cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelReferenceImport.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 static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_ARTICLE;
  13 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_BOOK;
  14 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_CONFERENCE_PROCEEDINGS;
  15 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_DATABASE;
  16 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_INFORMAL;
  17 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_JOURNAL;
  18 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_JOURNAL_VOLUME;
  19 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_PART_OF_OTHER_TITLE;
  20 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_PRINT_SERIES;
  21 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_UNKNOWN;
  22 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_WEBSITE;
  23 import static eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES.ALL;
  24 import static eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES.CONCEPT_REFERENCES;
  25 import static eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES.NOMENCLATURAL;
  26 import static eu.etaxonomy.cdm.io.common.ImportHelper.NO_OVERWRITE;
  27 import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
  28 import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;
  29
  30 import java.sql.ResultSet;
  31 import java.sql.SQLException;
  32 import java.util.ArrayList;
  33 import java.util.Arrays;
  34 import java.util.HashMap;
  35 import java.util.HashSet;
  36 import java.util.List;
  37 import java.util.Map;
  38 import java.util.Set;
  39 import java.util.UUID;
  40
  41 import org.apache.log4j.Logger;
  42 import org.springframework.stereotype.Component;
  43
  44 import eu.etaxonomy.cdm.common.CdmUtils;
  45 import eu.etaxonomy.cdm.io.berlinModel.CdmOneToManyMapper;
  46 import eu.etaxonomy.cdm.io.berlinModel.CdmStringMapper;
  47 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelReferenceImportValidator;
  48 import eu.etaxonomy.cdm.io.common.ICdmIO;
  49 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  50 import eu.etaxonomy.cdm.io.common.ImportHelper;
  51 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  52 import eu.etaxonomy.cdm.io.common.Source;
  53 import eu.etaxonomy.cdm.io.common.mapping.CdmAttributeMapperBase;
  54 import eu.etaxonomy.cdm.io.common.mapping.CdmIoMapping;
  55 import eu.etaxonomy.cdm.io.common.mapping.CdmSingleAttributeMapperBase;
  56 import eu.etaxonomy.cdm.io.common.mapping.DbImportExtensionMapper;
  57 import eu.etaxonomy.cdm.io.common.mapping.DbImportMarkerMapper;
  58 import eu.etaxonomy.cdm.model.agent.Team;
  59 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  60 import eu.etaxonomy.cdm.model.common.CdmBase;
  61 import eu.etaxonomy.cdm.model.common.ExtensionType;
  62 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  63 import eu.etaxonomy.cdm.model.common.Marker;
  64 import eu.etaxonomy.cdm.model.common.MarkerType;
  65 import eu.etaxonomy.cdm.model.reference.IArticle;
  66 import eu.etaxonomy.cdm.model.reference.IBook;
  67 import eu.etaxonomy.cdm.model.reference.IBookSection;
  68 import eu.etaxonomy.cdm.model.reference.IJournal;
  69 import eu.etaxonomy.cdm.model.reference.IPrintSeries;
  70 import eu.etaxonomy.cdm.model.reference.Reference;
  71 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  72 import eu.etaxonomy.cdm.model.reference.ReferenceType;
  73
  74 /**
  75  * @author a.mueller
  76  * @created 20.03.2008
  77  * @version 1.0
  78  */
  79 @Component
  80 public class BerlinModelReferenceImport extends BerlinModelImportBase {
  81         private static final Logger logger = Logger.getLogger(BerlinModelReferenceImport.class);
  82
  83         public static final String NOM_REFERENCE_NAMESPACE = "NomReference";
  84         public static final String BIBLIO_REFERENCE_NAMESPACE = "BiblioReference";
  85
  86         public static final UUID REF_DEPOSITED_AT_UUID = UUID.fromString("23ca88c7-ce73-41b2-8ca3-2cb22f013beb");
  87         public static final UUID REF_SOURCE_UUID = UUID.fromString("d6432582-2216-4b08-b0db-76f6c1013141");
  88         public static final UUID DATE_STRING_UUID = UUID.fromString("e4130eae-606e-4b0c-be4f-e93dc161be7d");
  89         public static final UUID IS_PAPER_UUID = UUID.fromString("8a326129-d0d0-4f9d-bbdf-8d86b037c65e");
  90
  91
  92         private int modCount = 1000;
  93         private static final String pluralString = "references";
  94         private static final String dbTableName = "reference";
  95
  96
  97         public BerlinModelReferenceImport(){
  98                 super();
  99         }
 100
 101         protected void initializeMappers(BerlinModelImportState state){
 102                 for (CdmAttributeMapperBase mapper: classMappers){
 103                         if (mapper instanceof DbImportExtensionMapper){
 104                                 ((DbImportExtensionMapper)mapper).initialize(state, Reference.class);
 105                         }
 106                 }
 107                 return;
 108         }
 109
 110         protected static CdmAttributeMapperBase[] classMappers = new CdmAttributeMapperBase[]{
 111                 new CdmStringMapper("edition", "edition"),
 112                 new CdmStringMapper("volume", "volume"),
 113                 new CdmStringMapper("publisher", "publisher"),
 114                 new CdmStringMapper("publicationTown", "placePublished"),
 115                 new CdmStringMapper("isbn", "isbn"),
 116                 new CdmStringMapper("isbn", "isbn"),
 117                 new CdmStringMapper("pageString", "pages"),
 118                 new CdmStringMapper("series", "series"),
 119                 new CdmStringMapper("issn", "issn"),
 120                 new CdmStringMapper("url", "uri"),
 121                 DbImportExtensionMapper.NewInstance("NomStandard", ExtensionType.NOMENCLATURAL_STANDARD()),
 122                 DbImportExtensionMapper.NewInstance("DateString", DATE_STRING_UUID, "Date String", "Date String", "dates"),
 123                 DbImportExtensionMapper.NewInstance("RefDepositedAt", REF_DEPOSITED_AT_UUID, "RefDepositedAt", "reference is deposited at", "at"),
 124                 DbImportExtensionMapper.NewInstance("RefSource", REF_SOURCE_UUID, "RefSource", "reference source", "source"),
 125                 DbImportMarkerMapper.NewInstance("isPaper", IS_PAPER_UUID, "is paper", "is paper", "paper")
 126         };
 127
 128
 129         protected static String[] operationalAttributes = new String[]{
 130                 "refId", "refCache", "nomRefCache", "preliminaryFlag", "inRefFk", "title", "nomTitleAbbrev",
 131                 "refAuthorString", "nomAuthorTeamFk",
 132                 "refCategoryFk", "thesisFlag", "informalRefCategory", "idInSource"
 133         };
 134
 135         protected static String[] createdAndNotesAttributes = new String[]{
 136                         "created_When", "updated_When", "created_Who", "updated_Who", "notes"
 137         };
 138
 139         protected static String[] unclearMappers = new String[]{
 140                         /*"isPaper",*/ "exportDate",
 141         };
