cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java

   1 /**
   2 * Copyright (C) 2017 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 package eu.etaxonomy.cdm.io.cdmLight;
  10
  11 import java.io.File;
  12 import java.util.ArrayList;
  13 import java.util.Collections;
  14 import java.util.Comparator;
  15 import java.util.HashSet;
  16 import java.util.Iterator;
  17 import java.util.List;
  18 import java.util.Map;
  19 import java.util.Map.Entry;
  20 import java.util.Set;
  21
  22 import org.apache.commons.lang3.StringUtils;
  23 import org.springframework.stereotype.Component;
  24
  25 import eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager;
  26 import eu.etaxonomy.cdm.common.CdmUtils;
  27 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  28 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  29 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  30 import eu.etaxonomy.cdm.io.common.CdmExportBase;
  31 import eu.etaxonomy.cdm.io.common.ExportResult.ExportResultState;
  32 import eu.etaxonomy.cdm.io.common.ICdmExport;
  33 import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
  34 import eu.etaxonomy.cdm.io.common.XmlExportState;
  35 import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
  36 import eu.etaxonomy.cdm.model.agent.AgentBase;
  37 import eu.etaxonomy.cdm.model.agent.Person;
  38 import eu.etaxonomy.cdm.model.agent.Team;
  39 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  40 import eu.etaxonomy.cdm.model.common.Annotation;
  41 import eu.etaxonomy.cdm.model.common.AnnotationType;
  42 import eu.etaxonomy.cdm.model.common.CdmBase;
  43 import eu.etaxonomy.cdm.model.common.ICdmBase;
  44 import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;
  45 import eu.etaxonomy.cdm.model.common.Language;
  46 import eu.etaxonomy.cdm.model.common.LanguageString;
  47 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  48 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  49 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  50 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  51 import eu.etaxonomy.cdm.model.description.Distribution;
  52 import eu.etaxonomy.cdm.model.description.Feature;
  53 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  54 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  55 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  56 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  57 import eu.etaxonomy.cdm.model.description.TextData;
  58 import eu.etaxonomy.cdm.model.location.NamedArea;
  59 import eu.etaxonomy.cdm.model.media.Media;
  60 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  61 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  62 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  63 import eu.etaxonomy.cdm.model.name.HomotypicalGroupNameComparator;
  64 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  65 import eu.etaxonomy.cdm.model.name.Rank;
  66 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  67 import eu.etaxonomy.cdm.model.name.TaxonName;
  68 import eu.etaxonomy.cdm.model.name.TypeComparator;
  69 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  70 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  71 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  72 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  73 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  74 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  75 import eu.etaxonomy.cdm.model.reference.Reference;
  76 import eu.etaxonomy.cdm.model.reference.ReferenceType;
  77 import eu.etaxonomy.cdm.model.taxon.Synonym;
  78 import eu.etaxonomy.cdm.model.taxon.Taxon;
  79 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  80 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  81 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  82 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  83 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
  84 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDtoByRankAndNameComparator;
  85 import eu.etaxonomy.cdm.strategy.cache.TagEnum;
  86 import eu.etaxonomy.cdm.strategy.cache.TaggedText;
  87 import eu.etaxonomy.cdm.strategy.cache.reference.DefaultReferenceCacheStrategy;
  88 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  89
  90 /**
  91  * @author k.luther
  92  * @since 15.03.2017
  93  */
  94 @Component
  95 public class CdmLightClassificationExport
  96             extends CdmExportBase<CdmLightExportConfigurator, CdmLightExportState, IExportTransformer, File>
  97             implements ICdmExport<CdmLightExportConfigurator, CdmLightExportState>{
  98
  99
 100     private static final long serialVersionUID = 2518643632756927053L;
 101     private static final String STD_TEAM_CONCATINATION = ", ";
 102     private static final String FINAL_TEAM_CONCATINATION = " & ";
 103
 104
 105     private static final String IPNI_NAME_IDENTIFIER = "Ipni Name Identifier";
 106     private static final String TROPICOS_NAME_IDENTIFIER = "Tropicos Name Identifier";
 107     private static final String WFO_NAME_IDENTIFIER = "WFO Name Identifier";
 108
 109     public CdmLightClassificationExport() {
 110         super();
 111         this.ioName = this.getClass().getSimpleName();
 112
 113     }
 114
 115     @Override
 116     public long countSteps(CdmLightExportState state) {
 117         TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
 118         return taxonNodeService.count(filter);
 119     }
 120
 121
 122     /**
 123      * {@inheritDoc}
 124      */
 125     @Override
 126     protected void doInvoke(CdmLightExportState state) {
 127         try {
 128
 129             IProgressMonitor monitor = state.getConfig().getProgressMonitor();
 130             CdmLightExportConfigurator config = state.getConfig();
 131             config.setFieldsTerminatedBy(",");
 132
 133 //            if (config.getTaxonNodeFilter().getTaxonNodesFilter().isEmpty() && config.getTaxonNodeFilter().getClassificationFilter().isEmpty()){
 134 //                //TODO
 135 //                state.setEmptyData();
 136 //                return;
 137 //            }
 138
 139
 140
 141 //            for (LogicFilter<Classification> classificationFilter : config.getTaxonNodeFilter().getClassificationFilter()){
 142 //                UUID classificationUuid = classificationFilter.getUuid();
 143 //                Classification classification = getClassificationService().find(classificationUuid);
 144 //                if (classification == null){
 145 //                    String message = String.format("Classification for given classification UUID not found. No data imported for %s", classificationUuid.toString());
 146 //                    state.getResult().addWarning(message);
 147 //                }else{
 148 //                    TaxonNode root = classification.getRootNode();
 149 //                    UUID uuid = root.getUuid();
 150 //                    root = getTaxonNodeService().load(uuid);
 151 //                    handleSingleClassification(state, root.getUuid());
 152 //                }
 153 //            }
 154
 155
 156             @SuppressWarnings("unchecked")
 157             TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
 158                   = TaxonNodeOutStreamPartitioner.NewInstance(
 159                           this, state, state.getConfig().getTaxonNodeFilter(),
 160                           100, monitor, null);
 161
 162
 163                 monitor.subTask("Start partitioning");
 164
 165                 TaxonNode node = partitioner.next();
 166                 while (node != null){
 167                     handleTaxonNode(state, node);
 168                     node = partitioner.next();
 169                 }
 170               //create sortIndex for nodes
 171                 for(Entry<Integer, List<TaxonNodeDto>> entry :state.getNodeChildrenMap().entrySet()){
 172                     List<TaxonNodeDto> children = entry.getValue();
 173                     Comparator<TaxonNodeDto> comp = state.getConfig().getComparator();
 174                     if (comp == null){
 175                         comp = new TaxonNodeDtoByRankAndNameComparator();
 176                     }
 177                     Collections.sort(children, comp);
 178                     int index = 0;
 179                     for (TaxonNodeDto child:children) {
 180                         if (state.getProcessor().hasRecord(CdmLightExportTable.TAXON, child.getTaxonUuid().toString())){
 181                             String[] csvLine = state.getProcessor().getRecord(CdmLightExportTable.TAXON,child.getTaxonUuid().toString());
 182                             csvLine[CdmLightExportTable.TAXON.getIndex(CdmLightExportTable.SORT_INDEX)] =  String.valueOf(index);
 183                             index++;
 184                         }
 185
 186                     }
 187                }
 188
 189
 190 //            for (LogicFilter<TaxonNode> taxonNodeFilter : config.getTaxonNodeFilter().getTaxonNodesFilter()){
 191 //                UUID nodeUuid = taxonNodeFilter.getUuid();
 192 //                handleSingleClassification(state, nodeUuid);
 193 //            }
 194             state.getProcessor().createFinalResult(state);
 195         } catch (Exception e) {
 196             state.getResult().addException(e, "An unexpected error occurred in main method doInvoke() " +
 197                     e.getMessage());
 198         }
 199     }
 200
 201     /**
 202      * @param state
 203      * @param classificationUuid
 204      */
 205     private void handleTaxonNode(CdmLightExportState state, TaxonNode taxonNode) {
 206
 207             if (taxonNode == null){
 208                 String message = "TaxonNode for given taxon node UUID not found. ";
 209                 //TODO
 210                 state.getResult().addWarning(message);
 211             }else{
 212                 try {
 213                     TaxonNode root = taxonNode;
 214                     List<TaxonNodeDto> childNodes;
 215                     if (root.hasChildNodes()){
 216                         childNodes = new ArrayList();
 217                         for (TaxonNode child: root.getChildNodes()){
 218                             childNodes.add(new TaxonNodeDto(child));
 219                         }
 220                         state.getNodeChildrenMap().put(root.getId(),childNodes);
 221                     }
 222                     if (root.hasTaxon()){
 223                         handleTaxon(state, root);
 224
 225                     }
 226                 } catch (Exception e) {
 227                     state.getResult().addException(e, "An unexpected error occurred when handling classification " +
 228                             taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace());
 229                 }
 230             }
 231     }
 232
 233     /**
 234      * @param state
 235      * @param taxon
 236      */
 237     private void handleTaxon(CdmLightExportState state, TaxonNode taxonNode) {
 238         try{
 239       //  Taxon taxon = taxonNode.getTaxon();
 240         if (taxonNode == null){
 241             state.getResult().addError ("The taxonNode was null.", "handleTaxon");
 242             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 243             return;
 244         }
 245         if (taxonNode.getTaxon() == null){
 246             state.getResult().addError ("There was a taxon node without a taxon: " + taxonNode.getUuid(), "handleTaxon");
 247             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 248         }else{
 249             Taxon taxon = HibernateProxyHelper.deproxy(taxonNode.getTaxon(), Taxon.class);
 250
 251              try{
 252                 TaxonName name = taxon.getName();
 253                 handleName(state, name);
 254                 for (Synonym syn : taxon.getSynonyms()){
 255                     handleSynonym(state, syn);
