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.BerlinModelTransformer;
  30 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelCommonNamesImportValidator;
  31 import eu.etaxonomy.cdm.io.common.IOValidator;
  32 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  33 import eu.etaxonomy.cdm.io.common.Source;
  34 import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;
  35 import eu.etaxonomy.cdm.model.common.Annotation;
  36 import eu.etaxonomy.cdm.model.common.AnnotationType;
  37 import eu.etaxonomy.cdm.model.common.CdmBase;
  38 import eu.etaxonomy.cdm.model.common.Extension;
  39 import eu.etaxonomy.cdm.model.common.ExtensionType;
  40 import eu.etaxonomy.cdm.model.common.Language;
  41 import eu.etaxonomy.cdm.model.common.Marker;
  42 import eu.etaxonomy.cdm.model.common.MarkerType;
  43 import eu.etaxonomy.cdm.model.common.Representation;
  44 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  45 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  46 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  47 import eu.etaxonomy.cdm.model.location.NamedArea;
  48 import eu.etaxonomy.cdm.model.location.Country;
  49 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  50 import eu.etaxonomy.cdm.model.reference.Reference;
  51 import eu.etaxonomy.cdm.model.taxon.Taxon;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  53
  54 /**
  55  *
  56  * @author a.mueller
  57  * @created 20.03.2008
  58  * @version 1.0
  59  */
  60 @Component
  61 public class BerlinModelCommonNamesImport  extends BerlinModelImportBase {
  62         private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);
  63
  64         public static final UUID REFERENCE_LANGUAGE_ISO639_2_UUID = UUID.fromString("40c4f8dd-3d9c-44a4-b77a-76e137a89a5f");
  65         public static final UUID REFERENCE_LANGUAGE_STRING_UUID = UUID.fromString("2a1b678f-c27d-48c1-b43e-98fd0d426305");
  66         public static final UUID STATUS_ANNOTATION_UUID = UUID.fromString("e3f7b80a-1286-458d-812c-5e818f731968");
  67
  68         public static final String NAMESPACE = "common name";
  69
  70
  71         private static final String pluralString = "common names";
  72         private static final String dbTableName = "emCommonName";
  73
  74
  75         //map that stores the regions (named areas) and makes them accessible via the regionFk
  76         private Map<String, NamedArea> regionMap = new HashMap<String, NamedArea>();
  77
  78
  79
  80         public BerlinModelCommonNamesImport(){
  81                 super(dbTableName, pluralString);
  82         }
  83
  84
  85
  86         @Override
  87         protected String getIdQuery(BerlinModelImportState state) {
  88                 String result = " SELECT CommonNameId FROM emCommonName WHERE (1=1) ";
  89                 if (StringUtils.isNotBlank(state.getConfig().getCommonNameFilter())){
  90                         result += " AND " + state.getConfig().getCommonNameFilter();
  91                 }
  92
  93                 return result;
  94         }
  95
  96
  97
  98         /* (non-Javadoc)
  99          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
 100          */
 101         @Override
 102         protected String getRecordQuery(BerlinModelImportConfigurator config) {
 103                 String recordQuery = "";
 104                 recordQuery =
 105                                 " SELECT     cn.CommonNameId, cn.CommonName, PTaxon.RIdentifier AS taxonId, cn.PTNameFk, cn.RefFk AS refId, cn.Status, cn.RegionFks, cn.MisNameRefFk, " +
 106                                                "               cn.NameInSourceFk, cn.Created_When, cn.Updated_When, cn.Created_Who, cn.Updated_Who, cn.Note AS Notes, languageCommonName.Language, " +
 107                                                "               languageCommonName.LanguageOriginal, languageCommonName.ISO639_1, languageCommonName.ISO639_2,   " +
 108                                                "               emLanguageReference.RefFk AS languageRefRefFk, emLanguageReference.ReferenceShort, emLanguageReference.ReferenceLong,  " +
 109                                                "               emLanguageReference.LanguageFk, languageReferenceLanguage.Language AS refLanguage, languageReferenceLanguage.ISO639_2 AS refLanguageIso639_2,  "+
 110                                                "               misappliedTaxon.RIdentifier AS misappliedTaxonId " +
 111                                         " FROM         PTaxon AS misappliedTaxon RIGHT OUTER JOIN " +
 112                                             "                  emLanguage AS languageReferenceLanguage RIGHT OUTER JOIN " +
 113                                                        "       emLanguageReference ON languageReferenceLanguage.LanguageId = emLanguageReference.LanguageFk RIGHT OUTER JOIN " +
 114                                                        "       emCommonName AS cn INNER JOIN " +
 115                                                        "       PTaxon ON cn.PTNameFk = PTaxon.PTNameFk AND cn.PTRefFk = PTaxon.PTRefFk ON  " +
 116                                                        "       emLanguageReference.ReferenceId = cn.LanguageRefFk LEFT OUTER JOIN " +