 142
 143         //TODO isPaper
 144         //
 145
 146
 147
 148         //type to count the references nomReferences that have been created and saved
 149         private class RefCounter{
 150                 RefCounter() {nomRefCount = 0; referenceCount = 0;};
 151                 int nomRefCount;
 152                 int referenceCount;
 153                 public String toString(){return String.valueOf(nomRefCount) + "," +String.valueOf(referenceCount);};
 154         }
 155
 156
 157         /* (non-Javadoc)
 158          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
 159          */
 160         @Override
 161         protected String getRecordQuery(BerlinModelImportConfigurator config) {
 162                 return null;  //not needed
 163         }
 164
 165
 166         @Override
 167         protected void doInvoke(BerlinModelImportState state){
 168                 logger.info("start make " + getPluralString() + " ...");
 169
 170                 boolean success = true;
 171                 initializeMappers(state);
 172                 BerlinModelImportConfigurator config = state.getConfig();
 173                 Source source = config.getSource();
 174
 175                 String strSelectId = "Select Reference.RefId as refId";
 176                 String strSelectFull =
 177                         " SELECT Reference.* , InReference.RefId as InRefId, InReference.RefCategoryFk as InRefCategoryFk,  " +
 178                         " InInReference.RefId as InInRefId, InInReference.RefCategoryFk as InInRefCategoryFk, " +
 179                         " InReference.InRefFk AS InRefInRefFk, InInReference.InRefFk AS InInRefInRefFk, RefSource.RefSource " ;
 180                 String strFrom =  " FROM Reference AS InInReference " +
 181                         " RIGHT OUTER JOIN Reference AS InReference ON InInReference.RefId = InReference.InRefFk " +
 182                         " RIGHT OUTER JOIN Reference ON InReference.RefId = dbo.Reference.InRefFk " +
 183                         " LEFT OUTER JOIN RefSource ON Reference.RefSourceFk = RefSource.RefSourceId " +
 184                         " WHERE (1=1) ";
 185                 String strWherePartitioned = " AND (Reference.refId IN ("+ ID_LIST_TOKEN + ") ) ";
 186
 187                 //test max number of recursions
 188                 String strQueryTestMaxRecursion = strSelectId + strFrom +
 189                         " AND (Reference.InRefFk is NOT NULL) AND (InReference.InRefFk is NOT NULL) AND (InInReference.InRefFk is NOT NULL) ";
 190                 ResultSet testMaxRecursionResultSet = source.getResultSet(strQueryTestMaxRecursion);
 191                 try {
 192                         if (testMaxRecursionResultSet.next() == true){
 193                                 logger.error("Maximum allowed InReference recursions exceeded in Berlin Model. Maximum recursion level is 2.");
 194                                 state.setUnsuccessfull();
 195                                 return;
 196                         }
 197                 } catch (SQLException e1) {
 198                         e1.printStackTrace();
 199                         logger.error("There are references with more then 2 in-reference recursion. Maximum number of allowed recursions is 2. Records will not be stored.");
 200                         success = false;
 201                 }
 202
 203                 String strSelectIdBase = strSelectId + strFrom;
 204
 205                 String strIdQueryNoInRef = strSelectIdBase +
 206                         " AND (Reference.InRefFk is NULL) ";
 207                 String strIdQuery1InRef = strSelectIdBase +
 208                         " AND (Reference.InRefFk is NOT NULL) AND (InReference.InRefFk is NULL) ";
 209                 String strIdQuery2InRefs = strSelectIdBase +
 210                         " AND (Reference.InRefFk is NOT NULL) AND (InReference.InRefFk is NOT NULL) AND (InInReference.InRefFk is NULL) ";
 211
 212                 if (config.getDoReferences() == CONCEPT_REFERENCES){
 213                         strIdQueryNoInRef += " AND ( Reference.refId IN ( SELECT ptRefFk FROM PTaxon) ) ";
 214                 }
 215
 216                 String strRecordQuery = strSelectFull + strFrom + strWherePartitioned;
 217
 218                 int recordsPerTransaction = config.getRecordsPerTransaction();
 219                 try{
 220                         //NoInRefs
 221                         ResultSetPartitioner partitioner = ResultSetPartitioner.NewInstance(source, strIdQueryNoInRef, strRecordQuery, recordsPerTransaction);
 222                         while (partitioner.nextPartition()){
 223                                 partitioner.doPartition(this, state);
 224                         }
 225                         logger.info("end make references with no in-references ... " + getSuccessString(success));
 226
 227                         if (config.getDoReferences() == ALL || config.getDoReferences() == NOMENCLATURAL){
 228
 229                                 //1InRef
 230                                 partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery1InRef, strRecordQuery, recordsPerTransaction);
 231                                 while (partitioner.nextPartition()){
 232                                         partitioner.doPartition(this, state);
 233                                 }
 234                                 logger.info("end make references with no 1 in-reference ... " + getSuccessString(success));
 235
 236                                 //2InRefs
 237                                 partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery2InRefs, strRecordQuery, recordsPerTransaction);
 238                                 while (partitioner.nextPartition()){
 239                                         partitioner.doPartition(this, state);
 240                                 }
 241                                 logger.info("end make references with no 2 in-reference ... " + getSuccessString(success));
 242                         }
 243
 244                 } catch (SQLException e) {
 245                         logger.error("SQLException:" +  e);
 246                         state.setUnsuccessfull();
 247                         return;
 248                 }
 249                 logger.info("end make " + getPluralString() + " ... " + getSuccessString(success));
 250                 if (! success){
 251                         state.setUnsuccessfull();
 252                 }
 253                 return;
 254         }
 255
 256
 257
 258         /* (non-Javadoc)
 259          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
 260          */
 261         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
 262                 boolean success = true;
 263 //              MapWrapper<Reference> referenceStore= new MapWrapper<Reference>(null);
 264 //              MapWrapper<Reference> nomRefStore= new MapWrapper<Reference>(null);
 265
 266                 Map<Integer, Reference> nomRefToSave = new HashMap<Integer, Reference>();
 267                 Map<Integer, Reference> biblioRefToSave = new HashMap<Integer, Reference>();
 268
