app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.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.redlist.gefaesspflanzen;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.regex.Matcher;
  19 import java.util.regex.Pattern;
  20
  21 import org.apache.log4j.Logger;
  22 import org.springframework.stereotype.Component;
  23
  24 import eu.etaxonomy.cdm.common.CdmUtils;
  25 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  26 import eu.etaxonomy.cdm.io.common.DbImportBase;
  27 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  28 import eu.etaxonomy.cdm.io.common.ImportHelper;
  29 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  30 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  31 import eu.etaxonomy.cdm.model.agent.AgentBase;
  32 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  33 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  34 import eu.etaxonomy.cdm.model.common.Annotation;
  35 import eu.etaxonomy.cdm.model.common.AnnotationType;
  36 import eu.etaxonomy.cdm.model.common.CdmBase;
  37 import eu.etaxonomy.cdm.model.common.Language;
  38 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  39 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  40 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  41 import eu.etaxonomy.cdm.model.name.BotanicalName;
  42 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
  43 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  44 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  45 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  46 import eu.etaxonomy.cdm.model.name.NonViralName;
  47 import eu.etaxonomy.cdm.model.name.Rank;
  48 import eu.etaxonomy.cdm.model.name.RankClass;
  49 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  50 import eu.etaxonomy.cdm.model.taxon.Synonym;
  51 import eu.etaxonomy.cdm.model.taxon.Taxon;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  53 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  54 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  55 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  56
  57 /**
  58  *
  59  * @author pplitzner
  60  * @date Mar 1, 2016
  61  *
  62  */
  63
  64 @Component
  65 @SuppressWarnings("serial")
  66 public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
  67
  68     private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
  69
  70     private static final String tableName = "Rote Liste Gefäßpflanzen";
  71
  72     private static final String pluralString = "names";
  73
  74     private static final boolean STRICT_TITLE_CHECK = false;
  75
  76     public RedListGefaesspflanzenImportNames() {
  77         super(tableName, pluralString);
  78     }
  79
  80     @Override
  81     protected String getIdQuery(RedListGefaesspflanzenImportState state) {
  82         return "SELECT NAMNR "
  83                 + "FROM V_TAXATLAS_D20_EXPORT t "
  84                 + " ORDER BY NAMNR";
  85     }
  86
  87     @Override
  88     protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
  89         String result = " SELECT * "
  90                 + " FROM V_TAXATLAS_D20_EXPORT t "
  91                 + " WHERE t.NAMNR IN (@IDSET)";
  92         result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
  93         return result;
  94     }
  95
  96     @Override
  97     protected void doInvoke(RedListGefaesspflanzenImportState state) {
  98         super.doInvoke(state);
  99     }
 100
 101
 102     @Override
 103     public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
 104         ResultSet rs = partitioner.getResultSet();
 105         Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
 106         Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
 107         try {
 108             while (rs.next()){
 109                 makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);
 110
 111             }
 112         } catch (SQLException e) {
 113             e.printStackTrace();
 114         }
 115
 116         getNameService().saveOrUpdate(namesToSave);
 117         getTaxonService().saveOrUpdate(taxaToSave);
 118         return true;
 119     }
 120
 121     private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
 122             throws SQLException {
 123         long id = rs.getLong(RedListUtil.NAMNR);
 124         String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
 125         String relationE = rs.getString(RedListUtil.E);
 126         String relationW = rs.getString(RedListUtil.W);
 127         String relationK = rs.getString(RedListUtil.K);
 128         String relationAW = rs.getString(RedListUtil.AW);
 129         String relationAO = rs.getString(RedListUtil.AO);
 130         String relationR = rs.getString(RedListUtil.R);
 131         String relationO = rs.getString(RedListUtil.O);
 132         String relationS = rs.getString(RedListUtil.S);
 133
 134         //---NAME---
 135         NonViralName<?> name = importName(state, rs, namesToSave);
 136
 137
 138         //--- AUTHORS ---
 139         importAuthors(state, rs, name);
 140
 141         //---TAXON---
 142         TaxonBase<?> taxonBase = importTaxon(rs, name, state);
 143         if(taxonBase==null){
 144             RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
 145             return;
 146         }
 147
 148         //---CONCEPT RELATIONSHIPS---
 149         //E, W, K, AW, AO, R, O, S
 150         cloneTaxon(taxonBase, relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxaToSave, id, state);
 151         cloneTaxon(taxonBase, relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxaToSave, id, state);
 152         cloneTaxon(taxonBase, relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxaToSave, id, state);
 153         cloneTaxon(taxonBase, relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxaToSave, id, state);
 154         cloneTaxon(taxonBase, relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxaToSave, id, state);
 155         cloneTaxon(taxonBase, relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxaToSave, id, state);
