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.api.service.name.TypeDesignationSetManager;
  24 import eu.etaxonomy.cdm.common.CdmUtils;
  25 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  26 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  27 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  28 import eu.etaxonomy.cdm.io.common.CdmExportBase;
  29 import eu.etaxonomy.cdm.io.common.ExportResult.ExportResultState;
  30 import eu.etaxonomy.cdm.io.common.ICdmExport;
  31 import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
  32 import eu.etaxonomy.cdm.io.common.XmlExportState;
  33 import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
  34 import eu.etaxonomy.cdm.model.agent.AgentBase;
  35 import eu.etaxonomy.cdm.model.agent.Person;
  36 import eu.etaxonomy.cdm.model.agent.Team;
  37 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  38 import eu.etaxonomy.cdm.model.common.Annotation;
  39 import eu.etaxonomy.cdm.model.common.AnnotationType;
  40 import eu.etaxonomy.cdm.model.common.CdmBase;
  41 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  42 import eu.etaxonomy.cdm.model.common.ICdmBase;
  43 import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;
  44 import eu.etaxonomy.cdm.model.common.Language;
  45 import eu.etaxonomy.cdm.model.common.LanguageString;
  46 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  47 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  48 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  49 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  50 import eu.etaxonomy.cdm.model.description.Distribution;
  51 import eu.etaxonomy.cdm.model.description.Feature;
  52 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  53 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  54 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  55 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  56 import eu.etaxonomy.cdm.model.description.TextData;
  57 import eu.etaxonomy.cdm.model.location.NamedArea;
  58 import eu.etaxonomy.cdm.model.media.Media;
  59 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  60 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  61 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  62 import eu.etaxonomy.cdm.model.name.HomotypicalGroupNameComparator;
  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.cache.TagEnum;
  82 import eu.etaxonomy.cdm.strategy.cache.TaggedText;
  83 import eu.etaxonomy.cdm.strategy.cache.reference.DefaultReferenceCacheStrategy;
  84 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  85
  86 /**
  87  * @author k.luther
  88  * @since 15.03.2017
  89  */
  90 @Component
  91 public class CdmLightClassificationExport
  92             extends CdmExportBase<CdmLightExportConfigurator, CdmLightExportState, IExportTransformer, File>
  93             implements ICdmExport<CdmLightExportConfigurator, CdmLightExportState>{
  94
  95
  96     private static final long serialVersionUID = 2518643632756927053L;
  97     private static final String STD_TEAM_CONCATINATION = ", ";
  98     private static final String FINAL_TEAM_CONCATINATION = " & ";
  99
 100
 101     private static final String IPNI_NAME_IDENTIFIER = "Ipni Name Identifier";
 102     private static final String TROPICOS_NAME_IDENTIFIER = "Tropicos Name Identifier";
 103     private static final String WFO_NAME_IDENTIFIER = "WFO Name Identifier";
 104
 105     public CdmLightClassificationExport() {
 106         super();
 107         this.ioName = this.getClass().getSimpleName();
 108
 109     }
 110
 111     @Override
 112     public long countSteps(CdmLightExportState state) {
 113         TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
 114         return taxonNodeService.count(filter);
 115     }
 116
 117
 118     /**
 119      * {@inheritDoc}
 120      */
 121     @Override
 122     protected void doInvoke(CdmLightExportState state) {
 123         try {
 124
 125             IProgressMonitor monitor = state.getConfig().getProgressMonitor();
 126             CdmLightExportConfigurator config = state.getConfig();
 127             config.setFieldsTerminatedBy(",");
 128
 129 //            if (config.getTaxonNodeFilter().getTaxonNodesFilter().isEmpty() && config.getTaxonNodeFilter().getClassificationFilter().isEmpty()){
 130 //                //TODO
 131 //                state.setEmptyData();
 132 //                return;
 133 //            }
 134
 135
 136
 137 //            for (LogicFilter<Classification> classificationFilter : config.getTaxonNodeFilter().getClassificationFilter()){
 138 //                UUID classificationUuid = classificationFilter.getUuid();
 139 //                Classification classification = getClassificationService().find(classificationUuid);
 140 //                if (classification == null){
 141 //                    String message = String.format("Classification for given classification UUID not found. No data imported for %s", classificationUuid.toString());
 142 //                    state.getResult().addWarning(message);
 143 //                }else{
 144 //                    TaxonNode root = classification.getRootNode();