 269                 Map<String, Reference> relatedNomReferences = partitioner.getObjectMap(NOM_REFERENCE_NAMESPACE);
 270                 Map<String, Reference> relatedBiblioReferences = partitioner.getObjectMap(BIBLIO_REFERENCE_NAMESPACE);
 271
 272                 BerlinModelImportConfigurator config = state.getConfig();
 273
 274                 try {
 275 //                      //get data from database
 276 //                              //strQueryBase += " AND Reference.refId = 1933 " ; //7000000
 277 //
 278 //                      int j = 0;
 279 //                      Iterator<ResultSet> resultSetListIterator =  resultSetList.listIterator();
 280 //                      //for each resultsetlist
 281 //                      while (resultSetListIterator.hasNext()){
 282                                 int i = 0;
 283                                 RefCounter refCounter  = new RefCounter();
 284
 285 //                              ResultSet rs = resultSetListIterator.next();
 286                                 ResultSet rs = partitioner.getResultSet();
 287                                 //for each resultset
 288                                 while (rs.next()){
 289                                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("References handled: " + (i-1) + " in round -" );}
 290
 291                                         success &= makeSingleReferenceRecord(rs, state, partitioner, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences, refCounter);
 292                                 } // end resultSet
 293
 294                                 //for the concept reference a fixed uuid may be needed -> change uuid
 295                                 Integer sourceSecId = (Integer)config.getSourceSecId();
 296                                 Reference<?> sec = biblioRefToSave.get(sourceSecId);
 297                                 if (sec == null){
 298                                         sec = nomRefToSave.get(sourceSecId);
 299                                 }
 300                                 if (sec != null){
 301                                         sec.setUuid(config.getSecUuid());
 302                                         logger.info("SecUuid changed to: " + config.getSecUuid());
 303                                 }
 304
 305                                 //save and store in map
 306                                 logger.info("Save nomenclatural references (" + refCounter.nomRefCount + ")");
 307                                 getReferenceService().save(nomRefToSave.values());
 308                                 logger.info("Save bibliographical references (" + refCounter.referenceCount +")");
 309                                 getReferenceService().save(biblioRefToSave.values());
 310 //                              j++;
 311 //                      }//end resultSetList
 312
 313                         logger.info("end makeReferences ..." + getSuccessString(success));;
 314                         return success;
 315                 } catch (SQLException e) {
 316                         logger.error("SQLException:" +  e);
 317                         return false;
 318                 }
 319         }
 320
 321
 322
 323         /* (non-Javadoc)
 324          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 325          */
 326         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 327                 String nameSpace;
 328                 Class cdmClass;
 329                 Set<String> idSet;
 330
 331                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 332
 333                 try{
 334                         Set<String> teamIdSet = new HashSet<String>();
 335                         Set<String> referenceIdSet = new HashSet<String>();
 336
 337                         while (rs.next()){
 338                                 handleForeignKey(rs, teamIdSet, "NomAuthorTeamFk");
 339                                 handleForeignKey(rs, referenceIdSet, "InRefFk");
 340                         }
 341
 342                         //team map
 343                         nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;
 344                         cdmClass = Team.class;
 345                         idSet = teamIdSet;
 346                         Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 347                         result.put(nameSpace, teamMap);
 348
 349
 350                         //nom reference map
 351                         nameSpace = NOM_REFERENCE_NAMESPACE;
 352                         cdmClass = Reference.class;
 353                         idSet = referenceIdSet;
 354                         Map<String, Reference> nomRefMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 355                         result.put(nameSpace, nomRefMap);
 356
 357                         //biblio reference map
 358                         nameSpace = BIBLIO_REFERENCE_NAMESPACE;
 359                         cdmClass = Reference.class;
 360                         idSet = referenceIdSet;
 361                         Map<String, Reference> biblioRefMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 362                         result.put(nameSpace, biblioRefMap);
 363
 364                 } catch (SQLException e) {
 365                         throw new RuntimeException(e);
 366                 }
 367                 return result;
 368         }
 369
 370
 371         /**
 372          * Handles a single reference record
 373          * @param rs
 374          * @param state
 375          * @param biblioRefToSave
 376          * @param nomRefToSave
 377          * @param relatedBiblioReferences
 378          * @param relatedNomReferences
 379          * @param refCounter
 380          * @return
 381          */
 382         private boolean makeSingleReferenceRecord(
 383                                 ResultSet rs,
 384                                 BerlinModelImportState state,
 385                                 ResultSetPartitioner<BerlinModelImportState> partitioner,
 386                                 Map<Integer, Reference> biblioRefToSave,
 387                                 Map<Integer, Reference> nomRefToSave,
 388                                 Map<String, Reference> relatedBiblioReferences,
 389                                 Map<String, Reference> relatedNomReferences,
 390                                 RefCounter refCounter){
 391                 boolean success = true;
 392
 393                 Integer refId = null;
 394                 try {
 395                         Map<String, Object> valueMap = getValueMap(rs);
 396
 397                         Integer categoryFk = (Integer)valueMap.get("refCategoryFk".toLowerCase());
 398                         refId = (Integer)valueMap.get("refId".toLowerCase());
 399                         Boolean thesisFlag = (Boolean)valueMap.get("thesisFlag".toLowerCase());
 400
 401
 402                         Reference<?> referenceBase;
 403                         logger.debug("RefCategoryFk: " + categoryFk);
 404
 405                         if (thesisFlag){
 406                                 referenceBase = makeThesis(valueMap);