 256                 }
 257                 for (TaxonRelationship rel : taxon.getProParteAndPartialSynonymRelations()){
 258                     handleProPartePartialMisapplied(state, rel);
 259                 }
 260                 for (TaxonRelationship rel : taxon.getMisappliedNameRelations()){
 261                     handleProPartePartialMisapplied(state, rel);
 262                 }
 263
 264                 CdmLightExportTable table = CdmLightExportTable.TAXON;
 265                 String[] csvLine = new String[table.getSize()];
 266
 267                 csvLine[table.getIndex(CdmLightExportTable.TAXON_ID)] = getId(state, taxon);
 268                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 269                 Taxon parent = (taxonNode.getParent()==null) ? null : taxonNode.getParent().getTaxon();
 270                 csvLine[table.getIndex(CdmLightExportTable.PARENT_FK)] = getId(state, parent);
 271                 csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
 272                 if (taxon.getSec()!= null && taxon.getSec().getDatePublished() != null && taxon.getSec().getDatePublished().getFreeText() != null){
 273                     String sec_string = taxon.getSec().getTitleCache() + ". " + taxon.getSec().getDatePublished().getFreeText();
 274                     sec_string = sec_string.replace("..", ".");
 275                     csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = sec_string;
 276                 }else{
 277                     csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(taxon.getSec());
 278                 }
 279                 if (taxon.getSec() != null){
 280                     if (state.getReferenceFromStore(taxon.getSec().getId()) == null){
 281                         handleReference(state, taxon.getSec());
 282                     }
 283                 }
 284                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_ID)] = getId(state, taxonNode.getClassification());
 285                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification().getTitleCache();
 286
 287                 state.getProcessor().put(table, taxon, csvLine);
 288                 handleDescriptions(state, taxon);
 289              }catch(Exception e){
 290                  state.getResult().addException (e, "An unexpected problem occurred when trying to export "
 291                          + "taxon with id " + taxon.getId());
 292                  state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 293              }
 294        }
 295
 296        taxonNode.removeNullValueFromChildren();
 297 //       for (TaxonNode child: taxonNode.getChildNodes()){
 298 //           handleTaxon(state, child);
 299 //       }
 300         }catch (Exception e){
 301             state.getResult().addException(e, "An unexpected error occurred when handling the taxon node of " +
 302                     cdmBaseStr(taxonNode.getTaxon()) + ": " + e.getMessage());
 303         }
 304     }
 305
 306
 307     /**
 308      * @param state
 309      * @param taxon
 310      */
 311     private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
 312         try{
 313         if (cdmBase instanceof Taxon){
 314             Taxon taxon = HibernateProxyHelper.deproxy(cdmBase, Taxon.class);
 315             Set<TaxonDescription> descriptions = taxon.getDescriptions();
 316             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 317             List<DescriptionElementBase> specimenFacts = new ArrayList<>();
 318             List<DescriptionElementBase> distributionFacts = new ArrayList<>();
 319             List<DescriptionElementBase> commonNameFacts = new ArrayList<>();
 320             List<DescriptionElementBase> usageFacts = new ArrayList<>();
 321             for (TaxonDescription description: descriptions){
 322                 if (description.getElements() != null){
 323                     for (DescriptionElementBase element: description.getElements()){
 324                         element = CdmBase.deproxy(element);
 325                         if (element.getFeature().equals(Feature.COMMON_NAME())){
 326                             commonNameFacts.add(element);
 327                         }else if (element.getFeature().equals(Feature.DISTRIBUTION())){
 328                             distributionFacts.add(element);
 329                         }else if (element instanceof IndividualsAssociation || isSpecimenFeature(element.getFeature())){
 330                             specimenFacts.add(element);
 331                         }else{
 332                             simpleFacts.add(element);
 333                         }
 334                     }
 335                 }
 336             }
 337             if (!commonNameFacts.isEmpty()){
 338                 handleCommonNameFacts(state, taxon, commonNameFacts);
 339             }
 340             if (!distributionFacts.isEmpty()){
 341                 handleDistributionFacts(state, taxon, distributionFacts);
 342             }
 343             if (!specimenFacts.isEmpty()){
 344                 handleSpecimenFacts(state, taxon, specimenFacts);
 345             }
 346             if (!simpleFacts.isEmpty()){
 347                 handleSimpleFacts(state, taxon, simpleFacts);
 348             }
 349         } else if (cdmBase instanceof TaxonName){
 350             TaxonName name = CdmBase.deproxy(cdmBase, TaxonName.class);
 351             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 352             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 353             for (TaxonNameDescription description: descriptions){
 354                 if (description.getElements() != null){
 355                     for (DescriptionElementBase element: description.getElements()){
 356                         simpleFacts.add(element);
 357
 358                     }
 359                 }
 360              }
 361             if (!simpleFacts.isEmpty()){
 362                 handleSimpleFacts(state, name, simpleFacts);
 363             }
 364         }
 365         }catch (Exception e){
 366             state.getResult().addException(e, "An unexpected error occurred when handling description of" +
 367                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 368         }
 369     }
 370
 371
 372     /**
 373      * @param feature
 374      * @return
 375      */
 376     private boolean isSpecimenFeature(Feature feature) {
 377         //TODO allow user defined specimen features
 378         if (feature == null){
 379             return false;
 380         }else if (feature.isSupportsIndividualAssociation()){
 381             return true;
 382         }else{
 383             return feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.INDIVIDUALS_ASSOCIATION())
 384                     || feature.equals(Feature.MATERIALS_EXAMINED()) || feature.equals(Feature.OBSERVATION())
 385                     || feature.equals(Feature.OCCURRENCE())
 386                      ;
 387         }
 388     }
 389
 390     /**
 391      * @param state
 392      * @param taxon
 393      * @param simpleFacts
 394      */
 395     private void handleSimpleFacts(CdmLightExportState state, CdmBase cdmBase,
 396             List<DescriptionElementBase> simpleFacts) {
 397         try {
 398             CdmLightExportTable table = CdmLightExportTable.SIMPLE_FACT;
 399             CdmLightExportTable tableMedia = CdmLightExportTable.MEDIA;
 400             for (DescriptionElementBase element: simpleFacts){
 401                 if (element.getModifyingText().isEmpty() && !element.getMedia().isEmpty()){
 402                     handleSimpleMediaFact(state, cdmBase, tableMedia, element);
 403                 }else{
 404                     handleSingleSimpleFact(state, cdmBase, table, element);
 405                 }
 406             }
 407         } catch (Exception e) {
 408             state.getResult().addException(e, "An unexpected error occurred when handling simple facts for " +
 409                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 410         }
 411     }
 412
 413     /**
 414      * @param state
 415      * @param cdmBase
 416      * @param tableMedia
 417      * @param element
 418      */
 419     private void handleSimpleMediaFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 420             DescriptionElementBase element) {
 421         try {
 422             String[] csvLine;
 423             handleSource(state, element, CdmLightExportTable.MEDIA);
 424
 425             if (element instanceof TextData){
 426                TextData textData = (TextData)element;
 427                csvLine = new String[table.getSize()];
 428                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 429                if (cdmBase instanceof Taxon){
 430                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 431                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 432                }else if (cdmBase instanceof TaxonName){
 433                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 434                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 435                }
 436
 437
 438                String mediaUris = "";
 439                for (Media media: textData.getMedia()){
 440                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 441                    if (!StringUtils.isBlank(mediaString)){
 442                        mediaUris +=  mediaString + ";";
 443                    }
 444                    else{
 445                        state.getResult().addWarning("Empty Media object for "
 446                                + cdmBase.getUserFriendlyTypeName() + " " + cdmBase.getUuid()
 447                                + " (media: " + media.getUuid() + ")");
 448                    }
 449                }
 450                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 451
 452             }
 453         } catch (Exception e) {
 454             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 455                     cdmBaseStr(element) + ": " + e.getMessage());
 456         }
 457
 458     }
 459
 460     /**
 461      * @param state
 462      * @param cdmBase
 463      * @param table
 464      * @param element
 465      */
 466     private void handleSingleSimpleFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 467             DescriptionElementBase element) {
 468         try {
 469             String[] csvLine;
 470             handleSource(state, element, CdmLightExportTable.SIMPLE_FACT);
 471
 472             if (element instanceof TextData){
 473                TextData textData = (TextData)element;
 474                csvLine = new String[table.getSize()];
 475                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 476                if (cdmBase instanceof Taxon){
 477                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 478                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 479                }else if (cdmBase instanceof TaxonName){
 480                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 481                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 482                }
 483                csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = textData.getFeature().getLabel();
 484
 485                String mediaUris = "";
 486                for (Media media: textData.getMedia()){
 487                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 488                    if (!StringUtils.isBlank(mediaString)){
 489                        mediaUris +=  mediaString + ";";
 490                    }
 491                    else{
 492                        state.getResult().addWarning("Empty Media object for uuid: " +
 493                                cdmBase.getUuid() + " uuid of media: " + media.getUuid());
 494                    }
 495                }