 117                                                         "      emLanguage AS languageCommonName ON cn.LanguageFk = languageCommonName.LanguageId ON misappliedTaxon.PTNameFk = cn.NameInSourceFk AND  " +
 118                                                         "      misappliedTaxon.PTRefFk = cn.MisNameRefFk " +
 119                         " WHERE cn.CommonNameId IN (" + ID_LIST_TOKEN + ")";
 120                 return recordQuery;
 121         }
 122
 123
 124
 125         @Override
 126         protected void doInvoke(BerlinModelImportState state) {
 127                 try {
 128                         makeRegions(state);
 129                 } catch (Exception e) {
 130                         logger.error("Error when creating common name regions:" + e.getMessage());
 131                         e.printStackTrace();
 132                         state.setUnsuccessfull();
 133                 }
 134                 super.doInvoke(state);
 135                 return;
 136         }
 137
 138         /**
 139          * @param state
 140          *
 141          */
 142         private void makeRegions(BerlinModelImportState state) {
 143                 try {
 144                         SortedSet<Integer> regionFks = new TreeSet<Integer>();
 145                         Source source = state.getConfig().getSource();
 146
 147                         //fill set with all regionFk from emCommonName.regionFks
 148                         getRegionFks(state, regionFks, source);
 149                         //concat filter string
 150                         String sqlWhere = getSqlWhere(regionFks);
 151
 152                         //get E+M - TDWG Mapping
 153                         Map<String, String> emTdwgMap = getEmTdwgMap(source);
 154                         //fill regionMap
 155                         fillRegionMap(state, sqlWhere, emTdwgMap);
 156
 157                         return;
 158                 } catch (NumberFormatException e) {
 159                         e.printStackTrace();
 160                         state.setUnsuccessfull();
 161                         return;
 162                 } catch (SQLException e) {
 163                         e.printStackTrace();
 164                         state.setUnsuccessfull();
 165                         return;
 166                 }
 167         }
 168
 169
 170         /* (non-Javadoc)
 171          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
 172          */
 173         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state)  {
 174                 boolean success = true ;
 175                 BerlinModelImportConfigurator config = state.getConfig();
 176                 Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
 177                 Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
 178                 Map<String, TaxonNameBase> taxonNameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
 179
 180                 Map<String, Reference> biblioRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
 181                 Map<String, Reference> nomRefMap = (Map<String, Reference>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);
 182
 183                 Map<String, Language> iso6392Map = new HashMap<String, Language>();
 184
 185         //      logger.warn("MisappliedNameRefFk  not yet implemented for Common Names");
 186
 187                 ResultSet rs = partitioner.getResultSet();
 188                 try{
 189                         while (rs.next()){
 190
 191                                 //create TaxonName element
 192                                 Object commonNameId = rs.getObject("CommonNameId");
 193                                 int taxonId = rs.getInt("taxonId");
 194                                 Object refId = rs.getObject("refId");
 195                                 Object ptNameFk = rs.getObject("PTNameFk");
 196                                 String commonNameString = rs.getString("CommonName");
 197                                 String iso639_2 = rs.getString("ISO639_2");
 198                                 String iso639_1 = rs.getString("ISO639_1");
 199                                 String languageString = rs.getString("Language");
 200                                 String originalLanguageString = rs.getString("LanguageOriginal");
 201                                 Object misNameRefFk = rs.getObject("MisNameRefFk");
 202                                 Object languageRefRefFk = rs.getObject("languageRefRefFk");
 203                                 String refLanguage = rs.getString("refLanguage");
 204                                 String refLanguageIso639_2 = rs.getString("refLanguageIso639_2");
 205                                 String status = rs.getString("Status");
 206                                 Object nameInSourceFk = rs.getObject("NameInSourceFk");
 207                                 Object misappliedTaxonId = rs.getObject("misappliedTaxonId");
 208
 209                                 //regions
 210                                 String regionFks  = rs.getString("RegionFks");