 407                         }else if (categoryFk == REF_JOURNAL){
 408                                 referenceBase = makeJournal(valueMap);
 409                         }else if(categoryFk == REF_BOOK){
 410                                 referenceBase = makeBook(valueMap, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences);
 411                         }else if(categoryFk == REF_DATABASE){
 412                                 referenceBase = makeDatabase(valueMap);
 413                         }else if(categoryFk == REF_INFORMAL){
 414                                 referenceBase = makeInformal(valueMap);
 415                         }else if(categoryFk == REF_WEBSITE){
 416                                 referenceBase = makeWebSite(valueMap);
 417                         }else if(categoryFk == REF_UNKNOWN){
 418                                 referenceBase = makeUnknown(valueMap);
 419                         }else if(categoryFk == REF_PRINT_SERIES){
 420                                 referenceBase = makePrintSeries(valueMap);
 421                         }else if(categoryFk == REF_CONFERENCE_PROCEEDINGS){
 422                                 referenceBase = makeProceedings(valueMap);
 423                         }else if(categoryFk == REF_ARTICLE){
 424                                 referenceBase = makeArticle(valueMap, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences);
 425                         }else if(categoryFk == REF_JOURNAL_VOLUME){
 426                                 referenceBase = makeJournalVolume(valueMap);
 427                         }else if(categoryFk == REF_PART_OF_OTHER_TITLE){
 428                                 referenceBase = makePartOfOtherTitle(valueMap, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences);
 429                         }else{
 430                                 logger.warn("Unknown categoryFk (" + categoryFk + "). Create 'Generic instead'");
 431                                 referenceBase = ReferenceFactory.newGeneric();
 432                                 success = false;
 433                         }
 434
 435                         //refYear
 436                         String refYear = (String)valueMap.get("refYear".toLowerCase());
 437                         referenceBase.setDatePublished(ImportHelper.getDatePublished(refYear));
 438
 439                         //created, updated, notes
 440                         doCreatedUpdatedNotes(state, referenceBase, rs);
 441
 442                         //isPaper
 443                         if ((Boolean)valueMap.get("isPaper".toLowerCase())){
 444                                 logger.warn("IsPaper is not yet implemented, but reference " +  refId + " is paper");
 445                         }
 446
 447                         //idInSource
 448                         String idInSource = (String)valueMap.get("IdInSource".toLowerCase());
 449                         if (CdmUtils.isNotEmpty(idInSource)){
 450                                 IdentifiableSource source = IdentifiableSource.NewInstance(idInSource);
 451                                 source.setIdNamespace("import to Berlin Model");
 452                                 referenceBase.addSource(source);
 453                         }
 454
 455                         //nom&BiblioReference  - must be last because a clone is created
 456                         success &= makeNomAndBiblioReference(rs, state, partitioner, refId, referenceBase, refCounter,
 457                                         biblioRefToSave, nomRefToSave );
 458
 459
 460                 } catch (Exception e) {
 461                         logger.warn("Reference with BM refId '" + CdmUtils.Nz(refId) +  "' threw Exception and could not be saved");
 462                         e.printStackTrace();
 463                         success = false;
 464                 }
 465                 return success;
 466         }
 467
 468
 469         /**
 470          * Creates and saves a nom. reference and a biblio. reference after checking necessity
 471          * @param rs
 472          * @param refId
 473          * @param referenceBase
 474          * @param refCounter
 475          * @param biblioRefToSave
 476          * @param nomRefToSave
 477          * @param teamMap
 478          * @param stores
 479          * @return
 480          * @throws SQLException
 481          */
 482         private boolean makeNomAndBiblioReference(
 483                                 ResultSet rs,
 484                                 BerlinModelImportState state,
 485                                 ResultSetPartitioner partitioner,
 486                                 int refId,
 487                                 Reference<?> referenceBase,
 488                                 RefCounter refCounter,
 489                                 Map<Integer, Reference> biblioRefToSave,
 490                                 Map<Integer, Reference> nomRefToSave
 491                                 ) throws SQLException{
 492
 493                 Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);
 494
 495                 String refCache = rs.getString("refCache");
 496                 String nomRefCache = rs.getString("nomRefCache");
 497                 String title = rs.getString("title");
 498                 String nomTitleAbbrev = rs.getString("nomTitleAbbrev");
 499                 boolean isPreliminary = rs.getBoolean("PreliminaryFlag");
 500                 String refAuthorString = rs.getString("refAuthorString");
 501                 Integer nomAuthorTeamFk = rs.getInt("NomAuthorTeamFk");
 502                 String strNomAuthorTeamFk = String.valueOf(nomAuthorTeamFk);
 503                 TeamOrPersonBase<?> nomAuthor = teamMap.get(strNomAuthorTeamFk);
 504                 Reference nomReference = null;
 505
 506                 boolean hasNomRef = false;
 507                 boolean hasBiblioRef = false;
 508                 Reference sourceReference = state.getConfig().getSourceReference();
 509
 510                 //is Nomenclatural Reference
 511                 if ( (CdmUtils.isNotEmpty(nomRefCache) && isPreliminary) || (CdmUtils.isNotEmpty(nomTitleAbbrev) && ! isPreliminary) ){
 512                         referenceBase.setTitle(nomTitleAbbrev);
 513                         TeamOrPersonBase<?> author = getAuthorTeam(refAuthorString , nomAuthor, true);
 514                         referenceBase.setAuthorTeam(author);
 515                         //referenceBase.setNomenclaturallyRelevant(true);
 516                         if (isPreliminary){
 517                                 referenceBase.setTitleCache(nomRefCache, true);
 518                         }
 519                         if (! nomRefToSave.containsKey(refId)){
 520                                 if (referenceBase == null){
 521                                         logger.warn("refBase is null");
 522                                 }
 523                                 nomRefToSave.put(refId, referenceBase);
 524                         }else{
 525                                 logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");
 526                         }
 527
 528 //                      ???
