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

   1 /**
   2 * Copyright (C) 2017 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.io.cdmLight;
  10
  11 import java.io.File;
  12 import java.util.ArrayList;
  13 import java.util.Collections;
  14 import java.util.HashSet;
  15 import java.util.Iterator;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.commons.lang3.StringUtils;
  22 import org.springframework.stereotype.Component;
  23
  24 import eu.etaxonomy.cdm.common.CdmUtils;
  25 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  26 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  27 import eu.etaxonomy.cdm.io.common.CdmExportBase;
  28 import eu.etaxonomy.cdm.io.common.ExportResult.ExportResultState;
  29 import eu.etaxonomy.cdm.io.common.ICdmExport;
  30 import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
  31 import eu.etaxonomy.cdm.io.common.XmlExportState;
  32 import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
  33 import eu.etaxonomy.cdm.model.agent.AgentBase;
  34 import eu.etaxonomy.cdm.model.agent.Person;
  35 import eu.etaxonomy.cdm.model.agent.Team;
  36 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  37 import eu.etaxonomy.cdm.model.common.Annotation;
  38 import eu.etaxonomy.cdm.model.common.AnnotationType;
  39 import eu.etaxonomy.cdm.model.common.CdmBase;
  40 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  41 import eu.etaxonomy.cdm.model.common.ICdmBase;
  42 import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;
  43 import eu.etaxonomy.cdm.model.common.Language;
  44 import eu.etaxonomy.cdm.model.common.LanguageString;
  45 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  46 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  47 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  48 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  49 import eu.etaxonomy.cdm.model.description.Distribution;
  50 import eu.etaxonomy.cdm.model.description.Feature;
  51 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  52 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  53 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  54 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  55 import eu.etaxonomy.cdm.model.description.TextData;
  56 import eu.etaxonomy.cdm.model.location.NamedArea;
  57 import eu.etaxonomy.cdm.model.media.Media;
  58 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  59 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  60 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  61 import eu.etaxonomy.cdm.model.name.HomotypicalGroupNameComparator;
  62 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  63 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  64 import eu.etaxonomy.cdm.model.name.Rank;
  65 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  66 import eu.etaxonomy.cdm.model.name.TaxonName;
  67 import eu.etaxonomy.cdm.model.name.TypeComparator;
  68 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  69 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  70 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  71 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  72 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  73 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  74 import eu.etaxonomy.cdm.model.reference.Reference;
  75 import eu.etaxonomy.cdm.model.reference.ReferenceType;
  76 import eu.etaxonomy.cdm.model.taxon.Synonym;
  77 import eu.etaxonomy.cdm.model.taxon.Taxon;
  78 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  79 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  80
  81 /**
  82  * @author k.luther
  83  * @date 15.03.2017
  84  */
  85 @Component
  86 public class CdmLightClassificationExport
  87             extends CdmExportBase<CdmLightExportConfigurator, CdmLightExportState, IExportTransformer, File>
  88             implements ICdmExport<CdmLightExportConfigurator, CdmLightExportState>{
  89
  90
  91     private static final long serialVersionUID = 2518643632756927053L;
  92     private static final String STD_TEAM_CONCATINATION = ", ";
  93     private static final String FINAL_TEAM_CONCATINATION = " & ";
  94
  95     private static final String IPNI_NAME_IDENTIFIER = "Ipni Name Identifier";
  96     private static final String TROPICOS_NAME_IDENTIFIER = "Tropicos Name Identifier";
  97     private static final String WFO_NAME_IDENTIFIER = "WFO Name Identifier";
  98
  99     public CdmLightClassificationExport() {
 100         super();
 101         this.ioName = this.getClass().getSimpleName();
 102
 103     }
 104
 105     /**
 106      * {@inheritDoc}
 107      */
 108     @Override
 109     protected void doInvoke(CdmLightExportState state) {
 110         try {
 111
 112             IProgressMonitor monitor = state.getConfig().getProgressMonitor();
 113             CdmLightExportConfigurator config = state.getConfig();
 114             config.setFieldsTerminatedBy(",");
 115
 116 //            if (config.getTaxonNodeFilter().getTaxonNodesFilter().isEmpty() && config.getTaxonNodeFilter().getClassificationFilter().isEmpty()){
 117 //                //TODO
 118 //                state.setEmptyData();
 119 //                return;
 120 //            }
 121
 122
 123
 124 //            for (LogicFilter<Classification> classificationFilter : config.getTaxonNodeFilter().getClassificationFilter()){
 125 //                UUID classificationUuid = classificationFilter.getUuid();
 126 //                Classification classification = getClassificationService().find(classificationUuid);
 127 //                if (classification == null){
 128 //                    String message = String.format("Classification for given classification UUID not found. No data imported for %s", classificationUuid.toString());
 129 //                    state.getResult().addWarning(message);
 130 //                }else{
 131 //                    TaxonNode root = classification.getRootNode();
 132 //                    UUID uuid = root.getUuid();
 133 //                    root = getTaxonNodeService().load(uuid);
 134 //                    handleSingleClassification(state, root.getUuid());
 135 //                }
 136 //            }
 137
 138
 139             @SuppressWarnings("unchecked")
 140             TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
 141               = TaxonNodeOutStreamPartitioner.NewInstance(
 142                     this, state, state.getConfig().getTaxonNodeFilter(),
 143                     100, monitor, null);
 144
 145
 146                 monitor.subTask("Start partitioning");
 147
 148                 TaxonNode node = partitioner.next();
 149                 while (node != null){
 150                   handleTaxonNode(state, node.getUuid());
 151                   node = partitioner.next();
 152                 }
 153
 154
 155 //            for (LogicFilter<TaxonNode> taxonNodeFilter : config.getTaxonNodeFilter().getTaxonNodesFilter()){
 156 //                UUID nodeUuid = taxonNodeFilter.getUuid();
 157 //                handleSingleClassification(state, nodeUuid);
 158 //            }
 159             state.getProcessor().createFinalResult(state);
 160         } catch (Exception e) {
 161             state.getResult().addException(e, "An unexpected error occurred in main method doInvoke() " +
 162                     e.getMessage());
 163         }
 164     }
 165
 166     /**
 167      * @param state
 168      * @param classificationUuid
 169      */
 170     private void handleTaxonNode(CdmLightExportState state, UUID taxonNodeUuid) {
 171         try {
 172             TaxonNode taxonNode = getTaxonNodeService().find(taxonNodeUuid);
 173
 174             if (taxonNode == null){
 175                 String message = String.format("TaxonNode for given taxon node UUID not found. No data imported for %s", taxonNodeUuid.toString());
 176                 //TODO
 177                 state.getResult().addWarning(message);
 178             }else{
 179                 TaxonNode root = taxonNode;
 180                 if (root.hasTaxon()){
 181                     handleTaxon(state, root);
 182                 }else{
 183                     for (TaxonNode child : root.getChildNodes()){
 184                         handleTaxon(state, child);
 185                         //TODO progress monitor
 186                     }
 187                 }
 188             }
 189         } catch (Exception e) {
 190             state.getResult().addException(e, "An unexpected error occurred when handling classification " +
 191                     taxonNodeUuid + ": " + e.getMessage() + e.getStackTrace());
 192         }
 193     }
 194
 195     /**
 196      * @param state
 197      * @param taxon
 198      */
 199     private void handleTaxon(CdmLightExportState state, TaxonNode taxonNode) {
 200         try{
 201       //  Taxon taxon = taxonNode.getTaxon();
 202         if (taxonNode == null){
 203             state.getResult().addError ("The taxonNode was null.", "handleTaxon");
 204             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 205             return;
 206         }
 207         if (taxonNode.getTaxon() == null){
 208             state.getResult().addError ("There was a taxon node without a taxon: " + taxonNode.getUuid(), "handleTaxon");
 209             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 210         }else{
 211             Taxon taxon = taxonNode.getTaxon();
 212              try{
 213                 TaxonName name = taxon.getName();
 214                 handleName(state, name);
 215                 for (Synonym syn : taxon.getSynonyms()){
 216                     handleSynonym(state, syn);
 217                 }
 218
 219
 220                 CdmLightExportTable table = CdmLightExportTable.TAXON;
 221                 String[] csvLine = new String[table.getSize()];
 222
 223                 csvLine[table.getIndex(CdmLightExportTable.TAXON_ID)] = getId(state, taxon);
 224                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 225                 Taxon parent = (taxonNode.getParent()==null) ? null : taxonNode.getParent().getTaxon();
 226                 csvLine[table.getIndex(CdmLightExportTable.PARENT_FK)] = getId(state, parent);
 227                 csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
 228                 csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(taxon.getSec());