 156         cloneTaxon(taxonBase, relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxaToSave, id, state);
 157         cloneTaxon(taxonBase, relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxaToSave, id, state);
 158         //checklist
 159         TaxonBase<?> checklistTaxon = null;
 160         if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
 161             checklistTaxon = (TaxonBase<?>) taxonBase.clone();
 162             if(checklistTaxon.isInstanceOf(Taxon.class)){
 163                 TaxonRelationship relation = HibernateProxyHelper.deproxy(checklistTaxon, Taxon.class).addTaxonRelation(HibernateProxyHelper.deproxy(taxonBase, Taxon.class), TaxonRelationshipType.CONGRUENT_TO(), null, null);
 164                 relation.setDoubtful(true);
 165             }
 166
 167             ImportHelper.setOriginalSource(checklistTaxon, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
 168             taxaToSave.add(checklistTaxon);
 169         }
 170
 171         //NOTE: the source has to be added after cloning or otherwise the clone would also get the source
 172         ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
 173         taxaToSave.add(taxonBase);
 174     }
 175
 176     private void cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String relationString, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
 177         if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
 178             Taxon clonedTaxon = null;
 179
 180             if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
 181                 clonedTaxon = HibernateProxyHelper.deproxy(gesamtListeTaxon.clone(), Taxon.class);
 182             }
 183             else if(gesamtListeTaxon.isInstanceOf(Synonym.class)){
 184                 clonedTaxon = Taxon.NewInstance(gesamtListeTaxon.getName(), gesamtListeTaxon.getSec());
 185             }
 186             else{
 187                 RedListUtil.logMessage(id, "Taxon base "+gesamtListeTaxon+" is neither taxon nor synonym! Taxon could not be cloned", logger);
 188                 return;
 189             }
 190             ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace);
 191             taxaToSave.add(clonedTaxon);
 192         }
 193     }
 194
 195     private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name, RedListGefaesspflanzenImportState state) throws SQLException {
 196
 197         long id = rs.getLong(RedListUtil.NAMNR);
 198         String taxNameString = rs.getString(RedListUtil.TAXNAME);
 199         String epi1String = rs.getString(RedListUtil.EPI1);
 200         String gueltString = rs.getString(RedListUtil.GUELT);
 201         String trivialString = rs.getString(RedListUtil.TRIVIAL);
 202         String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
 203         String hybString = rs.getString(RedListUtil.HYB);
 204         String florString = rs.getString(RedListUtil.FLOR);
 205         String atlasIdxString = rs.getString(RedListUtil.ATLAS_IDX);
 206         String kartString = rs.getString(RedListUtil.KART);
 207         String rl2015String = rs.getString(RedListUtil.RL2015);
 208         String ehrdString = rs.getString(RedListUtil.EHRD);
 209         String wisskString = rs.getString(RedListUtil.WISSK);
 210
 211         TaxonBase<?> taxonBase = null;
 212         if(authorBasiString.trim().contains(RedListUtil.AUCT)){
 213             taxonBase = Taxon.NewInstance(name, null);
 214             taxonBase.setAppendedPhrase(RedListUtil.AUCT);
 215         }
 216         else if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON)){
 217             taxonBase = Taxon.NewInstance(name, null);
 218         }
 219         else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
 220             taxonBase = Synonym.NewInstance(name, null);
 221         }
 222         else{
 223             return null;
 224         }
 225
 226         //common name
 227         if(taxonBase.isInstanceOf(Taxon.class) && trivialString!=null){
 228             Taxon taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
 229             TaxonDescription description = TaxonDescription.NewInstance(taxon);
 230             description.addElement(CommonTaxonName.NewInstance(trivialString, Language.GERMAN()));
 231         }
 232
 233         //add annotations
 234         addAnnotation(RedListUtil.FLOR+": "+florString, taxonBase);
 235         addAnnotation(RedListUtil.ATLAS_IDX+": "+atlasIdxString, taxonBase);
 236         addAnnotation(RedListUtil.KART+": "+kartString, taxonBase);
 237         addAnnotation(RedListUtil.RL2015+": "+rl2015String, taxonBase);
 238         addAnnotation(RedListUtil.EHRD+": "+ehrdString, taxonBase);
 239         addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase);
 240
 241         //check taxon name consistency
 242         checkTaxonConsistency(id, taxNameString, hybString, epi1String, taxonBase, state);
 243         return taxonBase;
 244     }
 245
 246     private void addAnnotation(String string, AnnotatableEntity entity) {
 247         if(CdmUtils.isNotBlank(string)){
 248             entity.addAnnotation(Annotation.NewInstance(string, AnnotationType.TECHNICAL(), Language.GERMAN()));
 249         }
 250     }
 251
 252     private void importAuthors(RedListGefaesspflanzenImportState state, ResultSet rs, NonViralName<?> name) throws SQLException {
 253
 254         long id = rs.getLong(RedListUtil.NAMNR);
 255         String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
 256         String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
 257         String zusatzString = rs.getString(RedListUtil.ZUSATZ);
 258         String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
 259         String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
 260         String hybString = rs.getString(RedListUtil.HYB);
 261
 262         //combination author
 263         if(authorKombString.contains(RedListUtil.EX)){
 264             //TODO: what happens with multiple ex authors??
