cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/specimen/SpecimenImportBase.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.specimen;
  11
  12
  13 import java.util.ArrayList;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.log4j.Logger;
  22
  23 import eu.etaxonomy.cdm.api.application.ICdmRepository;
  24 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  25 import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;
  26 import eu.etaxonomy.cdm.api.service.pager.Pager;
  27 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  28 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  29 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  30 import eu.etaxonomy.cdm.io.specimen.abcd206.in.Identification;
  31 import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
  32 import eu.etaxonomy.cdm.model.agent.AgentBase;
  33 import eu.etaxonomy.cdm.model.agent.Institution;
  34 import eu.etaxonomy.cdm.model.agent.Person;
  35 import eu.etaxonomy.cdm.model.agent.Team;
  36 import eu.etaxonomy.cdm.model.common.CdmBase;
  37 import eu.etaxonomy.cdm.model.common.ISourceable;
  38 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  39 import eu.etaxonomy.cdm.model.common.LanguageString;
  40 import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
  41 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  42 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  43 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  44 import eu.etaxonomy.cdm.model.description.Feature;
  45 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  46 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  47 import eu.etaxonomy.cdm.model.name.INonViralName;
  48 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  49 import eu.etaxonomy.cdm.model.name.Rank;
  50 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  51 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  52 import eu.etaxonomy.cdm.model.name.TaxonName;
  53 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
  54 import eu.etaxonomy.cdm.model.occurrence.Collection;
  55 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  56 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  57 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  58 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  59 import eu.etaxonomy.cdm.model.reference.Reference;
  60 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  61 import eu.etaxonomy.cdm.model.taxon.Classification;
  62 import eu.etaxonomy.cdm.model.taxon.Synonym;
  63 import eu.etaxonomy.cdm.model.taxon.Taxon;
  64 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  65 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  66 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  67 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  68 import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
  69 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
  70
  71
  72 /**
  73  * @author p.kelbert
  74  * @created 20.10.2008
  75  */
  76 public abstract class SpecimenImportBase<CONFIG extends IImportConfigurator, STATE extends SpecimenImportStateBase>
  77         extends CdmImportBase<CONFIG, STATE> {
  78
  79     private static final long serialVersionUID = 4423065367998125678L;
  80     private static final Logger logger = Logger.getLogger(SpecimenImportBase.class);
  81
  82         protected static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
  83
  84         private static final String COLON = ":";
  85
  86
  87         @Override
  88     protected abstract void doInvoke(STATE state);
  89
  90         /**
  91          * Handle a single unit
  92          * @param state
  93          * @param item
  94          */
  95         protected abstract void handleSingleUnit(STATE state, Object item) ;
  96
  97
  98
  99         protected TaxonName getOrCreateTaxonName(String scientificName, Rank rank, boolean preferredFlag, STATE state, int unitIndexInAbcdFile){
 100             TaxonName taxonName = null;
 101         SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
 102
 103         //check atomised name data for rank
 104         //new name will be created
 105         TaxonName atomisedTaxonName = null;
 106         if (rank==null && unitIndexInAbcdFile>=0 && ((state.getDataHolder().getAtomisedIdentificationList() != null && !state.getDataHolder().getAtomisedIdentificationList().isEmpty())|| state.getDataHolder().getAtomisedIdentificationList().size() > 0)) {
 107             atomisedTaxonName = setTaxonNameByType(state.getDataHolder().getAtomisedIdentificationList().get(unitIndexInAbcdFile), scientificName, state);
 108             if(atomisedTaxonName!=null){
 109                 rank = atomisedTaxonName.getRank();
 110             }
 111         }
 112         if(config.isReuseExistingTaxaWhenPossible()){
 113             TaxonName parsedName = atomisedTaxonName;
 114             if(parsedName==null){
 115
 116                 parsedName = parseScientificName(scientificName, state, state.getReport(), rank);
 117
 118             }
 119             atomisedTaxonName = parsedName;
 120             if(config.isIgnoreAuthorship() && parsedName!=null){// && preferredFlag){
 121                 // do not ignore authorship for non-preferred names because they need
 122                 // to be created for the determination history
 123                 String nameCache = TaxonName.castAndDeproxy(parsedName).getNameCache();
 124                 List<TaxonName> names = getNameService().findNamesByNameCache(nameCache, MatchMode.EXACT, null);
 125                 if (!names.isEmpty()){
 126                      taxonName = getBestMatchingName(scientificName, new ArrayList<>(names), state);
 127                 }
 128                 if (taxonName == null && !names.isEmpty()){
 129                     taxonName = names.get(0);
 130                 }
 131
 132             } else {
 133                 //search for existing names
 134                 List<TaxonName> names = getNameService().listByTitle(TaxonName.class, scientificName, MatchMode.EXACT, null, null, null, null, null);
 135                 taxonName = getBestMatchingName(scientificName, names, state);
 136                 //still nothing found -> try with the atomised name full title cache
 137                 if(taxonName==null && atomisedTaxonName!=null){
 138                     names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getFullTitleCache(), MatchMode.EXACT, null, null, null, null, null);
 139                     taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
 140                     //still nothing found -> try with the atomised name title cache
 141                     if(taxonName==null){
 142                         names = getNameService().listByTitle(TaxonName.class, atomisedTaxonName.getTitleCache(), MatchMode.EXACT, null, null, null, null, null);
 143                         taxonName = getBestMatchingName(atomisedTaxonName.getTitleCache(), names, state);
 144                     }
 145                 }
 146
 147             }
 148
 149         }
 150
 151         if(taxonName==null && atomisedTaxonName!=null){
 152             taxonName = atomisedTaxonName;
 153             state.getReport().addName(taxonName);
 154             logger.info("Created new taxon name "+taxonName);
 155             if(taxonName.hasProblem()){
 156                 state.getReport().addInfoMessage(String.format("Created %s with parsing problems", taxonName));
 157             }
 158             if(!atomisedTaxonName.getTitleCache().equals(scientificName)){
 159                 state.getReport().addInfoMessage(String.format("Taxon %s was parsed as %s", scientificName, atomisedTaxonName.getTitleCache()));
 160             }
 161         }
 162         else if(taxonName==null){
 163             //create new taxon name
 164
 165             if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP)){
 166                 taxonName = TaxonNameFactory.NewBotanicalInstance(rank);
 167             }else if (state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN)){
 168                 taxonName = TaxonNameFactory.NewZoologicalInstance(rank);
 169             }else{
 170                 taxonName = TaxonNameFactory.NewNonViralInstance(rank);
 171             }
 172             taxonName.setFullTitleCache(scientificName,true);
 173             taxonName.setTitleCache(scientificName, true);
 174             state.getReport().addName(taxonName);
 175             logger.info("Created new taxon name "+taxonName);
 176         }
 177         save(taxonName, state);
 178         return taxonName;
 179     }
 180
 181          protected TaxonName getBestMatchingName(String scientificName, java.util.Collection<TaxonName> names, STATE state){
 182                 Set<TaxonName> namesWithAcceptedTaxa = new HashSet<>();
 183                 List<TaxonName> namesWithAcceptedTaxaInClassification = new ArrayList<>();
 184                 for (TaxonName name : names) {
 185                     if(!name.getTaxa().isEmpty()){
 186                         Set<Taxon> taxa = name.getTaxa();
 187                         for (Taxon taxon:taxa){
 188                             if (!taxon.getTaxonNodes().isEmpty()){
 189                                 //use only taxa included in a classification
 190                                 for (TaxonNode node:taxon.getTaxonNodes()){
 191                                     if (state.getClassification() != null && node.getClassification().equals(state.getClassification())){