 211                                 String[] regionFkSplit = regionFks.split(",");
 212
 213                                 //commonNameString
 214                                 if (CdmUtils.isBlank(commonNameString)){
 215                                         String message = "CommonName is empty or null. Do not import record for taxon " + taxonId;
 216                                         logger.warn(message);
 217                                         continue;
 218                                 }
 219
 220                                 //taxon
 221                                 Taxon taxon = null;
 222                                 TaxonBase taxonBase  = taxonMap.get(String.valueOf(taxonId));
 223                                 if (taxonBase == null){
 224                                         logger.warn("Taxon (" + taxonId + ") could not be found. Common name " + commonNameString + "(" + commonNameId + ") not imported");
 225                                         continue;
 226                                 }else if (! taxonBase.isInstanceOf(Taxon.class)){
 227                                         logger.warn("taxon (" + taxonId + ") is not accepted. Can't import common name " +  commonNameId);
 228                                         continue;
 229                                 }else{
 230                                         taxon = CdmBase.deproxy(taxonBase, Taxon.class);
 231                                 }
 232
 233                                 //Language
 234                                 Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString, state);
 235
 236                                 //CommonTaxonName
 237                                 List<CommonTaxonName> commonTaxonNames = new ArrayList<CommonTaxonName>();
 238                                 for (String regionFk : regionFkSplit){ //
 239                                         CommonTaxonName commonTaxonName;
 240                                         if (commonTaxonNames.size() == 0){
 241                                                 commonTaxonName = CommonTaxonName.NewInstance(commonNameString, language);
 242                                         }else{
 243                                                 commonTaxonName = (CommonTaxonName)commonTaxonNames.get(0).clone();
 244                                         }
 245                                         commonTaxonNames.add(commonTaxonName);
 246                                         regionFk = regionFk.trim();
 247                                         NamedArea area = regionMap.get(regionFk);
 248                                         if (area == null){
 249                                                 if (regionFkSplit.length > 1 && StringUtils.isNotBlank(regionFk)){
 250                                                         logger.warn("Area for " + regionFk + " not defined in regionMap.");
 251                                                 }else{
 252                                                         //no region is defined
 253                                                 }
 254                                         }else{
 255                                                 commonTaxonName.setArea(area);
 256                                                 TaxonDescription description = getDescription(taxon);
 257                                                 description.addElement(commonTaxonName);
 258                                         }
 259                                 }
 260
 261                                 //Reference/Source
 262                                 String strRefId = String.valueOf(refId);
 263                                 String languageRefFk = String.valueOf(languageRefRefFk);
 264                                 if (! CdmUtils.nullSafeEqual(strRefId, languageRefFk)){
 265                                         //use strRefId if languageRefFk is null
 266                                         if (languageRefRefFk == null){
 267                                                 languageRefFk = strRefId;
 268                                         }else{
 269                                                 logger.warn("CommonName.RefFk (" + CdmUtils.Nz(strRefId) + ") and LanguageReference.RefFk " + CdmUtils.Nz(languageRefFk) + " are not equal. I will import only languageReference.RefFk");
 270                                         }
 271                                 }
 272
 273                                 Reference<?> reference = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(languageRefRefFk));
 274                                 String microCitation = null;
 275                                 String originalNameString = null;
 276
 277                                 TaxonNameBase<?,?> nameUsedInSource = taxonNameMap.get(String.valueOf(nameInSourceFk));
 278                                 if (nameInSourceFk != null && nameUsedInSource == null){
 279                                         logger.warn("Name used in source (" + nameInSourceFk + ") was not found for common name " + commonNameId);
 280                                 }