 496                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 497                if (textData.getFeature().equals(Feature.CITATION())){
 498                   // csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 499                    state.getProcessor().put(table, textData, csvLine);
 500                }else if (!textData.getMultilanguageText().isEmpty()){
 501                    for (Language language: textData.getMultilanguageText().keySet()){
 502                        String[] csvLineLanguage = csvLine.clone();
 503                        LanguageString langString = textData.getLanguageText(language);
 504                        String text = langString.getText();
 505                        if (state.getConfig().isFilterIntextReferences()){
 506                            text = filterIntextReferences(langString.getText());
 507                        }
 508                        csvLineLanguage[table.getIndex(CdmLightExportTable.FACT_TEXT)] = text;
 509                        csvLineLanguage[table.getIndex(CdmLightExportTable.LANGUAGE)] = language.getLabel();
 510                        state.getProcessor().put(table, textData, csvLineLanguage);
 511                    }
 512                } else{
 513                    state.getProcessor().put(table, textData, csvLine);
 514                }
 515             }
 516         } catch (Exception e) {
 517             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 518                     cdmBaseStr(element) + ": " + e.getMessage());
 519         }
 520     }
 521
 522
 523     /**
 524      * @param text
 525      * @return
 526      */
 527     private String filterIntextReferences(String text) {
 528         /*
 529          * (<cdm:reference cdmId='fbd19251-efee-4ded-b780-915000f66d41' intextId='1352d42c-e201-4155-a02a-55360d3b563e'>Ridley in Fl. Malay Pen. 3 (1924) 22</cdm:reference>)
 530          */
 531
 532        String newText = text.replaceAll("<cdm:reference cdmId='[a-z0-9\\-]*' intextId='[a-z0-9\\-]*'>","");
 533        newText = newText.replaceAll("</cdm:reference>","");
 534
 535        newText = newText.replaceAll("<cdm:key cdmId='[a-z0-9\\-]*' intextId='[a-z0-9\\-]*'>","");
 536        newText = newText.replaceAll("</cdm:key>","");
 537        return newText;
 538     }
 539
 540     /**
 541      * @param state
 542      * @param specimenFacts
 543      */
 544     private void handleSpecimenFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> specimenFacts) {
 545         CdmLightExportTable table = CdmLightExportTable.SPECIMEN_FACT;
 546
 547         for (DescriptionElementBase element: specimenFacts){
 548             try {
 549                 String[] csvLine = new String[table.getSize()];
 550                 csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 551                 csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 552                 handleSource(state, element, table);
 553                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_NOTES)] = createAnnotationsString(element.getAnnotations());
 554
 555                 if (element instanceof IndividualsAssociation){
 556
 557                     IndividualsAssociation indAssociation = (IndividualsAssociation)element;
 558                     if (indAssociation.getAssociatedSpecimenOrObservation() == null){
 559                         state.getResult().addWarning("There is an individual association with no specimen associated (Taxon "+ taxon.getTitleCache() + "(" + taxon.getUuid() +"). Could not be exported.");
 560                         continue;
 561                     }else{
 562                         if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
 563                             SpecimenOrObservationBase<?> specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 564
 565                             handleSpecimen(state, specimenBase);
 566                             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
 567
 568                         }
 569                     }
 570                 } else if (element instanceof TextData){
 571                     TextData textData = HibernateProxyHelper.deproxy(element, TextData.class);
 572                     csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_DESCRIPTION)] = createMultilanguageString(textData.getMultilanguageText());
 573                 }
 574                 state.getProcessor().put(table, element, csvLine);
 575             } catch (Exception e) {
 576                 state.getResult().addException(e, "An unexpected error occurred when handling single specimen fact " +
 577                         cdmBaseStr(element) + ": " + e.getMessage());
 578             }
 579         }
 580     }
 581
 582     /**
 583      * @param multilanguageText
 584      * @return
 585      */
 586     private String createMultilanguageString(Map<Language, LanguageString> multilanguageText) {
 587        String text = "";
 588        int index = multilanguageText.size();
 589        for(LanguageString langString: multilanguageText.values()){
 590            text += langString.getText();
 591            if (index > 1){
 592                text += "; ";
 593            }
 594            index --;
 595        }
 596
 597         return text;
 598     }
 599
 600     /**
 601      * @param annotations
 602      * @return
 603      */
 604     private String createAnnotationsString(Set<Annotation> annotations) {
 605         StringBuffer strBuff = new StringBuffer();
 606
 607         for (Annotation ann:annotations){
 608             if (ann.getAnnotationType() == null ||!ann.getAnnotationType().equals(AnnotationType.TECHNICAL())){
 609                 strBuff.append(ann.getText());
 610                 strBuff.append("; ");
 611             }
 612         }
 613
 614         if (strBuff.length() > 2){
 615             return strBuff.substring(0, strBuff.length()-2);
 616         }else{
 617             return null;
 618         }
 619     }
 620
 621     /**
 622      * @param state
 623      * @param taxon
 624      * @param element
 625      */
 626     private void handleSource(CdmLightExportState state, DescriptionElementBase element, CdmLightExportTable factsTable) {
 627         CdmLightExportTable table = CdmLightExportTable.FACT_SOURCES;
 628         try {
 629         Set<DescriptionElementSource> sources = element.getSources();
 630
 631         for (DescriptionElementSource source: sources){
 632
 633                 String[] csvLine = new  String[table.getSize()];
 634                 Reference ref = source.getCitation();
 635                 if ((ref == null) && (source.getNameUsedInSource() == null)){
 636                     continue;
 637                 }
 638                 if (ref != null){
 639                     if (state.getReferenceFromStore(ref.getId()) == null){
 640                         handleReference(state, ref);
 641
 642                     }
 643                     csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, ref);
 644                 }
 645                 csvLine[table.getIndex(CdmLightExportTable.FACT_FK)] = getId(state, element);
 646
 647                 csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)] = getId(state, source.getNameUsedInSource());
 648                 csvLine[table.getIndex(CdmLightExportTable.FACT_TYPE)] = factsTable.getTableName();
 649                 if ( StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)])  && StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)])){
 650                     continue;
 651                 }
 652                 state.getProcessor().put(table, source, csvLine);
 653
 654         }
 655         } catch (Exception e) {
 656             state.getResult().addException(e, "An unexpected error occurred when handling single source " +
 657                     cdmBaseStr(element) + ": " + e.getMessage());
 658         }
 659
 660     }
 661
 662     /**
 663      * @param state
 664      * @param distributionFacts
 665      */
 666     private void handleDistributionFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> distributionFacts) {
 667         CdmLightExportTable table = CdmLightExportTable.GEOGRAPHIC_AREA_FACT;
 668
 669         for (DescriptionElementBase element: distributionFacts){
 670             try {
 671                 if (element instanceof Distribution){
 672                     String[] csvLine = new  String[table.getSize()];
 673                     Distribution distribution = (Distribution)element;
 674                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 675                     handleSource(state, element, table);
 676                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 677                     if (distribution.getArea() != null){
 678                         csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = distribution.getArea().getLabel();
 679                     }
 680                     if (distribution.getStatus() != null){
 681                         csvLine[table.getIndex(CdmLightExportTable.STATUS_LABEL)] = distribution.getStatus().getLabel();
 682                     }
 683                     state.getProcessor().put(table, distribution, csvLine);
 684                 } else{
 685                     state.getResult().addError("The distribution description for the taxon " + taxon.getUuid() + " is not of type distribution. Could not be exported. UUID of the description element: " + element.getUuid());
 686                 }
 687             } catch (Exception e) {
 688                 state.getResult().addException(e, "An unexpected error occurred when handling single distribution " +
 689                         cdmBaseStr(element) + ": " + e.getMessage());
 690             }
 691         }
 692     }
 693
 694     /**
 695      * @param state
 696      * @param commonNameFacts
 697      */
 698     private void handleCommonNameFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> commonNameFacts) {
 699         CdmLightExportTable table = CdmLightExportTable.COMMON_NAME_FACT;
 700
 701         for (DescriptionElementBase element: commonNameFacts){
 702             try {
 703                 if (element instanceof CommonTaxonName){
 704                     String[] csvLine = new  String[table.getSize()];
 705                     CommonTaxonName commonName = (CommonTaxonName)element;
 706                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 707                     handleSource(state, element, table);
 708                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 709                     if (commonName.getName() != null){csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = commonName.getName();}
 710                     if (commonName.getLanguage() != null){csvLine[table.getIndex(CdmLightExportTable.LANGUAGE)] = commonName.getLanguage().getLabel();}
 711                     if (commonName.getArea() != null){ csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = commonName.getArea().getLabel();}
 712                     state.getProcessor().put(table, commonName, csvLine);
 713                 } else{
 714                     state.getResult().addError("The distribution description for the taxon " + taxon.getUuid() + " is not of type distribution. Could not be exported. UUID of the description element: " + element.getUuid());
 715                 }
 716             } catch (Exception e) {
 717                 state.getResult().addException(e, "An unexpected error occurred when handling single common name " +
 718                         cdmBaseStr(element) + ": " + e.getMessage());
 719             }
 720         }
 721     }
 722
 723     /**
 724      * @param sec
 725      * @return
 726      */
 727     private String getTitleCache(IIdentifiableEntity identEntity) {
 728         if (identEntity == null){
 729             return "";
 730         }
 731         //TODO refresh?