 192                                         namesWithAcceptedTaxaInClassification.add(name);
 193                                     }else {
 194                                         namesWithAcceptedTaxa.add(name);
 195                                     }
 196                                 }
 197
 198                             }
 199                         }
 200
 201                     }
 202                 }
 203                 String message = String.format("More than one taxon name was found for %s, maybe in other classifications!", scientificName);
 204                 //check for names with accepted taxa in classification
 205                 if(namesWithAcceptedTaxaInClassification.size()>0){
 206                 if(namesWithAcceptedTaxaInClassification.size()>1){
 207
 208                     state.getReport().addInfoMessage(message);
 209                     logger.warn(message);
 210                     return null;
 211                 }
 212                 return namesWithAcceptedTaxaInClassification.iterator().next();
 213             }
 214               //check for any names with accepted taxa
 215                 if(namesWithAcceptedTaxa.size()>0){
 216                     if(namesWithAcceptedTaxa.size()>1){
 217
 218                         state.getReport().addInfoMessage(message);
 219                         logger.warn(message);
 220                         return null;
 221                     }
 222                     return namesWithAcceptedTaxa.iterator().next();
 223                 }
 224                 //no names with accepted taxa found -> check accepted taxa of synonyms
 225                 List<Taxon> taxaFromSynonyms = new ArrayList<>();
 226                 for (TaxonName name : names) {
 227                     Set<TaxonBase> taxonBases = name.getTaxonBases();
 228                     for (TaxonBase taxonBase : taxonBases) {
 229                         if(taxonBase.isInstanceOf(Synonym.class)){
 230                             Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
 231                             taxaFromSynonyms.add(synonym.getAcceptedTaxon());
 232                         }
 233                     }
 234                 }
 235                 if(taxaFromSynonyms.size()>0){
 236                     if(taxaFromSynonyms.size()>1){
 237                         state.getReport().addInfoMessage(message);
 238                         logger.warn(message);
 239                         return null;
 240                     }
 241                     return taxaFromSynonyms.iterator().next().getName();
 242                 }
 243                 //no accepted and no synonyms -> return one of the names and create a new taxon
 244                 if (names.isEmpty()){
 245                     return null;
 246                 }else{
 247                     return names.iterator().next();
 248                 }
 249             }
 250          /**
 251              * Parse automatically the scientific name
 252              * @param scientificName the scientific name to parse
 253              * @param state the current import state
 254              * @param report the import report
 255              * @return a parsed name
 256              */
 257
 258             protected TaxonName parseScientificName(String scientificName, STATE state, SpecimenImportReport report, Rank rank) {
 259
 260                 NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
 261                 TaxonName taxonName = null;
 262                 boolean problem = false;
 263
 264                 if (logger.isDebugEnabled()){
 265                     logger.debug("parseScientificName " + state.getDataHolder().getNomenclatureCode().toString());
 266                 }
 267
 268                 if (state.getDataHolder().getNomenclatureCode().toString().equals("Zoological") || state.getDataHolder().getNomenclatureCode().toString().contains("ICZN")) {
 269                     taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICZN, rank);
 270                     if (taxonName.hasProblem()) {
 271                         problem = true;
 272                     }
 273                 }
 274                 else if (state.getDataHolder().getNomenclatureCode().toString().equals("Botanical") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
 275                     taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNAFP, rank);
 276                     if (taxonName.hasProblem()) {
 277                         problem = true;
 278                     }
 279                 }
 280                 else if (state.getDataHolder().getNomenclatureCode().toString().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().toString().contains("ICBN")) {
 281                     taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNB, rank);
 282                     if (taxonName.hasProblem()) {
 283                         problem = true;
 284                     }
 285                 }
 286                 else if (state.getDataHolder().getNomenclatureCode().toString().equals("Cultivar") || state.getDataHolder().getNomenclatureCode().toString().contains("ICNCP")) {
 287                     taxonName = (TaxonName)nvnpi.parseFullName(scientificName, NomenclaturalCode.ICNCP, rank);
 288                     if (taxonName.hasProblem()) {
 289                         problem = true;
 290                     }
 291                 }
 292                 if (problem) {
 293                     String message = String.format("Parsing problems for %s", scientificName);
 294                     if(taxonName!=null){
 295                         for (ParserProblem parserProblem : taxonName.getParsingProblems()) {
 296                             message += "\n\t- "+parserProblem;
 297                         }
 298                     }
 299                     report.addInfoMessage(message);
 300                     logger.info(message);
 301                 }
 302                 return taxonName;
 303
 304             }
 305
 306             /**
 307              * Create the name without automatic parsing, either because it failed, or because the user deactivated it.
 308              * The name is built upon the ABCD fields
 309              * @param atomisedMap : the ABCD atomised fields
 310              * @param fullName : the full scientific name
 311              * @param state
 312              * @return the corresponding Botanical or Zoological or... name
 313              */
 314             protected TaxonName setTaxonNameByType(
 315                     HashMap<String, String> atomisedMap, String fullName, STATE state) {
 316                 boolean problem = false;
 317                 if (logger.isDebugEnabled()){
 318                     logger.debug("settaxonnamebytype " + state.getDataHolder().getNomenclatureCode().toString());
 319                 }
 320
 321                 if (state.getDataHolder().getNomenclatureCode().equals("Zoological") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICZN.getUuid())) {
 322                     TaxonName taxonName = TaxonNameFactory.NewZoologicalInstance(null);
 323                     taxonName.setFullTitleCache(fullName, true);
 324                     taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
 325                     taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
 326                     taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap,"SpeciesEpithet")));
 327                     taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap,"SubspeciesEpithet")));
 328
 329                     if (taxonName.getGenusOrUninomial() != null){
 330                         taxonName.setRank(Rank.GENUS());
 331                     }
 332
 333                     if (taxonName.getInfraGenericEpithet() != null){
 334                         taxonName.setRank(Rank.SUBGENUS());
 335                     }
 336
 337                     if (taxonName.getSpecificEpithet() != null){
 338                         taxonName.setRank(Rank.SPECIES());
 339                     }
 340
 341                     if (taxonName.getInfraSpecificEpithet() != null){
 342                         taxonName.setRank(Rank.SUBSPECIES());
 343                     }
 344
 345                     Team team = null;
 346                     if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
 347                         team = Team.NewInstance();
 348                         team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
 349                     }
 350                     else {
 351                         if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
 352                             team = Team.NewInstance();
 353                             team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
 354                         }
 355                     }
 356                     if (team != null) {
 357                         taxonName.setBasionymAuthorship(team);
 358                     }
 359                     else {
 360                         if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
 361                             taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
 362                         }
 363                         else if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
 364                             taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamAndYear"));
 365                         }