 229                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_ID)] = getId(state, taxonNode.getClassification());
 230                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification().getTitleCache();
 231
 232                 state.getProcessor().put(table, taxon, csvLine);
 233                 handleDescriptions(state, taxon);
 234              }catch(Exception e){
 235                  state.getResult().addException (e, "An unexpected problem occurred when trying to export "
 236                          + "taxon with id " + taxon.getId());
 237                  state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 238              }
 239        }
 240
 241        taxonNode.removeNullValueFromChildren();
 242 //       for (TaxonNode child: taxonNode.getChildNodes()){
 243 //           handleTaxon(state, child);
 244 //       }
 245         }catch (Exception e){
 246             state.getResult().addException(e, "An unexpected error occurred when handling the taxon node of " +
 247                     cdmBaseStr(taxonNode.getTaxon()) + ": " + e.getMessage());
 248         }
 249     }
 250
 251     /**
 252      * @param state
 253      * @param taxon
 254      */
 255     private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
 256         try{
 257         if (cdmBase instanceof Taxon){
 258             Taxon taxon = HibernateProxyHelper.deproxy(cdmBase, Taxon.class);
 259             Set<TaxonDescription> descriptions = taxon.getDescriptions();
 260             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 261             List<DescriptionElementBase> specimenFacts = new ArrayList<>();
 262             List<DescriptionElementBase> distributionFacts = new ArrayList<>();
 263             List<DescriptionElementBase> commonNameFacts = new ArrayList<>();
 264             List<DescriptionElementBase> usageFacts = new ArrayList<>();
 265             for (TaxonDescription description: descriptions){
 266                 if (description.getElements() != null){
 267                     for (DescriptionElementBase element: description.getElements()){
 268                         element = CdmBase.deproxy(element);
 269                         if (element.getFeature().equals(Feature.COMMON_NAME())){
 270                             commonNameFacts.add(element);
 271                         }else if (element.getFeature().equals(Feature.DISTRIBUTION())){
 272                             distributionFacts.add(element);
 273                         }else if (element instanceof IndividualsAssociation || isSpecimenFeature(element.getFeature())){
 274                             specimenFacts.add(element);
 275                         }else{
 276                             simpleFacts.add(element);
 277                         }
 278                     }
 279                 }
 280             }
 281             if (!commonNameFacts.isEmpty()){
 282                 handleCommonNameFacts(state, taxon, commonNameFacts);
 283             }
 284             if (!distributionFacts.isEmpty()){
 285                 handleDistributionFacts(state, taxon, distributionFacts);
 286             }
 287             if (!specimenFacts.isEmpty()){
 288                 handleSpecimenFacts(state, taxon, specimenFacts);
 289             }
 290             if (!simpleFacts.isEmpty()){
 291                 handleSimpleFacts(state, taxon, simpleFacts);
 292             }
 293         } else if (cdmBase instanceof TaxonName){
 294             TaxonName name = CdmBase.deproxy(cdmBase, TaxonName.class);
 295             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 296             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 297             for (TaxonNameDescription description: descriptions){
 298                 if (description.getElements() != null){
 299                     for (DescriptionElementBase element: description.getElements()){
 300                         if (!element.getFeature().equals(Feature.PROTOLOGUE())){
 301                             simpleFacts.add(element);
 302                         }
 303                     }
 304                 }
 305              }
 306             if (!simpleFacts.isEmpty()){
 307                 handleSimpleFacts(state, name, simpleFacts);
 308             }
 309         }
 310         }catch (Exception e){
 311             state.getResult().addException(e, "An unexpected error occurred when handling description of" +
 312                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 313         }
 314     }
 315
 316
 317     /**
 318      * @param feature
 319      * @return
 320      */
 321     private boolean isSpecimenFeature(Feature feature) {
 322         //TODO allow user defined specimen features
 323         if (feature == null){
 324             return false;
 325         }else if (feature.isSupportsIndividualAssociation()){
 326             return true;
 327         }else{
 328             return feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.INDIVIDUALS_ASSOCIATION())
 329                     || feature.equals(Feature.MATERIALS_EXAMINED()) || feature.equals(Feature.OBSERVATION())
 330                     || feature.equals(Feature.OCCURRENCE())
 331                      ;
 332         }
 333     }
 334
 335     /**
 336      * @param state
 337      * @param taxon
 338      * @param simpleFacts
 339      */
 340     private void handleSimpleFacts(CdmLightExportState state, CdmBase cdmBase,
 341             List<DescriptionElementBase> simpleFacts) {
 342         try {
 343             CdmLightExportTable table = CdmLightExportTable.SIMPLE_FACT;
 344             CdmLightExportTable tableMedia = CdmLightExportTable.MEDIA;
 345             for (DescriptionElementBase element: simpleFacts){
 346                 if (element.getModifyingText().isEmpty() && !element.getMedia().isEmpty()){
 347                     handleSimpleMediaFact(state, cdmBase, tableMedia, element);
 348                 }else{
 349                     handleSingleSimpleFact(state, cdmBase, table, element);
 350                 }
 351             }
 352         } catch (Exception e) {
 353             state.getResult().addException(e, "An unexpected error occurred when handling simple facts for " +
 354                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 355         }
 356     }
 357
 358     /**
 359      * @param state
 360      * @param cdmBase
 361      * @param tableMedia
 362      * @param element
 363      */
 364     private void handleSimpleMediaFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 365             DescriptionElementBase element) {
 366         try {
 367             String[] csvLine;
 368             handleSource(state, element, CdmLightExportTable.MEDIA);
 369
 370             if (element instanceof TextData){
 371                TextData textData = (TextData)element;
 372                csvLine = new String[table.getSize()];
 373                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 374                if (cdmBase instanceof Taxon){
 375                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 376                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 377                }else if (cdmBase instanceof TaxonName){
 378                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 379                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 380                }
 381
 382
 383                String mediaUris = "";
 384                for (Media media: textData.getMedia()){
 385                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 386                    if (!StringUtils.isBlank(mediaString)){
 387                        mediaUris +=  mediaString + ";";
 388                    }
 389                    else{
 390                        state.getResult().addWarning("Empty Media object for uuid: " +
 391                                cdmBase.getUuid() + " uuid of media: " + media.getUuid());
 392                    }
 393                }
 394                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 395
 396             }
 397         } catch (Exception e) {
 398             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 399                     cdmBaseStr(element) + ": " + e.getMessage());
 400         }
 401
 402     }
 403
 404     /**
 405      * @param state
 406      * @param cdmBase
 407      * @param table
 408      * @param element
 409      */
 410     private void handleSingleSimpleFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 411             DescriptionElementBase element) {
 412         try {
 413             String[] csvLine;
 414             handleSource(state, element, CdmLightExportTable.SIMPLE_FACT);
 415
 416             if (element instanceof TextData){
 417                TextData textData = (TextData)element;
 418                csvLine = new String[table.getSize()];
 419                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 420                if (cdmBase instanceof Taxon){
 421                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 422                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 423                }else if (cdmBase instanceof TaxonName){
 424                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 425                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 426                }
 427                csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = textData.getFeature().getLabel();
 428
 429                String mediaUris = "";
 430                for (Media media: textData.getMedia()){
 431                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 432                    if (!StringUtils.isBlank(mediaString)){
 433                        mediaUris +=  mediaString + ";";
 434                    }
 435                    else{
 436                        state.getResult().addWarning("Empty Media object for uuid: " +
 437                                cdmBase.getUuid() + " uuid of media: " + media.getUuid());
 438                    }
 439                }
 440                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 441                if (textData.getFeature().equals(Feature.CITATION())){
 442                   // csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 443                    state.getProcessor().put(table, textData, csvLine);
