
 381
 382
 383
 384         /**
 385          * @param iso6392Map
 386          * @param iso639_2
 387          * @param languageString
 388          * @param originalLanguageString
 389          * @return
 390          */
 391         private Language getAndHandleLanguage(Map<String, Language> iso639Map,  String iso639_2, String iso639_1, String languageString, String originalLanguageString) {
 392                 Language language;
 393                 if (CdmUtils.isNotEmpty(iso639_2)|| CdmUtils.isNotEmpty(iso639_1)  ){
 394                         //TODO test performance, implement in state
 395                         language = getLanguageFromIsoMap(iso639Map, iso639_2, iso639_1);
 396
 397                         if (language == null){
 398                                 language = getTermService().getLanguageByIso(iso639_2);
 399                                 iso639Map.put(iso639_2, language);
 400                                 if (language == null){
 401                                         language = getTermService().getLanguageByIso(iso639_1);
 402                                         iso639Map.put(iso639_1, language);
 403                                 }
 404                                 if (language == null){
 405                                         logger.warn("Language for code ISO693-2 '" + iso639_2 + "' and ISO693-1 '" + iso639_1 + "' was not found");
 406                                 }
 407                         }
 408                 }else{
 409                         logger.warn("language ISO 639_1 and ISO 639_2 were empty for " + languageString);
 410                         language = null;
 411                 }
 412                 addOriginalLanguage(language, originalLanguageString);
 413                 return language;
 414         }
 415
 416
 417         /**
 418          * @param iso639Map
 419          * @param iso639_2
 420          * @param iso639_1
 421          * @return
 422          */
 423         private Language getLanguageFromIsoMap(Map<String, Language> iso639Map, String iso639_2, String iso639_1) {
 424                 Language language;
 425                 language = iso639Map.get(iso639_2);
 426                 if (language == null){
 427                         language = iso639Map.get(iso639_1);
 428                 }
 429                 return language;
 430         }
 431
 432         /**
 433          * @param language
 434          * @param originalLanguageString
 435          */
 436         private void addOriginalLanguage(Language language,     String originalLanguageString) {
 437                 if (CdmUtils.isEmpty(originalLanguageString)){
 438                         return;
 439                 }else if (language == null){
 440                         logger.warn("Language could not be defined, but originalLanguageString exists: " + originalLanguageString);
 441                 }else {
 442                         Representation representation = language.getRepresentation(language);
 443                         if (representation == null){
 444                                 language.addRepresentation(Representation.NewInstance(originalLanguageString, originalLanguageString, originalLanguageString, language));
 445                                 getTermService().saveOrUpdate(language);
 446                         }
 447                 }
 448
 449         }
 450
 451
 452
 453         /**
 454          * @param result
 455          * @param regionFks
 456          * @param source
 457          * @return
 458          * @throws SQLException
 459          */
 460         private boolean getRegionFks(boolean result, SortedSet<Integer> regionFks,
 461                         Source source) throws SQLException {
 462                 String sql = " SELECT DISTINCT RegionFks FROM emCommonName";
 463                 ResultSet rs = source.getResultSet(sql);
 464                 while (rs.next()){
 465                         String strRegionFks = rs.getString("RegionFks");
 466                         String[] regionFkArray = strRegionFks.split(",");
 467                         for (String regionFk: regionFkArray){
 468                                 regionFk = regionFk.trim();
 469                                 if (! StringUtils.isNumeric(regionFk) || "".equals(regionFk)  ){
 470                                         result = false;
 471                                         logger.warn("RegionFk is not numeric: " + regionFk);
 472                                 }else{
 473                                         regionFks.add(Integer.valueOf(regionFk));
 474                                 }
 475                         }
 476                 }
 477                 return result;
 478         }
 479
 480
 481
 482         /**
 483          * @param source
 484          * @param sqlWhere
 485          * @param emTdwgMap