 145 //                    UUID uuid = root.getUuid();
 146 //                    root = getTaxonNodeService().load(uuid);
 147 //                    handleSingleClassification(state, root.getUuid());
 148 //                }
 149 //            }
 150
 151
 152             @SuppressWarnings("unchecked")
 153             TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
 154                   = TaxonNodeOutStreamPartitioner.NewInstance(
 155                           this, state, state.getConfig().getTaxonNodeFilter(),
 156                           100, monitor, null);
 157
 158
 159                 monitor.subTask("Start partitioning");
 160
 161                 TaxonNode node = partitioner.next();
 162                 while (node != null){
 163                     handleTaxonNode(state, node);
 164                     node = partitioner.next();
 165                 }
 166
 167
 168 //            for (LogicFilter<TaxonNode> taxonNodeFilter : config.getTaxonNodeFilter().getTaxonNodesFilter()){
 169 //                UUID nodeUuid = taxonNodeFilter.getUuid();
 170 //                handleSingleClassification(state, nodeUuid);
 171 //            }
 172             state.getProcessor().createFinalResult(state);
 173         } catch (Exception e) {
 174             state.getResult().addException(e, "An unexpected error occurred in main method doInvoke() " +
 175                     e.getMessage());
 176         }
 177     }
 178
 179     /**
 180      * @param state
 181      * @param classificationUuid
 182      */
 183     private void handleTaxonNode(CdmLightExportState state, TaxonNode taxonNode) {
 184
 185             if (taxonNode == null){
 186                 String message = "TaxonNode for given taxon node UUID not found. ";
 187                 //TODO
 188                 state.getResult().addWarning(message);
 189             }else{
 190                 try {
 191                     TaxonNode root = taxonNode;
 192                     if (root.hasTaxon()){
 193                         handleTaxon(state, root);
 194                     }else{
 195     //                    for (TaxonNode child : root.getChildNodes()){
 196     //                        handleTaxon(state, child);
 197     //                        //TODO progress monitor
 198     //                    }
 199                     }
 200                 } catch (Exception e) {
 201                     state.getResult().addException(e, "An unexpected error occurred when handling classification " +
 202                             taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace());
 203                 }
 204             }
 205     }
 206
 207     /**
 208      * @param state
 209      * @param taxon
 210      */
 211     private void handleTaxon(CdmLightExportState state, TaxonNode taxonNode) {
 212         try{
 213       //  Taxon taxon = taxonNode.getTaxon();
 214         if (taxonNode == null){
 215             state.getResult().addError ("The taxonNode was null.", "handleTaxon");
 216             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 217             return;
 218         }
 219         if (taxonNode.getTaxon() == null){
 220             state.getResult().addError ("There was a taxon node without a taxon: " + taxonNode.getUuid(), "handleTaxon");
 221             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 222         }else{
 223             Taxon taxon = HibernateProxyHelper.deproxy(taxonNode.getTaxon(), Taxon.class);
 224
 225              try{
 226                 TaxonName name = taxon.getName();
 227                 handleName(state, name);
 228                 for (Synonym syn : taxon.getSynonyms()){
 229                     handleSynonym(state, syn);
 230                 }
 231                 for (TaxonRelationship rel : taxon.getProParteAndPartialSynonymRelations()){
 232                     handleProPartePartialMisapplied(state, rel);
 233                 }
 234                 for (TaxonRelationship rel : taxon.getMisappliedNameRelations()){
 235                     handleProPartePartialMisapplied(state, rel);
 236                 }
 237
 238                 CdmLightExportTable table = CdmLightExportTable.TAXON;
 239                 String[] csvLine = new String[table.getSize()];
 240
 241                 csvLine[table.getIndex(CdmLightExportTable.TAXON_ID)] = getId(state, taxon);
 242                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 243                 Taxon parent = (taxonNode.getParent()==null) ? null : taxonNode.getParent().getTaxon();
 244                 csvLine[table.getIndex(CdmLightExportTable.PARENT_FK)] = getId(state, parent);
 245                 csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
 246                 if (taxon.getSec()!= null && taxon.getSec().getDatePublished() != null && taxon.getSec().getDatePublished().getFreeText() != null){
 247                     String sec_string = taxon.getSec().getTitleCache() + ". " + taxon.getSec().getDatePublished().getFreeText();
 248                     sec_string = sec_string.replace("..", ".");