 444                }else if (!textData.getMultilanguageText().isEmpty()){
 445                    for (Language language: textData.getMultilanguageText().keySet()){
 446                        String[] csvLineLanguage = csvLine.clone();
 447                        LanguageString langString = textData.getLanguageText(language);
 448
 449                        csvLineLanguage[table.getIndex(CdmLightExportTable.FACT_TEXT)] = langString.getText();
 450                        csvLineLanguage[table.getIndex(CdmLightExportTable.LANGUAGE)] = language.getLabel();
 451                        state.getProcessor().put(table, textData, csvLineLanguage);
 452                    }
 453                } else{
 454                    state.getProcessor().put(table, textData, csvLine);
 455                }
 456             }
 457         } catch (Exception e) {
 458             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 459                     cdmBaseStr(element) + ": " + e.getMessage());
 460         }
 461     }
 462
 463
 464     /**
 465      * @param state
 466      * @param specimenFacts
 467      */
 468     private void handleSpecimenFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> specimenFacts) {
 469         CdmLightExportTable table = CdmLightExportTable.SPECIMEN_FACT;
 470
 471         for (DescriptionElementBase element: specimenFacts){
 472             try {
 473                 String[] csvLine = new String[table.getSize()];
 474                 csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 475                 csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 476                 handleSource(state, element, table);
 477                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_NOTES)] = createAnnotationsString(element.getAnnotations());
 478
 479                 if (element instanceof IndividualsAssociation){
 480
 481                     IndividualsAssociation indAssociation = (IndividualsAssociation)element;
 482                     if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
 483                         SpecimenOrObservationBase<?> specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation());
 484
 485                         if (specimenBase instanceof SpecimenOrObservationBase){
 486                             SpecimenOrObservationBase derivedUnit = specimenBase;
 487                             handleSpecimen(state, derivedUnit);
 488                             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
 489                         }else{
 490                             //field units are not supported
 491                             state.getResult().addError("The associated Specimen of taxon " + taxon.getUuid() + " is not an DerivedUnit. Could not be exported.");
 492                         }
 493                     }
 494                 } else if (element instanceof TextData){
 495                     TextData textData = HibernateProxyHelper.deproxy(element, TextData.class);
 496                     csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_DESCRIPTION)] = createMultilanguageString(textData.getMultilanguageText());
 497                 }
 498                 state.getProcessor().put(table, element, csvLine);
 499             } catch (Exception e) {
 500                 state.getResult().addException(e, "An unexpected error occurred when handling single specimen fact " +
 501                         cdmBaseStr(element) + ": " + e.getMessage());
 502             }
 503         }
 504     }
 505
 506     /**
 507      * @param multilanguageText
 508      * @return
 509      */
 510     private String createMultilanguageString(Map<Language, LanguageString> multilanguageText) {
 511        String text = "";
 512        int index = multilanguageText.size();
 513        for(LanguageString langString: multilanguageText.values()){
 514            text += langString.getText();
 515            if (index > 1){
 516                text += "; ";
 517            }
 518            index --;
 519        }
 520
 521         return text;
 522     }
 523
 524     /**
 525      * @param annotations
 526      * @return
 527      */
 528     private String createAnnotationsString(Set<Annotation> annotations) {
 529         StringBuffer strBuff = new StringBuffer();
 530
 531         for (Annotation ann:annotations){
 532             if (ann.getAnnotationType() == null ||!ann.getAnnotationType().equals(AnnotationType.TECHNICAL())){
 533                 strBuff.append(ann.getText());
 534                 strBuff.append("; ");
 535             }
 536         }
 537
 538         if (strBuff.length() > 2){
 539             return strBuff.substring(0, strBuff.length()-2);
 540         }else{
 541             return null;
 542         }
 543     }
 544
 545     /**
 546      * @param state
 547      * @param taxon
 548      * @param element
 549      */
 550     private void handleSource(CdmLightExportState state, DescriptionElementBase element, CdmLightExportTable factsTable) {
 551         CdmLightExportTable table = CdmLightExportTable.FACT_SOURCES;
 552         try {
 553         Set<DescriptionElementSource> sources = element.getSources();
 554
 555         for (DescriptionElementSource source: sources){
 556
 557                 String[] csvLine = new  String[table.getSize()];
 558                 Reference ref = source.getCitation();
 559                 if ((ref == null) && (source.getNameUsedInSource() == null)){
 560                     continue;
 561                 }
 562                 if (ref != null){
 563                     if (state.getReferenceFromStore(ref.getId()) == null){
 564                         handleReference(state, ref);
 565
 566                     }
 567                     csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, ref);
 568                 }
 569                 csvLine[table.getIndex(CdmLightExportTable.FACT_FK)] = getId(state, element);
 570
 571                 csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)] = getId(state, source.getNameUsedInSource());
 572                 csvLine[table.getIndex(CdmLightExportTable.FACT_TYPE)] = factsTable.getTableName();
 573                 if ( StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)])  && StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)])){
 574                     continue;
 575                 }
 576                 state.getProcessor().put(table, source, csvLine);
 577
 578         }
 579         } catch (Exception e) {
 580             state.getResult().addException(e, "An unexpected error occurred when handling single source " +
 581                     cdmBaseStr(element) + ": " + e.getMessage());
 582         }
 583
 584     }
 585
 586     /**
 587      * @param state
 588      * @param distributionFacts
 589      */
 590     private void handleDistributionFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> distributionFacts) {
 591         CdmLightExportTable table = CdmLightExportTable.GEOGRAPHIC_AREA_FACT;
 592
 593         for (DescriptionElementBase element: distributionFacts){
 594             try {
 595                 if (element instanceof Distribution){
 596                     String[] csvLine = new  String[table.getSize()];
 597                     Distribution distribution = (Distribution)element;
 598                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 599                     handleSource(state, element, table);
 600                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 601                     if (distribution.getArea() != null){
 602                         csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = distribution.getArea().getLabel();
 603                     }
 604                     if (distribution.getStatus() != null){
 605                         csvLine[table.getIndex(CdmLightExportTable.STATUS_LABEL)] = distribution.getStatus().getLabel();
 606                     }
 607                     state.getProcessor().put(table, distribution, csvLine);
 608                 } else{
 609                     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());
 610                 }
 611             } catch (Exception e) {
 612                 state.getResult().addException(e, "An unexpected error occurred when handling single distribution " +
 613                         cdmBaseStr(element) + ": " + e.getMessage());
 614             }
 615         }
 616     }
 617
 618     /**
 619      * @param state
 620      * @param commonNameFacts
 621      */
 622     private void handleCommonNameFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> commonNameFacts) {
 623         CdmLightExportTable table = CdmLightExportTable.COMMON_NAME_FACT;
 624
 625         for (DescriptionElementBase element: commonNameFacts){
 626             try {
 627                 if (element instanceof CommonTaxonName){
 628                     String[] csvLine = new  String[table.getSize()];
 629                     CommonTaxonName commonName = (CommonTaxonName)element;
 630                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 631                     handleSource(state, element, table);
 632                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 633                     if (commonName.getName() != null){csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = commonName.getName();}
 634                     if (commonName.getLanguage() != null){csvLine[table.getIndex(CdmLightExportTable.LANGUAGE)] = commonName.getLanguage().getLabel();}
 635                     if (commonName.getArea() != null){ csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = commonName.getArea().getLabel();}
 636                     state.getProcessor().put(table, commonName, csvLine);
 637                 } else{
 638                     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());
 639                 }
 640             } catch (Exception e) {
 641                 state.getResult().addException(e, "An unexpected error occurred when handling single common name " +
 642                         cdmBaseStr(element) + ": " + e.getMessage());
 643             }
 644         }
 645     }
 646
 647     /**
 648      * @param sec
 649      * @return
 650      */
 651     private String getTitleCache(IIdentifiableEntity identEntity) {
 652         if (identEntity == null){
 653             return "";
 654         }
 655         //TODO refresh?