 281                                 DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation, nameUsedInSource, originalNameString);
 282                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 283                                         commonTaxonName.addSource(source);
 284                                 }
 285
 286
 287                                 //MisNameRef
 288                                 if (misNameRefFk != null){
 289                                         //Taxon misappliedName = getMisappliedName(biblioRefMap, nomRefMap, misNameRefFk, taxon);
 290                                         Taxon misappliedNameTaxon = null;
 291                                         if (misappliedTaxonId != null){
 292                                                 TaxonBase misTaxonBase =  taxonMap.get(String.valueOf(misappliedTaxonId));
 293                                                 if (misTaxonBase == null){
 294                                                         logger.warn("MisappliedName not found for misappliedTaxonId " + misappliedTaxonId + "; commonNameId: " + commonNameId);
 295                                                 }else if (misTaxonBase.isInstanceOf(Taxon.class)){
 296                                                         misappliedNameTaxon = CdmBase.deproxy(misTaxonBase, Taxon.class);
 297                                                 }else{
 298                                                         logger.warn("Misapplied name taxon is not of type Taxon but " + misTaxonBase.getClass().getSimpleName());
 299                                                 }
 300                                         }else{
 301
 302                                                 Reference<?> sec = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));
 303                                                 if (nameUsedInSource == null || sec == null){
 304                                                         logger.warn("Taxon name or misapplied name reference is null for common name " + commonNameId);
 305                                                 }else{
 306                                                         misappliedNameTaxon = Taxon.NewInstance(nameUsedInSource, sec);
 307                                                         MarkerType misCommonNameMarker = getMarkerType(state, BerlinModelTransformer.uuidMisappliedCommonName,"Misapplied Common Name in Berlin Model", "Misapplied taxon was automatically created by Berlin Model import for a common name with a misapplied name reference", "MCN");
 308                                                         Marker marker = Marker.NewInstance(misCommonNameMarker, true);
 309                                                         misappliedNameTaxon.addMarker(marker);
 310                                                         taxaToSave.add(misappliedNameTaxon);
 311                                                         logger.warn("Misapplied name taxon could not be found in database but misapplied name reference exists for common name. " +
 312                                                                         "New misapplied name for misapplied reference common name was added. CommonNameId: " + commonNameId);
 313                                                 }
 314                                         }
 315                                         if (misappliedNameTaxon != null){
 316
 317                                                 if (! taxon.getMisappliedNames().contains(misappliedNameTaxon)){
 318                                                         taxon.addMisappliedName(misappliedNameTaxon,state.getTransactionalSourceReference(), null);
 319                                                         logger.warn("Misapplied name for common name was not found related to the accepted taxon. Created new relationship. CommonNameId: " + commonNameId);
 320                                                 }
 321
 322                                                 TaxonDescription misappliedNameDescription = getDescription(misappliedNameTaxon);
 323                                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 324                                                         CommonTaxonName commonNameClone = (CommonTaxonName)commonTaxonName.clone();
 325                                                         misappliedNameDescription.addElement(commonNameClone);
 326                                                 }
 327                                         }else{
 328                                                 logger.warn("Misapplied name is null for common name " + commonNameId);
 329                                         }
 330
 331                                 }
 332
 333
 334                                 //reference extensions
 335                                 if (reference != null){
 336                                         if (CdmUtils.isNotEmpty(refLanguage)){
 337                                                 ExtensionType refLanguageExtensionType = getExtensionType( state, REFERENCE_LANGUAGE_STRING_UUID, "reference language","The language of the reference","ref. lang.");