 366                     }
 367                     if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
 368                         team = Team.NewInstance();
 369                         team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
 370                         taxonName.setCombinationAuthorship(team);
 371                     }
 372                     if (taxonName.hasProblem()) {
 373                         logger.info("pb ICZN");
 374                         problem = true;
 375                     }
 376                     else {
 377                         return taxonName;
 378                     }
 379                 }
 380                 else if (state.getDataHolder().getNomenclatureCode().equals("Botanical") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNAFP.getUuid())) {
 381                     TaxonName taxonName = parseScientificName(fullName, state, state.getReport(), null);
 382                     if (taxonName != null){
 383                         return taxonName;
 384                     }
 385                     else{
 386                         taxonName = TaxonNameFactory.NewBotanicalInstance(null);
 387                     }
 388                     taxonName.setFullTitleCache(fullName, true);
 389                     taxonName.setGenusOrUninomial(NB(getFromMap(atomisedMap, "Genus")));
 390                     taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "FirstEpithet")));
 391                     taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "InfraSpeEpithet")));
 392                     try {
 393                         taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap, "Rank")));
 394                     } catch (Exception e) {
 395                         if (taxonName.getInfraSpecificEpithet() != null){
 396                             taxonName.setRank(Rank.SUBSPECIES());
 397                         }
 398                         else if (taxonName.getSpecificEpithet() != null){
 399                             taxonName.setRank(Rank.SPECIES());
 400                         }
 401                         else if (taxonName.getInfraGenericEpithet() != null){
 402                             taxonName.setRank(Rank.SUBGENUS());
 403                         }
 404                         else if (taxonName.getGenusOrUninomial() != null){
 405                             taxonName.setRank(Rank.GENUS());
 406                         }
 407                     }
 408                     Team team = null;
 409                     if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
 410                         team = Team.NewInstance();
 411                         team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"), true);
 412                         taxonName.setBasionymAuthorship(team);
 413                     }
 414                     if (getFromMap(atomisedMap, "AuthorTeam") != null) {
 415                         team = Team.NewInstance();
 416                         team.setTitleCache(getFromMap(atomisedMap, "AuthorTeam"), true);
 417                         taxonName.setCombinationAuthorship(team);
 418                     }
 419                     if (team == null) {
 420                         if (getFromMap(atomisedMap, "AuthorTeamParenthesis") != null) {
 421                             taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeamParenthesis"));
 422                         }
 423                         else if (getFromMap(atomisedMap, "AuthorTeam") != null) {
 424                             taxonName.setAuthorshipCache(getFromMap(atomisedMap, "AuthorTeam"));
 425                         }
 426                     }
 427                     if (getFromMap(atomisedMap, "CombinationAuthorTeamAndYear") != null) {
 428                         team = Team.NewInstance();
 429                         team.setTitleCache(getFromMap(atomisedMap, "CombinationAuthorTeamAndYear"), true);
 430                         taxonName.setCombinationAuthorship(team);
 431                     }
 432                     if (taxonName.hasProblem()) {
 433                         logger.info("pb ICBN");
 434                         problem = true;
 435                     }
 436                     else {
 437                         return taxonName;
 438                     }
 439                 }
 440                 else if (state.getDataHolder().getNomenclatureCode().equals("Bacterial") || state.getDataHolder().getNomenclatureCode().equals(NomenclaturalCode.ICNB.getUuid())) {
 441                     TaxonName taxonName = TaxonNameFactory.NewBacterialInstance(null);
 442                     taxonName.setFullTitleCache(fullName, true);
 443                     taxonName.setGenusOrUninomial(getFromMap(atomisedMap, "Genus"));
 444                     taxonName.setInfraGenericEpithet(NB(getFromMap(atomisedMap, "SubGenus")));
 445                     taxonName.setSpecificEpithet(NB(getFromMap(atomisedMap, "Species")));
 446                     taxonName.setInfraSpecificEpithet(NB(getFromMap(atomisedMap, "SubspeciesEpithet")));
 447
 448                     if (taxonName.getGenusOrUninomial() != null){
 449                         taxonName.setRank(Rank.GENUS());
 450                     }
 451                     else if (taxonName.getInfraGenericEpithet() != null){
 452                         taxonName.setRank(Rank.SUBGENUS());
 453                     }
 454                     else if (taxonName.getSpecificEpithet() != null){
 455                         taxonName.setRank(Rank.SPECIES());
 456                     }
 457                     else if (taxonName.getInfraSpecificEpithet() != null){
 458                         taxonName.setRank(Rank.SUBSPECIES());
 459                     }
 460
 461                     if (getFromMap(atomisedMap, "AuthorTeamAndYear") != null) {
 462                         Team team = Team.NewInstance();
 463                         team.setTitleCache(getFromMap(atomisedMap, "AuthorTeamAndYear"), true);
 464                         taxonName.setCombinationAuthorship(team);
 465                     }
 466                     if (getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear") != null) {
 467                         Team team = Team.NewInstance();
 468                         team.setTitleCache(getFromMap(atomisedMap, "ParentheticalAuthorTeamAndYear"), true);
 469                         taxonName.setBasionymAuthorship(team);
 470                     }
 471                     if (taxonName.hasProblem()) {
 472                         logger.info("pb ICNB");
 473                         problem = true;
 474                     }
 475                     else {
 476                         return taxonName;
 477                     }
 478                 }
 479                 else if (state.getDataHolder().getNomenclatureCode().equals("Cultivar")) {
 480                     TaxonName taxonName = TaxonNameFactory.NewCultivarInstance(null);
 481
 482                     if (taxonName.hasProblem()) {
 483                         logger.info("pb ICNCP");
 484                         problem = true;
 485                     }
 486                     else {
 487                         return taxonName;
 488                     }
 489                     return taxonName;
 490                 }
 491
 492                 if (problem) {
 493                     logger.info("Problem im setTaxonNameByType ");
 494                     TaxonName taxonName = TaxonNameFactory.NewNonViralInstance(null);
 495                     taxonName.setFullTitleCache(fullName, true);
 496                     return taxonName;
 497                 }
 498                 TaxonName tn = TaxonNameFactory.NewNonViralInstance(null);
 499                 return tn;
 500             }
 501
 502             /**
 503              * Get a formated string from a hashmap
 504              * @param atomisedMap
 505              * @param key
 506              * @return
 507              */
 508             private String getFromMap(HashMap<String, String> atomisedMap, String key) {
 509                 String value = null;
 510                 if (atomisedMap.containsKey(key)) {
 511                     value = atomisedMap.get(key);
 512                 }
 513
 514                 try {
 515                     if (value != null && key.matches(".*Year.*")) {
 516                         value = value.trim();
 517                         if (value.matches("[a-z A-Z ]*[0-9]{4}$")) {
 518                             String tmp = value.split("[0-9]{4}$")[0];
 519                             int year = Integer.parseInt(value.split(tmp)[1]);
 520                             if (year >= 1752) {
 521                                 value = tmp;
 522                             }
 523                             else {
 524                                 value = null;
 525                             }
 526                         }
 527                         else {
 528                             value = null;
 529                         }
 530                     }
 531                 }
 532                 catch (Exception e) {
 533                     value = null;
 534                 }
 535                 return value;
 536             }
 537
 538             /**
 539              * Very fast and dirty implementation to allow handling of transient objects as described in
 540              * https://dev.e-taxonomy.eu/trac/ticket/3726
 541              *
 542              * Not yet complete.