 529 //                      nomRefToSave.put(refId, referenceBase);
 530                         hasNomRef = true;
 531                         nomReference = referenceBase;
 532                         refCounter.nomRefCount++;
 533                 }
 534                 //is bibliographical Reference
 535                 if ((CdmUtils.isNotEmpty(refCache) && isPreliminary && ! refCache.equalsIgnoreCase(nomRefCache))
 536                                 || (CdmUtils.isNotEmpty(title) && ! isPreliminary && ! title.equalsIgnoreCase(nomTitleAbbrev))
 537                                 || hasNomRef == false){
 538                         if (hasNomRef){
 539                                 referenceBase = (Reference)referenceBase.clone();
 540                                 copyCreatedUpdated(referenceBase, nomReference);
 541                         }
 542                         referenceBase.setTitle(title);
 543                         TeamOrPersonBase author = getAuthorTeam(refAuthorString , nomAuthor, false);
 544                         referenceBase.setAuthorTeam(author);
 545                         referenceBase.setNomenclaturallyRelevant(false);
 546                         if (isPreliminary){
 547                                 referenceBase.setTitleCache(refCache, true);
 548                         }
 549                         if (! biblioRefToSave.containsKey(refId)){
 550                                 biblioRefToSave.put(refId, referenceBase);
 551                         }else{
 552                                 logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");
 553                         }
 554                         hasBiblioRef = true;
 555
 556                         //??
 557                         //biblioRefToSave.put(refId, referenceBase);
 558                         refCounter.referenceCount++;
 559                 }
 560                 //refId
 561                 if (hasNomRef){
 562                         ImportHelper.setOriginalSource(nomReference, sourceReference, refId, NOM_REFERENCE_NAMESPACE);
 563                 }
 564                 if (hasBiblioRef){
 565                         ImportHelper.setOriginalSource(referenceBase, sourceReference, refId, BIBLIO_REFERENCE_NAMESPACE);
 566                 }
 567
 568                 return true;
 569
 570         }
 571
 572         /**
 573          * Copies the created and updated information from the nomReference to the cloned bibliographic reference
 574          * @param referenceBase
 575          * @param nomReference
 576          */
 577         private void copyCreatedUpdated(Reference<?> biblioReference, Reference nomReference) {
 578                 biblioReference.setCreatedBy(nomReference.getCreatedBy());
 579                 biblioReference.setCreated(nomReference.getCreated());
 580                 biblioReference.setUpdatedBy(nomReference.getUpdatedBy());
 581                 biblioReference.setUpdated(nomReference.getUpdated());
 582
 583         }
 584
 585         private Reference<?> makeArticle (Map<String, Object> valueMap, Map<Integer, Reference> biblioRefToSave, Map<Integer, Reference> nomRefToSave, Map<String, Reference> relatedBiblioReferences, Map<String, Reference> relatedNomReferences){
 586
 587                 IArticle article = ReferenceFactory.newArticle();
 588                 Object inRefFk = valueMap.get("inRefFk".toLowerCase());
 589                 Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
 590                 Integer refId = (Integer)valueMap.get("refId".toLowerCase());
 591
 592                 if (inRefFk != null){
 593                         if (inRefCategoryFk == REF_JOURNAL){
 594                                 int inRefFkInt = (Integer)inRefFk;
 595                                 if (existsInMapOrToSave(inRefFkInt, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences)){
 596                                         Reference<?> inJournal = getReferenceFromMaps(inRefFkInt, nomRefToSave, relatedNomReferences);
 597                                         if (inJournal == null){
 598                                                 inJournal = getReferenceFromMaps(inRefFkInt, biblioRefToSave, relatedBiblioReferences);
 599                                                 logger.info("inJournal (" + inRefFkInt + ") found in referenceStore instead of nomRefStore.");
 600                                                 nomRefToSave.put(inRefFkInt, inJournal);
 601                                         }
 602                                         if (inJournal == null){
 603                                                 logger.warn("inJournal for " + inRefFkInt + " is null. "+
 604                                                         " InReference relation could not be set");
 605                                         //}else if (Reference.class.isAssignableFrom(inJournal.getClass())){
 606                                         }else if (inJournal.getType().equals(ReferenceType.Journal)){
 607                                                 article.setInJournal((IJournal)inJournal);
 608                                         }else{
 609                                                 logger.warn("InJournal is not of type journal but of type " + inJournal.getType() +
 610                                                         " Inreference relation could not be set");
 611                                         }
 612                                 }else{
 613                                         logger.error("Journal (refId = " + inRefFkInt + " ) for Article (refID = " + refId +") could not be found in nomRefStore. Inconsistency error. ");
 614                                         //success = false;;
 615                                 }
 616                         }else{
 617                                 logger.warn("Wrong inrefCategory for Article (refID = " + refId +"). Type must be 'Journal' but was not (RefCategoryFk=" + inRefCategoryFk + "))." +
 618                                         " InReference was not added to Article! ");
 619                         }
 620                 }
 621                 makeStandardMapper(valueMap, (Reference)article); //url, pages, series, volume
 622                 return (Reference)article;
 623         }
 624
 625         private Reference<?> makePartOfOtherTitle (Map<String, Object> valueMap, Map<Integer, Reference> biblioRefToSave, Map<Integer, Reference> nomRefToSave, Map<String, Reference> relatedBiblioReferences, Map<String, Reference> relatedNomReferences){
 626                 Reference<?> result;
 627                 Object inRefFk = valueMap.get("inRefFk".toLowerCase());
 628                 Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
 629                 Integer refId = (Integer)valueMap.get("refId".toLowerCase());
 630
 631                 if (inRefCategoryFk == null){
 632                         //null -> error