 338                                                 Extension.NewInstance(reference, refLanguage, refLanguageExtensionType);
 339                                         }
 340
 341                                         if (CdmUtils.isNotEmpty(refLanguageIso639_2)){
 342                                                 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");
 343                                                 Extension.NewInstance(reference, refLanguageIso639_2, refLanguageIsoExtensionType);
 344                                         }
 345                                 }else if (CdmUtils.isNotEmpty(refLanguage) || CdmUtils.isNotEmpty(refLanguageIso639_2)){
 346                                         logger.warn("Reference is null (" + languageRefRefFk + ") but refLanguage (" + CdmUtils.Nz(refLanguage) + ") or iso639_2 (" + CdmUtils.Nz(refLanguageIso639_2) + ") was not null for common name ("+ commonNameId +")");
 347                                 }
 348
 349                                 //status
 350                                 if (CdmUtils.isNotEmpty(status)){
 351                                         AnnotationType statusAnnotationType = getAnnotationType( state, STATUS_ANNOTATION_UUID, "status","The status of this object","status", null);
 352                                         Annotation annotation = Annotation.NewInstance(status, statusAnnotationType, Language.DEFAULT());
 353                                         for (CommonTaxonName commonTaxonName : commonTaxonNames){
 354                                                 commonTaxonName.addAnnotation(annotation);
 355                                         }
 356
 357                                 }
 358
 359                                 //Notes
 360                                 for (CommonTaxonName commonTaxonName : commonTaxonNames){
 361                                         doIdCreatedUpdatedNotes(state, commonTaxonName, rs, String.valueOf(commonNameId), NAMESPACE);
 362                                 }
 363                                 partitioner.startDoSave();
 364                                 taxaToSave.add(taxon);
 365
 366                         }
 367                 } catch (SQLException e) {
 368                         logger.error("SQLException:" +  e);
 369                         return false;
 370                 } catch (ClassCastException e) {
 371                         e.printStackTrace();
 372                 }
 373
 374                 //      logger.info( i + " names handled");
 375                 getTaxonService().save(taxaToSave);
 376                 return success;
 377
 378         }
 379
 380
 381
 382         /**
 383          * Not used anymore. Use MisappliedName RIdentifier instead
 384          * @param biblioRefMap
 385          * @param nomRefMap
 386          * @param misNameRefFk
 387          * @param taxon
 388          */
 389         private boolean isFirstMisappliedName = true;
 390         private Taxon getMisappliedName(Map<String, Reference> biblioRefMap, Map<String, Reference> nomRefMap, Object misNameRefFk, Taxon taxon) {
 391                 Taxon misappliedTaxon = null;
 392                 Reference<?> misNameRef = getReferenceOnlyFromMaps(biblioRefMap, nomRefMap, String.valueOf(misNameRefFk));
 393                 misappliedTaxon = Taxon.NewInstance(taxon.getName(), misNameRef);
 394                 Set<String> includeProperty = new HashSet<String>();
 395                 try {
 396 //                      //IMatchStrategy matchStrategy = DefaultMatchStrategy.NewInstance(TaxonBase.class);
 397 //                      //List<TaxonBase> misappliedList1 = getCommonService().findMatching(misappliedTaxon, matchStrategy);
 398                         List<TaxonBase> misappliedList = getTaxonService().list(misappliedTaxon, includeProperty, null, null, null, null);
 399                         if (misappliedList.size() > 0){
 400                                 misappliedTaxon = CdmBase.deproxy(misappliedList.get(0), Taxon.class);
 401                         }
 402                 } catch (ClassCastException e) {
 403                         logger.error(e.getMessage());
 404                         if (isFirstMisappliedName){
 405                                 e.printStackTrace();
 406                                 isFirstMisappliedName = false;
 407                         }
 408                 }
 409                 return misappliedTaxon;
 410         }
 411
 412
 413
 414         /**
 415          * @param iso6392Map
 416          * @param iso639_2
 417          * @param languageString
 418          * @param originalLanguageString
 419          * @param state
 420          * @return
 421          */
 422         private Language getAndHandleLanguage(Map<String, Language> iso639Map,  String iso639_2, String iso639_1, String languageString, String originalLanguageString, BerlinModelImportState state) {
 423                 Language language;
 424                 if (CdmUtils.isNotEmpty(iso639_2)|| CdmUtils.isNotEmpty(iso639_1)  ){
 425                         //TODO test performance, implement in state