 486          * @throws SQLException
 487          */
 488         private void fillRegionMap(Source source, String sqlWhere,
 489                         Map<String, String> emTdwgMap) throws SQLException {
 490                 String sql;
 491                 ResultSet rs;
 492                 sql = " SELECT RegionId, Region FROM emLanguageRegion WHERE RegionId IN ("+ sqlWhere+ ") ";
 493                 rs = source.getResultSet(sql);
 494                 while (rs.next()){
 495                         Object regionId = rs.getObject("RegionId");
 496                         String region = rs.getString("Region");
 497                         String[] splitRegion = region.split("-");
 498                         if (splitRegion.length <= 1){
 499                                 NamedArea newArea = NamedArea.NewInstance(region, region, null);
 500                                 getTermService().save(newArea);
 501                                 regionMap.put(String.valueOf(regionId), newArea);
 502                                 logger.warn("Found new area: " +  region);
 503                         }else if (splitRegion.length == 2){
 504                                 String emCode = splitRegion[1].trim();
 505                                 String tdwgCode = emTdwgMap.get(emCode);
 506                                 if (StringUtils.isNotBlank(tdwgCode) ){
 507                                         NamedArea tdwgArea = getNamedArea(tdwgCode);
 508                                         regionMap.put(String.valueOf(regionId), tdwgArea);
 509                                 }else{
 510                                         logger.warn("emCode did not map to valid tdwgCode: " +  CdmUtils.Nz(emCode) + "->" + CdmUtils.Nz(tdwgCode));
 511                                 }
 512                         }
 513                 }
 514         }
 515
 516
 517         /**
 518          * @param tdwgCode
 519          */
 520         private NamedArea getNamedArea(String tdwgCode) {
 521                 NamedArea area;
 522                 if (tdwgCode.equalsIgnoreCase("Ab")){
 523                         area = NamedArea.NewInstance("Azerbaijan (including Nakhichevan)", "Azerbaijan & Nakhichevan", "Ab");
 524                         getTermService().save(area);
 525                 }else if (tdwgCode.equalsIgnoreCase("Rf")){
 526                         area = NamedArea.NewInstance("The Russian Federation", "The Russian Federation", "Rf");
 527                         getTermService().save(area);
 528                 }else if (tdwgCode.equalsIgnoreCase("Uk")){
 529                         area = NamedArea.NewInstance("Ukraine (including Crimea)", "Ukraine & Crimea", "Uk");
 530                         getTermService().save(area);
 531                 }else{
 532                         area = TdwgArea.getAreaByTdwgAbbreviation(tdwgCode);
 533                 }
 534                 return area;
 535         }
 536
 537
 538
 539         /**
 540          * @param regionFks
 541          * @return
 542          */
 543         private String getSqlWhere(SortedSet<Integer> regionFks) {
 544                 String sqlWhere = "";
 545                 for (Integer regionFk : regionFks){
 546                         sqlWhere += regionFk + ",";
 547                 }
 548                 sqlWhere = sqlWhere.substring(0, sqlWhere.length()-1);
 549                 return sqlWhere;
 550         }
 551
 552
 553
 554         /**
 555          * @param source
 556          * @throws SQLException
 557          */
 558         private Map<String, String> getEmTdwgMap(Source source) throws SQLException {
 559                 String sql;
 560                 ResultSet rs;
 561                 Map<String, String> emTdwgMap = new HashMap<String, String>();
 562                 sql = " SELECT EmCode, TDWGCode FROM emArea ";
 563                 rs = source.getResultSet(sql);
 564                 while (rs.next()){
 565                         String emCode = rs.getString("EMCode");
 566                         String TDWGCode = rs.getString("TDWGCode");
 567                         if (StringUtils.isNotBlank(emCode) ){
 568                                 emCode = emCode.trim();
 569                                 if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")|| emCode.equalsIgnoreCase("Uk") ){
 570                                         emTdwgMap.put(emCode, emCode);
 571                                 }else if (StringUtils.isNotBlank(TDWGCode)){
 572                                         emTdwgMap.put(emCode, TDWGCode.trim());
 573                                 }
 574                         }
 575                 }
 576                 return emTdwgMap;
 577         }
 578
 579
 580
 581
 582         /**
 583          * Returns the first non-image gallery description. Creates a new one if no description exists.