 543              *
 544              * @param cdmBase
 545              * @param state
 546              */
 547             protected UUID save(CdmBase cdmBase, SpecimenImportStateBase state) {
 548                 ICdmRepository cdmRepository = state.getConfig().getCdmAppController();
 549                 if (cdmRepository == null){
 550                     cdmRepository = this;
 551                 }
 552
 553                 if (cdmBase.isInstanceOf(LanguageString.class)){
 554                     return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
 555                 }else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
 556                     SpecimenOrObservationBase specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
 557
 558                     return cdmRepository.getOccurrenceService().saveOrUpdate(specimen);
 559                 }else if (cdmBase.isInstanceOf(Reference.class)){
 560                     return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
 561                 }else if (cdmBase.isInstanceOf(Classification.class)){
 562                     return cdmRepository.getClassificationService().saveOrUpdate(CdmBase.deproxy(cdmBase, Classification.class));
 563                 }else if (cdmBase.isInstanceOf(AgentBase.class)){
 564                     return cdmRepository.getAgentService().saveOrUpdate(CdmBase.deproxy(cdmBase, AgentBase.class));
 565                 }else if (cdmBase.isInstanceOf(Collection.class)){
 566                     return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
 567                 }else if (cdmBase.isInstanceOf(DescriptionBase.class)){
 568                     DescriptionBase description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
 569
 570                     return cdmRepository.getDescriptionService().saveOrUpdate(description);
 571                 }else if (cdmBase.isInstanceOf(TaxonBase.class)){
 572                     return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
 573                 }else if (cdmBase.isInstanceOf(TaxonName.class)){
 574                     return cdmRepository.getNameService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonName.class));
 575                 }else if (cdmBase.isInstanceOf(TaxonNode.class)){
 576                 return cdmRepository.getTaxonNodeService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonNode.class));
 577             }else{
 578                     throw new IllegalArgumentException("Class not supported in save method: " + CdmBase.deproxy(cdmBase, CdmBase.class).getClass().getSimpleName());
 579                 }
 580
 581             }
 582
 583
 584             protected SpecimenOrObservationBase findExistingSpecimen(String unitId, SpecimenImportStateBase state){
 585                 ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
 586                 if(cdmAppController==null){
 587                     cdmAppController = this;
 588                 }
 589                 FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();
 590                 config.setSignificantIdentifier(unitId);
 591                 Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
 592                 if(!existingSpecimens.getRecords().isEmpty()){
 593                     if(existingSpecimens.getRecords().size()==1){
 594                         return existingSpecimens.getRecords().iterator().next();
 595                     }
 596                 }
 597                 return null;
 598             }
 599
 600             protected abstract void importAssociatedUnits(STATE state, Object item, DerivedUnitFacade derivedUnitFacade);
 601
 602             /**
 603              * getFacade : get the DerivedUnitFacade based on the recordBasis
 604              * @param state
 605              *
 606              * @return DerivedUnitFacade
 607              */
 608             protected DerivedUnitFacade getFacade(STATE state) {
 609                 if (logger.isDebugEnabled()){
 610                     logger.info("getFacade()");
 611                 }
 612                 SpecimenOrObservationType type = null;
 613
 614                 // create specimen
 615                 if (NB((state.getDataHolder().getRecordBasis())) != null) {
 616                     if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
 617                         type = SpecimenOrObservationType.PreservedSpecimen;
 618                     }
 619                     if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
 620                         type = SpecimenOrObservationType.Observation;
 621                     }
 622                     if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
 623                         type = SpecimenOrObservationType.Fossil;
 624                     }
 625                     if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
 626                         type = SpecimenOrObservationType.LivingSpecimen;
 627                     }
 628                     if (type == null) {
 629                         logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
 630                         type = SpecimenOrObservationType.DerivedUnit;
 631                     }
 632                     // TODO fossils?
 633                 } else {
 634                     logger.info("The basis of record is null");
 635                     type = SpecimenOrObservationType.DerivedUnit;
 636                 }
 637                 DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
 638                 return derivedUnitFacade;
 639             }
 640
 641             /**
 642              * Look if the Institution does already exist
 643              * @param institutionCode: a string with the institutioncode
 644              * @param config : the configurator
 645              * @return the Institution (existing or new)
 646              */
 647             protected Institution getInstitution(String institutionCode, STATE state) {
 648                 SpecimenImportConfiguratorBase config = state.getConfig();
 649                 Institution institution=null;
 650                 institution = (Institution)state.institutions.get(institutionCode);
 651                 if (institution != null){
 652                     return institution;
 653                 }
 654                 List<Institution> institutions;
 655                 try {
 656                     institutions = getAgentService().searchInstitutionByCode(institutionCode);
 657
 658                 } catch (Exception e) {
 659                     institutions = new ArrayList<Institution>();
 660                     logger.warn(e);
 661                 }
 662                 if (institutions.size() > 0 && config.isReuseExistingMetaData()) {
 663                     for (Institution institut:institutions){
 664                         try{
 665                             if (institut.getCode().equalsIgnoreCase(institutionCode)) {
 666                                 institution=institut;
 667                                 break;
 668                             }
 669                         }catch(Exception e){logger.warn("no institution code in the db");}
 670                     }
 671                 }
 672                 if (logger.isDebugEnabled()){
 673                     if(institution !=null) {
 674                         logger.info("getinstitution " + institution.toString());
 675                     }
 676                 }
 677                 if (institution == null){
 678                     // create institution
 679                     institution = Institution.NewInstance();
 680                     institution.setCode(institutionCode);
 681                     institution.setTitleCache(institutionCode, true);
 682                     UUID uuid = save(institution, state);
 683                 }
 684
 685
 686                 state.institutions.put(institutionCode, institution);
 687                 return institution;
 688             }
 689
 690             /**
 691              * Look if the Collection does already exist
 692              * @param collectionCode
 693              * @param collectionCode: a string
 694              * @param config : the configurator
 695              * @return the Collection (existing or new)
 696              */
 697             protected Collection getCollection(Institution institution, String collectionCode, STATE state) {
 698                 SpecimenImportConfiguratorBase config = state.getConfig();
 699                 Collection collection = null;
 700                 List<Collection> collections;
 701                 collection = (Collection) state.collections.get(collectionCode);
 702                 if (collection != null){
 703                     return collection;
 704                 }
 705                 try {
 706                     collections = getCollectionService().searchByCode(collectionCode);
 707                 } catch (Exception e) {
 708                     collections = new ArrayList<Collection>();
 709                 }
 710                 if (collections.size() > 0 && config.isReuseExistingMetaData()) {
 711                     for (Collection coll:collections){
 712                         if (coll.getCode() != null && coll.getInstitute() != null
 713                                 && coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
 714                             collection = coll;
 715                             break;
 716                         }
 717                     }
 718                 }
 719
 720                 if(collection == null){
 721                     collection =Collection.NewInstance();
 722                     collection.setCode(collectionCode);
 723                     collection.setInstitute(institution);
 724                     collection.setTitleCache(collectionCode);
 725                     UUID uuid = save(collection, state);
 726                 }
 727
 728
 729
 730                 state.collections.put(collectionCode, collection);
 731
 732                 return collection;
 733             }
 734
 735             /**
 736              * @param reference
 737              * @param citationDetail
 738              * @return
 739              */
 740             //FIXME this method is highly critical, because
 741             //  * it will have serious performance and memory problems with large databases
 742             //        (databases may easily have >1 Mio source records)
 743             //  * it does not make sense to search for existing sources and then clone them
 744             //    we need to search for existing references instead and use them (if exist)
 745             //    for our new source.