 426                         language = getLanguageFromIsoMap(iso639Map, iso639_2, iso639_1);
 427
 428                         if (language == null){
 429                                 language = getTermService().getLanguageByIso(iso639_2);
 430                                 iso639Map.put(iso639_2, language);
 431                                 if (language == null){
 432                                         language = getTermService().getLanguageByIso(iso639_1);
 433                                         iso639Map.put(iso639_1, language);
 434                                 }
 435                                 if (language == null){
 436                                         logger.warn("Language for code ISO693-2 '" + iso639_2 + "' and ISO693-1 '" + iso639_1 + "' was not found");
 437                                 }
 438                         }
 439                 } else if ("unknown".equals(languageString)){
 440                         language = Language.UNKNOWN_LANGUAGE();
 441                 } else if ("Majorcan".equalsIgnoreCase(languageString)){
 442                         language = getLanguage(state, BerlinModelTransformer.uuidLangMajorcan, "Majorcan", "Majorcan (original 'mallorqu\u00EDn')", null);
 443                 }else{
 444                         logger.warn("language ISO 639_1 and ISO 639_2 were empty for " + languageString);
 445                         language = null;
 446                 }
 447                 addOriginalLanguage(language, originalLanguageString);
 448                 return language;
 449         }
 450
 451
 452         /**
 453          * @param iso639Map
 454          * @param iso639_2
 455          * @param iso639_1
 456          * @return
 457          */
 458         private Language getLanguageFromIsoMap(Map<String, Language> iso639Map, String iso639_2, String iso639_1) {
 459                 Language language;
 460                 language = iso639Map.get(iso639_2);
 461                 if (language == null){
 462                         language = iso639Map.get(iso639_1);
 463                 }
 464                 return language;
 465         }
 466
 467         /**
 468          * @param language
 469          * @param originalLanguageString
 470          */
 471         private void addOriginalLanguage(Language language,     String originalLanguageString) {
 472                 if (CdmUtils.isBlank(originalLanguageString)){
 473                         return;
 474                 }else if (language == null){
 475                         logger.warn("Language could not be defined, but originalLanguageString exists: " + originalLanguageString);
 476                 }else {
 477                         Representation representation = language.getRepresentation(language);
 478                         if (representation == null){
 479                                 language.addRepresentation(Representation.NewInstance(originalLanguageString, originalLanguageString, originalLanguageString, language));
 480                                 getTermService().saveOrUpdate(language);
 481                         }
 482                 }
 483
 484         }
 485
 486
 487
 488         /**
 489          * Fills the regionFks with all regionFks from emCommonName. Comma separated regionFks will be split.
 490          * @param state
 491          * @param regionFks
 492          * @param source
 493          * @return
 494          * @throws SQLException
 495          *
 496          */
 497         private void getRegionFks(BerlinModelImportState state, SortedSet<Integer> regionFks, Source source) throws SQLException {
 498                 String sql = " SELECT DISTINCT RegionFks FROM emCommonName";
 499                 if (state.getConfig().getCommonNameFilter() != null){
 500                         sql += " WHERE " + state.getConfig().getCommonNameFilter();
 501                 }
 502
 503                 ResultSet rs = source.getResultSet(sql);
 504                 while (rs.next()){
 505                         String strRegionFks = rs.getString("RegionFks");
 506                         if (StringUtils.isBlank(strRegionFks)){
 507                                 continue;
 508                         }
 509
 510                         String[] regionFkArray = strRegionFks.split(",");
 511                         for (String regionFk: regionFkArray){
 512                                 regionFk = regionFk.trim();
 513                                 if (! StringUtils.isNumeric(regionFk) || "".equals(regionFk)  ){
 514                                         state.setUnsuccessfull();
 515                                         logger.warn("RegionFk is not numeric: " + regionFk +  " ( part of " + strRegionFks + ")");
 516                                 }else{
 517                                         regionFks.add(Integer.valueOf(regionFk));
 518                                 }
 519                         }
 520                 }
 521                 return;
 522         }
 523
 524
 525
 526         /**
 527          * Fills the {@link #regionMap} by all emLanguageRegion regions defined in the sql filter.
 528          * {@link #regionMap} maps emLanguageRegion.RegionId to named areas.
