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