 249                     csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = sec_string;
 250                 }else{
 251                     csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(taxon.getSec());
 252                 }
 253                 if (taxon.getSec() != null){
 254                     if (state.getReferenceFromStore(taxon.getSec().getId()) == null){
 255                         handleReference(state, taxon.getSec());
 256                     }
 257                 }
 258                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_ID)] = getId(state, taxonNode.getClassification());
 259                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification().getTitleCache();
 260
 261                 state.getProcessor().put(table, taxon, csvLine);
 262                 handleDescriptions(state, taxon);
 263              }catch(Exception e){
 264                  state.getResult().addException (e, "An unexpected problem occurred when trying to export "
 265                          + "taxon with id " + taxon.getId());
 266                  state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 267              }
 268        }
 269
 270        taxonNode.removeNullValueFromChildren();
 271 //       for (TaxonNode child: taxonNode.getChildNodes()){
 272 //           handleTaxon(state, child);
 273 //       }
 274         }catch (Exception e){
 275             state.getResult().addException(e, "An unexpected error occurred when handling the taxon node of " +
 276                     cdmBaseStr(taxonNode.getTaxon()) + ": " + e.getMessage());
 277         }
 278     }
 279
 280
 281     /**
 282      * @param state
 283      * @param taxon
 284      */
 285     private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
 286         try{
 287         if (cdmBase instanceof Taxon){
 288             Taxon taxon = HibernateProxyHelper.deproxy(cdmBase, Taxon.class);
 289             Set<TaxonDescription> descriptions = taxon.getDescriptions();
 290             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 291             List<DescriptionElementBase> specimenFacts = new ArrayList<>();
 292             List<DescriptionElementBase> distributionFacts = new ArrayList<>();
 293             List<DescriptionElementBase> commonNameFacts = new ArrayList<>();
 294             List<DescriptionElementBase> usageFacts = new ArrayList<>();
 295             for (TaxonDescription description: descriptions){
 296                 if (description.getElements() != null){
 297                     for (DescriptionElementBase element: description.getElements()){
 298                         element = CdmBase.deproxy(element);
 299                         if (element.getFeature().equals(Feature.COMMON_NAME())){
 300                             commonNameFacts.add(element);
 301                         }else if (element.getFeature().equals(Feature.DISTRIBUTION())){
 302                             distributionFacts.add(element);
 303                         }else if (element instanceof IndividualsAssociation || isSpecimenFeature(element.getFeature())){
 304                             specimenFacts.add(element);
 305                         }else{
 306                             simpleFacts.add(element);
 307                         }
 308                     }
 309                 }
 310             }
 311             if (!commonNameFacts.isEmpty()){
 312                 handleCommonNameFacts(state, taxon, commonNameFacts);
 313             }
 314             if (!distributionFacts.isEmpty()){
 315                 handleDistributionFacts(state, taxon, distributionFacts);
 316             }
 317             if (!specimenFacts.isEmpty()){
 318                 handleSpecimenFacts(state, taxon, specimenFacts);
 319             }
 320             if (!simpleFacts.isEmpty()){
 321                 handleSimpleFacts(state, taxon, simpleFacts);
 322             }
 323         } else if (cdmBase instanceof TaxonName){
 324             TaxonName name = CdmBase.deproxy(cdmBase, TaxonName.class);
 325             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 326             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 327             for (TaxonNameDescription description: descriptions){
 328                 if (description.getElements() != null){
 329                     for (DescriptionElementBase element: description.getElements()){
 330                         if (!element.getFeature().equals(Feature.PROTOLOGUE())){
 331                             simpleFacts.add(element);
 332                         }
 333                     }
 334                 }
 335              }
 336             if (!simpleFacts.isEmpty()){
 337                 handleSimpleFacts(state, name, simpleFacts);
 338             }
 339         }
 340         }catch (Exception e){
 341             state.getResult().addException(e, "An unexpected error occurred when handling description of" +
 342                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 343         }
 344     }
 345
 346
 347     /**
 348      * @param feature
 349      * @return
 350      */