 584          * @param taxon
 585          * @return
 586          */
 587         private TaxonDescription getDescription(Taxon taxon) {
 588                 TaxonDescription result = null;
 589                 for (TaxonDescription taxonDescription : taxon.getDescriptions()){
 590                         if (! taxonDescription.isImageGallery()){
 591                                 result = taxonDescription;
 592                         }
 593                 }
 594                 if (result == null){
 595                         result = TaxonDescription.NewInstance(taxon);
 596                 }
 597                 return result;
 598         }
 599
 600         /* (non-Javadoc)
 601          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 602          */
 603         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 604                 String nameSpace;
 605                 Class cdmClass;
 606                 Set<String> idSet;
 607                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 608
 609                 try{
 610                         Set<String> taxonIdSet = new HashSet<String>();
 611                         Set<String> nameIdSet = new HashSet<String>();
 612                         Set<String> referenceIdSet = new HashSet<String>();
 613                         while (rs.next()){
 614                                 handleForeignKey(rs, taxonIdSet, "taxonId");
 615                                 handleForeignKey(rs, taxonIdSet, "misappliedTaxonId");
 616                                 handleForeignKey(rs, referenceIdSet, "refId");
 617                                 handleForeignKey(rs, referenceIdSet, "languageRefRefFk");
 618                                 handleForeignKey(rs, nameIdSet, "NameInSourceFk");
 619                                 handleForeignKey(rs, nameIdSet, "PTNameFk");
 620                                 handleForeignKey(rs, referenceIdSet, "MisNameRefFk");
 621                         }
 622
 623                         //name map
 624                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 625                         cdmClass = TaxonNameBase.class;
 626                         idSet = nameIdSet;
 627                         Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 628                         result.put(nameSpace, nameMap);
 629
 630                         //name map
 631                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 632                         cdmClass = Taxon.class;
 633                         idSet = taxonIdSet;
 634                         Map<String, TaxonNameBase> taxonMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 635                         result.put(nameSpace, taxonMap);
 636
 637                         //nom reference map
 638                         nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
 639                         cdmClass = Reference.class;
 640                         idSet = referenceIdSet;
 641                         Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 642                         result.put(nameSpace, nomReferenceMap);
 643
 644                         //biblio reference map
 645                         nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
 646                         cdmClass = Reference.class;
 647                         idSet = referenceIdSet;
 648                         Map<String, Reference> biblioReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 649                         result.put(nameSpace, biblioReferenceMap);
 650
 651                 } catch (SQLException e) {
 652                         throw new RuntimeException(e);
 653                 } catch (NullPointerException nep){
 654                         logger.error("NullPointerException in getRelatedObjectsForPartition()");
 655                 }
 656                 return result;
 657         }
 658
 659
 660
 661         /* (non-Javadoc)
 662          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 663          */
 664         @Override
 665         protected boolean doCheck(BerlinModelImportState state){
 666                 IOValidator<BerlinModelImportState> validator = new BerlinModelCommonNamesImportValidator();
 667                 return validator.validate(state);
 668         }
 669
 670
 671         /* (non-Javadoc)
 672          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
 673          */
 674         @Override
 675         protected String getTableName() {
 676                 return dbTableName;
 677         }
 678
 679         /* (non-Javadoc)
 680          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
 681          */
 682         @Override
 683         public String getPluralString() {
 684                 return pluralString;
 685         }
 686
 687         /* (non-Javadoc)
 688          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 689          */
 690         protected boolean isIgnore(BerlinModelImportState state){
 691                 return ! state.getConfig().isDoCommonNames();
 692         }
 693
 694 }