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 final String pluralString = "common names";
  68         private static final String dbTableName = "emCommonName";
  69
  70
  71         //map that stores the regions (named areas) and makes them accessible via the regionFk
  72         private Map<String, NamedArea> regionMap = new HashMap<String, NamedArea>();
  73
  74
  75
  76         public BerlinModelCommonNamesImport(){
  77                 super();
  78         }
  79
  80
  81
  82         @Override
  83         protected String getIdQuery() {
  84                 String result = " SELECT CommonNameId FROM emCommonName ";
  85                 return result;
  86         }
  87
  88
  89
  90         /* (non-Javadoc)
  91          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  92          */
  93         @Override
  94         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  95                 String recordQuery = "";
  96                 recordQuery =
  97                         " SELECT emCommonName.CommonNameId, emCommonName.CommonName, PTaxon.RIdentifier AS taxonId, emCommonName.PTNameFk, emCommonName.RefFk AS refId, emCommonName.Status, " +
  98                                 " emCommonName.RegionFks, emCommonName.MisNameRefFk, emCommonName.NameInSourceFk , emCommonName.Created_When, emCommonName.Updated_When, emCommonName.Created_Who, emCommonName.Updated_Who, emCommonName.Note as Notes," +
  99                         " regionLanguage.Language AS regionLanguage, languageCommonName.Language, languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2, " +
 100                         " emLanguageRegion.Region, emLanguageReference.RefFk as languageRefRefFk, emLanguageReference.ReferenceShort, " +
 101                         " emLanguageReference.ReferenceLong, emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, " +
 102                         " languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2, regionLanguage.ISO639_2 AS regionLanguageIso, " +
 103                         " misappliedTaxon.RIdentifier AS misappliedTaxonId " +
 104                 " FROM emLanguage as regionLanguage RIGHT OUTER JOIN " +
 105                         " emLanguageRegion ON regionLanguage.LanguageId = emLanguageRegion.LanguageFk RIGHT OUTER JOIN " +
 106                         " emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " +
 107                         " emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " +
 108                         " emCommonName INNER JOIN " +
 109                         " PTaxon ON emCommonName.PTNameFk = PTaxon.PTNameFk AND emCommonName.PTRefFk = PTaxon.PTRefFk ON " +
 110                         " emLanguageReference.ReferenceId = emCommonName.LanguageRefFk LEFT OUTER JOIN " +
 111                         " emLanguage AS languageCommonName ON emCommonName.LanguageFk = languageCommonName.LanguageId ON " +
 112                         " emLanguageRegion.RegionId = emCommonName.RegionFks LEFT OUTER JOIN " +
 113                         " PTaxon as misappliedTaxon ON emCommonName.PTNameFk = misappliedTaxon.PTNameFk AND emCommonName.MisNameRefFk = misappliedTaxon.PTRefFk " +
 114                         " WHERE emCommonName.CommonNameId IN (" + ID_LIST_TOKEN + ")";
 115                 return recordQuery;
 116         }
 117
 118
 119
 120         @Override
 121         protected boolean doInvoke(BerlinModelImportState state) {
 122                 boolean result = true;
 123                 try {
 124                         result &= makeRegions(state);
 125                 } catch (Exception e) {
 126                         logger.error("Error when creating common name regions:" + e.getMessage());
 127                         result = false;
 128                 }
 129                 result &= super.doInvoke(state);
 130                 return result;
 131         }
 132
 133         /**
 134          * @param state
 135          *
 136          */
 137         private boolean makeRegions(BerlinModelImportState state) {
 138                 boolean result = true;
 139                 try {
 140                         SortedSet<Integer> regionFks = new TreeSet<Integer>();
 141                         Source source = state.getConfig().getSource();
 142
 143                         result = getRegionFks(result, regionFks, source);
 144                         //concat filter string
 145                         String sqlWhere = getSqlWhere(regionFks);
 146
 147                         //get E+M - TDWG Mapping
 148                         Map<String, String> emTdwgMap = getEmTdwgMap(source);
 149                         //fill regionMap
 150                         fillRegionMap(source, sqlWhere, emTdwgMap);
 151
 152                         return result;
 153                 } catch (NumberFormatException e) {
 154                         e.printStackTrace();
 155                         return false;
 156                 } catch (SQLException e) {
 157                         e.printStackTrace();
 158                         return false;
 159                 }
 160         }
 161
 162
 163         /* (non-Javadoc)
 164          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
 165          */
 166         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state)  {
 167                 boolean success = true ;
 168                 BerlinModelImportConfigurator config = state.getConfig();
 169                 Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
 170                 Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
 171                 Map<String, TaxonNameBase> taxonNameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
 172
 173                 Map<String, Reference> biblioRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
 174                 Map<String, Reference> nomRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);
 175
 176                 Map<String, Language> iso6392Map = new HashMap<String, Language>();