 732         return identEntity.getTitleCache();
 733     }
 734
 735     /**
 736      * @param state
 737      * @param taxon
 738      * @return
 739      */
 740     private String getId(CdmLightExportState state, ICdmBase cdmBase) {
 741         if (cdmBase == null){
 742             return "";
 743         }
 744         //TODO make configurable
 745         return cdmBase.getUuid().toString();
 746     }
 747
 748     /**
 749      * @param state
 750      * @param synonym
 751      */
 752     private void handleSynonym(CdmLightExportState state, Synonym synonym) {
 753        try {
 754            if (isUnpublished(state.getConfig(), synonym)){
 755                return;
 756            }
 757            TaxonName name = synonym.getName();
 758            handleName(state, name);
 759
 760            CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 761            String[] csvLine = new String[table.getSize()];
 762
 763            csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, synonym);
 764            csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, synonym.getAcceptedTaxon());
 765            csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 766            csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, synonym.getSec());
 767            csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(synonym.getSec());
 768
 769            state.getProcessor().put(table, synonym, csvLine);
 770         } catch (Exception e) {
 771             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
 772                     cdmBaseStr(synonym) + ": " + e.getMessage());
 773         }
 774     }
 775
 776
 777     /**
 778      * Handles Misapplied names (including pro parte and partial as well as
 779      * pro parte and partial synonyms
 780      * @param state
 781      * @param rel
 782      */
 783     private void handleProPartePartialMisapplied(CdmLightExportState state, TaxonRelationship rel) {
 784         try {
 785             Taxon ppSyonym = rel.getFromTaxon();
 786             if (isUnpublished(state.getConfig(), ppSyonym)){
 787                 return;
 788             }
 789             TaxonName name = ppSyonym.getName();
 790             handleName(state, name);
 791
 792             CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 793             String[] csvLine = new String[table.getSize()];
 794
 795             csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, rel);
 796             csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, rel.getToTaxon());
 797             csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 798
 799             Reference secRef = ppSyonym.getSec();
 800             csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef);
 801             csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef);
 802             Reference synSecRef = rel.getCitation();
 803             csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, synSecRef);
 804             csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(synSecRef);
 805
 806             //pro parte type
 807             TaxonRelationshipType type = rel.getType();
 808             csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = type.isProParte()? "1":"0";
 809             csvLine[table.getIndex(CdmLightExportTable.IS_PARTIAL)] = type.isPartial()? "1":"0";
 810             csvLine[table.getIndex(CdmLightExportTable.IS_MISAPPLIED)] = type.isAnyMisappliedName()? "1":"0";
 811
 812             state.getProcessor().put(table, ppSyonym, csvLine);
 813          } catch (Exception e) {
 814              state.getResult().addException(e, "An unexpected error occurred when handling "
 815                      + "pro parte/partial synonym relationship " +
 816                      cdmBaseStr(rel) + ": " + e.getMessage());
 817          }
 818
 819     }
 820
 821
 822     /**
 823      * @param state
 824      * @param name
 825      */
 826     private void handleName(CdmLightExportState state, TaxonName name) {
 827         if (name == null){
 828             return;
 829         }
 830         try {
 831             Rank rank = name.getRank();
 832             CdmLightExportTable table = CdmLightExportTable.SCIENTIFIC_NAME;
 833             name = HibernateProxyHelper.deproxy(name);
 834             String[] csvLine = new String[table.getSize()];
 835
 836             csvLine[table.getIndex(CdmLightExportTable.NAME_ID)] = getId(state, name);
 837             if (name.getLsid() != null){
 838                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = name.getLsid().getLsid();
 839             }else{
 840                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = "";
 841             }
 842
 843             handleIdentifier(state, name);
 844             handleDescriptions(state, name);
 845
 846             csvLine[table.getIndex(CdmLightExportTable.RANK)] = getTitleCache(rank);
 847             if (rank != null){
 848                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
 849                 if (rank.isInfraGeneric()){
 850                     try {
 851                         csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
 852                     } catch (UnknownCdmTypeException e) {
 853                         state.getResult().addError("Infrageneric marker expected but not available for rank " + name.getRank().getTitleCache());
 854                     }
 855                 }
 856                 if (rank.isInfraSpecific()){
 857                     csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
 858                 }
 859             }else{
 860                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = "";
 861             }
 862             if (name.isProtectedTitleCache()){
 863                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] =name.getTitleCache();
 864             }else{
 865                 //TODO: adapt the tropicos titlecache creation
 866                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
 867             }
 868             csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
 869             csvLine[table.getIndex(CdmLightExportTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
 870
 871             csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
 872             csvLine[table.getIndex(CdmLightExportTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
 873
 874             csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
 875             csvLine[table.getIndex(CdmLightExportTable.BAS_AUTHORTEAM_FK)] = getId(state,name.getBasionymAuthorship());
 876             if (name.getBasionymAuthorship() != null){
 877                 if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
 878                     handleAuthor(state, name.getBasionymAuthorship());
 879                 }
 880             }
 881             csvLine[table.getIndex(CdmLightExportTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
 882             if (name.getExBasionymAuthorship() != null){
 883                 if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
 884                     handleAuthor(state, name.getExBasionymAuthorship());
 885                 }
 886
 887             }
 888             csvLine[table.getIndex(CdmLightExportTable.COMB_AUTHORTEAM_FK)] = getId(state,name.getCombinationAuthorship());
 889             if (name.getCombinationAuthorship() != null){
 890                 if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
 891                     handleAuthor(state, name.getCombinationAuthorship());
 892                 }
 893             }
 894             csvLine[table.getIndex(CdmLightExportTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
 895             if (name.getExCombinationAuthorship() != null){
 896                 if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
 897                     handleAuthor(state, name.getExCombinationAuthorship());
 898                 }
 899
 900             }
 901
 902             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
 903
 904             Reference nomRef = name.getNomenclaturalReference();
 905
 906             if (nomRef != null){
 907                 if (state.getReferenceFromStore(nomRef.getId()) == null){
 908                     handleReference(state, nomRef);
 909                 }
 910                 csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, nomRef);
 911                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = nomRef.getType().name();
 912                 if (nomRef.getVolume() != null){
 913                     csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = nomRef.getVolume();
 914                     csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 915                 }
 916                 if (nomRef.getDatePublished() != null){
 917                     csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = nomRef.getTimePeriodPublishedString();
 918                     csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
 919                     csvLine[table.getIndex(CdmLightExportTable.VERBATIM_DATE)] = nomRef.getDatePublished().getVerbatimDate();
 920                 }
 921                 if (name.getNomenclaturalMicroReference() != null){
 922                     csvLine[table.getIndex(CdmLightExportTable.DETAIL)] = name.getNomenclaturalMicroReference();
 923                 }
 924                 nomRef = HibernateProxyHelper.deproxy(nomRef);
 925                 if (nomRef.getInReference() != null){
 926                     Reference inReference = nomRef.getInReference();
 927                     if (inReference.getDatePublished() != null && nomRef.getDatePublished() == null){
 928                         csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = inReference.getDatePublishedString();
 929                         csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = inReference.getDatePublished().getYear();
 930                     }
 931                     if (nomRef.getVolume() == null && inReference.getVolume() != null){
 932                         csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = inReference.getVolume();
 933                         csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 934                     }
 935                     if (inReference.getInReference() != null){
 936                         inReference = inReference.getInReference();
 937                     }
 938                     if (inReference.getAbbrevTitle() == null){
 939                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitleCache());
 940                     }else{
 941                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
 942                     }
 943                     if (inReference.getTitle() == null){
 944                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitleCache());
 945                     }else{
 946                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
 947                     }
 948
 949
 950                     TeamOrPersonBase<?> author = inReference.getAuthorship();