 633                         logger.warn("Part-Of-Other-Title has not inRefCategoryFk! RefId = " + refId + ". ReferenceType set to Generic.");
 634                         result = makeUnknown(valueMap);
 635                 }else if (inRefCategoryFk == REF_BOOK){
 636                         //BookSection
 637                         IBookSection bookSection = ReferenceFactory.newBookSection();
 638                         result = (Reference)bookSection;
 639                         if (inRefFk != null){
 640                                 int inRefFkInt = (Integer)inRefFk;
 641                                 if (existsInMapOrToSave(inRefFkInt, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences)){
 642                                         Reference<?> inBook = getReferenceFromMaps(inRefFkInt, nomRefToSave, relatedNomReferences);
 643                                         if (inBook == null){
 644                                                 inBook = getReferenceFromMaps(inRefFkInt, biblioRefToSave, relatedBiblioReferences);
 645                                                 logger.info("inBook (" + inRefFkInt + ") found in referenceStore instead of nomRefStore.");
 646                                                 nomRefToSave.put(inRefFkInt, inBook);
 647                                         }
 648                                         if (inBook == null){
 649                                                 logger.warn("inBook for " + inRefFkInt + " is null. "+
 650                                                 " InReference relation could not be set");;
 651                                         //}else if (Book.class.isAssignableFrom(inBook.getClass())){
 652                                         }else if (inBook.getType().equals(ReferenceType.Book)){
 653                                                 bookSection.setInBook((IBook)inBook);
 654                                                 //TODO
 655                                         }else{
 656                                                 logger.warn("InBook is not of type book but of type " + inBook.getClass().getSimpleName() +
 657                                                                 " Inreference relation could not be set");
 658                                         }
 659                                 }else{
 660                                         logger.error("Book (refId = " + inRefFkInt + ") for part_of_other_title (refID = " + refId +") could not be found in nomRefStore. Inconsistency error. ");
 661                                         //success = false;
 662                                 }
 663                         }
 664                 }else if (inRefCategoryFk == REF_ARTICLE){
 665                         //Article
 666                         //TODO
 667                         logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' is part of 'article'." +
 668                                         " This type is not implemented yet. Generic reference created instead") ;
 669                         result = ReferenceFactory.newGeneric();
 670                 }else if (inRefCategoryFk == REF_JOURNAL){
 671                         //TODO
 672                         logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference of type 'journal'." +
 673                                         " This is not allowed! Generic reference created instead") ;
 674                         result = ReferenceFactory.newGeneric();
 675                         result.addMarker(Marker.NewInstance(MarkerType.TO_BE_CHECKED(), true));
 676                 }else{
 677                         logger.warn("InReference type (catFk = " + inRefCategoryFk + ") of part-of-reference not recognized for refId " + refId + "." +
 678                                 " Create 'Generic' reference instead");
 679                         result = ReferenceFactory.newGeneric();
 680                 }
 681                 makeStandardMapper(valueMap, result); //url, pages
 682                 return result;
 683         }
 684
 685
 686         /**
 687          * @param inRefFkInt
 688          * @param biblioRefToSave
 689          * @param nomRefToSave
 690          * @param relatedBiblioReferences
 691          * @param relatedNomReferences
 692          * @return
 693          */
 694         private boolean existsInMapOrToSave(Integer inRefFkInt, Map<Integer, Reference> biblioRefToSave, Map<Integer, Reference> nomRefToSave, Map<String, Reference> relatedBiblioReferences, Map<String, Reference> relatedNomReferences) {
 695                 boolean result = false;
 696                 if (inRefFkInt == null){
 697                         return false;
 698                 }
 699                 result |= nomRefToSave.containsKey(inRefFkInt);
 700                 result |= biblioRefToSave.containsKey(inRefFkInt);
 701                 result |= relatedBiblioReferences.containsKey(String.valueOf(inRefFkInt));
 702                 result |= relatedNomReferences.containsKey(String.valueOf(inRefFkInt));
 703                 return result;
 704         }
 705
 706         private Reference<?> makeWebSite(Map<String, Object> valueMap){
 707                 if (logger.isDebugEnabled()){logger.debug("RefType 'Website'");}
 708                 Reference webPage = ReferenceFactory.newWebPage();
 709                 makeStandardMapper(valueMap, webPage); //placePublished, publisher
 710                 return webPage;
 711         }
 712
 713         private Reference<?> makeUnknown(Map<String, Object> valueMap){
 714                 if (logger.isDebugEnabled()){logger.debug("RefType 'Unknown'");}
 715                 Reference generic = ReferenceFactory.newGeneric();
 716 //              generic.setSeries(series);
 717                 makeStandardMapper(valueMap, generic); //pages, placePublished, publisher, series, volume
 718                 return generic;
 719         }
 720
 721         private Reference<?> makeInformal(Map<String, Object> valueMap){
 722                 if (logger.isDebugEnabled()){logger.debug("RefType 'Informal'");}
 723                 Reference generic = ReferenceFactory.newGeneric();
 724 //              informal.setSeries(series);
 725                 makeStandardMapper(valueMap, generic);//editor, pages, placePublished, publisher, series, volume
 726                 String informal = (String)valueMap.get("InformalRefCategory".toLowerCase());
 727                 if (CdmUtils.isNotEmpty(informal) ){
 728                         generic.addExtension(informal, ExtensionType.INFORMAL_CATEGORY());
 729                 }
 730                 return generic;
 731         }
 732
 733         private Reference<?> makeDatabase(Map<String, Object> valueMap){
 734                 if (logger.isDebugEnabled()){logger.debug("RefType 'Database'");}
 735                 Reference database =  ReferenceFactory.newDatabase();
 736                 makeStandardMapper(valueMap, database); //?
