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