 265             String[] kombSplit = authorKombString.split(RedListUtil.EX);
 266             if(kombSplit.length!=2){
 267                 RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);
 268             }
 269             for (int i = 0; i < kombSplit.length; i++) {
 270                 if(i==0){
 271                     //first author is ex author
 272                     TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
 273                     name.setExCombinationAuthorship(authorKomb);
 274                 }
 275                 else{
 276                     TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
 277                     name.setCombinationAuthorship(authorKomb);
 278                 }
 279             }
 280         }
 281         else if(authorKombString.trim().contains(RedListUtil.AUCT)){
 282             RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
 283         }
 284         else if(CdmUtils.isNotBlank(authorKombString)){
 285             TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
 286             name.setCombinationAuthorship(authorKomb);
 287         }
 288         //basionym author
 289         if(authorBasiString.contains(RedListUtil.EX)){
 290             String[] basiSplit = authorBasiString.split(RedListUtil.EX);
 291             for (int i = 0; i < basiSplit.length; i++) {
 292                 if(basiSplit.length!=2){
 293                     RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);
 294                 }
 295                 if(i==0){
 296                     TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
 297                     if(CdmUtils.isBlank(authorKombString)){
 298                         name.setExCombinationAuthorship(authorBasi);
 299                     }
 300                     else{
 301                         name.setExBasionymAuthorship(authorBasi);
 302                     }
 303                 }
 304                 else{
 305                     TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
 306                     if(CdmUtils.isBlank(authorKombString)){
 307                         name.setCombinationAuthorship(authorBasi);
 308                     }
 309                     else{
 310                         name.setBasionymAuthorship(authorBasi);
 311                     }
 312                 }
 313             }
 314         }
 315         else if(CdmUtils.isNotBlank(authorBasiString)){
 316             //this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used
 317             TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
 318             if(CdmUtils.isBlank(authorKombString)){
 319                 name.setCombinationAuthorship(authorBasi);
 320             }
 321             else{
 322                 name.setBasionymAuthorship(authorBasi);
 323             }
 324         }
 325
 326         //check authorship consistency
 327         String authorString = rs.getString(RedListUtil.AUTOR);
 328         checkNameConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, hybString, name);
 329     }
 330
 331     private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
 332
 333         long id = rs.getLong(RedListUtil.NAMNR);
 334         String taxNameString = rs.getString(RedListUtil.TAXNAME);
 335         String rangString = rs.getString(RedListUtil.RANG);
 336         String ep1String = rs.getString(RedListUtil.EPI1);
 337         String ep2String = rs.getString(RedListUtil.EPI2);
 338         String ep3String = rs.getString(RedListUtil.EPI3);
 339         String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
 340         String hybString = rs.getString(RedListUtil.HYB);
 341         String formelString = rs.getString(RedListUtil.FORMEL);
 342
 343         if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
 344             RedListUtil.logMessage(id, "No name found!", logger);
 345         }
 346
 347         NonViralName<?> name = null;
 348         Rank rank = makeRank(id, state, rangString, ep3String!=null);
 349         //cultivar
 350         if(rank!= null && rank.equals(Rank.CULTIVAR())){
 351             CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank);
 352             cultivar.setGenusOrUninomial(ep1String);
 353             cultivar.setSpecificEpithet(ep2String);
 354             cultivar.setCultivarName(ep3String);
 355             name = cultivar;
 356         }
 357         //botanical names
 358         else{
 359             name = BotanicalName.NewInstance(rank);
 360
 361             //ep1 should always be present
 362             if(CdmUtils.isBlank(ep1String)){
 363                 RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
 364             }
 365             name.setGenusOrUninomial(ep1String);
 366             if(CdmUtils.isNotBlank(ep2String)){
 367                 if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
 368                     name.setInfraGenericEpithet(ep2String);
 369                 }
 370                 else{
 371                     name.setSpecificEpithet(ep2String);
 372                 }
 373             }
 374             if(CdmUtils.isNotBlank(ep3String)){
 375                 name.setInfraSpecificEpithet(ep3String);
 376             }
 377
 378
 379             //nomenclatural status
 380             if(CdmUtils.isNotBlank(nomZusatzString)){
 381                 NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
 382                 if(statusType!=null){
 383                     NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType);
 384                     //special case for invalid names where the DB entry contains
 385                     //additional information in brackets e.g. "nom. inval. (sine basion.)"