 656         return identEntity.getTitleCache();
 657     }
 658
 659     /**
 660      * @param state
 661      * @param taxon
 662      * @return
 663      */
 664     private String getId(CdmLightExportState state, ICdmBase cdmBase) {
 665         if (cdmBase == null){
 666             return "";
 667         }
 668         //TODO make configurable
 669         return cdmBase.getUuid().toString();
 670     }
 671
 672     /**
 673      * @param state
 674      * @param syn
 675      */
 676     private void handleSynonym(CdmLightExportState state, Synonym syn) {
 677        try {
 678
 679            TaxonName name = syn.getName();
 680            handleName(state, name);
 681
 682            CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 683            String[] csvLine = new String[table.getSize()];
 684
 685            csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, syn);
 686            csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, syn.getAcceptedTaxon());
 687            csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 688            csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, syn.getSec());
 689            csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(syn.getSec());
 690
 691            state.getProcessor().put(table, syn, csvLine);
 692         } catch (Exception e) {
 693             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
 694                     cdmBaseStr(syn) + ": " + e.getMessage());
 695         }
 696     }
 697
 698     /**
 699      * @param state
 700      * @param name
 701      */
 702     private void handleName(CdmLightExportState state, TaxonName name) {
 703         if (name == null){
 704             return;
 705         }
 706         try {
 707             Rank rank = name.getRank();
 708             CdmLightExportTable table = CdmLightExportTable.SCIENTIFIC_NAME;
 709             name = HibernateProxyHelper.deproxy(name);
 710             String[] csvLine = new String[table.getSize()];
 711
 712             csvLine[table.getIndex(CdmLightExportTable.NAME_ID)] = getId(state, name);
 713             if (name.getLsid() != null){
 714                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = name.getLsid().getLsid();
 715             }else{
 716                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = "";
 717             }
 718
 719             handleIdentifier(state, name);
 720             handleDescriptions(state, name);
 721
 722             csvLine[table.getIndex(CdmLightExportTable.RANK)] = getTitleCache(rank);
 723             if (rank != null){
 724                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
 725                 if (rank.isInfraGeneric()){
 726                     try {
 727                         csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
 728                     } catch (UnknownCdmTypeException e) {
 729                         state.getResult().addError("Infrageneric marker expected but not available for rank " + name.getRank().getTitleCache());
 730                     }
 731                 }
 732                 if (rank.isInfraSpecific()){
 733                     csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
 734                 }
 735             }else{
 736                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = "";
 737             }
 738             if (name.isProtectedTitleCache()){
 739                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] =name.getTitleCache();
 740             }else{
 741                 //TODO: adapt the tropicos titlecache creation
 742                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
 743             }
 744             csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
 745             csvLine[table.getIndex(CdmLightExportTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
 746
 747             csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
 748             csvLine[table.getIndex(CdmLightExportTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
 749
 750             csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
 751             csvLine[table.getIndex(CdmLightExportTable.BAS_AUTHORTEAM_FK)] = getId(state,name.getBasionymAuthorship());
 752             if (name.getBasionymAuthorship() != null){
 753                 if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
 754                     handleAuthor(state, name.getBasionymAuthorship());
 755                 }
 756             }
 757             csvLine[table.getIndex(CdmLightExportTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
 758             if (name.getExBasionymAuthorship() != null){
 759                 if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
 760                     handleAuthor(state, name.getExBasionymAuthorship());
 761                 }
 762
 763             }
 764             csvLine[table.getIndex(CdmLightExportTable.COMB_AUTHORTEAM_FK)] = getId(state,name.getCombinationAuthorship());
 765             if (name.getCombinationAuthorship() != null){
 766                 if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
 767                     handleAuthor(state, name.getCombinationAuthorship());
 768                 }
 769             }
 770             csvLine[table.getIndex(CdmLightExportTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
 771             if (name.getExCombinationAuthorship() != null){
 772                 if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
 773                     handleAuthor(state, name.getExCombinationAuthorship());
 774                 }
 775
 776             }
 777
 778             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
 779
 780             Reference nomRef = (Reference)name.getNomenclaturalReference();
 781
 782             if (nomRef != null){
 783                 if (state.getReferenceFromStore(nomRef.getId()) == null){
 784                     handleReference(state, nomRef);
 785                 }
 786                 csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, nomRef);
 787                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = nomRef.getType().name();
 788                 if (nomRef.getVolume() != null){
 789                     csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = nomRef.getVolume();
 790                     csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 791                 }
 792                 if (nomRef.getDatePublished() != null){
 793                     csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = nomRef.getTimePeriodPublishedString();
 794                     csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
 795                     csvLine[table.getIndex(CdmLightExportTable.VERBATIM_DATE)] = null;
 796                 }
 797                 if (name.getNomenclaturalMicroReference() != null){
 798                     csvLine[table.getIndex(CdmLightExportTable.DETAIL)] = name.getNomenclaturalMicroReference();
 799                 }
 800                 nomRef = HibernateProxyHelper.deproxy(nomRef);
 801                 if (nomRef.getInReference() != null){
 802                     Reference inReference = nomRef.getInReference();
 803                     if (inReference.getDatePublished() != null && nomRef.getDatePublished() == null){
 804                         csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = inReference.getDatePublishedString();
 805                         csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = inReference.getDatePublished().getYear();
 806                     }
 807                     if (nomRef.getVolume() == null && inReference.getVolume() != null){
 808                         csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = inReference.getVolume();
 809                         csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 810                     }
 811                     if (inReference.getInReference() != null){
 812                         inReference = inReference.getInReference();
 813                     }
 814                     if (inReference.getAbbrevTitle() == null){
 815                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitleCache());
 816                     }else{
 817                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
 818                     }
 819                     if (inReference.getTitle() == null){
 820                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitleCache());
 821                     }else{
 822                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
 823                     }
 824
 825
 826                     TeamOrPersonBase<?> author = inReference.getAuthorship();
 827                     if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))){
 828                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
 829                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 830                     }else{
 831                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 832                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 833                     }
 834                 }else{
 835                     if (nomRef.getAbbrevTitle() == null){
 836                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitleCache());
 837                     }else{
 838                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle());
 839                     }
 840                     if (nomRef.getTitle() == null){
 841                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitleCache());
 842                     }else{
 843                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitle());
 844                     }
 845                     TeamOrPersonBase<?> author = nomRef.getAuthorship();
 846                     if (author != null ){
 847                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
 848                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 849                     }else{
 850                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 851                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 852                     }
 853
 854                 }
 855             }else{
 856                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = "";
 857             }
 858
 859
 860
 861             /*
 862             * Collation
 863
 864             Detail
 865
 866
 867             TitlePageYear
 868             */