 737                 return database;
 738         }
 739
 740         private Reference<?> makeJournal(Map<String, Object> valueMap){
 741                 if (logger.isDebugEnabled()){logger.debug("RefType 'Journal'");}
 742                 Reference journal = ReferenceFactory.newJournal();
 743
 744                 Set<String> omitAttributes = new HashSet<String>();
 745                 String series = "series";
 746 //              omitAttributes.add(series);
 747
 748                 makeStandardMapper(valueMap, journal, omitAttributes); //issn,placePublished,publisher
 749 //              if (valueMap.get(series) != null){
 750 //                      logger.warn("Series not yet implemented for journal!");
 751 //              }
 752                 return journal;
 753         }
 754
 755         private Reference<?> makeBook(
 756                                 Map<String, Object> valueMap,
 757                                 Map<Integer, Reference> biblioRefToSave,
 758                                 Map<Integer, Reference> nomRefToSave,
 759                                 Map<String, Reference> relatedBiblioReferences,
 760                                 Map<String, Reference> relatedNomReferences){
 761                 if (logger.isDebugEnabled()){logger.debug("RefType 'Book'");}
 762                 Reference book = ReferenceFactory.newBook();
 763                 Integer refId = (Integer)valueMap.get("refId".toLowerCase());
 764
 765                 //Set bookAttributes = new String[]{"edition", "isbn", "pages","publicationTown","publisher","volume"};
 766
 767                 Set<String> omitAttributes = new HashSet<String>();
 768                 String attrSeries = "series";
 769 //              omitAttributes.add(attrSeries);
 770
 771                 makeStandardMapper(valueMap, book, omitAttributes);
 772
 773                 //Series (as String)
 774                 IPrintSeries printSeries = null;
 775                 if (valueMap.get(attrSeries) != null){
 776                         String series = (String)valueMap.get("title".toLowerCase());
 777                         if (series == null){
 778                                 String nomTitle = (String)valueMap.get("nomTitleAbbrev".toLowerCase());
 779                                 series = nomTitle;
 780                         }
 781                         printSeries = ReferenceFactory.newPrintSeries(series);
 782                         logger.info("Implementation of printSeries is preliminary");
 783                 }
 784                 Object inRefFk = valueMap.get("inRefFk".toLowerCase());
 785                 //Series (as Reference)
 786                 if (inRefFk != null){
 787                         int inRefFkInt = (Integer)inRefFk;
 788                         if (existsInMapOrToSave(inRefFkInt, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences)){
 789                                 Reference<?> inSeries = getReferenceFromMaps(inRefFkInt, nomRefToSave, relatedNomReferences);
 790                                 if (inSeries == null){
 791                                         inSeries = getReferenceFromMaps(inRefFkInt, biblioRefToSave, relatedBiblioReferences);
 792                                         logger.info("inSeries (" + inRefFkInt + ") found in referenceStore instead of nomRefStore.");
 793                                         nomRefToSave.put(inRefFkInt, inSeries);
 794                                 }
 795                                 if (inSeries == null){
 796                                         logger.warn("inSeries for " + inRefFkInt + " is null. "+
 797                                         " InReference relation could not be set");;
 798                                 //}else if (PrintSeries.class.isAssignableFrom(inSeries.getClass())){
 799                                 }else if (inSeries.getType().equals(ReferenceType.PrintSeries)){
 800                                         book.setInSeries((IPrintSeries)inSeries);
 801                                         //TODO
 802                                 }else{
 803                                         logger.warn("inSeries is not of type PrintSeries but of type " + inSeries.getType().getMessage() +
 804                                                         ". In-reference relation could not be set for refId " + refId + " and inRefFk " + inRefFk);
 805                                 }
 806                         }else{
 807                                 logger.error("PrintSeries (refId = " + inRefFkInt + ") for book (refID = " + refId +") could not be found in nomRefStore. Inconsistency error. ");
 808                                 //success = false;
 809                         }
 810                 }
 811                 if (book.getInSeries() != null && printSeries != null){
 812                         logger.warn("Book has series string and inSeries reference. Can not take both. Series string neglected");
 813                 }else{
 814                         book.setInSeries(printSeries);
 815                 }
 816                 book.setEditor(null);
 817                 return book;
 818
 819         }
 820
 821         /**
 822          * Returns the requested object if it exists in one of both maps. Prefers the refToSaveMap in ambigious cases.
 823          * @param inRefFkInt
 824          * @param nomRefToSave
 825          * @param relatedNomReferences
 826          * @return
 827          */
 828         private Reference<?> getReferenceFromMaps(
 829                         int inRefFkInt,
 830                         Map<Integer, Reference> refToSaveMap,
 831                         Map<String, Reference> relatedRefMap) {
 832                 Reference result = null;
 833                 result = refToSaveMap.get(inRefFkInt);
 834                 if (result == null){
 835                         result = relatedRefMap.get(String.valueOf(inRefFkInt));
 836                 }
 837                 return result;
 838         }
 839
 840         private Reference<?> makePrintSeries(Map<String, Object> valueMap){
 841                 if (logger.isDebugEnabled()){logger.debug("RefType 'PrintSeries'");}
 842                 Reference printSeries = ReferenceFactory.newPrintSeries();
 843                 makeStandardMapper(valueMap, printSeries, null);
 844                 return printSeries;
 845         }
 846
 847         private Reference<?> makeProceedings(Map<String, Object> valueMap){
 848                 if (logger.isDebugEnabled()){logger.debug("RefType 'Proceedings'");}
 849                 Reference proceedings = ReferenceFactory.newProceedings();
 850                 makeStandardMapper(valueMap, proceedings, null);
 851                 return proceedings;
 852         }
 853
 854         private Reference<?> makeThesis(Map<String, Object> valueMap){
 855                 if (logger.isDebugEnabled()){logger.debug("RefType 'Thesis'");}
 856                 Reference thesis = ReferenceFactory.newThesis();
 857                 makeStandardMapper(valueMap, thesis, null);
 858                 return thesis;
 859         }
 860
 861
 862         private Reference<?> makeJournalVolume(Map<String, Object> valueMap){
 863                 if (logger.isDebugEnabled()){logger.debug("RefType 'JournalVolume'");}
 864                 //Proceedings proceedings = Proceedings.NewInstance();
 865                 Reference journalVolume = ReferenceFactory.newGeneric();
 866                 makeStandardMapper(valueMap, journalVolume, null);
 867                 logger.warn("Journal volumes not yet implemented. Generic created instead but with errors");
 868                 return journalVolume;
 869         }
 870
 871         private boolean makeStandardMapper(Map<String, Object> valueMap, Reference<?> ref){
 872                 return makeStandardMapper(valueMap, ref, null);
 873         }
 874
 875
 876         private boolean makeStandardMapper(Map<String, Object> valueMap, CdmBase cdmBase, Set<String> omitAttributes){