 951                     if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))){
 952                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = author.isProtectedTitleCache()? author.getTitleCache(): CdmUtils.Nz(author.getNomenclaturalTitle());
 953                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 954                     }else{
 955                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 956                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 957                     }
 958                 }else{
 959                     if (nomRef.getAbbrevTitle() == null){
 960                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitleCache());
 961                     }else{
 962                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle());
 963                     }
 964                     if (nomRef.getTitle() == null){
 965                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitleCache());
 966                     }else{
 967                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitle());
 968                     }
 969                     TeamOrPersonBase<?> author = nomRef.getAuthorship();
 970                     if (author != null ){
 971                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = author.isProtectedTitleCache()? author.getTitleCache(): CdmUtils.Nz(author.getNomenclaturalTitle());
 972                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 973                     }else{
 974                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 975                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 976                     }
 977
 978                 }
 979             }else{
 980                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = "";
 981             }
 982
 983
 984
 985             /*
 986             * Collation
 987
 988             Detail
 989
 990
 991             TitlePageYear
 992             */
 993             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 994             String protologueUriString = extractURIs(state, descriptions, Feature.PROTOLOGUE());
 995
 996             csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_URI)] = protologueUriString;
 997
 998             if (name.getStatus() == null || name.getStatus().isEmpty()){
 999                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = "";
1000                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = "";
1001             }else{
1002
1003                 String statusStringAbbrev = extractStatusString(state, name, true);
1004                 String statusString = extractStatusString(state, name, false);
1005
1006                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = statusString.trim();
1007                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
1008             }
1009
1010             HomotypicalGroup group =name.getHomotypicalGroup();
1011
1012             if (state.getHomotypicalGroupFromStore(group.getId()) == null){
1013                 handleHomotypicalGroup(state, HibernateProxyHelper.deproxy(group, HomotypicalGroup.class));
1014             }
1015             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
1016             List<TaxonName> typifiedNames = new ArrayList<>();
1017             typifiedNames.addAll(group.getTypifiedNames());
1018             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
1019             Integer  seqNumber= typifiedNames.indexOf(name);
1020             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
1021             state.getProcessor().put(table, name, csvLine);
1022
1023             /*
1024              *
1025             Tropicos_ID
1026             IPNI_ID
1027
1028
1029             InfragenericRank
1030
1031
1032             InfraspecificRank
1033             Collation
1034             Volume (Issue)
1035             Detail
1036             DatePublished
1037             YearPublished
1038             TitlePageYear
1039
1040
1041
1042             HomotypicGroupSequenceNumber
1043
1044
1045              *
1046              */
1047         } catch (Exception e) {
1048             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
1049                     cdmBaseStr(name) + ": " + e.getMessage());
1050         }
1051     }
1052
1053     /**
1054      * @return
1055      */
1056     private String createCollatation(TaxonName name) {
1057         String collation = "";
1058         if (name.getNomenclaturalReference() != null){
1059             Reference ref = name.getNomenclaturalReference();
1060             collation = getVolume(ref);
1061         }
1062         if (name.getNomenclaturalMicroReference() != null){
1063             if (!StringUtils.isBlank(collation)){
1064                 collation += ":";
1065             }
1066             collation +=name.getNomenclaturalMicroReference();
1067         }
1068
1069         return collation;
1070     }
1071
1072     /**
1073      * @param nomenclaturalReference
1074      * @return
1075      */
1076     private String getVolume(Reference reference) {
1077         if (reference.getVolume() != null){
1078             return reference.getVolume();
1079         }else if (reference.getInReference() != null){
1080             if (reference.getInReference().getVolume() != null){
1081                 return reference.getInReference().getVolume();
1082             }
1083         }
1084         return null;
1085     }
1086
1087     /**
1088      * @param state
1089      * @param name
1090      */
1091     private void handleIdentifier(CdmLightExportState state, TaxonName name) {
1092         CdmLightExportTable table = CdmLightExportTable.IDENTIFIER;
1093         String[] csvLine;
1094         try {
1095             Set<String>  IPNIidentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_IPNI());
1096             Set<String>  tropicosIdentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_TROPICOS());
1097             Set<String>  WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
1098             if (!IPNIidentifiers.isEmpty()){
1099                 csvLine = new String[table.getSize()];
1100                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1101                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
1102                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(IPNIidentifiers);
1103                 state.getProcessor().put(table, name, csvLine);
1104             }
1105             if (!tropicosIdentifiers.isEmpty()){
1106                 csvLine = new String[table.getSize()];
1107                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1108                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = TROPICOS_NAME_IDENTIFIER;
1109                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(tropicosIdentifiers);
1110                 state.getProcessor().put(table, name, csvLine);
1111             }
1112             if (!WFOIdentifiers.isEmpty()){
1113                 csvLine = new String[table.getSize()];
1114                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1115                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
1116                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(WFOIdentifiers);
1117                 state.getProcessor().put(table, name, csvLine);
1118             }
1119         } catch (Exception e) {
1120             state.getResult().addException(e, "An unexpected error occurred when handling identifiers for " +
1121                     cdmBaseStr(name) + ": " + e.getMessage());
1122
1123         }
1124     }
1125
1126     /**
1127      * @param tropicosIdentifiers
1128      */
1129     private String extractIdentifier(Set<String> identifierSet) {
1130
1131         String identifierString = "";
1132         for (String identifier: identifierSet){
1133             if (!StringUtils.isBlank(identifierString)){
1134                 identifierString += ", ";
1135             }
1136             identifierString += identifier;
1137         }
1138
1139         return identifierString;
1140     }
1141
1142     /**
1143      * @param state
1144      * @param descriptions
1145      * @return
1146      */
1147     private String extractURIs(CdmLightExportState state,
1148             Set<? extends DescriptionBase<?>> descriptionsSet, Feature feature) {
1149         String mediaUriString = "";
1150         SpecimenDescription specimenDescription;
1151         TaxonDescription taxonDescription;
1152         TaxonNameDescription nameDescription;
1153         Set<DescriptionElementBase> elements = new HashSet<>();
1154         for (DescriptionBase<?> description : descriptionsSet){
1155             try {
1156                 if (!description.getElements().isEmpty()){
1157                     if (description instanceof SpecimenDescription){
1158                         specimenDescription = (SpecimenDescription)description;
1159                         elements = specimenDescription.getElements();
1160                     }else if (description instanceof TaxonDescription){
1161                         taxonDescription = (TaxonDescription) description;
1162                         elements = taxonDescription.getElements();
1163                     } else if (description instanceof TaxonNameDescription){
1164                         nameDescription = (TaxonNameDescription) description;
1165                         elements = nameDescription.getElements();
1166                     }
1167
1168                     for (DescriptionElementBase element : elements){
1169                         Feature entityFeature = HibernateProxyHelper.deproxy(element.getFeature());
1170                         if (entityFeature.equals(feature)){
1171                             if (!element.getMedia().isEmpty()){
1172                                 List<Media> media = element.getMedia();
1173                                 for (Media mediaElement: media){
1174                                     Iterator<MediaRepresentation> it =  mediaElement.getRepresentations().iterator();
1175                                     mediaUriString = extractMediaUris(it);
1176                                 }
1177                             }
1178                         }
1179                     }
1180                 }
1181             } catch (Exception e) {
1182                 state.getResult().addException(e, "An unexpected error occurred when extracting media URIs for " +
1183                         cdmBaseStr(description) + ": " + e.getMessage());
1184             }
1185         }
1186         return mediaUriString;
1187     }
1188
1189     /**
1190      * @param state
1191      * @param basionymAuthorship
1192      */
1193     private void handleAuthor(CdmLightExportState state, TeamOrPersonBase<?> author) {
1194         try {
1195             if (state.getAuthorFromStore(author.getId()) != null){
1196                 return;
1197             }
1198             state.addAuthorToStore(author);
1199             CdmLightExportTable table = CdmLightExportTable.NOMENCLATURAL_AUTHOR;