 177
 178         //      logger.warn("MisappliedNameRefFk  not yet implemented for Common Names");
 179
 180                 ResultSet rs = partitioner.getResultSet();
 181                 try{
 182                         while (rs.next()){
 183
 184                                 //create TaxonName element
 185                                 Object commonNameId = rs.getObject("CommonNameId");
 186                                 int taxonId = rs.getInt("taxonId");
 187                                 Object refId = rs.getObject("refId");
 188                                 Object ptNameFk = rs.getObject("PTNameFk");
 189                                 String commonNameString = rs.getString("CommonName");
 190                                 String iso639_2 = rs.getString("ISO639_2");
 191                                 String iso639_1 = rs.getString("ISO639_1");
 192                                 String languageString = rs.getString("Language");
 193                                 String originalLanguageString = rs.getString("LanguageOriginal");
 194                                 Object misNameRefFk = rs.getObject("MisNameRefFk");
 195                                 Object languageRefRefFk = rs.getObject("languageRefRefFk");
 196                                 String refLanguage = rs.getString("refLanguage");
 197                                 String refLanguageIso639_2 = rs.getString("refLanguageIso639_2");
 198                                 String status = rs.getString("Status");
 199                                 Object nameInSourceFk = rs.getObject("NameInSourceFk");
 200                                 Object misappliedTaxonId = rs.getObject("misappliedTaxonId");
 201
 202                                 //regions
 203                                 String region = rs.getString("Region");
 204                                 String regionFks  = rs.getString("RegionFks");
 205                                 String[] regionFkSplit = regionFks.split(",");
 206
 207                                 //commonNameString
 208                                 if (CdmUtils.isEmpty(commonNameString)){
 209                                         String message = "CommonName is empty or null. Do not import record for taxon " + taxonId;
 210                                         logger.warn(message);
 211                                         continue;
 212                                 }
 213
 214                                 //taxon
 215                                 Taxon taxon = null;
 216                                 TaxonBase taxonBase = null;
 217                                 taxonBase  = taxonMap.get(String.valueOf(taxonId));
 218                                 if (taxonBase == null){
 219                                         logger.warn("Taxon (" + taxonId + ") could not be found. Common name " + commonNameString + " not imported");
 220                                         continue;
 221                                 }else if (! taxonBase.isInstanceOf(Taxon.class)){
 222                                         logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " +  commonNameId);
 223                                         continue;
 224                                 }else{
 225                                         taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 226                                 }
 227
 228                                 //Language
 229                                 Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString);
 230
 231                                 //CommonTaxonName
 232                                 List<CommonTaxonName> commonTaxonNames = new ArrayList<CommonTaxonName>();
 233                                 for (String regionFk : regionFkSplit){
 234                                         CommonTaxonName commonTaxonName;
 235                                         if (commonTaxonNames.size() == 0){
 236                                                 commonTaxonName = CommonTaxonName.NewInstance(commonNameString, language);
 237                                         }else{
 238                                                 commonTaxonName = (CommonTaxonName)commonTaxonNames.get(0).clone();
 239                                         }
 240                                         commonTaxonNames.add(commonTaxonName);
 241                                         regionFk = regionFk.trim();
 242                                         NamedArea area = regionMap.get(regionFk);
 243                                         if (area == null){
 244                                                 logger.warn("Area for " + regionFk + " not defined.");
 245                                         }else{
 246                                                 commonTaxonName.setArea(area);
 247                                                 TaxonDescription description = getDescription(taxon);
 248                                                 description.addElement(commonTaxonName);
 249                                         }
 250                                 }
 251
 252                                 //Reference/Source
 253                                 String strRefId = String.valueOf(refId);
 254                                 String languageRefFk = String.valueOf(languageRefRefFk);
 255                                 if (! CdmUtils.nullSafeEqual(strRefId, languageRefFk)){
 256                                         logger.warn("CommonName.RefFk (" + CdmUtils.Nz(strRefId) + ") and LanguageReference.RefFk " + CdmUtils.Nz(languageRefFk) + " are not equal. I will import only languageRefFk");
 257                                 }
 258
 259                                 Reference reference = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(languageRefRefFk));
 260                                 String microCitation = null;