 746             protected IdentifiableSource getIdentifiableSource(Reference reference, String citationDetail) {
 747
 748               /*  List<IdentifiableSource> issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
 749
 750
 751                 if (reference != null){
 752                     try {
 753                         for (OriginalSourceBase<?> osb: issTmp){
 754                             if (osb.getCitation() != null && osb.getCitation().getTitleCache().equalsIgnoreCase(reference.getTitleCache())){
 755                                 String osbDetail = osb.getCitationMicroReference();
 756                                 if ((StringUtils.isBlank(osbDetail) && StringUtils.isBlank(citationDetail))
 757                                         || (osbDetail != null && osbDetail.equalsIgnoreCase(citationDetail)) ) {
 758 //                                  System.out.println("REFERENCE FOUND RETURN EXISTING SOURCE");
 759                                     return (IdentifiableSource) osb.clone();
 760                                 }
 761                             }
 762                         }
 763                     } catch (CloneNotSupportedException e) {
 764                         throw new RuntimeException(e);
 765                     } catch (Exception e1){
 766                         e1.printStackTrace();
 767                     }
 768                 }
 769         */
 770                 IdentifiableSource sour = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
 771                 return sour;
 772             }
 773
 774             /**
 775              * Add the hierarchy for a Taxon(add higher taxa)
 776              * @param classification
 777              * @param taxon: a taxon to add as a node
 778              * @param state: the ABCD import state
 779              */
 780             protected void addParentTaxon(Taxon taxon, STATE state, boolean preferredFlag, Classification classification){
 781                 INonViralName  nvname = taxon.getName();
 782                 Rank rank = nvname.getRank();
 783                 Taxon genus =null;
 784                 Taxon subgenus =null;
 785                 Taxon species = null;
 786                 Taxon subspecies = null;
 787                 Taxon parent = null;
 788                 if(rank!=null){
 789                     if (rank.isLower(Rank.GENUS() )){
 790                         String genusOrUninomial = nvname.getGenusOrUninomial();
 791                         TaxonName taxonName = getOrCreateTaxonName(genusOrUninomial, Rank.GENUS(), preferredFlag, state, -1);
 792                         genus = getOrCreateTaxonForName(taxonName, state);
 793                         if (genus == null){
 794                             logger.debug("The genus should not be null " + taxonName);
 795                         }
 796                         if (preferredFlag) {
 797                             parent = linkParentChildNode(null, genus, classification, state);
 798                         }
 799
 800                     }
 801                     if (rank.isLower(Rank.SUBGENUS())){
 802                         String prefix = nvname.getGenusOrUninomial();
 803                         String name = nvname.getInfraGenericEpithet();
 804                         if (name != null){
 805                             TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SUBGENUS(), preferredFlag, state, -1);
 806                             subgenus = getOrCreateTaxonForName(taxonName, state);
 807                             if (preferredFlag) {
 808                                 parent = linkParentChildNode(genus, subgenus, classification, state);
 809                             }            }
 810                     }
 811                     if (rank.isLower(Rank.SPECIES())){
 812                         if (subgenus!=null){
 813                             String prefix = nvname.getGenusOrUninomial();
 814                             String name = nvname.getInfraGenericEpithet();
 815                             String spe = nvname.getSpecificEpithet();
 816                             if (spe != null){
 817                                 TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name+" "+spe, Rank.SPECIES(), preferredFlag, state, -1);
 818                                 species = getOrCreateTaxonForName(taxonName, state);
 819                                 if (preferredFlag) {
 820                                     parent = linkParentChildNode(subgenus, species, classification, state);
 821                                 }
 822                             }
 823                         }
 824                         else{
 825                             String prefix = nvname.getGenusOrUninomial();
 826                             String name = nvname.getSpecificEpithet();
 827                             if (name != null){
 828                                 TaxonName taxonName = getOrCreateTaxonName(prefix+" "+name, Rank.SPECIES(), preferredFlag, state, -1);
 829                                 species = getOrCreateTaxonForName(taxonName, state);
 830                                 if (preferredFlag) {
 831                                     parent = linkParentChildNode(genus, species, classification, state);
 832                                 }
 833                             }
 834                         }
 835                     }
 836                     if (rank.isLower(Rank.INFRASPECIES())){
 837                         TaxonName taxonName = getOrCreateTaxonName(nvname.getFullTitleCache(), Rank.SUBSPECIES(), preferredFlag, state, -1);
 838                         subspecies = getOrCreateTaxonForName(taxonName, state);
 839                         if (preferredFlag) {
 840                             parent = linkParentChildNode(species, subspecies, classification, state);
 841                         }
 842                     }
 843                 }
 844                 if (preferredFlag && parent!=taxon ) {
 845                     linkParentChildNode(parent, taxon, classification, state);
 846                 }
 847             }
 848
 849             /**
 850              * Link a parent to a child and save it in the current classification
 851              * @param parent: the higher Taxon
 852              * @param child : the lower (or current) Taxon
 853              * return the Taxon from the new created Node
 854              * @param classification
 855              * @param state
 856              */
 857             protected Taxon linkParentChildNode(Taxon parent, Taxon child, Classification classification, STATE state) {
 858                 TaxonNode node =null;
 859                 if (parent != null) {
 860                     parent = (Taxon) getTaxonService().find(parent.getUuid());
 861                     child = (Taxon) getTaxonService().find(child.getUuid());
 862                     //here we do not have to check if the taxon nodes already exists
 863                     //this is done by classification.addParentChild()
 864                     //do not add child node if it already exists
 865                     if(hasTaxonNodeInClassification(child, classification)){
 866                         return child;
 867                     }
 868                     else{
 869                         node = classification.addParentChild(parent, child, state.getRef(), "");
 870                         save(node, state);
 871                     }
 872                 }
 873                 else {
 874                     if (child == null){
 875                         logger.debug("The child should not be null!");
 876                     }
 877                     child = (Taxon) getTaxonService().find(child.getUuid());
 878                     //do not add child node if it already exists
 879                     if(hasTaxonNodeInClassification(child, classification)){
 880                         return child;
 881                     }
 882                     else{
 883                         node = classification.addChildTaxon(child, state.getRef(), null);
 884                         save(node, state);
 885                     }
 886                 }
 887                 if(node!=null){
 888                     state.getReport().addTaxonNode(node);
 889                     return node.getTaxon();
 890                 }
 891                 String message = "Could not create taxon node for " +child;
 892                 state.getReport().addInfoMessage(message);
 893                 logger.warn(message);
 894                 return null;
 895             }
 896
 897             protected Taxon getOrCreateTaxonForName(TaxonName taxonName, STATE state){
 898                 if (taxonName != null){
 899                 Set<Taxon> acceptedTaxa = taxonName.getTaxa();
 900                 if(acceptedTaxa.size()>0){
 901                     Taxon firstAcceptedTaxon = acceptedTaxa.iterator().next();
 902                     if(acceptedTaxa.size()>1){
 903                         String message = "More than one accepted taxon was found for taxon name: "
 904                                 + taxonName.getTitleCache() + "!\n" + firstAcceptedTaxon + "was chosen for "+state.getDerivedUnitBase();
 905                         state.getReport().addInfoMessage(message);
 906                         logger.warn(message);
 907                     }
 908                     else{
 909                         return firstAcceptedTaxon;
 910                     }
 911                 }
 912                 else{