1200             String[] csvLine = new String[table.getSize()];
1201             CdmLightExportTable tableAuthorRel = CdmLightExportTable.NOMENCLATURAL_AUTHOR_TEAM_RELATION;
1202             String[] csvLineRel = new String[tableAuthorRel.getSize()];
1203             String[] csvLineMember = new String[table.getSize()];
1204             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, author);
1205             csvLine[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = author.isProtectedTitleCache()? author.getTitleCache(): author.getNomenclaturalTitle();
1206             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = author.getTitleCache();
1207             author = HibernateProxyHelper.deproxy(author);
1208             if (author instanceof Person){
1209                 Person authorPerson = (Person)author;
1210                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_GIVEN_NAME)] = authorPerson.getGivenName();
1211                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FAMILY_NAME)] = authorPerson.getFamilyName();
1212                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = authorPerson.getPrefix();
1213                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = authorPerson.getSuffix();
1214             } else{
1215                 // create an entry in rel table and all members in author table, check whether the team members already in author table
1216
1217                 Team authorTeam = (Team)author;
1218                 int index = 0;
1219                 for (Person member: authorTeam.getTeamMembers()){
1220                     csvLineRel = new String[tableAuthorRel.getSize()];
1221                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_FK)] = getId(state, authorTeam);
1222                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state, member);
1223                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_SEQ_NUMBER)] = String.valueOf(index);
1224                     state.getProcessor().put(tableAuthorRel, authorTeam.getId() +":" +member.getId(), csvLineRel);
1225
1226                     if (state.getAuthorFromStore(member.getId()) == null){
1227                         state.addAuthorToStore(member);
1228                         csvLineMember = new String[table.getSize()];
1229                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, member);
1230                         csvLineMember[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = member.isProtectedTitleCache()? member.getTitleCache(): member.getNomenclaturalTitle();
1231                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = member.getTitleCache();
1232                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_GIVEN_NAME)] = member.getGivenName();
1233                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_FAMILY_NAME)] = member.getFamilyName();
1234                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = member.getPrefix();
1235                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = member.getSuffix();
1236                         state.getProcessor().put(table, member, csvLineMember);
1237                     }
1238                     index++;
1239
1240                 }
1241             }
1242             state.getProcessor().put(table, author, csvLine);
1243         } catch (Exception e) {
1244             state.getResult().addException(e, "An unexpected error occurred when handling author " +
1245                     cdmBaseStr(author) + ": " + e.getMessage());
1246         }
1247     }
1248
1249     /**
1250      * @param state
1251      * @param name
1252      * @param statusString
1253      * @return
1254      */
1255     private String extractStatusString(CdmLightExportState state, TaxonName name, boolean abbrev) {
1256         try {
1257             Set<NomenclaturalStatus> status = name.getStatus();
1258             if (status.isEmpty()){
1259                 return "";
1260             }
1261             String statusString = "";
1262             for (NomenclaturalStatus nameStatus: status){
1263                 if (nameStatus != null){
1264                     if (abbrev){
1265                         if (nameStatus.getType() != null){
1266                             statusString += nameStatus.getType().getIdInVocabulary();
1267                         }
1268                     }else{
1269                         if (nameStatus.getType() != null){
1270                             statusString += nameStatus.getType().getTitleCache();
1271                         }
1272                     }
1273                     if (!abbrev){
1274
1275                         if (nameStatus.getRuleConsidered() != null && !StringUtils.isBlank(nameStatus.getRuleConsidered())){
1276                             statusString += " " + nameStatus.getRuleConsidered();
1277                         }
1278                         if (nameStatus.getCitation() != null){
1279                             statusString += " " + nameStatus.getCitation().getTitleCache();
1280                         }
1281                         if (nameStatus.getCitationMicroReference() != null && !StringUtils.isBlank(nameStatus.getCitationMicroReference())){
1282                             statusString += " " + nameStatus.getCitationMicroReference();
1283                         }
1284                     }
1285                     statusString += " ";
1286                 }
1287             }
1288             return statusString;
1289         } catch (Exception e) {
1290             state.getResult().addException(e, "An unexpected error occurred when extracting status string for " +
1291                     cdmBaseStr(name) + ": " + e.getMessage());
1292             return "";
1293         }
1294     }
1295
1296     /**
1297      * @param group
1298      */
1299     private void handleHomotypicalGroup(CdmLightExportState state, HomotypicalGroup group) {
1300         try {
1301            state.addHomotypicalGroupToStore(group);
1302             CdmLightExportTable table = CdmLightExportTable.HOMOTYPIC_GROUP;
1303             String[] csvLine = new String[table.getSize()];
1304
1305             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_ID)] = getId(state, group);
1306             List<TaxonName> typifiedNames = new ArrayList<>();
1307             typifiedNames.addAll(group.getTypifiedNames());
1308             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
1309             String typifiedNamesString = "";
1310             for (TaxonName name: typifiedNames){
1311                 //Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)
1312                 //TODO: nameRelations, which and how to display
1313
1314
1315                 typifiedNamesString += name.getTitleCache()+ extractStatusString(state, name, true) + "; ";
1316             }
1317             typifiedNamesString = typifiedNamesString.substring(0, typifiedNamesString.length()-2);
1318             if (typifiedNamesString != null){
1319                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = typifiedNamesString.trim();
1320             }else{
1321                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = "";
1322             }
1323             Set<TypeDesignationBase<?>> typeDesigantionSet = group.getTypeDesignations();
1324             List<TypeDesignationBase<?>> designationList = new ArrayList<>();
1325             designationList.addAll(typeDesigantionSet);
1326             Collections.sort(designationList, new TypeComparator());
1327             StringBuffer typeDesignationString = new StringBuffer();
1328             List<TaggedText> list = new ArrayList<>();
1329             if (!designationList.isEmpty()){
1330                 TypeDesignationSetManager manager = new TypeDesignationSetManager(group);
1331
1332                 list.addAll( manager.toTaggedTextWithCitation());
1333             }
1334             StringBuffer homotypicalGroupTypeDesignationString = new StringBuffer();
1335
1336             for (TaggedText text:list){
1337                 if (text != null && text.getText() != null && (text.getText().equals("Type:") || text.getText().equals("NameType:"))){
1338                   //do nothing
1339                 } else if (text.getType().equals(TagEnum.reference)){
1340                     homotypicalGroupTypeDesignationString.append(text.getText());
1341                 }else if (text.getType().equals(TagEnum.typeDesignation)){
1342                     homotypicalGroupTypeDesignationString.append(text.getText().replace(").", "").replace("(", "").replace(")", "") );
1343                 } else{
1344                     homotypicalGroupTypeDesignationString.append(text.getText());
1345                 }
1346             }
1347
1348
1349             String typeDesignations= homotypicalGroupTypeDesignationString.toString();
1350             typeDesignations = typeDesignations.trim();
1351
1352             typeDesignations += ".";
1353             typeDesignations = typeDesignations.replace("..", ".");
1354             typeDesignations = typeDesignations.replace(". .", ".");
1355             if (typeDesignations.equals(".")){
1356                 typeDesignations = null;
1357             }
1358
1359        /*     for (TypeDesignationBase typeDesignation: designationList){
1360                 //[Vorschlag Soll:]
1361                // Sumatra Utara, Kab. Karo, around Sidikalang areas, 1000─1500 m, Dec 11, 2003, Nepenthes Team (Hernawati, P. Akhriadi & I. Petra), NP 354 (‘ANDA’–Holo, BO–Iso) [fide Akhriadi & al. 2004]
1362                 if (typeDesignation != null && typeDesignation.getTypeStatus() != null){
1363                     typeDesignationString.append(typeDesignation.getTypeStatus().getTitleCache() + ":");
1364                 }
1365                 if (typeDesignation instanceof SpecimenTypeDesignation){
1366                     if (((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen() != null){
1367                         typeDesignationString.append(" "+((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen().getTitleCache());
1368                         if (typeDesignationString.lastIndexOf(".") == typeDesignationString.length()){
1369                             typeDesignationString.deleteCharAt(typeDesignationString.lastIndexOf("."));
1370                         }
1371                         handleSpecimen(state, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
1372                     }
1373                 }else{
1374                     if (((NameTypeDesignation)typeDesignation).getTypeName() != null){
1375                         typeDesignationString.append(((NameTypeDesignation)typeDesignation).getTypeName().getTitleCache());
1376                     }
1377                 }
1378                 if(typeDesignation.getCitation() != null ){
1379                     typeDesignationString.append(" [fide " + ((DefaultReferenceCacheStrategy)typeDesignation.getCitation().getCacheStrategy()).createShortCitation(typeDesignation.getCitation()) +"]");
1380                 }
1381                 //TODO...