 261                                 String originalNameString = null;
 262
 263                                 TaxonNameBase nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));
 264                                 if (nameInSourceFk != null && nameUsedInSource == null){
 265                                         logger.warn("Name used in source (" + nameInSourceFk + ") was not found");
 266                                 }
 267                                 DescriptionElementSource source = DescriptionElementSource.NewInstance(reference, microCitation, nameUsedInSource, originalNameString);
 268                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 269                                         commonTaxonName.addSource(source);
 270                                 }
 271
 272                                 //MisNameRef
 273                                 if (misNameRefFk != null){
 274                                         //Taxon misappliedName = getMisappliedName(biblioRefMap, nomRefMap, misNameRefFk, taxon);
 275                                         Taxon misappliedName = null;
 276                                         if (misappliedTaxonId != null){
 277                                                 misappliedName = taxonMap.get(String.valueOf(misappliedTaxonId));
 278                                         }else{
 279                                                 TaxonNameBase taxonName = taxonNameMap.get(String.valueOf(ptNameFk));
 280                                                 Reference sec = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));
 281                                                 if (taxonName == null || sec == null){
 282                                                         logger.info("Taxon name or misapplied name reference is null for common name " + commonNameId);
 283                                                 }else{
 284                                                         misappliedName = Taxon.NewInstance(taxonName, sec);
 285                                                         taxaToSave.add(misappliedName);
 286                                                 }
 287                                         }
 288                                         if (misappliedName != null){
 289                                                 taxon.addMisappliedName(misappliedName, config.getSourceReference(), null);
 290                                                 TaxonDescription misappliedNameDescription = getDescription(misappliedName);
 291                                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 292                                                         CommonTaxonName commonNameClone = (CommonTaxonName)commonTaxonName.clone();
 293                                                         misappliedNameDescription.addElement(commonNameClone);
 294                                                 }
 295                                         }else{
 296                                                 logger.warn("Misapplied name is null for common name " + commonNameId);
 297                                         }
 298
 299                                 }
 300
 301
 302                                 //reference extensions
 303                                 if (reference != null){
 304                                         if (CdmUtils.isNotEmpty(refLanguage)){
 305                                                 ExtensionType refLanguageExtensionType = getExtensionType( state, REFERENCE_LANGUAGE_STRING_UUID, "reference language","The language of the reference","ref. lang.");
 306                                                 Extension.NewInstance(reference, refLanguage, refLanguageExtensionType);
 307                                         }
 308
 309                                         if (CdmUtils.isNotEmpty(refLanguageIso639_2)){
 310                                                 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");
 311                                                 Extension.NewInstance(reference, refLanguageIso639_2, refLanguageIsoExtensionType);
 312                                         }
 313                                 }else if (CdmUtils.isNotEmpty(refLanguage) || CdmUtils.isNotEmpty(refLanguageIso639_2)){
 314                                         logger.warn("Reference is null (" + languageRefRefFk + ") but refLanguage (" + CdmUtils.Nz(refLanguage) + ") or iso639_2 (" + CdmUtils.Nz(refLanguageIso639_2) + ") was not null");
 315                                 }
 316
 317                                 //status
 318                                 if (CdmUtils.isNotEmpty(status)){
 319                                         AnnotationType statusAnnotationType = getAnnotationType( state, STATUS_ANNOTATION_UUID, "status","The status of this object","status");
 320                                         Annotation annotation = Annotation.NewInstance(status, statusAnnotationType, Language.DEFAULT());
 321                                         for (CommonTaxonName commonTaxonName : commonTaxonNames){
 322                                                 commonTaxonName.addAnnotation(annotation);
 323                                         }
 324
 325                                 }
 326
 327                                 //Notes
 328                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 329                                         doIdCreatedUpdatedNotes(state, commonTaxonName, rs, String.valueOf(commonNameId), NAMESPACE);
 330                                 }
 331                                 partitioner.startDoSave();
 332                                 taxaToSave.add(taxon);
 333
 334                         }
 335                 } catch (SQLException e) {
 336                         logger.error("SQLException:" +  e);
 337                         return false;
 338                 } catch (ClassCastException e) {