 529          * @param state
 530          * @param sqlWhere
 531          * @param emTdwgMap
 532          * @throws SQLException
 533          */
 534         private void fillRegionMap(BerlinModelImportState state, String sqlWhere,
 535                         Map<String, String> emTdwgMap) throws SQLException {
 536                 Source source = state.getConfig().getSource();
 537                 String sql;
 538                 ResultSet rs;
 539                 sql = " SELECT RegionId, Region FROM emLanguageRegion WHERE RegionId IN ("+ sqlWhere+ ") ";
 540                 rs = source.getResultSet(sql);
 541                 while (rs.next()){
 542                         Object regionId = rs.getObject("RegionId");
 543                         String region = rs.getString("Region");
 544                         String[] splitRegion = region.split("-");
 545                         if (splitRegion.length <= 1){
 546                                 NamedArea newArea = getNamedArea(state, null, region, "Language region '" + region + "'", null, null, null);
 547 //                              getTermService().save(newArea);
 548                                 regionMap.put(String.valueOf(regionId), newArea);
 549                                 logger.warn("Found new area: " +  region);
 550                         }else if (splitRegion.length == 2){
 551                                 String emCode = splitRegion[1].trim();
 552                                 String tdwgCode = emTdwgMap.get(emCode);
 553                                 if (StringUtils.isNotBlank(tdwgCode) ){
 554                                         NamedArea tdwgArea = getNamedArea(state, tdwgCode);
 555                                         regionMap.put(String.valueOf(regionId), tdwgArea);
 556                                 }else {
 557                                         NamedArea area = getOtherAreas(state, emCode, tdwgCode);
 558                                         if (area != null){
 559                                                 regionMap.put(String.valueOf(regionId), area);
 560                                         }else{
 561                                                 logger.warn("emCode did not map to valid tdwgCode: " +  CdmUtils.Nz(emCode) + "->" + CdmUtils.Nz(tdwgCode));
 562                                         }
 563                                 }
 564                         }
 565                 }
 566         }
 567
 568
 569         /**
 570          * Returns the are for a given TDWG code. See {@link #getEmTdwgMap(Source)} for exceptions from
 571          * the TDWG code
 572          * @param state
 573          * @param tdwgCode
 574          */
 575         private NamedArea getNamedArea(BerlinModelImportState state, String tdwgCode) {
 576                 NamedArea area;
 577                 if (tdwgCode.equalsIgnoreCase("Ab")){
 578                         area = getNamedArea(state, BerlinModelTransformer.uuidAzerbaijanNakhichevan, "Azerbaijan & Nakhichevan", "Azerbaijan (including Nakhichevan)",  "Ab", null, null);
 579                         getTermService().saveOrUpdate(area);
 580                 }else if (tdwgCode.equalsIgnoreCase("Uk")){
 581                         area = getNamedArea(state, BerlinModelTransformer.uuidUkraineAndCrimea , "Ukraine & Crimea", "Ukraine (including Crimea)", "Uk", null, null);
 582                         getTermService().saveOrUpdate(area);
 583                 }else if (tdwgCode.equalsIgnoreCase("Rf")){
 584                         area = Country.RUSSIANFEDERATION();
 585                 }else if (tdwgCode.equalsIgnoreCase("Gg")){
 586                         area = Country.GEORGIA();
 587                 }else{
 588                         area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode);
 589                 }
 590                 if (area == null){
 591                         logger.warn("Area is null for " + tdwgCode);
 592                 }
 593                 return area;
 594         }
 595
 596         /**
 597          * @param regionFks
 598          * @return
 599          */
 600         private String getSqlWhere(SortedSet<Integer> regionFks) {
 601                 String sqlWhere = "";
 602                 for (Integer regionFk : regionFks){
 603                         sqlWhere += regionFk + ",";
 604                 }
 605                 sqlWhere = sqlWhere.substring(0, sqlWhere.length()-1);
 606                 return sqlWhere;
 607         }
 608
 609
 610
 611         /**
 612          * Returns a map which is filled by the emCode->TdwgCode mapping defined in emArea.
 613          * Some exceptions are defined for emCode 'Ab','Rf','Uk' and some additional mapping is added
 614          * for 'Ab / Ab(A)', 'Ga / Ga(F)', 'It / It(I)', 'Ar / Ar(A)','Hs / Hs(S)'
 615          * @param source
 616          * @throws SQLException
 617          */
 618         private Map<String, String> getEmTdwgMap(Source source) throws SQLException {
 619                 String sql;
 620                 ResultSet rs;
 621                 Map<String, String> emTdwgMap = new HashMap<String, String>();
 622                 sql = " SELECT EmCode, TDWGCode FROM emArea ";
 623                 rs = source.getResultSet(sql);
 624                 while (rs.next()){
 625                         String emCode = rs.getString("EMCode");
 626                         String TDWGCode = rs.getString("TDWGCode");
 627                         if (StringUtils.isNotBlank(emCode) ){
 628                                 emCode = emCode.trim();
 629                                 if (emCode.equalsIgnoreCase("Ab") || emCode.equalsIgnoreCase("Rf")||
 630                                                 emCode.equalsIgnoreCase("Uk") || emCode.equalsIgnoreCase("Gg")){
 631                                         emTdwgMap.put(emCode, emCode);
 632                                 }else if (StringUtils.isNotBlank(TDWGCode)){
 633                                         emTdwgMap.put(emCode, TDWGCode.trim());
 634                                 }
 635                         }
 636                 }
 637                 emTdwgMap.put("Ab / Ab(A)", "Ab");
 638                 emTdwgMap.put("Ga / Ga(F)", "FRA-FR");
 639                 emTdwgMap.put("It / It(I)", "ITA");
 640                 emTdwgMap.put("Uk / Uk(U)", "Uk");
 641                 emTdwgMap.put("Ar / Ar(A)", "TCS-AR");
 642                 emTdwgMap.put("Hs / Hs(S)", "SPA-SP");
 643
 644                 return emTdwgMap;
 645         }
 646
 647
 648
 649
 650         /**
 651          * Returns the first non-image gallery description. Creates a new one if no description exists.