1382                 /*
1383                  * Sortierung:
1384                 1.  Status der Typen: a) holo, lecto, neo, syn, b) epi, paralecto, c) para (wenn überhaupt) – die jeweiligen iso immer direct mit dazu
1385                 2.  Land
1386                 3.  Sammler
1387                 4.  Nummer
1388
1389                 Aufbau der Typusinformationen:
1390                 Land: Lokalität mit Höhe und Koordinaten; Datum; Sammler Nummer (Herbar/Barcode, Typusart; Herbar/Barcode, Typusart …)
1391
1392
1393             }*/
1394            // typeDesignations = typeDesignationString.toString();
1395             if (typeDesignations != null){
1396                 if (!typeDesignations.endsWith(".") ){
1397                     typeDesignations =typeDesignations + ".";
1398                 }
1399                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = typeDesignations;
1400
1401             }else{
1402                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = "";
1403             }
1404             state.getProcessor().put(table, String.valueOf(group.getId()), csvLine);
1405         } catch (Exception e) {
1406             e.printStackTrace();
1407             state.getResult().addException(e, "An unexpected error occurred when handling homotypic group " +
1408                     cdmBaseStr(group) + ": " + e.getMessage());
1409         }
1410     }
1411
1412     /**
1413      * @param name
1414      * @return
1415      */
1416     private String getTropicosTitleCache(CdmLightExportState state, TaxonName name) {
1417         try {
1418             String basionymStart = "(";
1419             String basionymEnd = ") ";
1420             String exAuthorSeperator = " ex ";
1421             TeamOrPersonBase<?> combinationAuthor = name.getCombinationAuthorship();
1422             TeamOrPersonBase<?> exCombinationAuthor = name.getExCombinationAuthorship();
1423             TeamOrPersonBase<?> basionymAuthor = name.getBasionymAuthorship();
1424             TeamOrPersonBase<?> exBasionymAuthor = name.getExBasionymAuthorship();
1425
1426             String combinationAuthorString = "";
1427             if (combinationAuthor != null){
1428                 combinationAuthor = HibernateProxyHelper.deproxy(combinationAuthor);
1429                 if (combinationAuthor instanceof Team){
1430                     combinationAuthorString = createTropicosTeamTitle(combinationAuthor);
1431                 }else{
1432                     Person person = HibernateProxyHelper.deproxy(combinationAuthor, Person.class);
1433                     combinationAuthorString = createTropicosAuthorString(person);
1434                 }
1435             }
1436             String exCombinationAuthorString = "";
1437             if (exCombinationAuthor != null){
1438                 exCombinationAuthor = HibernateProxyHelper.deproxy(exCombinationAuthor);
1439                 if (exCombinationAuthor instanceof Team){
1440                    exCombinationAuthorString = createTropicosTeamTitle(exCombinationAuthor);
1441                 }else{
1442                     Person person = HibernateProxyHelper.deproxy(exCombinationAuthor, Person.class);
1443                     exCombinationAuthorString = createTropicosAuthorString(person);
1444                 }
1445             }
1446
1447             String basionymAuthorString = "";
1448             if (basionymAuthor != null){
1449                 basionymAuthor = HibernateProxyHelper.deproxy(basionymAuthor);
1450                 if (basionymAuthor instanceof Team){
1451                     basionymAuthorString =  createTropicosTeamTitle(basionymAuthor);
1452                 }else{
1453                     Person person = HibernateProxyHelper.deproxy(basionymAuthor, Person.class);
1454                     basionymAuthorString = createTropicosAuthorString(person);
1455                 }
1456             }
1457
1458             String exBasionymAuthorString = "";
1459
1460             if (exBasionymAuthor != null){
1461                 exBasionymAuthor = HibernateProxyHelper.deproxy(exBasionymAuthor);
1462                 if (exBasionymAuthor instanceof Team){
1463                     exBasionymAuthorString = createTropicosTeamTitle(exBasionymAuthor);
1464
1465                 }else{
1466                     Person person = HibernateProxyHelper.deproxy(exBasionymAuthor, Person.class);
1467                     exBasionymAuthorString = createTropicosAuthorString(person);
1468                 }
1469             }
1470             String completeAuthorString =  name.getNameCache() + " ";
1471
1472             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymStart: "";
1473             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString)) ? (CdmUtils.Nz(exBasionymAuthorString) + exAuthorSeperator): "" ;
1474             completeAuthorString += (!CdmUtils.isBlank(basionymAuthorString))? CdmUtils.Nz(basionymAuthorString):"";
1475             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ?  basionymEnd:"";
1476             completeAuthorString += (!CdmUtils.isBlank(exCombinationAuthorString)) ? (CdmUtils.Nz(exCombinationAuthorString) + exAuthorSeperator): "" ;
1477             completeAuthorString += (!CdmUtils.isBlank(combinationAuthorString))? CdmUtils.Nz(combinationAuthorString):"";
1478
1479
1480             return completeAuthorString;
1481         } catch (Exception e) {
1482             state.getResult().addException(e, "An unexpected error occurred when handling tropicos title cache for " +
1483                     cdmBaseStr(name) + ": " + e.getMessage());
1484             return null;
1485         }
1486     }
1487
1488     /**
1489      * @param combinationAuthor
1490      * @return
1491      */
1492     private String createTropicosTeamTitle(TeamOrPersonBase<?> combinationAuthor) {
1493         String combinationAuthorString;
1494         Team team = HibernateProxyHelper.deproxy(combinationAuthor, Team.class);
1495         Team tempTeam = Team.NewInstance();
1496         for (Person teamMember:team.getTeamMembers()){
1497             combinationAuthorString = createTropicosAuthorString(teamMember);
1498             Person tempPerson = Person.NewTitledInstance(combinationAuthorString);
1499             tempTeam.addTeamMember(tempPerson);
1500         }
1501         combinationAuthorString = tempTeam.generateTitle();
1502         return combinationAuthorString;
1503     }
1504
1505     /**
1506      * @param teamMember
1507      */
1508     private String createTropicosAuthorString(Person teamMember) {
1509         String nomAuthorString = "";
1510         String[] splittedAuthorString = null;
1511         if (teamMember == null){
1512             return nomAuthorString;
1513         }
1514
1515         if (teamMember.getGivenName() != null){
1516             String givenNameString = teamMember.getGivenName().replaceAll("\\.", "\\. ");
1517             splittedAuthorString = givenNameString.split("\\s");
1518             for (String split: splittedAuthorString){
1519                 if (!StringUtils.isBlank(split)){
1520                     nomAuthorString += split.substring(0, 1);
1521                     nomAuthorString += ".";
1522                 }
1523             }
1524         }
1525         if (teamMember.getFamilyName() != null){
1526             String familyNameString = teamMember.getFamilyName().replaceAll("\\.", "\\. ");
1527             splittedAuthorString = familyNameString.split("\\s");
1528             for (String split: splittedAuthorString){
1529                 nomAuthorString += " " +split;
1530             }
1531         }
1532         if (isBlank(nomAuthorString.trim())){
1533             if (teamMember.getTitleCache() != null) {
1534                 String titleCacheString = teamMember.getTitleCache().replaceAll("\\.", "\\. ");
1535                 splittedAuthorString = titleCacheString.split("\\s");
1536             }else{
1537                 splittedAuthorString = new String[0];
1538             }
1539
1540             int index = 0;
1541             for (String split: splittedAuthorString){
1542                 if ( index < splittedAuthorString.length-1 && (split.length()==1 || split.endsWith("."))){
1543                     nomAuthorString += split;
1544                 }else{
1545                     nomAuthorString = nomAuthorString +" "+ split;
1546                 }
1547                 index++;
1548             }
1549         }
1550         return nomAuthorString.trim();
1551     }
1552
1553     /**
1554      * @param state
1555      * @param name
1556      */
1557     private void handleReference(CdmLightExportState state, Reference reference) {
1558         try {
1559             state.addReferenceToStore(reference);
1560             CdmLightExportTable table = CdmLightExportTable.REFERENCE;
1561             reference = HibernateProxyHelper.deproxy(reference,Reference.class);
1562             String[] csvLine = new String[table.getSize()];
1563             csvLine[table.getIndex(CdmLightExportTable.REFERENCE_ID)] = getId(state, reference);
1564             //TODO short citations correctly
1565             String shortCitation = ((DefaultReferenceCacheStrategy)reference.getCacheStrategy()).createShortCitation(reference);  //Should be Author(year) like in Taxon.sec
1566             csvLine[table.getIndex(CdmLightExportTable.BIBLIO_SHORT_CITATION)] = shortCitation;
1567             //TODO get preferred title
1568             csvLine[table.getIndex(CdmLightExportTable.REF_TITLE)] = reference.isProtectedTitleCache()? reference.getTitleCache() : reference.getTitle();
1569             csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_TITLE)] = reference.isProtectedAbbrevTitleCache()? reference.getAbbrevTitleCache(): reference.getAbbrevTitle();
1570             csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = reference.getDatePublishedString();
1571             //TBC
1572             csvLine[table.getIndex(CdmLightExportTable.EDITION)] = reference.getEdition();
1573             csvLine[table.getIndex(CdmLightExportTable.EDITOR)] = reference.getEditor();
1574             csvLine[table.getIndex(CdmLightExportTable.ISBN)] = reference.getIsbn();
1575             csvLine[table.getIndex(CdmLightExportTable.ISSN)] = reference.getIssn();
1576             csvLine[table.getIndex(CdmLightExportTable.ORGANISATION)] = reference.getOrganization();
1577             csvLine[table.getIndex(CdmLightExportTable.PAGES)] = reference.getPages();
1578             csvLine[table.getIndex(CdmLightExportTable.PLACE_PUBLISHED)] = reference.getPlacePublished();
1579             csvLine[table.getIndex(CdmLightExportTable.PUBLISHER)] = reference.getPublisher();
1580             csvLine[table.getIndex(CdmLightExportTable.REF_ABSTRACT)] = reference.getReferenceAbstract();
1581             csvLine[table.getIndex(CdmLightExportTable.SERIES_PART)] = reference.getSeriesPart();
1582             csvLine[table.getIndex(CdmLightExportTable.VOLUME)] = reference.getVolume();
1583             csvLine[table.getIndex(CdmLightExportTable.YEAR)] = reference.getYear();
1584
1585             if ( reference.getAuthorship() != null){
1586                 csvLine[table.getIndex(CdmLightExportTable.AUTHORSHIP_TITLE)] = createFullAuthorship(reference);
1587                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state,reference.getAuthorship());
1588             }
1589
1590             csvLine[table.getIndex(CdmLightExportTable.IN_REFERENCE)] = getId(state, reference.getInReference());
1591             if (reference.getInReference() != null && state.getReferenceFromStore(reference.getInReference().getId()) == null){
1592                 handleReference(state, reference.getInReference());
1593             }
1594             if ( reference.getInstitution() != null){ csvLine[table.getIndex(CdmLightExportTable.INSTITUTION)] = reference.getInstitution().getTitleCache();}
1595             if ( reference.getLsid() != null){ csvLine[table.getIndex(CdmLightExportTable.LSID)] = reference.getLsid().getLsid();}
1596             if ( reference.getSchool() != null){ csvLine[table.getIndex(CdmLightExportTable.SCHOOL)] = reference.getSchool().getTitleCache();}
1597             if ( reference.getUri() != null){ csvLine[table.getIndex(CdmLightExportTable.URI)] = reference.getUri().toString();}
1598             csvLine[table.getIndex(CdmLightExportTable.REF_TYPE)] = reference.getType().getKey();
