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