 386                     if(statusType.equals(NomenclaturalStatusType.INVALID()) || statusType.equals(NomenclaturalStatusType.REJECTED()) ){
 387                         Pattern pattern = Pattern.compile("\\((.*?)\\)");
 388                         Matcher matcher = pattern.matcher(nomZusatzString);
 389                         if (matcher.find()){
 390                             status.setRuleConsidered(matcher.group(1));
 391                         }
 392                     }
 393                     name.addStatus(status);
 394                 }
 395             }
 396             //hybrid
 397             if(CdmUtils.isNotBlank(hybString)){
 398                 //save hybrid formula
 399                 if(CdmUtils.isNotBlank(formelString)){
 400                     Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
 401                     annotation.setAnnotationType(AnnotationType.TECHNICAL());
 402                     name.addAnnotation(annotation);
 403                 }
 404                 //more than two hybrids not yet handled by name parser
 405                 //TODO: use parser when implemented to fully support hybrids
 406                 if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
 407                     name = BotanicalName.NewInstance(rank);
 408                     name.setTitleCache(taxNameString, true);
 409                 }
 410                 else if(hybString.equals(RedListUtil.HYB_X)){
 411                     name.setBinomHybrid(true);
 412                 }
 413                 else if(hybString.equals(RedListUtil.HYB_G)){
 414                     name.setMonomHybrid(true);
 415                 }
 416                 else if(hybString.equals(RedListUtil.HYB_XF) || hybString.equals(RedListUtil.HYB_XU)){
 417                     name.setHybridFormula(true);
 418                     if(ep1String.contains(RedListUtil.HYB_SIGN)){
 419                         name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String, NomenclaturalCode.ICNAFP, rank);
 420                     }
 421                     else if(ep2String.contains(RedListUtil.HYB_SIGN)){
 422                         String[] split = ep2String.split(RedListUtil.HYB_SIGN);
 423                         String hybridFormula1 = ep1String+" "+split[0].trim();
 424                         String hybridFormula2 = ep1String+" "+split[1].trim();
 425                         //check if the genus is mentioned in EP2 or not
 426                         String[] secondHybrid = split[1].trim().split(" ");
 427                         //check if the genus is abbreviated like e.g. Centaurea jacea × C. decipiens
 428                         if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
 429                             hybridFormula2 = ep1String+" "+split[1].trim().substring(2);
 430                         }
 431                         else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
 432                             hybridFormula2 = split[1];
 433                         }
 434                         if(CdmUtils.isNotBlank(ep3String)){
 435                             hybridFormula1 += " "+ep3String;
 436                             hybridFormula2 += " "+ep3String;
 437                         }
 438                         String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
 439                         name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
 440                     }
 441                     else if(ep3String.contains(RedListUtil.HYB_SIGN)){
 442                         String[] split = ep3String.split(RedListUtil.HYB_SIGN);
 443                         String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
 444                         String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
 445                         //check if the genus is mentioned in EP3 or not
 446                         String[] secondHybrid = split[1].trim().split(" ");
 447                         //check if the genus is abbreviated like e.g. Centaurea jacea jacea × C. jacea subsp. decipiens
 448                         if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
 449                             hybridFormula2 = ep1String+" "+split[1].trim().substring(2);
 450                         }
 451                         else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
 452                             hybridFormula2 = split[1];
 453                         }
 454                         String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
 455                         name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
 456                     }
 457                 }
 458                 else if(hybString.equals(RedListUtil.HYB_N)){
 459                     name = NonViralNameParserImpl.NewInstance().parseFullName(taxNameString, NomenclaturalCode.ICNAFP, rank);
 460                 }
 461                 else if(hybString.equals(RedListUtil.HYB_GF)){
 462                     if(ep1String.contains(RedListUtil.HYB_SIGN)){
 463                         name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String, NomenclaturalCode.ICNAFP, rank);
 464                     }
 465                     else{
 466                         RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
 467                     }
 468                 }
 469                 else if(hybString.equals(RedListUtil.HYB_XS)){
