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