 339                         e.printStackTrace();
 340                 }
 341
 342                 //      logger.info( i + " names handled");
 343                 getTaxonService().save(taxaToSave);
 344                 return success;
 345
 346         }
 347
 348
 349
 350         /**
 351          * Not used anymore. Use MisappliedName RIdentifier instead
 352          * @param biblioRefMap
 353          * @param nomRefMap
 354          * @param misNameRefFk
 355          * @param taxon
 356          */
 357         private boolean isFirstMisappliedName = true;
 358         private Taxon getMisappliedName(Map<String, Reference> biblioRefMap, Map<String, Reference> nomRefMap,
 359                         Object misNameRefFk, Taxon taxon) {
 360                 Taxon misappliedTaxon = null;
 361                 Reference misNameRef = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));
 362                 misappliedTaxon = Taxon.NewInstance(taxon.getName(), misNameRef);
 363                 Set<String> includeProperty = new HashSet<String>();
 364                 try {
 365 //                      //IMatchStrategy matchStrategy = DefaultMatchStrategy.NewInstance(TaxonBase.class);
 366 //                      //List<TaxonBase> misappliedList1 = getCommonService().findMatching(misappliedTaxon, matchStrategy);
 367                         List<TaxonBase> misappliedList = getTaxonService().list(misappliedTaxon, includeProperty, null, null, null, null);
 368                         if (misappliedList.size() > 0){
 369                                 misappliedTaxon = CdmBase.deproxy(misappliedList.get(0), Taxon.class);
 370                         }
 371                 } catch (ClassCastException e) {
 372                         logger.error(e.getMessage());
 373                         if (isFirstMisappliedName){
 374                                 e.printStackTrace();
 375                                 isFirstMisappliedName = false;
 376                         }
 377                 }
 378                 return misappliedTaxon;
 379         }
 380
 381
 382
 383         /**
 384          * @param iso6392Map
 385          * @param iso639_2
 386          * @param languageString
 387          * @param originalLanguageString
 388          * @return
 389          */
 390         private Language getAndHandleLanguage(Map<String, Language> iso639Map,  String iso639_2, String iso639_1, String languageString, String originalLanguageString) {
 391                 Language language;
 392                 if (CdmUtils.isNotEmpty(iso639_2)|| CdmUtils.isNotEmpty(iso639_1)  ){
 393                         //TODO test performance, implement in state
 394                         language = getLanguageFromIsoMap(iso639Map, iso639_2, iso639_1);
 395
 396                         if (language == null){
 397                                 language = getTermService().getLanguageByIso(iso639_2);
 398                                 iso639Map.put(iso639_2, language);
 399                                 if (language == null){
 400                                         language = getTermService().getLanguageByIso(iso639_1);
 401                                         iso639Map.put(iso639_1, language);
 402                                 }
 403                                 if (language == null){
 404                                         logger.warn("Language for code ISO693-2 '" + iso639_2 + "' and ISO693-1 '" + iso639_1 + "' was not found");
 405                                 }
 406                         }
 407                 } else if ("unknown".equals(languageString)){
 408                         language = Language.UNKNOWN_LANGUAGE();
 409                 }else{
 410                         logger.warn("language ISO 639_1 and ISO 639_2 were empty for " + languageString);
 411                         language = null;
 412                 }
 413                 addOriginalLanguage(language, originalLanguageString);
 414                 return language;
 415         }
 416
 417
 418         /**
 419          * @param iso639Map
 420          * @param iso639_2
 421          * @param iso639_1
 422          * @return
 423          */
 424         private Language getLanguageFromIsoMap(Map<String, Language> iso639Map, String iso639_2, String iso639_1) {
 425                 Language language;
 426                 language = iso639Map.get(iso639_2);
 427                 if (language == null){
 428                         language = iso639Map.get(iso639_1);
 429                 }
 430                 return language;
 431         }
 432
 433         /**
 434          * @param language
 435          * @param originalLanguageString
 436          */
 437         private void addOriginalLanguage(Language language,     String originalLanguageString) {
 438                 if (CdmUtils.isEmpty(originalLanguageString)){
 439                         return;
 440                 }else if (language == null){
 441                         logger.warn("Language could not be defined, but originalLanguageString exists: " + originalLanguageString);
 442                 }else {
 443                         Representation representation = language.getRepresentation(language);
 444                         if (representation == null){
 445                                 language.addRepresentation(Representation.NewInstance(originalLanguageString, originalLanguageString, originalLanguageString, language));
 446                                 getTermService().saveOrUpdate(language);
 447                         }
 448                 }
 449
 450         }
 451
 452
 453
 454         /**
 455          * @param result
 456          * @param regionFks
 457          * @param source
 458          * @return
 459          * @throws SQLException
 460          */
 461         private boolean getRegionFks(boolean result, SortedSet<Integer> regionFks,
 462                         Source source) throws SQLException {