1599
1600             state.getProcessor().put(table, reference, csvLine);
1601         } catch (Exception e) {
1602             state.getResult().addException(e, "An unexpected error occurred when handling reference " +
1603                     cdmBaseStr(reference) + ": " + e.getMessage());
1604         }
1605
1606     }
1607
1608
1609
1610
1611     /**
1612      * @param reference
1613      * @return
1614      */
1615     private String createFullAuthorship(Reference reference) {
1616         TeamOrPersonBase<?> authorship = reference.getAuthorship();
1617         String fullAuthorship = "";
1618         if (authorship == null) {
1619             return null;
1620         }
1621         authorship = HibernateProxyHelper.deproxy(authorship);
1622         if (authorship instanceof Person){
1623             fullAuthorship = ((Person)authorship).getTitleCache();
1624
1625         }
1626         else if (authorship instanceof Team){
1627
1628             Team authorTeam = HibernateProxyHelper.deproxy(authorship, Team.class);
1629             int index = 0;
1630
1631             for (Person teamMember : authorTeam.getTeamMembers()){
1632                 index++;
1633                 String concat = concatString(authorTeam, authorTeam.getTeamMembers(), index);
1634                 fullAuthorship += concat + teamMember.getTitleCache();
1635             }
1636
1637         }
1638
1639         return fullAuthorship;
1640     }
1641
1642     private static String concatString(Team team, List<Person> teamMembers, int i) {
1643         String concat;
1644         if (i <= 1){
1645             concat = "";
1646         }else if (i < teamMembers.size() || ( team.isHasMoreMembers() && i == teamMembers.size())){
1647             concat = STD_TEAM_CONCATINATION;
1648         }else{
1649             concat = FINAL_TEAM_CONCATINATION;
1650         }
1651         return concat;
1652     }
1653
1654     /*
1655      * TypeDesignation table
1656      * Specimen_Fk
1657      *  EditName_Fk
1658      *   TypeVerbatimCitation
1659      *   TypeCategory
1660      *   TypeDesignatedByString
1661      *   TypeDesignatedByRef_Fk
1662      */
1663
1664     private void handleSpecimenTypeDesignations(CdmLightExportState state, TaxonName name){
1665        try {
1666            Set<SpecimenTypeDesignation> typeDesignations = name.getSpecimenTypeDesignations();
1667            CdmLightExportTable table = CdmLightExportTable.TYPE_DESIGNATION;
1668            String nameId = getId(state, name);
1669            String[] csvLine = new String[table.getSize()];
1670             for (SpecimenTypeDesignation specimenType: typeDesignations){
1671                 csvLine = new String[table.getSize()];
1672                 DerivedUnit specimen = specimenType.getTypeSpecimen();
1673                 if (state.getSpecimenFromStore(specimen.getId()) == null){
1674                     handleSpecimen(state, specimen);
1675                 }
1676                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
1677                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = nameId;
1678                 csvLine[table.getIndex(CdmLightExportTable.TYPE_VERBATIM_CITATION)] = specimenType.getTypeSpecimen().generateTitle();
1679                 //TODO: add link to existing Vorcabulary
1680                 csvLine[table.getIndex(CdmLightExportTable.TYPE_CATEGORY)] = "";
1681                 csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_STRING)] = specimenType.getCitation().getTitleCache();
1682                 csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_REF_FK)] = getId(state, specimenType.getCitation());
1683             }
1684         } catch (Exception e) {
1685             state.getResult().addException(e, "An unexpected error occurred when handling specimen type designations for " +
1686                     cdmBaseStr(name) + ": " + e.getMessage());
1687         }
1688     }
1689
1690     /**
1691      * @param state
1692      * @param specimen
1693      */
1694     private void handleSpecimen(CdmLightExportState state, SpecimenOrObservationBase specimen) {
1695         try {
1696             state.addSpecimenToStore(specimen);
1697             CdmLightExportTable table = CdmLightExportTable.SPECIMEN;
1698             String specimenId = getId(state, specimen);
1699             String[] csvLine = new String[table.getSize()];
1700
1701             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_ID)] = specimenId;
1702             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
1703             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractURIs(state, specimen.getDescriptions(), Feature.IMAGE());
1704             if (specimen instanceof DerivedUnit){
1705                     DerivedUnit derivedUnit = (DerivedUnit)specimen;
1706                     if (derivedUnit.getCollection() != null){ csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection().getCode();}
1707
1708                 if (specimen instanceof MediaSpecimen){
1709                     MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
1710                     Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
1711                     String mediaUris = extractMediaUris(it);
1712                     csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
1713
1714                 }
1715
1716                 if (derivedUnit.getDerivedFrom() != null){
1717                     for (SpecimenOrObservationBase<?> original: derivedUnit.getDerivedFrom().getOriginals()){
1718                         //TODO: What to do if there are more then one FieldUnit??
1719                         if (original instanceof FieldUnit){
1720                             FieldUnit fieldUnit = (FieldUnit)original;
1721                             csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
1722
1723                             GatheringEvent gathering = fieldUnit.getGatheringEvent();
1724                             if (gathering != null){
1725                                 if (gathering.getLocality() != null){ csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();}
1726                                 if (gathering.getCountry() != null){csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();}
1727                                 csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
1728
1729                                 if (gathering.getGatheringDate() != null){csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
1730                                 if (!gathering.getCollectingAreas().isEmpty()){
1731                                     int index = 0;
1732                                     csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
1733                                     for (NamedArea area: gathering.getCollectingAreas()){
1734                                         if (index == 0){
1735                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getTermType().getKey();
1736                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
1737                                         }
1738                                         if (index == 1){
1739                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getTermType().getKey();
1740                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
1741                                         }
1742                                         if (index == 2){
1743                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getTermType().getKey();
1744                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
1745                                         }
1746                                         if (index == 3){
1747                                             csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
1748                                             break;
1749                                         }
1750                                         index++;
1751                                     }
1752                                 }
1753                             }
1754                         }
1755                     }
1756                 }else{
1757                     state.getResult().addError("The specimen with uuid " + specimen.getUuid() + " is not an DerivedUnit. Could not be exported.");
1758                 }
1759             }
1760
1761             state.getProcessor().put(table, specimen, csvLine);
1762         } catch (Exception e) {
1763             state.getResult().addException(e, "An unexpected error occurred when handling specimen " +
1764                     cdmBaseStr(specimen) + ": " + e.getMessage());
1765         }
1766     }
1767
1768     /**
1769      * @param it
1770      */
1771     private String extractMediaUris(Iterator<MediaRepresentation> it) {
1772
1773         String mediaUriString = "";
1774         boolean first = true;
1775         while(it.hasNext()){
1776             MediaRepresentation rep = it.next();
1777             List<MediaRepresentationPart> parts = rep.getParts();
1778             for (MediaRepresentationPart part: parts){
1779                 if (first){
1780                     if (part.getUri() != null){
1781                         mediaUriString += part.getUri().toString();
1782                         first = false;
1783                     }
1784                 }else{
1785                     if (part.getUri() != null){
1786                         mediaUriString += ", " +part.getUri().toString();
1787                     }
1788                 }
1789             }
1790         }
1791
1792         return mediaUriString;
1793     }
1794
1795     /**
1796      * @param gathering
1797      * @return
1798      */
1799     private String createCollectorString(CdmLightExportState state, GatheringEvent gathering, FieldUnit fieldUnit) {
1800         try {
1801             String collectorString = "";
1802             AgentBase<?> collectorA = CdmBase.deproxy(gathering.getCollector());
1803             if (gathering.getCollector() != null){
1804                if (collectorA instanceof TeamOrPersonBase
1805                        && state.getConfig().isHighLightPrimaryCollector()){
1806
1807                    Person primaryCollector = fieldUnit.getPrimaryCollector();
1808                    if (collectorA instanceof Team){
1809                        Team collectorTeam = (Team)collectorA;
1810                        boolean isFirst = true;
1811                        for (Person member: collectorTeam.getTeamMembers()){
1812                            if (!isFirst){
1813                                collectorString += "; ";
1814                            }
1815                            if (member.equals(primaryCollector)){
1816                                //highlight
1817                                collectorString += "<b>" + member.getTitleCache() + "</b>";
1818                            }else{
1819                                collectorString += member.getTitleCache();
1820                            }
1821                        }
1822                    }
1823                } else{
1824                    collectorString = collectorA.getTitleCache();
1825                }
1826            }
1827            return collectorString;
1828         } catch (Exception e) {
1829             state.getResult().addException(e, "An unexpected error occurred when creating collector string for " +
1830                     cdmBaseStr(fieldUnit) + ": " + e.getMessage());
1831             return "";
1832         }
1833     }
1834
1835
1836     /**
1837      * Returns a string representation of the {@link CdmBase cdmBase} object
1838      * for result messages.
1839      */
1840     private String cdmBaseStr(CdmBase cdmBase) {
1841         if (cdmBase == null){
1842             return "-no object available-";
1843         }else{
1844             return cdmBase.getClass().getSimpleName() + ": " + cdmBase.getUuid();
1845         }
1846     }
1847
1848     /**
1849      * {@inheritDoc}
1850      */
1851     @Override
1852     protected boolean doCheck(CdmLightExportState state) {
1853         return false;
1854     }
1855
1856     /**
1857      * {@inheritDoc}
1858      */
1859     @Override
1860     protected boolean isIgnore(CdmLightExportState state) {
1861         return false;
1862     }
1863
1864 }