 913                     Set<TaxonBase> taxonAndSynonyms = taxonName.getTaxonBases();
 914                     for (TaxonBase taxonBase : taxonAndSynonyms) {
 915                         if(taxonBase.isInstanceOf(Synonym.class)){
 916                             Synonym synonym = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
 917                             Taxon acceptedTaxonOfSynonym = synonym.getAcceptedTaxon();
 918                             if(acceptedTaxonOfSynonym == null){
 919                                 String message = "No accepted taxon could be found for taxon name: "
 920                                         + taxonName.getTitleCache()
 921                                         + "!";
 922                                 state.getReport().addInfoMessage(message);
 923                                 logger.warn(message);
 924                             }
 925                             else{
 926                                 return acceptedTaxonOfSynonym;
 927                             }
 928                         }
 929                     }
 930                 }
 931                 Taxon taxon = Taxon.NewInstance(taxonName, state.getRef());
 932                 save(taxon, state);
 933                 state.getReport().addTaxon(taxon);
 934                 logger.info("Created new taxon "+ taxon);
 935                 return taxon;
 936                 }
 937                 return null;
 938
 939             }
 940
 941             private boolean hasTaxonNodeInClassification(Taxon taxon, Classification classification){
 942                 if(taxon.getTaxonNodes()!=null){
 943                     for (TaxonNode node : taxon.getTaxonNodes()){
 944                         if(node.getClassification().equals(classification)){
 945                             return true;
 946                         }
 947                     }
 948                 }
 949                 return false;
 950             }
 951
 952             /**
 953              * HandleIdentifications : get the scientific names present in the ABCD
 954              * document and store link them with the observation/specimen data
 955              * @param state: the current ABCD import state
 956              * @param derivedUnitFacade : the current derivedunitfacade
 957              */
 958             protected void handleIdentifications(STATE state, DerivedUnitFacade derivedUnitFacade) {
 959                SpecimenImportConfiguratorBase config = state.getConfig();
 960
 961
 962                 String scientificName = "";
 963                 boolean preferredFlag = false;
 964
 965                 if (state.getDataHolder().getNomenclatureCode() == ""){
 966                     if (config.getNomenclaturalCode() != null){
 967                         if (config.getNomenclaturalCode() != null){
 968                             state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().toString());
 969
 970                         }
 971                     }
 972                 }
 973
 974                 for (int i = 0; i < state.getDataHolder().getIdentificationList().size(); i++) {
 975                     Identification identification = state.getDataHolder().getIdentificationList().get(i);
 976                     scientificName = identification.getScientificName().replaceAll(" et ", " & ");
 977
 978                     String preferred = identification.getPreferred();
 979                     preferredFlag = false;
 980                     if (preferred != null){
 981                     if (preferred.equals("1") || preferred.toLowerCase().indexOf("true") != -1 || state.getDataHolder().getIdentificationList().size()==1) {
 982                         preferredFlag = true;
 983                     }
 984
 985                     }
 986                     if (identification.getCode() != null){
 987                     if (identification.getCode().indexOf(':') != -1) {
 988                         state.getDataHolder().setNomenclatureCode(identification.getCode().split(COLON)[1]);
 989                     }
 990                     else{
 991                         state.getDataHolder().setNomenclatureCode(identification.getCode());
 992                     }
 993                     }
 994                     TaxonName taxonName = getOrCreateTaxonName(scientificName, null, preferredFlag, state, i);
 995                     Taxon taxon = getOrCreateTaxonForName(taxonName, state);
 996                     addTaxonNode(taxon, state,preferredFlag);
 997                     linkDeterminationEvent(state, taxon, preferredFlag, derivedUnitFacade, identification.getIdentifier(), identification.getDate());
 998                 }
 999             }
1000
1001             /**
1002              * @param taxon : a taxon to add as a node
1003              * @param state : the ABCD import state
1004              */
1005             protected void addTaxonNode(Taxon taxon, STATE state, boolean preferredFlag) {
1006                 SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
1007                 logger.info("link taxon to a taxonNode "+taxon.getTitleCache());
1008                 //only add nodes if not already existing in current classification or default classification
1009
1010                 //check if node exists in current classification
1011                 //NOTE: we cannot use hasTaxonNodeInClassification() here because we are first creating it here
1012                 if (!existsInClassification(taxon,state.getClassification(), state)){
1013                     if(config.isMoveNewTaxaToDefaultClassification()){
1014                         //check if node exists in default classification
1015                         if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
1016                             addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
1017                         }
1018                     }else{
1019                         //add non-existing taxon to current classification
1020                         addParentTaxon(taxon, state, preferredFlag, state.getClassification());
1021                     }
1022
1023                 }
1024             }
1025
1026
1027             private boolean existsInClassification(Taxon taxon, Classification classification, STATE state){
1028                 boolean exist = false;
1029                 ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
1030             if(cdmAppController==null){
1031                 cdmAppController = this;
1032             }
1033             if (classification != null){
1034                 if (!taxon.getTaxonNodes().isEmpty()){
1035                     for (TaxonNode node:taxon.getTaxonNodes()){
1036                         if (node.getClassification().equals(classification)){
1037                             return true;
1038                         }
1039                     }
1040                 }
1041 // we do not need this because we already searched for taxa in db in the previous steps
1042 //              List<UuidAndTitleCache<TaxonNode>> uuidAndTitleCacheOfAllTaxa = cdmAppController.getClassificationService().getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification.getUuid());
1043 //              if (uuidAndTitleCacheOfAllTaxa != null){
1044 //                      for (UuidAndTitleCache p : uuidAndTitleCacheOfAllTaxa){
1045 //                          try{
1046 //                              if(p.getTitleCache().equals(taxon.getTitleCache())) {
1047 //                                  exist = true;
1048 //                              }
1049 //                          }
1050 //                          catch(Exception e){
1051 //                              logger.warn("TaxonNode doesn't seem to have a taxon");
1052 //                          }
1053 //                      }
1054 //              }
1055             }
1056                 return exist;
1057             }
1058
1059             /**
1060              * join DeterminationEvent to the Taxon Object
1061              * @param state : the ABCD import state
1062              * @param taxon: the current Taxon
1063              * @param preferredFlag :if the current name is preferred
1064              * @param derivedFacade : the derived Unit Facade
1065              */
1066             @SuppressWarnings("rawtypes")
1067         protected void linkDeterminationEvent(STATE state, Taxon taxon, boolean preferredFlag,  DerivedUnitFacade derivedFacade, String identifierStr, String dateStr) {
1068                 SpecimenImportConfiguratorBase config = state.getConfig();
1069                 if (logger.isDebugEnabled()){
1070                     logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
1071                 }
1072
1073                 DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
1074                 determinationEvent.setTaxonName(taxon.getName());
1075                 determinationEvent.setPreferredFlag(preferredFlag);
1076
1077
1078                 determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
1079                 if (state.getPersonStore().get(identifierStr) != null){
1080                     determinationEvent.setActor((AgentBase)state.getPersonStore().get(identifierStr));
1081                 } else if (identifierStr != null){
1082                     Person identifier = Person.NewTitledInstance(identifierStr);
1083                     determinationEvent.setActor(identifier);
1084                 }
1085                 if (dateStr != null){
1086                     determinationEvent.setTimeperiod(TimePeriodParser.parseString(dateStr));
1087                 }