 463                 String sql = " SELECT DISTINCT RegionFks FROM emCommonName";
 464                 ResultSet rs = source.getResultSet(sql);
 465                 while (rs.next()){
 466                         String strRegionFks = rs.getString("RegionFks");
 467                         String[] regionFkArray = strRegionFks.split(",");
 468                         for (String regionFk: regionFkArray){
 469                                 regionFk = regionFk.trim();
 470                                 if (! StringUtils.isNumeric(regionFk) || "".equals(regionFk)  ){
 471                                         result = false;
 472                                         logger.warn("RegionFk is not numeric: " + regionFk);
 473                                 }else{
 474                                         regionFks.add(Integer.valueOf(regionFk));
 475                                 }
 476                         }
 477                 }
 478                 return result;
 479         }
 480
 481
 482
 483         /**
 484          * @param source
 485          * @param sqlWhere
 486          * @param emTdwgMap
 487          * @throws SQLException
 488          */
 489         private void fillRegionMap(Source source, String sqlWhere,
 490                         Map<String, String> emTdwgMap) throws SQLException {
 491                 String sql;
 492                 ResultSet rs;
 493                 sql = " SELECT RegionId, Region FROM emLanguageRegion WHERE RegionId IN ("+ sqlWhere+ ") ";
 494                 rs = source.getResultSet(sql);
 495                 while (rs.next()){
 496                         Object regionId = rs.getObject("RegionId");
 497                         String region = rs.getString("Region");
 498                         String[] splitRegion = region.split("-");
 499                         if (splitRegion.length <= 1){
 500                                 NamedArea newArea = NamedArea.NewInstance(region, region, null);
 501                                 getTermService().save(newArea);
 502                                 regionMap.put(String.valueOf(regionId), newArea);
 503                                 logger.warn("Found new area: " +  region);
 504                         }else if (splitRegion.length == 2){
 505                                 String emCode = splitRegion[1].trim();
 506                                 String tdwgCode = emTdwgMap.get(emCode);
 507                                 if (StringUtils.isNotBlank(tdwgCode) ){
 508                                         NamedArea tdwgArea = getNamedArea(tdwgCode);
 509                                         regionMap.put(String.valueOf(regionId), tdwgArea);
 510                                 }else{
 511                                         logger.warn("emCode did not map to valid tdwgCode: " +  CdmUtils.Nz(emCode) + "->" + CdmUtils.Nz(tdwgCode));
 512                                 }
 513                         }
 514                 }
 515         }
 516
 517
 518         /**
 519          * @param tdwgCode
 520          */
 521         private NamedArea getNamedArea(String tdwgCode) {
 522                 NamedArea area;
 523                 if (tdwgCode.equalsIgnoreCase("Ab")){
 524                         area = NamedArea.NewInstance("Azerbaijan (including Nakhichevan)", "Azerbaijan & Nakhichevan", "Ab");
 525                         getTermService().save(area);
 526                 }else if (tdwgCode.equalsIgnoreCase("Rf")){
 527                         area = NamedArea.NewInstance("The Russian Federation", "The Russian Federation", "Rf");
 528                         getTermService().save(area);
 529                 }else if (tdwgCode.equalsIgnoreCase("Uk")){
 530                         area = NamedArea.NewInstance("Ukraine (including Crimea)", "Ukraine & Crimea", "Uk");
 531                         getTermService().save(area);
 532                 }else{
 533                         area = TdwgArea.getAreaByTdwgAbbreviation(tdwgCode);
 534                 }
 535                 return area;
 536         }
 537
 538
 539
 540         /**
 541          * @param regionFks
 542          * @return
 543          */
 544         private String getSqlWhere(SortedSet<Integer> regionFks) {
 545                 String sqlWhere = "";
 546                 for (Integer regionFk : regionFks){
 547                         sqlWhere += regionFk + ",";
 548                 }
 549                 sqlWhere = sqlWhere.substring(0, sqlWhere.length()-1);
 550                 return sqlWhere;
 551         }
 552
 553
 554
 555         /**
 556          * @param source
 557          * @throws SQLException
 558          */
 559         private Map<String, String> getEmTdwgMap(Source source) throws SQLException {
 560                 String sql;
 561                 ResultSet rs;
 562                 Map<String, String> emTdwgMap = new HashMap<String, String>();
 563                 sql = " SELECT EmCode, TDWGCode FROM emArea ";
 564                 rs = source.getResultSet(sql);
 565                 while (rs.next()){
 566                         String emCode = rs.getString("EMCode");
 567                         String TDWGCode = rs.getString("TDWGCode");
 568                         if (StringUtils.isNotBlank(emCode) ){
 569                                 emCode = emCode.trim();
 570                                 if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")|| emCode.equalsIgnoreCase("Uk") ){
 571                                         emTdwgMap.put(emCode, emCode);
 572                                 }else if (StringUtils.isNotBlank(TDWGCode)){
 573                                         emTdwgMap.put(emCode, TDWGCode.trim());
 574                                 }
 575                         }
 576                 }
 577                 return emTdwgMap;
 578         }
 579
 580
 581
 582
 583         /**
 584          * Returns the first non-image gallery description. Creates a new one if no description exists.