 869             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 870             String protologueUriString = extractURIs(state, descriptions, Feature.PROTOLOGUE());
 871
 872             csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_URI)] = protologueUriString;
 873
 874             if (name.getStatus() == null || name.getStatus().isEmpty()){
 875                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = "";
 876                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = "";
 877             }else{
 878
 879                 String statusStringAbbrev = extractStatusString(state, name, true);
 880                 String statusString = extractStatusString(state, name, false);
 881
 882                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = statusString.trim();
 883                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
 884             }
 885
 886             HomotypicalGroup group =name.getHomotypicalGroup();
 887
 888             if (state.getHomotypicalGroupFromStore(group.getId()) == null){
 889                 handleHomotypicalGroup(state, group);
 890             }
 891             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
 892             List<TaxonName> typifiedNames = new ArrayList<>();
 893             typifiedNames.addAll(group.getTypifiedNames());
 894             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
 895             Integer  seqNumber= typifiedNames.indexOf(name);
 896             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
 897             state.getProcessor().put(table, name, csvLine);
 898
 899             /*
 900              *
 901             Tropicos_ID
 902             IPNI_ID
 903
 904
 905             InfragenericRank
 906
 907
 908             InfraspecificRank
 909             Collation
 910             Volume (Issue)
 911             Detail
 912             DatePublished
 913             YearPublished
 914             TitlePageYear
 915
 916
 917
 918             HomotypicGroupSequenceNumber
 919
 920
 921              *
 922              */
 923         } catch (Exception e) {
 924             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
 925                     cdmBaseStr(name) + ": " + e.getMessage());
 926         }
 927     }
 928
 929     /**
 930      * @return
 931      */
 932     private String createCollatation(TaxonName name) {
 933         String collation = "";
 934         if (name.getNomenclaturalReference() != null){
 935             Reference ref = (Reference) name.getNomenclaturalReference();
 936             collation = getVolume(ref);
 937         }
 938         if (name.getNomenclaturalMicroReference() != null){
 939             if (!StringUtils.isBlank(collation)){
 940                 collation += ":";
 941             }
 942             collation +=name.getNomenclaturalMicroReference();
 943         }
 944
 945         return collation;
 946     }
 947
 948     /**
 949      * @param nomenclaturalReference
 950      * @return
 951      */
 952     private String getVolume(Reference reference) {
 953         if (reference.getVolume() != null){
 954             return reference.getVolume();
 955         }else if (reference.getInReference() != null){
 956             if (reference.getInReference().getVolume() != null){
 957                 return reference.getInReference().getVolume();
 958             }
 959         }
 960         return null;
 961     }
 962
 963     /**
 964      * @param state
 965      * @param name
 966      */
 967     private void handleIdentifier(CdmLightExportState state, TaxonName name) {
 968         CdmLightExportTable table = CdmLightExportTable.IDENTIFIER;
 969         String[] csvLine;
 970         try {
 971             Set<String>  IPNIidentifiers = name.getIdentifiers(DefinedTerm.IPNI_NAME_IDENTIFIER());
 972             Set<String>  tropicosIdentifiers = name.getIdentifiers(DefinedTerm.TROPICOS_NAME_IDENTIFIER());
 973             Set<String>  WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
 974             if (!IPNIidentifiers.isEmpty()){
 975                 csvLine = new String[table.getSize()];
 976                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
 977                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
 978                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(IPNIidentifiers);
 979                 state.getProcessor().put(table, name, csvLine);
 980             }
 981             if (!tropicosIdentifiers.isEmpty()){
 982                 csvLine = new String[table.getSize()];
 983                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
 984                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = TROPICOS_NAME_IDENTIFIER;
 985                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(tropicosIdentifiers);
 986                 state.getProcessor().put(table, name, csvLine);
 987             }
 988             if (!WFOIdentifiers.isEmpty()){
 989                 csvLine = new String[table.getSize()];
 990                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
 991                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
 992                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(WFOIdentifiers);
 993                 state.getProcessor().put(table, name, csvLine);
 994             }
 995         } catch (Exception e) {
 996             state.getResult().addException(e, "An unexpected error occurred when handling identifiers for " +
 997                     cdmBaseStr(name) + ": " + e.getMessage());
 998
 999         }
1000     }
1001
1002     /**
1003      * @param tropicosIdentifiers
1004      */
1005     private String extractIdentifier(Set<String> identifierSet) {
1006
1007         String identifierString = "";
1008         for (String identifier: identifierSet){
1009             if (!StringUtils.isBlank(identifierString)){
1010                 identifierString += ", ";
1011             }
1012             identifierString += identifier;
1013         }
1014
1015         return identifierString;
1016     }
1017
1018     /**
1019      * @param state
1020      * @param descriptions
1021      * @return
1022      */
1023     private String extractURIs(CdmLightExportState state,
1024             Set<? extends DescriptionBase<?>> descriptionsSet, Feature feature) {
1025         String mediaUriString = "";
1026         SpecimenDescription specimenDescription;
1027         TaxonDescription taxonDescription;
1028         TaxonNameDescription nameDescription;
1029         Set<DescriptionElementBase> elements = new HashSet<>();
1030         for (DescriptionBase<?> description : descriptionsSet){
1031             try {
1032                 if (!description.getElements().isEmpty()){
1033                     if (description instanceof SpecimenDescription){
1034                         specimenDescription = (SpecimenDescription)description;
1035                         elements = specimenDescription.getElements();
1036                     }else if (description instanceof TaxonDescription){
1037                         taxonDescription = (TaxonDescription) description;
1038                         elements = taxonDescription.getElements();
1039                     } else if (description instanceof TaxonNameDescription){
1040                         nameDescription = (TaxonNameDescription) description;
1041                         elements = nameDescription.getElements();
1042                     }
1043
1044                     for (DescriptionElementBase element : elements){
1045                         Feature entityFeature = HibernateProxyHelper.deproxy(element.getFeature());
1046                         if (entityFeature.equals(feature)){
1047                             if (!element.getMedia().isEmpty()){
1048                                 List<Media> media = element.getMedia();
1049                                 for (Media mediaElement: media){
1050                                     Iterator<MediaRepresentation> it =  mediaElement.getRepresentations().iterator();
1051                                     mediaUriString = extractMediaUris(it);
1052                                 }
1053                             }
1054                         }
1055                     }
1056                 }
1057             } catch (Exception e) {
1058                 state.getResult().addException(e, "An unexpected error occurred when extracting media URIs for " +
1059                         cdmBaseStr(description) + ": " + e.getMessage());
1060             }
1061         }
1062         return mediaUriString;
1063     }
1064
1065     /**
1066      * @param state
1067      * @param basionymAuthorship
1068      */
1069     private void handleAuthor(CdmLightExportState state, TeamOrPersonBase<?> author) {
1070         try {
1071             if (state.getAuthorFromStore(author.getId()) != null){
1072                 return;
1073             }
1074             state.addAuthorToStore(author);
1075             CdmLightExportTable table = CdmLightExportTable.NOMENCLATURAL_AUTHOR;
1076             String[] csvLine = new String[table.getSize()];
1077             CdmLightExportTable tableAuthorRel = CdmLightExportTable.NOMENCLATURAL_AUTHOR_TEAM_RELATION;
1078             String[] csvLineRel = new String[tableAuthorRel.getSize()];
1079             String[] csvLineMember = new String[table.getSize()];
1080             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, author);
1081             csvLine[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = author.getNomenclaturalTitle();
1082             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = author.getTitleCache();
1083             author = HibernateProxyHelper.deproxy(author);
1084             if (author instanceof Person){
1085                 Person authorPerson = (Person)author;
1086                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FIRST_NAME)] = authorPerson.getFirstname();
1087                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_LASTNAME)] = authorPerson.getLastname();
1088                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = authorPerson.getPrefix();
1089                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = authorPerson.getSuffix();
1090             } else{
1091                 // create an entry in rel table and all members in author table, check whether the team members already in author table
1092
1093                 Team authorTeam = (Team)author;
1094                 int index = 0;
1095                 for (Person member: authorTeam.getTeamMembers()){