1088                 state.getDerivedUnitBase().addDetermination(determinationEvent);
1089
1090                 if (logger.isDebugEnabled()){
1091                     logger.debug("NB TYPES INFO: "+ state.getDataHolder().getStatusList().size());
1092                 }
1093                 for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().getStatusList()) {
1094                     if (specimenTypeDesignationstatus != null) {
1095                         if (logger.isDebugEnabled()){
1096                             logger.debug("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
1097                         }
1098
1099                         ICdmRepository cdmAppController = config.getCdmAppController();
1100                         if(cdmAppController == null){
1101                             cdmAppController = this;
1102                         }
1103                         specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid());
1104                         //Designation
1105                         TaxonName name = taxon.getName();
1106                         SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
1107
1108                         designation.setTypeStatus(specimenTypeDesignationstatus);
1109                         designation.setTypeSpecimen(state.getDerivedUnitBase());
1110                         name.addTypeDesignation(designation, true);
1111                     }
1112                 }
1113
1114                 for (String[] fullReference : state.getDataHolder().getReferenceList()) {
1115
1116
1117                     String strReference=fullReference[0];
1118                     String citationDetail = fullReference[1];
1119                     String citationURL = fullReference[2];
1120                     List<Reference> references = getReferenceService().listByTitle(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
1121
1122                     if (!references.isEmpty()){
1123                         Reference reference = null;
1124                         for (Reference refe: references) {
1125                             if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
1126                                 reference =refe;
1127                                 break;
1128                             }
1129                         }
1130                         if (reference ==null){
1131                             reference = ReferenceFactory.newGeneric();
1132                             reference.setTitleCache(strReference, true);
1133                             save(reference, state);
1134                         }
1135                         determinationEvent.addReference(reference);
1136                     }
1137                 }
1138                 save(state.getDerivedUnitBase(), state);
1139
1140                 if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
1141                     //do not add IndividualsAssociation to non-preferred taxa
1142                     if (logger.isDebugEnabled()){
1143                         logger.debug("isDoCreateIndividualsAssociations");
1144                     }
1145
1146                     makeIndividualsAssociation(state, taxon, determinationEvent);
1147
1148                     save(state.getDerivedUnitBase(), state);
1149                 }
1150             }
1151
1152             /**
1153              * create and link each association (specimen, observation..) to the accepted taxon
1154              * @param state : the ABCD import state
1155              * @param taxon: the current Taxon
1156              * @param determinationEvent:the determinationevent
1157              */
1158             protected void makeIndividualsAssociation(STATE state, Taxon taxon, DeterminationEvent determinationEvent) {
1159                 SpecimenImportConfiguratorBase<?,?,?> config = state.getConfig();
1160                 SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
1161
1162                 if (logger.isDebugEnabled()){
1163                     logger.info("MAKE INDIVIDUALS ASSOCIATION");
1164                 }
1165
1166                 TaxonDescription taxonDescription = null;
1167                 Set<TaxonDescription> descriptions= taxon.getDescriptions();
1168                if (!descriptions.isEmpty()){ taxonDescription = descriptions.iterator().next();}
1169
1170 //                  for (TaxonDescription description : descriptions){
1171 //                      Set<IdentifiableSource> sources =  new HashSet<>();
1172 //                      sources.addAll(description.getTaxon().getSources());
1173 //                      sources.addAll(description.getSources());
1174 //                      for (IdentifiableSource source:sources){
1175 //                          if(state.getRef().equals(source.getCitation())) {
1176 //                              taxonDescription = description;
1177 //                          }
1178 //                      }
1179 //                  }
1180               //  }
1181                 if (taxonDescription == null){
1182                     taxonDescription = TaxonDescription.NewInstance(taxon, false);
1183                     if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
1184                         taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
1185                     }
1186                     state.setDescriptionGroup(taxonDescription);
1187                     taxon.addDescription(taxonDescription);
1188                 }
1189
1190                 //PREPARE REFERENCE QUESTIONS
1191
1192                 Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
1193
1194                 List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
1195                 List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
1196
1197                 Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
1198                 if(issTmp2!=null) {
1199                     osbSet.addAll(issTmp2);
1200                 }
1201                 if(issTmp!=null) {
1202                     osbSet.addAll(issTmp);
1203                 }
1204
1205
1206                 addToSourceMap(sourceMap, osbSet);
1207
1208 //              if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
1209 //                  List<OriginalSourceBase<?>> res = null;
1210 //                  if(!state.isDescriptionSourcesSet()){
1211 //                      res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
1212 //                              "The current reference is "+state.getRef().getTitleCache(),getReferenceService(), state.getDataHolder().docSources);
1213 //                      state.setDescriptionRefs(res);
1214 //                      state.setDescriptionSourcesSet(true);
1215 //                  }
1216 //                  else{
1217 //                      res=state.getDescriptionRefs();
1218 //                  }
1219 //                  if(res !=null) {
1220 //                      for (OriginalSourceBase<?> sour:res){
1221 //                          if(sour.isInstanceOf(IdentifiableSource.class)){
1222 //                              try {
1223 //                                  if(sourceNotLinkedToElement(taxonDescription,sour)) {
1224 //                                      taxonDescription.addSource((IdentifiableSource)sour.clone());
1225 //                                  }
1226 //                              } catch (CloneNotSupportedException e) {
1227 //                                  logger.warn("no cloning?");
1228 //                              }
1229 //                          }else{
1230 //                              if(sourceNotLinkedToElement(taxonDescription,sour)) {
1231 //                                  taxonDescription.addSource(OriginalSourceType.Import,null, null, sour.getCitation(),sour.getCitationMicroReference());
1232 //                              }
1233 //                          }
1234 //                      }
1235 //                  }
1236 //              }
1237 //              else {
1238                     if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
1239                         taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
1240                     }
1241 //              }
1242                 state.setDescriptionGroup(taxonDescription);
1243
1244                 IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
1245                 Feature feature = makeFeature(state.getDerivedUnitBase());
1246                 indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
1247                 indAssociation.setFeature(feature);
1248 //
1249 //              if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
1250 //                  sourceMap = new HashMap<String, OriginalSourceBase<?>>();
1251 //
1252 //                  issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
1253 //                  issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
1254 //
1255 //                  osbSet = new HashSet<OriginalSourceBase>();
1256 //                  if(issTmp2!=null) {
1257 //                      osbSet.addAll(issTmp2);
1258 //                  }
1259 //                  if(issTmp!=null) {
1260 //                      osbSet.addAll(issTmp);
1261 //                  }
1262 //
1263 //
1264 //                  addToSourceMap(sourceMap, osbSet);
1265 //
1266 //                  List<OriginalSourceBase<?>> sources =null;
1267 //                  if(!state.isAssociationSourcesSet()) {
1268 //                      sources = sui.askForSource(sourceMap,  "descriptive element (association) ",taxon.toString(),
1269 //                              getReferenceService(),state.getDataHolder().getDocSources());