 585          * @param taxon
 586          * @return
 587          */
 588         private TaxonDescription getDescription(Taxon taxon) {
 589                 TaxonDescription result = null;
 590                 for (TaxonDescription taxonDescription : taxon.getDescriptions()){
 591                         if (! taxonDescription.isImageGallery()){
 592                                 result = taxonDescription;
 593                         }
 594                 }
 595                 if (result == null){
 596                         result = TaxonDescription.NewInstance(taxon);
 597                 }
 598                 return result;
 599         }
 600
 601         /* (non-Javadoc)
 602          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 603          */
 604         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 605                 String nameSpace;
 606                 Class cdmClass;
 607                 Set<String> idSet;
 608                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 609
 610                 try{
 611                         Set<String> taxonIdSet = new HashSet<String>();
 612                         Set<String> nameIdSet = new HashSet<String>();
 613                         Set<String> referenceIdSet = new HashSet<String>();
 614                         while (rs.next()){
 615                                 handleForeignKey(rs, taxonIdSet, "taxonId");
 616                                 handleForeignKey(rs, taxonIdSet, "misappliedTaxonId");
 617                                 handleForeignKey(rs, referenceIdSet, "refId");
 618                                 handleForeignKey(rs, referenceIdSet, "languageRefRefFk");
 619                                 handleForeignKey(rs, nameIdSet, "NameInSourceFk");
 620                                 handleForeignKey(rs, nameIdSet, "PTNameFk");
 621                                 handleForeignKey(rs, referenceIdSet, "MisNameRefFk");
 622                         }
 623
 624                         //name map
 625                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 626                         cdmClass = TaxonNameBase.class;
 627                         idSet = nameIdSet;
 628                         Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 629                         result.put(nameSpace, nameMap);
 630
 631                         //name map
 632                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 633                         cdmClass = Taxon.class;
 634                         idSet = taxonIdSet;
 635                         Map<String, TaxonNameBase> taxonMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 636                         result.put(nameSpace, taxonMap);
 637
 638                         //nom reference map
 639                         nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
 640                         cdmClass = Reference.class;
 641                         idSet = referenceIdSet;
 642                         Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 643                         result.put(nameSpace, nomReferenceMap);
 644
 645                         //biblio reference map
 646                         nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
 647                         cdmClass = Reference.class;
 648                         idSet = referenceIdSet;
 649                         Map<String, Reference> biblioReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 650                         result.put(nameSpace, biblioReferenceMap);
 651
 652                 } catch (SQLException e) {
 653                         throw new RuntimeException(e);
 654                 } catch (NullPointerException nep){
 655                         logger.error("NullPointerException in getRelatedObjectsForPartition()");
 656                 }
 657                 return result;
 658         }
 659
 660
 661
 662         /* (non-Javadoc)
 663          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 664          */
 665         @Override
 666         protected boolean doCheck(BerlinModelImportState state){
 667                 IOValidator<BerlinModelImportState> validator = new BerlinModelCommonNamesImportValidator();
 668                 return validator.validate(state);
 669         }
 670
 671
 672         /* (non-Javadoc)
 673          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
 674          */
 675         @Override
 676         protected String getTableName() {
 677                 return dbTableName;
 678         }
 679
 680         /* (non-Javadoc)
 681          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
 682          */
 683         @Override
 684         public String getPluralString() {
 685                 return pluralString;
 686         }
 687
 688         /* (non-Javadoc)
 689          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 690          */
 691         protected boolean isIgnore(BerlinModelImportState state){
 692                 return ! state.getConfig().isDoCommonNames();
 693         }
 694
 695 }