 470                     //nothing to do
 471                 }
 472                 else{
 473                     logger.error("HYB value "+hybString+" not yet handled");
 474                 }
 475             }
 476         }
 477
 478         //add source
 479         ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
 480
 481         namesToSave.add(name);
 482         return name;
 483     }
 484
 485     private void checkNameConsistency(long id, String nomZusatzString, String taxZusatzString,
 486             String zusatzString, String authorString, String hybString, NonViralName<?> name) {
 487         String authorshipCache = name.getAuthorshipCache();
 488         //FIXME: remove split length check when name parser can parse multiple hybrid parents
 489         if(hybString.equals(RedListUtil.HYB_XF) && name.getTitleCache().split(RedListUtil.HYB_SIGN).length==2){
 490             if(name.getHybridChildRelations().isEmpty()){
 491                 RedListUtil.logMessage(id, "Hybrid formula but no hybrid child relations: "+name.getTitleCache(), logger);
 492                 return;
 493             }
 494             return;
 495         }
 496
 497         if(CdmUtils.isNotBlank(zusatzString)){
 498             authorString = authorString.replace(", "+zusatzString, "");
 499         }
 500         if(CdmUtils.isNotBlank(nomZusatzString)){
 501             authorString = authorString.replace(", "+nomZusatzString, "");
 502         }
 503         if(CdmUtils.isNotBlank(taxZusatzString)){
 504             authorString = authorString.replace(", "+taxZusatzString, "");
 505         }
 506         if(authorString.equals(RedListUtil.AUCT)){
 507             authorString = "";
 508         }
 509         if(STRICT_TITLE_CHECK){
 510             if(!authorString.equals(authorshipCache)){
 511                 RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
 512             }
 513         }
 514         else{
 515             if(CdmUtils.isNotBlank(authorString) && !authorString.startsWith(authorshipCache)){
 516                 RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
 517             }
 518         }
 519     }
 520
 521     private void checkTaxonConsistency(long id, String taxNameString, String hybString, String epi1String, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {
 522         if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
 523             RedListUtil.logInfoMessage(id, "multiple hybrid signs. No name check for "+taxNameString, logger);
 524             return;
 525         }
 526
 527         String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim();
 528         taxNameString = taxNameString.trim();
 529         taxNameString = taxNameString.replaceAll(" +", " ");
 530
 531
 532         if(hybString.equals(RedListUtil.HYB_X) || hybString.equals(RedListUtil.HYB_N)){
 533             taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);//hybrid sign has no space after it in titleCache for binomial hybrids
 534             taxNameString = taxNameString.replace(" x ", " "+RedListUtil.HYB_SIGN);//in some cases a standard 'x' is used
 535         }
 536         else if(hybString.equals(RedListUtil.HYB_G)){
 537             taxNameString = taxNameString.replace("X ", RedListUtil.HYB_SIGN);
 538         }
 539         else if(hybString.equals(RedListUtil.HYB_GF)){
 540             taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);
 541         }
 542         else if(hybString.equals(RedListUtil.HYB_XF)){
 543             nameCache = taxonBase.getName().getTitleCache();
 544             if(nameCache.contains("sec")){
 545                 nameCache = nameCache.substring(0, nameCache.indexOf("sec"));
 546             }
 547             if(taxNameString.matches((".*[A-Z]\\..*"))){
 548                 taxNameString = taxNameString.replaceAll("[A-Z]\\.", epi1String);
 549             }
 550             if(taxNameString.matches((".*"+RedListUtil.HYB_SIGN+"\\s[a-z].*"))){
 551                 taxNameString = taxNameString.replaceAll(RedListUtil.HYB_SIGN+" ", RedListUtil.HYB_SIGN+" "+epi1String+" ");
 552             }
 553         }
 554
 555         if(taxNameString.endsWith("- Gruppe")){
 556             taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
 557         }
 558         if(taxNameString.endsWith("- group")){
 559             taxNameString = taxNameString.replaceAll("- group", "species group");
 560         }
 561
 562         taxNameString = taxNameString.replace("agg.", "aggr.");
 563         taxNameString = taxNameString.replace("[ranglos]", "[unranked]");
 564
 565         if(taxonBase.getName().getRank()!=null){
 566             if(taxonBase.getName().getRank().equals(Rank.PROLES())){
 567                 taxNameString = taxNameString.replace("proles", "prol.");
 568             }
 569             else if(taxonBase.getName().getRank().equals(state.getRank(RedListUtil.uuidRankCollectionSpecies))){
 570                 taxNameString = taxNameString.replace("\"Sammelart\"", "\"Coll. Species\"");
 571             }
 572         }
 573         if(STRICT_TITLE_CHECK){
 574             if(!taxNameString.trim().equals(nameCache)){
 575                 RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
 576             }
 577         }
 578         else{
 579             if(!taxNameString.startsWith(nameCache)){