1270 //                      state.setAssociationRefs(sources);
1271 //                      state.setAssociationSourcesSet(true);
1272 //                  }
1273 //                  else{
1274 //                      sources=state.getAssociationRefs();
1275 //                  }
1276 //                  if(sources !=null) {
1277 //                      for (OriginalSourceBase<?> source: sources) {
1278 //                          if(source !=null) {
1279 //                              if(source.isInstanceOf(DescriptionElementSource.class)){
1280 //                                  try {
1281 //                                      if(sourceNotLinkedToElement(indAssociation,source)) {
1282 //                                          indAssociation.addSource((DescriptionElementSource)source.clone());
1283 //                                      }
1284 //                                  } catch (CloneNotSupportedException e) {
1285 //                                      logger.warn("clone forbidden?");
1286 //                                  }
1287 //                              }else{
1288 //                                  if(sourceNotLinkedToElement(indAssociation,source)) {
1289 //                                      indAssociation.addSource(OriginalSourceType.Import,null, null, source.getCitation(),source.getCitationMicroReference());
1290 //                                  }
1291 //                                  try {
1292 //                                      if(sourceNotLinkedToElement(state.getDerivedUnitBase(), source)) {
1293 //                                          state.getDerivedUnitBase().addSource((IdentifiableSource) source.clone());
1294 //                                      }
1295 //                                  } catch (CloneNotSupportedException e) {
1296 //                                      // TODO Auto-generated catch block
1297 //                                      e.printStackTrace();
1298 //                                  }
1299 //                              }
1300 //
1301 //                          }
1302 //                      }
1303 //                  }
1304 //              }else {
1305                     if(sourceNotLinkedToElement(indAssociation,state.getRef(),null)) {
1306                         indAssociation.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
1307                     }
1308                     if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
1309                         state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
1310                     }
1311                     for (Reference citation : determinationEvent.getReferences()) {
1312                         if(sourceNotLinkedToElement(indAssociation,citation,null))
1313                         {
1314                             indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
1315                         }
1316                         if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
1317                             state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
1318                         }
1319                     }
1320            //     }
1321
1322                 taxonDescription.addElement(indAssociation);
1323
1324                 save(taxonDescription, state);
1325                 save(taxon, state);
1326                 state.getReport().addDerivate(state.getDerivedUnitBase(), config);
1327                 state.getReport().addIndividualAssociation(taxon, state.getDataHolder().getUnitID(), state.getDerivedUnitBase());
1328             }
1329
1330             /**
1331              * @param derivedUnitBase2
1332              * @param ref2
1333              * @param object
1334              * @return
1335              */
1336             private boolean sourceNotLinkedToElement(DerivedUnit derivedUnitBase2, Reference b, String d) {
1337                 Set<IdentifiableSource> linkedSources = derivedUnitBase2.getSources();
1338                 for (IdentifiableSource is:linkedSources){
1339                     Reference a = is.getCitation();
1340                     String c = is.getCitationMicroReference();
1341
1342                     boolean refMatch=false;
1343                     boolean microMatch=false;
1344
1345                     try{
1346                         if (a==null && b==null) {
1347                             refMatch=true;
1348                         }
1349                         if (a!=null && b!=null) {
1350                             if (a.getTitleCache().equalsIgnoreCase(b.getTitleCache())) {
1351                                 refMatch=true;
1352                             }
1353                         }
1354                     }catch(Exception e){}
1355
1356
1357                     try{
1358                         if (c==null && d==null) {
1359                             microMatch=true;
1360                         }
1361                         if(c!=null && d!=null) {
1362                             if(c.equalsIgnoreCase(d)) {
1363                                 microMatch=true;
1364                             }
1365                         }
1366                     }
1367                     catch(Exception e){}
1368
1369                     if (microMatch && refMatch) {
1370                         return false;
1371                     }
1372
1373
1374                 }
1375                 return true;
1376             }
1377
1378             private <T extends OriginalSourceBase<?>> boolean  sourceNotLinkedToElement(ISourceable<T> sourcable, Reference reference, String microReference) {
1379                 Set<T> linkedSources = sourcable.getSources();
1380                 for (T is:linkedSources){
1381                     Reference unitReference = is.getCitation();
1382                     String unitMicroReference = is.getCitationMicroReference();
1383
1384                     boolean refMatch=false;
1385                     boolean microMatch=false;
1386
1387                     try{
1388                         if (unitReference==null && reference==null) {
1389                             refMatch=true;
1390                         }
1391                         if (unitReference!=null && reference!=null) {
1392                             if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
1393                                 refMatch=true;
1394                             }
1395                         }
1396                     }catch(Exception e){}
1397
1398                     try{
1399                         if (unitMicroReference==null && microReference==null) {
1400                             microMatch=true;
1401                         }
1402                         if(unitMicroReference!=null && microReference!=null) {
1403                             if(unitMicroReference.equalsIgnoreCase(microReference)) {
1404                                 microMatch=true;
1405                             }
1406                         }
1407                     }
1408                     catch(Exception e){}
1409
1410                     if (microMatch && refMatch) {
1411                         return false;
1412                     }
1413                 }
1414                 return true;
1415             }
1416
1417             /**
1418              * look for the Feature object (FieldObs, Specimen,...)
1419              * @param unit : a specimen or obersvation base
1420              * @return the corresponding Feature
1421              */
1422             private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
1423                 SpecimenOrObservationType type = unit.getRecordBasis();
1424
1425
1426
1427                 if (type.isFeatureObservation()){
1428                     return Feature.OBSERVATION();
1429                 }else if (type.isFeatureSpecimen()){
1430                     return Feature.SPECIMEN();
1431                 }else if (type == SpecimenOrObservationType.DerivedUnit){
1432                     return Feature.OBSERVATION();
1433                     //            return getFeature("Specimen or observation");
1434                 }else{
1435                     String message = "Unhandled record basis '%s' for defining individuals association feature type. Use default.";
1436                     logger.warn(String.format(message, type.getMessage()));
1437                     return Feature.OBSERVATION();
1438                     //            return getFeature("Specimen or observation");
1439
1440                 }
1441             }
1442
1443
1444             /**
1445              * @param sourceMap
1446              * @param osbSet
1447              */
1448             protected void addToSourceMap(Map<String, OriginalSourceBase<?>> sourceMap, Set<OriginalSourceBase> osbSet) {
1449                 for( OriginalSourceBase<?> osb:osbSet) {
1450                     if(osb.getCitation()!=null && osb.getCitationMicroReference() !=null  && !osb.getCitationMicroReference().isEmpty()) {
1451                         try{
1452                             sourceMap.put(osb.getCitation().getTitleCache()+ "---"+osb.getCitationMicroReference(),osb);
1453                         }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
1454                     } else if(osb.getCitation()!=null){
1455                         try{
1456                             sourceMap.put(osb.getCitation().getTitleCache(),osb);
1457                         }catch(NullPointerException e){logger.warn("null pointer problem (no ref?) with "+osb);}
1458                     }
1459                 }
1460             }
1461
1462
1463 }