1096                     csvLineRel = new String[tableAuthorRel.getSize()];
1097                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_FK)] = getId(state, authorTeam);
1098                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state, member);
1099                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_SEQ_NUMBER)] = String.valueOf(index);
1100                     state.getProcessor().put(tableAuthorRel, authorTeam.getId() +":" +member.getId(), csvLineRel);
1101
1102                     if (state.getAuthorFromStore(member.getId()) == null){
1103                         state.addAuthorToStore(member);
1104                         csvLineMember = new String[table.getSize()];
1105                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, member);
1106                         csvLineMember[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = member.getNomenclaturalTitle();
1107                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = member.getTitleCache();
1108                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_FIRST_NAME)] = member.getFirstname();
1109                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_LASTNAME)] = member.getLastname();
1110                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = member.getPrefix();
1111                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = member.getSuffix();
1112                         state.getProcessor().put(table, member, csvLineMember);
1113                     }
1114                     index++;
1115
1116                 }
1117             }
1118             state.getProcessor().put(table, author, csvLine);
1119         } catch (Exception e) {
1120             state.getResult().addException(e, "An unexpected error occurred when handling author " +
1121                     cdmBaseStr(author) + ": " + e.getMessage());
1122         }
1123     }
1124
1125     /**
1126      * @param state
1127      * @param name
1128      * @param statusString
1129      * @return
1130      */
1131     private String extractStatusString(CdmLightExportState state, TaxonName name, boolean abbrev) {
1132         try {
1133             Set<NomenclaturalStatus> status = name.getStatus();
1134             if (status.isEmpty()){
1135                 return "";
1136             }
1137             String statusString = "";
1138             for (NomenclaturalStatus nameStatus: status){
1139                 if (nameStatus != null){
1140                     if (abbrev){
1141                         if (nameStatus.getType() != null){
1142                             statusString += nameStatus.getType().getIdInVocabulary();
1143                         }
1144                     }else{
1145                         if (nameStatus.getType() != null){
1146                             statusString += nameStatus.getType().getTitleCache();
1147                         }
1148                     }
1149                     if (!abbrev){
1150
1151                         if (nameStatus.getRuleConsidered() != null && !StringUtils.isBlank(nameStatus.getRuleConsidered())){
1152                             statusString += " " + nameStatus.getRuleConsidered();
1153                         }
1154                         if (nameStatus.getCitation() != null){
1155                             statusString += " " + nameStatus.getCitation().getTitleCache();
1156                         }
1157                         if (nameStatus.getCitationMicroReference() != null && !StringUtils.isBlank(nameStatus.getCitationMicroReference())){
1158                             statusString += " " + nameStatus.getCitationMicroReference();
1159                         }
1160                     }
1161                     statusString += " ";
1162                 }
1163             }
1164             return statusString;
1165         } catch (Exception e) {
1166             state.getResult().addException(e, "An unexpected error occurred when extracting status string for " +
1167                     cdmBaseStr(name) + ": " + e.getMessage());
1168             return "";
1169         }
1170     }
1171
1172     /**
1173      * @param group
1174      */
1175     private void handleHomotypicalGroup(CdmLightExportState state, HomotypicalGroup group) {
1176         try {
1177             state.addHomotypicalGroupToStore(group);
1178             CdmLightExportTable table = CdmLightExportTable.HOMOTYPIC_GROUP;
1179             String[] csvLine = new String[table.getSize()];
1180
1181             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_ID)] = getId(state, group);
1182             List<TaxonName> typifiedNames = new ArrayList<>();
1183             typifiedNames.addAll(group.getTypifiedNames());
1184             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
1185             String typifiedNamesString = "";
1186             for (TaxonName name: typifiedNames){
1187                 //Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)
1188                 //TODO: nameRelations, which and how to display
1189
1190
1191                 typifiedNamesString += name.getTitleCache()+ extractStatusString(state, name, true) + "; ";
1192             }
1193             typifiedNamesString = typifiedNamesString.substring(0, typifiedNamesString.length()-2);
1194             if (typifiedNamesString != null){
1195                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = typifiedNamesString.trim();
1196             }else{
1197                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = "";
1198             }
1199             Set<TypeDesignationBase> typeDesigantions = group.getTypeDesignations();
1200             List<TypeDesignationBase> designationList = new ArrayList<>();
1201             designationList.addAll(typeDesigantions);
1202             Collections.sort(designationList, new TypeComparator());
1203             StringBuffer typeDesignationString = new StringBuffer();
1204             for (TypeDesignationBase typeDesignation: typeDesigantions){
1205                 if (typeDesignation != null && typeDesignation.getTypeStatus() != null){
1206                     typeDesignationString.append(typeDesignation.getTypeStatus().getTitleCache() + ": ");
1207                 }
1208                 if (typeDesignation instanceof SpecimenTypeDesignation){
1209                     if (((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen() != null){
1210                         typeDesignationString.append(((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen().getTitleCache());
1211                         handleSpecimen(state, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
1212                     }
1213                 }else{
1214                     if (((NameTypeDesignation)typeDesignation).getTypeName() != null){
1215                         typeDesignationString.append(((NameTypeDesignation)typeDesignation).getTypeName().getTitleCache());
1216                     }
1217                 }
1218                 if(typeDesignation.getCitation() != null ){
1219                     typeDesignationString.append(", "+typeDesignation.getCitation().getTitleCache());
1220                 }
1221                 //TODO...
1222                 /*
1223                  * Sortierung:
1224                 1.  Status der Typen: a) holo, lecto, neo, syn, b) epi, paralecto, c) para (wenn überhaupt) – die jeweiligen iso immer direct mit dazu
1225                 2.  Land
1226                 3.  Sammler
1227                 4.  Nummer
1228
1229                 Aufbau der Typusinformationen:
1230                 Land: Lokalität mit Höhe und Koordinaten; Datum; Sammler Nummer (Herbar/Barcode, Typusart; Herbar/Barcode, Typusart …)
1231
1232                  */
1233             }
1234             String typeDesignations = typeDesignationString.toString();
1235             if (typeDesignations != null){
1236                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = typeDesignations;
1237             }else{
1238                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = "";
1239             }
1240             state.getProcessor().put(table, String.valueOf(group.getId()), csvLine);
1241         } catch (Exception e) {
1242             state.getResult().addException(e, "An unexpected error occurred when handling homotypic group " +
1243                     cdmBaseStr(group) + ": " + e.getMessage());
1244         }
1245     }
1246
1247     /**
1248      * @param name
1249      * @return
1250      */
1251     private String getTropicosTitleCache(CdmLightExportState state, TaxonName name) {
1252         try {
1253             String basionymStart = "(";
1254             String basionymEnd = ") ";
1255             String exAuthorSeperator = " ex ";
1256             TeamOrPersonBase<?> combinationAuthor = name.getCombinationAuthorship();
1257             TeamOrPersonBase<?> exCombinationAuthor = name.getExCombinationAuthorship();
1258             TeamOrPersonBase<?> basionymAuthor = name.getBasionymAuthorship();
1259             TeamOrPersonBase<?> exBasionymAuthor = name.getExBasionymAuthorship();
1260
1261             String combinationAuthorString = "";
1262             if (combinationAuthor != null){
1263                 combinationAuthor = HibernateProxyHelper.deproxy(combinationAuthor);
1264                 if (combinationAuthor instanceof Team){
1265                     combinationAuthorString = createTropicosTeamTitle(combinationAuthor);
1266                 }else{
1267                     Person person = HibernateProxyHelper.deproxy(combinationAuthor, Person.class);
1268                     combinationAuthorString = createTropicosAuthorString(person);
1269                 }
1270             }
1271             String exCombinationAuthorString = "";
1272             if (exCombinationAuthor != null){
1273                 exCombinationAuthor = HibernateProxyHelper.deproxy(exCombinationAuthor);
1274                 if (exCombinationAuthor instanceof Team){
1275                    exCombinationAuthorString = createTropicosTeamTitle(exCombinationAuthor);
1276                 }else{
1277                     Person person = HibernateProxyHelper.deproxy(exCombinationAuthor, Person.class);
1278                     exCombinationAuthorString = createTropicosAuthorString(person);
1279                 }
1280             }
1281
1282             String basionymAuthorString = "";
1283             if (basionymAuthor != null){
1284                 basionymAuthor = HibernateProxyHelper.deproxy(basionymAuthor);
1285                 if (basionymAuthor instanceof Team){