 351     private boolean isSpecimenFeature(Feature feature) {
 352         //TODO allow user defined specimen features
 353         if (feature == null){
 354             return false;
 355         }else if (feature.isSupportsIndividualAssociation()){
 356             return true;
 357         }else{
 358             return feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.INDIVIDUALS_ASSOCIATION())
 359                     || feature.equals(Feature.MATERIALS_EXAMINED()) || feature.equals(Feature.OBSERVATION())
 360                     || feature.equals(Feature.OCCURRENCE())
 361                      ;
 362         }
 363     }
 364
 365     /**
 366      * @param state
 367      * @param taxon
 368      * @param simpleFacts
 369      */
 370     private void handleSimpleFacts(CdmLightExportState state, CdmBase cdmBase,
 371             List<DescriptionElementBase> simpleFacts) {
 372         try {
 373             CdmLightExportTable table = CdmLightExportTable.SIMPLE_FACT;
 374             CdmLightExportTable tableMedia = CdmLightExportTable.MEDIA;
 375             for (DescriptionElementBase element: simpleFacts){
 376                 if (element.getModifyingText().isEmpty() && !element.getMedia().isEmpty()){
 377                     handleSimpleMediaFact(state, cdmBase, tableMedia, element);
 378                 }else{
 379                     handleSingleSimpleFact(state, cdmBase, table, element);
 380                 }
 381             }
 382         } catch (Exception e) {
 383             state.getResult().addException(e, "An unexpected error occurred when handling simple facts for " +
 384                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 385         }
 386     }
 387
 388     /**
 389      * @param state
 390      * @param cdmBase
 391      * @param tableMedia
 392      * @param element
 393      */
 394     private void handleSimpleMediaFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 395             DescriptionElementBase element) {
 396         try {
 397             String[] csvLine;
 398             handleSource(state, element, CdmLightExportTable.MEDIA);
 399
 400             if (element instanceof TextData){
 401                TextData textData = (TextData)element;
 402                csvLine = new String[table.getSize()];
 403                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 404                if (cdmBase instanceof Taxon){
 405                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 406                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 407                }else if (cdmBase instanceof TaxonName){
 408                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 409                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 410                }
 411
 412
 413                String mediaUris = "";
 414                for (Media media: textData.getMedia()){
 415                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 416                    if (!StringUtils.isBlank(mediaString)){
 417                        mediaUris +=  mediaString + ";";
 418                    }
 419                    else{
 420                        state.getResult().addWarning("Empty Media object for "
 421                                + cdmBase.getUserFriendlyTypeName() + " " + cdmBase.getUuid()
 422                                + " (media: " + media.getUuid() + ")");
 423                    }
 424                }
 425                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 426
 427             }
 428         } catch (Exception e) {
 429             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 430                     cdmBaseStr(element) + ": " + e.getMessage());
 431         }
 432
 433     }
 434
 435     /**
 436      * @param state
 437      * @param cdmBase
 438      * @param table
 439      * @param element
 440      */
 441     private void handleSingleSimpleFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 442             DescriptionElementBase element) {
 443         try {
 444             String[] csvLine;
 445             handleSource(state, element, CdmLightExportTable.SIMPLE_FACT);
 446
 447             if (element instanceof TextData){
 448                TextData textData = (TextData)element;
 449                csvLine = new String[table.getSize()];
 450                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 451                if (cdmBase instanceof Taxon){
 452                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 453                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 454                }else if (cdmBase instanceof TaxonName){
 455                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 456                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 457                }
 458                csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = textData.getFeature().getLabel();
 459
 460                String mediaUris = "";
 461                for (Media media: textData.getMedia()){
 462                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 463                    if (!StringUtils.isBlank(mediaString)){