 652          * @param taxon
 653          * @return
 654          */
 655         private TaxonDescription getDescription(Taxon taxon) {
 656                 TaxonDescription result = null;
 657                 for (TaxonDescription taxonDescription : taxon.getDescriptions()){
 658                         if (! taxonDescription.isImageGallery()){
 659                                 result = taxonDescription;
 660                         }
 661                 }
 662                 if (result == null){
 663                         result = TaxonDescription.NewInstance(taxon);
 664                 }
 665                 return result;
 666         }
 667
 668         /* (non-Javadoc)
 669          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 670          */
 671         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 672                 String nameSpace;
 673                 Class<?> cdmClass;
 674                 Set<String> idSet;
 675                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 676
 677                 int pos = -1;
 678                 try{
 679                         Set<String> taxonIdSet = new HashSet<String>();
 680                         Set<String> nameIdSet = new HashSet<String>();
 681                         Set<String> referenceIdSet = new HashSet<String>();
 682                         while (rs.next()){
 683                                 pos = 0;
 684                                 handleForeignKey(rs, taxonIdSet, "taxonId");
 685                                 pos = 1;
 686                                 handleForeignKey(rs, taxonIdSet, "misappliedTaxonId");
 687                                 pos = 2;
 688                                 handleForeignKey(rs, referenceIdSet, "refId");
 689                                 pos = 3;
 690                                 handleForeignKey(rs, referenceIdSet, "languageRefRefFk");
 691                                 pos = 4;
 692                                 handleForeignKey(rs, nameIdSet, "NameInSourceFk");
 693                                 pos = 5;
 694                                 handleForeignKey(rs, nameIdSet, "PTNameFk");
 695                                 pos = 6;
 696                                 handleForeignKey(rs, referenceIdSet, "MisNameRefFk");
 697                                 pos = -2;
 698
 699                         }
 700
 701                         pos = 7;
 702
 703                         //name map
 704                         nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
 705                         cdmClass = TaxonNameBase.class;
 706                         idSet = nameIdSet;
 707                         Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 708                         result.put(nameSpace, nameMap);
 709
 710                         pos = 8;
 711
 712                         //taxon map
 713                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 714                         cdmClass = TaxonBase.class;
 715                         idSet = taxonIdSet;
 716                         Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 717                         result.put(nameSpace, taxonMap);
 718
 719                         pos = 9;
 720
 721                         //nom reference map
 722                         nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
 723                         cdmClass = Reference.class;
 724                         idSet = referenceIdSet;
 725                         Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 726                         result.put(nameSpace, nomReferenceMap);
 727
 728                         pos = 10;
 729
 730                         //biblio reference map
 731                         nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
 732                         cdmClass = Reference.class;
 733                         idSet = referenceIdSet;
 734                         Map<String, Reference<?>> biblioReferenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 735                         result.put(nameSpace, biblioReferenceMap);
 736
 737                         pos = 11;
 738
 739                 } catch (SQLException e) {
 740                         throw new RuntimeException("pos: " +pos, e);
 741                 } catch (NullPointerException nep){
 742                         logger.error("NullPointerException in getRelatedObjectsForPartition()");
 743                 }
 744                 return result;
 745         }
 746
 747
 748
 749         /* (non-Javadoc)
 750          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 751          */
 752         @Override
 753         protected boolean doCheck(BerlinModelImportState state){
 754                 IOValidator<BerlinModelImportState> validator = new BerlinModelCommonNamesImportValidator();
 755                 return validator.validate(state);
 756         }
 757
 758         /* (non-Javadoc)
 759          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 760          */
 761         protected boolean isIgnore(BerlinModelImportState state){
 762                 return ! state.getConfig().isDoCommonNames();
 763         }
 764
 765 }