1286                     basionymAuthorString =  createTropicosTeamTitle(basionymAuthor);
1287                 }else{
1288                     Person person = HibernateProxyHelper.deproxy(basionymAuthor, Person.class);
1289                     basionymAuthorString = createTropicosAuthorString(person);
1290                 }
1291             }
1292
1293             String exBasionymAuthorString = "";
1294
1295             if (exBasionymAuthor != null){
1296                 exBasionymAuthor = HibernateProxyHelper.deproxy(exBasionymAuthor);
1297                 if (exBasionymAuthor instanceof Team){
1298                     exBasionymAuthorString = createTropicosTeamTitle(exBasionymAuthor);
1299
1300                 }else{
1301                     Person person = HibernateProxyHelper.deproxy(exBasionymAuthor, Person.class);
1302                     exBasionymAuthorString = createTropicosAuthorString(person);
1303                 }
1304             }
1305             String completeAuthorString =  name.getNameCache() + " ";
1306
1307             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymStart: "";
1308             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString)) ? (CdmUtils.Nz(exBasionymAuthorString) + exAuthorSeperator): "" ;
1309             completeAuthorString += (!CdmUtils.isBlank(basionymAuthorString))? CdmUtils.Nz(basionymAuthorString):"";
1310             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ?  basionymEnd:"";
1311             completeAuthorString += (!CdmUtils.isBlank(exCombinationAuthorString)) ? (CdmUtils.Nz(exCombinationAuthorString) + exAuthorSeperator): "" ;
1312             completeAuthorString += (!CdmUtils.isBlank(combinationAuthorString))? CdmUtils.Nz(combinationAuthorString):"";
1313
1314
1315             return completeAuthorString;
1316         } catch (Exception e) {
1317             state.getResult().addException(e, "An unexpected error occurred when handling tropicos title cache for " +
1318                     cdmBaseStr(name) + ": " + e.getMessage());
1319             return null;
1320         }
1321     }
1322
1323     /**
1324      * @param combinationAuthor
1325      * @return
1326      */
1327     private String createTropicosTeamTitle(TeamOrPersonBase<?> combinationAuthor) {
1328         String combinationAuthorString;
1329         Team team = HibernateProxyHelper.deproxy(combinationAuthor, Team.class);
1330         Team tempTeam = Team.NewInstance();
1331         for (Person teamMember:team.getTeamMembers()){
1332             combinationAuthorString = createTropicosAuthorString(teamMember);
1333             Person tempPerson = Person.NewTitledInstance(combinationAuthorString);
1334             tempTeam.addTeamMember(tempPerson);
1335         }
1336         combinationAuthorString = tempTeam.generateTitle();
1337         return combinationAuthorString;
1338     }
1339
1340     /**
1341      * @param teamMember
1342      */
1343     private String createTropicosAuthorString(Person teamMember) {
1344         String nomAuthorString = "";
1345         String[] splittedAuthorString = null;
1346         if (teamMember == null){
1347             return nomAuthorString;
1348         }
1349
1350         if (teamMember.getFirstname() != null){
1351             String firstNameString = teamMember.getFirstname().replaceAll("\\.", "\\. ");
1352             splittedAuthorString = firstNameString.split("\\s");
1353             for (String split: splittedAuthorString){
1354                 if (!StringUtils.isBlank(split)){
1355                     nomAuthorString += split.substring(0, 1);
1356                     nomAuthorString += ".";
1357                 }
1358             }
1359         }
1360         if (teamMember.getLastname() != null){
1361             String lastNameString = teamMember.getLastname().replaceAll("\\.", "\\. ");
1362             splittedAuthorString = lastNameString.split("\\s");
1363             for (String split: splittedAuthorString){
1364                 nomAuthorString += " " +split;
1365             }
1366         }
1367         if (StringUtils.isBlank(nomAuthorString.trim())){
1368             if (teamMember.getTitleCache() != null) {
1369                 String titleCacheString = teamMember.getTitleCache().replaceAll("\\.", "\\. ");
1370                 splittedAuthorString = titleCacheString.split("\\s");
1371             }
1372
1373
1374             int index = 0;
1375             for (String split: splittedAuthorString){
1376                 if ( index < splittedAuthorString.length-1 && (split.length()==1 || split.endsWith("."))){
1377                     nomAuthorString += split;
1378                 }else{
1379                     nomAuthorString = nomAuthorString +" "+ split;
1380                 }
1381                 index++;
1382             }
1383         }
1384         return nomAuthorString.trim();
1385     }
1386
1387     /**
1388      * @param state
1389      * @param name
1390      */
1391     private void handleReference(CdmLightExportState state, Reference reference) {
1392         try {
1393             state.addReferenceToStore(reference);
1394             CdmLightExportTable table = CdmLightExportTable.REFERENCE;
1395
1396             String[] csvLine = new String[table.getSize()];
1397             csvLine[table.getIndex(CdmLightExportTable.REFERENCE_ID)] = getId(state, reference);
1398             //TODO short citations correctly
1399             String shortCitation = createShortCitation(reference);  //Should be Author(year) like in Taxon.sec
1400             csvLine[table.getIndex(CdmLightExportTable.BIBLIO_SHORT_CITATION)] = shortCitation;
1401             //TODO get preferred title
1402             csvLine[table.getIndex(CdmLightExportTable.REF_TITLE)] = reference.getTitle();
1403             csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_TITLE)] = reference.getAbbrevTitle();
1404             csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = reference.getDatePublishedString();
1405             //TBC
1406             csvLine[table.getIndex(CdmLightExportTable.EDITION)] = reference.getEdition();
1407             csvLine[table.getIndex(CdmLightExportTable.EDITOR)] = reference.getEditor();
1408             csvLine[table.getIndex(CdmLightExportTable.ISBN)] = reference.getIsbn();
1409             csvLine[table.getIndex(CdmLightExportTable.ISSN)] = reference.getIssn();
1410             csvLine[table.getIndex(CdmLightExportTable.ORGANISATION)] = reference.getOrganization();
1411             csvLine[table.getIndex(CdmLightExportTable.PAGES)] = reference.getPages();
1412             csvLine[table.getIndex(CdmLightExportTable.PLACE_PUBLISHED)] = reference.getPlacePublished();
1413             csvLine[table.getIndex(CdmLightExportTable.PUBLISHER)] = reference.getPublisher();
1414             csvLine[table.getIndex(CdmLightExportTable.REF_ABSTRACT)] = reference.getReferenceAbstract();
1415             csvLine[table.getIndex(CdmLightExportTable.SERIES_PART)] = reference.getSeriesPart();
1416             csvLine[table.getIndex(CdmLightExportTable.VOLUME)] = reference.getVolume();
1417             csvLine[table.getIndex(CdmLightExportTable.YEAR)] = reference.getYear();
1418             if ( reference.getAuthorship() != null){
1419                 csvLine[table.getIndex(CdmLightExportTable.AUTHORSHIP_TITLE)] = reference.getAuthorship().getTitleCache();
1420                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state,reference.getAuthorship());
1421             }
1422
1423             csvLine[table.getIndex(CdmLightExportTable.IN_REFERENCE)] = getId(state, reference.getInReference());
1424             if (reference.getInReference() != null && state.getReferenceFromStore(reference.getInReference().getId()) == null){
1425                 handleReference(state, reference.getInReference());
1426             }
1427             if ( reference.getInstitution() != null){ csvLine[table.getIndex(CdmLightExportTable.INSTITUTION)] = reference.getInstitution().getTitleCache();}
1428             if ( reference.getLsid() != null){ csvLine[table.getIndex(CdmLightExportTable.LSID)] = reference.getLsid().getLsid();}
1429             if ( reference.getSchool() != null){ csvLine[table.getIndex(CdmLightExportTable.SCHOOL)] = reference.getSchool().getTitleCache();}
1430             if ( reference.getUri() != null){ csvLine[table.getIndex(CdmLightExportTable.URI)] = reference.getUri().toString();}
1431             csvLine[table.getIndex(CdmLightExportTable.REF_TYPE)] = reference.getType().getKey();
1432
1433             state.getProcessor().put(table, reference, csvLine);
1434         } catch (Exception e) {
1435             state.getResult().addException(e, "An unexpected error occurred when handling reference " +
1436                     cdmBaseStr(reference) + ": " + e.getMessage());
1437         }
1438
1439     }
1440
1441
1442     /**
1443      * @param reference
1444      * @return
1445      */
1446     private String createShortCitation(Reference reference) {
1447         TeamOrPersonBase<?> authorship = reference.getAuthorship();
1448         String shortCitation = "";
1449         if (authorship == null) {
1450             return null;
1451         }
1452         authorship = HibernateProxyHelper.deproxy(authorship);
1453         if (authorship instanceof Person){ shortCitation = ((Person)authorship).getLastname();}
1454         else if (authorship instanceof Team){
1455
1456             Team authorTeam = HibernateProxyHelper.deproxy(authorship, Team.class);
1457             int index = 0;
1458
1459             for (Person teamMember : authorTeam.getTeamMembers()){
1460                 index++;
1461                 String concat = concatString(authorTeam, authorTeam.getTeamMembers(), index);
1462                 shortCitation += concat + teamMember.getLastname();
1463             }
1464
1465         }
1466         if (reference.getYear() != null){
1467             shortCitation = shortCitation + " (" + reference.getYear() + ")";
1468         }
1469         return shortCitation;
1470     }
1471
1472     private static String concatString(Team team, List<Person> teamMembers, int i) {
1473         String concat;
1474         if (i <= 1){
1475             concat = "";
1476         }else if (i < teamMembers.size() || ( team.isHasMoreMembers() && i == teamMembers.size())){
1477             concat = STD_TEAM_CONCATINATION;
1478         }else{
1479             concat = FINAL_TEAM_CONCATINATION;
1480         }
1481         return concat;
1482     }
1483
1484     /*
1485      * TypeDesignation table
1486      * Specimen_Fk
1487      *  EditName_Fk
1488      *   TypeVerbatimCitation
1489      *   TypeCategory