 580                 RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
 581             }
 582         }
 583     }
 584
 585     private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr, boolean hasSpecificEpithet) {
 586         Rank rank = null;
 587         try {
 588             if(rankStr.equals("ORA")){
 589                 //special handling for ORA because of two possibilities
 590                 if(hasSpecificEpithet){
 591                     return Rank.UNRANKED_INFRASPECIFIC();
 592                 }
 593                 else{
 594                     return Rank.UNRANKED_INFRAGENERIC();
 595                 }
 596             }
 597             else if(rankStr.equals("SAM")){
 598                 return getRank(state, RedListUtil.uuidRankCollectionSpecies, "Collective Species", "Collective Species", "\"Coll. Species\"", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.SpeciesGroup);
 599             }
 600             else if(rankStr.equals("SPR")){
 601                 return getRank(state, RedListUtil.uuidRankSubproles, "Subproles", "Subproles", "subproles", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
 602             }
 603             else if(rankStr.equals("MOD")){
 604                 return getRank(state, RedListUtil.uuidRankModification, "Modification", "Modification", "modificatio", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
 605             }
 606             else if(rankStr.equals("LUS")){
 607                 return getRank(state, RedListUtil.uuidRankLusus, "Lusus", "Lusus", "lusus", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
 608             }
 609             else if(rankStr.equals("SPI")){
 610                 return getRank(state, RedListUtil.uuidRankSubspeciesPrincipes, "Subspecies principes", "Subspecies principes", "subsp. princ.", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
 611             }
 612             else if(rankStr.equals("KMB")){
 613                 return getRank(state, RedListUtil.uuidRankCombination, "Combination", "Combination", "", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
 614             }
 615             else{
 616                 rank = state.getTransformer().getRankByKey(rankStr);
 617             }
 618         } catch (UndefinedTransformerMethodException e) {
 619             e.printStackTrace();
 620         }
 621         if(rank==null){
 622             RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
 623         }
 624         return rank;
 625     }
 626
 627     private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
 628         NomenclaturalStatusType status = null;
 629         try {
 630             status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
 631         } catch (UndefinedTransformerMethodException e) {
 632             e.printStackTrace();
 633         }
 634         if(status==null){
 635             RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
 636         }
 637         return status;
 638     }
 639
 640
 641
 642     @Override
 643     public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
 644             RedListGefaesspflanzenImportState state) {
 645         Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 646         Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
 647
 648         try {
 649             while (rs.next()){
 650                 String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
 651
 652                 if(authorKombString.contains(RedListUtil.EX)){
 653                     String[] kombSplit = authorKombString.split(RedListUtil.EX);
 654                     for (int i = 0; i < kombSplit.length; i++) {
 655                         if(!authorMap.containsKey(kombSplit[i])){
 656                             authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
 657                         }
 658                     }
 659                 }
 660                 else if(CdmUtils.isNotBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
 661                     authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
 662                 }
 663
 664                 String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
 665                 //basionym author
 666                 if(authorBasiString.contains(RedListUtil.EX)){
 667                     String[] basiSplit = authorBasiString.split(RedListUtil.EX);
 668                     for (int i = 0; i < basiSplit.length; i++) {
 669                         if(!authorMap.containsKey(basiSplit[i])){
 670                             authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
 671                         }
 672                     }
 673                 }
 674                 else if(CdmUtils.isNotBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
 675                     authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
 676                 }
 677             }
 678         } catch (SQLException e) {
 679             e.printStackTrace();
 680         }
 681         result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
 682
 683         return result;
 684     }
 685
 686     @Override
 687     protected boolean doCheck(RedListGefaesspflanzenImportState state) {
 688         return false;
 689     }
 690
 691     @Override
 692     protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
 693         return false;
 694     }
 695
 696 }