 877                 boolean result = true;
 878                 for (CdmAttributeMapperBase mapper : classMappers){
 879                         if (mapper instanceof CdmSingleAttributeMapperBase){
 880                                 result &= makeStandardSingleMapper(valueMap, cdmBase, (CdmSingleAttributeMapperBase)mapper, omitAttributes);
 881                         }else if (mapper instanceof CdmOneToManyMapper){
 882                                 result &= makeMultipleValueAddMapper(valueMap, cdmBase, (CdmOneToManyMapper)mapper, omitAttributes);
 883                         }else{
 884                                 logger.error("Unknown mapper type");
 885                                 result = false;
 886                         }
 887                 }
 888                 return result;
 889         }
 890
 891         private boolean makeStandardSingleMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmSingleAttributeMapperBase mapper, Set<String> omitAttributes){
 892                 boolean result = true;
 893                 if (omitAttributes == null){
 894                         omitAttributes = new HashSet<String>();
 895                 }
 896                 if (mapper instanceof DbImportExtensionMapper){
 897                         result &= ((DbImportExtensionMapper)mapper).invoke(valueMap, cdmBase);
 898                 }else{
 899                         String sourceAttribute = mapper.getSourceAttributeList().get(0).toLowerCase();
 900                         Object value = valueMap.get(sourceAttribute);
 901                         if (value != null){
 902                                 String destinationAttribute = mapper.getDestinationAttribute();
 903                                 if (! omitAttributes.contains(destinationAttribute)){
 904                                         result &= ImportHelper.addValue(value, cdmBase, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
 905                                 }
 906                         }
 907                 }
 908                 return result;
 909         }
 910
 911
 912         private boolean makeMultipleValueAddMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmOneToManyMapper<CdmBase, CdmBase, CdmSingleAttributeMapperBase> mapper, Set<String> omitAttributes){
 913                 if (omitAttributes == null){
 914                         omitAttributes = new HashSet<String>();
 915                 }
 916                 boolean result = true;
 917                 String destinationAttribute = mapper.getSingleAttributeName();
 918                 List<Object> sourceValues = new ArrayList<Object>();
 919                 List<Class> classes = new ArrayList<Class>();
 920                 for (CdmSingleAttributeMapperBase singleMapper : mapper.getSingleMappers()){
 921                         String sourceAttribute = singleMapper.getSourceAttribute();
 922                         Object value = valueMap.get(sourceAttribute);
 923                         sourceValues.add(value);
 924                         Class<?> clazz = singleMapper.getTypeClass();
 925                         classes.add(clazz);
 926                 }
 927
 928                 result &= ImportHelper.addMultipleValues(sourceValues, cdmBase, destinationAttribute, classes, NO_OVERWRITE, OBLIGATORY);
 929 //              //only for testing
 930 //              if (cdmBase instanceof PublicationBase){
 931 //                      PublicationBase pub = ((PublicationBase)cdmBase);
 932 //                      pub.addPublisher("A new publisher for " + pub.getTitleCache(), "A nice place");
 933 //              }
 934                 return result;
 935         }
 936
 937
 938         private static TeamOrPersonBase<?> getAuthorTeam(String authorString, TeamOrPersonBase<?> nomAuthor, boolean preferNomeclaturalAuthor){
 939                 TeamOrPersonBase<?> result;
 940                 if (preferNomeclaturalAuthor){
 941                         if (nomAuthor != null){
 942                                 result = nomAuthor;
 943                         }else{
 944                                 if (CdmUtils.isEmpty(authorString)){
 945                                         result = null;
 946                                 }else{
 947                                         TeamOrPersonBase<?> team = Team.NewInstance();
 948                                         //TODO which one to use??
 949                                         team.setNomenclaturalTitle(authorString);
 950                                         team.setTitleCache(authorString, true);
 951                                         result = team;
 952                                 }
 953                         }
 954                 }else{ //prefer bibliographic
 955                         if (CdmUtils.isNotEmpty(authorString)){
 956                                 TeamOrPersonBase<?> team = Team.NewInstance();
 957                                 //TODO which one to use??
 958                                 team.setNomenclaturalTitle(authorString);
 959                                 team.setTitleCache(authorString, true);
 960                                 result = team;
 961                         }else{
 962                                 result = nomAuthor;
 963                         }
 964                 }
 965                 return result;
 966         }
 967
 968
 969         /**
 970          * @param lowerCase
 971          * @param config
 972          * @return
 973          */
 974         public Set<String> getObligatoryAttributes(boolean lowerCase, BerlinModelImportConfigurator config){
 975                 Set<String> result = new HashSet<String>();
 976                 Class<ICdmIO>[] ioClassList = config.getIoClassList();
 977                 logger.warn("getObligatoryAttributes has been commented because it still needs to be adapted to the new package structure");
 978                 result.addAll(Arrays.asList(unclearMappers));
 979                 result.addAll(Arrays.asList(createdAndNotesAttributes));
 980                 result.addAll(Arrays.asList(operationalAttributes));
 981                 CdmIoMapping mapping = new CdmIoMapping();
 982                 for (CdmAttributeMapperBase mapper : classMappers){
 983                         mapping.addMapper(mapper);
 984                 }
 985                 result.addAll(mapping.getSourceAttributes());
 986                 if (lowerCase){
 987                         Set<String> lowerCaseResult = new HashSet<String>();
 988                         for (String str : result){
 989                                 if (str != null){lowerCaseResult.add(str.toLowerCase());}
 990                         }
 991                         result = lowerCaseResult;
 992                 }
 993                 return result;
 994         }
 995
 996         /* (non-Javadoc)
 997          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 998          */
 999         @Override
1000         protected boolean doCheck(BerlinModelImportState state){
1001                 BerlinModelReferenceImportValidator validator = new BerlinModelReferenceImportValidator();
1002                 return validator.validate(state, this);
1003         }
1004
1005
1006         /* (non-Javadoc)
1007          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
1008          */
1009         @Override
1010         protected String getTableName() {
1011                 return dbTableName;
1012         }
1013
1014         /* (non-Javadoc)
1015          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
1016          */
1017         @Override
1018         public String getPluralString() {
1019                 return pluralString;
1020         }
1021
1022         /* (non-Javadoc)
1023          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
1024          */
1025         protected boolean isIgnore(BerlinModelImportState state){
1026                 return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
1027         }
1028
1029
1030
1031
1032 }