1490      *   TypeDesignatedByString
1491      *   TypeDesignatedByRef_Fk
1492      */
1493
1494     private void handleSpecimenTypeDesignations(CdmLightExportState state, TaxonName name){
1495        try {
1496            Set<SpecimenTypeDesignation> typeDesignations = name.getSpecimenTypeDesignations();
1497            CdmLightExportTable table = CdmLightExportTable.TYPE_DESIGNATION;
1498            String nameId = getId(state, name);
1499            String[] csvLine = new String[table.getSize()];
1500             for (SpecimenTypeDesignation specimenType: typeDesignations){
1501                 csvLine = new String[table.getSize()];
1502                 DerivedUnit specimen = specimenType.getTypeSpecimen();
1503                 if (state.getSpecimenFromStore(specimen.getId()) == null){
1504                     handleSpecimen(state, specimen);
1505                 }
1506                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
1507                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = nameId;
1508                 csvLine[table.getIndex(CdmLightExportTable.TYPE_VERBATIM_CITATION)] = specimenType.getTypeSpecimen().generateTitle();
1509                 //TODO: add link to existing Vorcabulary
1510                 csvLine[table.getIndex(CdmLightExportTable.TYPE_CATEGORY)] = "";
1511                 csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_STRING)] = specimenType.getCitation().getTitleCache();
1512                 csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_REF_FK)] = getId(state, specimenType.getCitation());
1513             }
1514         } catch (Exception e) {
1515             state.getResult().addException(e, "An unexpected error occurred when handling specimen type designations for " +
1516                     cdmBaseStr(name) + ": " + e.getMessage());
1517         }
1518     }
1519
1520     /**
1521      * @param state
1522      * @param specimen
1523      */
1524     private void handleSpecimen(CdmLightExportState state, SpecimenOrObservationBase specimen) {
1525         try {
1526             state.addSpecimenToStore(specimen);
1527             CdmLightExportTable table = CdmLightExportTable.SPECIMEN;
1528             String specimenId = getId(state, specimen);
1529             String[] csvLine = new String[table.getSize()];
1530
1531             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_ID)] = specimenId;
1532             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
1533             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractURIs(state, specimen.getDescriptions(), Feature.IMAGE());
1534             if (specimen instanceof DerivedUnit){
1535                     DerivedUnit derivedUnit = (DerivedUnit)specimen;
1536                     if (derivedUnit.getCollection() != null){ csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection().getCode();}
1537
1538                 if (specimen instanceof MediaSpecimen){
1539                     MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
1540                     Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
1541                     String mediaUris = extractMediaUris(it);
1542                     csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
1543
1544                 }
1545
1546                 if (derivedUnit.getDerivedFrom() != null){
1547                     for (SpecimenOrObservationBase<?> original: derivedUnit.getDerivedFrom().getOriginals()){
1548                         //TODO: What to do if there are more then one FieldUnit??
1549                         if (original instanceof FieldUnit){
1550                             FieldUnit fieldUnit = (FieldUnit)original;
1551                             csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
1552
1553                             GatheringEvent gathering = fieldUnit.getGatheringEvent();
1554                             if (gathering != null){
1555                                 if (gathering.getLocality() != null){ csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();}
1556                                 if (gathering.getCountry() != null){csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();}
1557                                 csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
1558                                 addCollectingAreas(state, gathering);
1559                                 if (gathering.getGatheringDate() != null){csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
1560                                 if (!gathering.getCollectingAreas().isEmpty()){
1561                                     int index = 0;
1562                                     csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
1563                                     for (NamedArea area: gathering.getCollectingAreas()){
1564                                         if (index == 0){
1565                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getTermType().getKey();
1566                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
1567                                         }
1568                                         if (index == 1){
1569                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getTermType().getKey();
1570                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
1571                                         }
1572                                         if (index == 2){
1573                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getTermType().getKey();
1574                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
1575                                         }
1576                                         if (index == 3){
1577                                             csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
1578                                             break;
1579                                         }
1580                                         index++;
1581                                     }
1582                                 }
1583                             }
1584                         }
1585                     }
1586                 }
1587             }
1588
1589             state.getProcessor().put(table, specimen, csvLine);
1590         } catch (Exception e) {
1591             state.getResult().addException(e, "An unexpected error occurred when handling specimen " +
1592                     cdmBaseStr(specimen) + ": " + e.getMessage());
1593         }
1594     }
1595
1596     /**
1597      * @param it
1598      */
1599     private String extractMediaUris(Iterator<MediaRepresentation> it) {
1600
1601         String mediaUriString = "";
1602         boolean first = true;
1603         while(it.hasNext()){
1604             MediaRepresentation rep = it.next();
1605             List<MediaRepresentationPart> parts = rep.getParts();
1606             for (MediaRepresentationPart part: parts){
1607                 if (first){
1608                     if (part.getUri() != null){
1609                         mediaUriString += part.getUri().toString();
1610                         first = false;
1611                     }
1612                 }else{
1613                     if (part.getUri() != null){
1614                         mediaUriString += ", " +part.getUri().toString();
1615                     }
1616                 }
1617             }
1618         }
1619
1620         return mediaUriString;
1621     }
1622
1623     /**
1624      * @param state
1625      * @param gathering
1626      */
1627     private void addCollectingAreas(CdmLightExportState state, GatheringEvent gathering) {
1628         // TODO implement !!!
1629
1630         if (!gathering.getCollectingAreas().isEmpty()){
1631             state.getResult().addWarning("Collecting areas not yet implemented but gathering " +
1632                     cdmBaseStr(gathering) + " has collecting areas.");
1633         }
1634
1635     }
1636
1637     /**
1638      * @param gathering
1639      * @return
1640      */
1641     private String createCollectorString(CdmLightExportState state, GatheringEvent gathering, FieldUnit fieldUnit) {
1642         try {
1643             String collectorString = "";
1644             AgentBase<?> collectorA = CdmBase.deproxy(gathering.getCollector());
1645             if (gathering.getCollector() != null){
1646                if (collectorA instanceof TeamOrPersonBase
1647                        && state.getConfig().isHighLightPrimaryCollector()){
1648
1649                    Person primaryCollector = fieldUnit.getPrimaryCollector();
1650                    if (collectorA instanceof Team){
1651                        Team collectorTeam = (Team)collectorA;
1652                        boolean isFirst = true;
1653                        for (Person member: collectorTeam.getTeamMembers()){
1654                            if (!isFirst){
1655                                collectorString += "; ";
1656                            }
1657                            if (member.equals(primaryCollector)){
1658                                //highlight
1659                                collectorString += "<b>" + member.getTitleCache() + "</b>";
1660                            }else{
1661                                collectorString += member.getTitleCache();
1662                            }
1663                        }
1664                    }
1665                } else{
1666                    collectorString = collectorA.getTitleCache();
1667                }
1668            }
1669            return collectorString;
1670         } catch (Exception e) {
1671             state.getResult().addException(e, "An unexpected error occurred when creating collector string for " +
1672                     cdmBaseStr(fieldUnit) + ": " + e.getMessage());
1673             return "";
1674         }
1675     }
1676
1677
1678     /**
1679      * Returns a string representation of the {@link CdmBase cdmBase} object
1680      * for result messages.
1681      */
1682     private String cdmBaseStr(CdmBase cdmBase) {
1683         if (cdmBase == null){
1684             return "-no object available-";
1685         }else{
1686             return cdmBase.getClass().getSimpleName() + ": " + cdmBase.getUuid();
1687         }
1688     }
1689
1690     /**
1691      * {@inheritDoc}
1692      */
1693     @Override
1694     protected boolean doCheck(CdmLightExportState state) {
1695         return false;
1696     }
1697
1698     /**
1699      * {@inheritDoc}
1700      */
1701     @Override
1702     protected boolean isIgnore(CdmLightExportState state) {
1703         return false;
1704     }
1705
1706 }