 464                        mediaUris +=  mediaString + ";";
 465                    }
 466                    else{
 467                        state.getResult().addWarning("Empty Media object for uuid: " +
 468                                cdmBase.getUuid() + " uuid of media: " + media.getUuid());
 469                    }
 470                }
 471                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 472                if (textData.getFeature().equals(Feature.CITATION())){
 473                   // csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 474                    state.getProcessor().put(table, textData, csvLine);
 475                }else if (!textData.getMultilanguageText().isEmpty()){
 476                    for (Language language: textData.getMultilanguageText().keySet()){
 477                        String[] csvLineLanguage = csvLine.clone();
 478                        LanguageString langString = textData.getLanguageText(language);
 479                        String text = langString.getText();
 480                        if (state.getConfig().isFilterIntextReferences()){
 481                            text = filterIntextReferences(langString.getText());
 482                        }
 483                        csvLineLanguage[table.getIndex(CdmLightExportTable.FACT_TEXT)] = text;
 484                        csvLineLanguage[table.getIndex(CdmLightExportTable.LANGUAGE)] = language.getLabel();
 485                        state.getProcessor().put(table, textData, csvLineLanguage);
 486                    }
 487                } else{
 488                    state.getProcessor().put(table, textData, csvLine);
 489                }
 490             }
 491         } catch (Exception e) {
 492             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 493                     cdmBaseStr(element) + ": " + e.getMessage());
 494         }
 495     }
 496
 497
 498     /**
 499      * @param text
 500      * @return
 501      */
 502     private String filterIntextReferences(String text) {
 503         /*
 504          * (<cdm:reference cdmId='fbd19251-efee-4ded-b780-915000f66d41' intextId='1352d42c-e201-4155-a02a-55360d3b563e'>Ridley in Fl. Malay Pen. 3 (1924) 22</cdm:reference>)
 505          */
 506
 507        String newText = text.replaceAll("<cdm:reference cdmId='[a-z0-9\\-]*' intextId='[a-z0-9\\-]*'>","");
 508        newText = newText.replaceAll("</cdm:reference>","");
 509
 510        newText = newText.replaceAll("<cdm:key cdmId='[a-z0-9\\-]*' intextId='[a-z0-9\\-]*'>","");
 511        newText = newText.replaceAll("</cdm:key>","");
 512        return newText;
 513     }
 514
 515     /**
 516      * @param state
 517      * @param specimenFacts
 518      */
 519     private void handleSpecimenFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> specimenFacts) {
 520         CdmLightExportTable table = CdmLightExportTable.SPECIMEN_FACT;
 521
 522         for (DescriptionElementBase element: specimenFacts){
 523             try {
 524                 String[] csvLine = new String[table.getSize()];
 525                 csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 526                 csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 527                 handleSource(state, element, table);
 528                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_NOTES)] = createAnnotationsString(element.getAnnotations());
 529
 530                 if (element instanceof IndividualsAssociation){
 531
 532                     IndividualsAssociation indAssociation = (IndividualsAssociation)element;
 533                     if (indAssociation.getAssociatedSpecimenOrObservation() == null){
 534                         state.getResult().addWarning("There is an individual association with no specimen associated (Taxon "+ taxon.getTitleCache() + "(" + taxon.getUuid() +"). Could not be exported.");
 535                         continue;
 536                     }else{
 537                         if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
 538                             SpecimenOrObservationBase<?> specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation());
 539
 540                             if (specimenBase instanceof SpecimenOrObservationBase){
 541                                 SpecimenOrObservationBase derivedUnit = specimenBase;
 542                                 handleSpecimen(state, derivedUnit);
 543                                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
 544                             }else{
 545                                 //field units are not supported
 546                                 state.getResult().addError("The associated Specimen of taxon " + taxon.getUuid() + " is not an DerivedUnit. Could not be exported.");
 547
 548                             }
 549                         }
 550                     }
 551                 } else if (element instanceof TextData){
 552                     TextData textData = HibernateProxyHelper.deproxy(element, TextData.class);
 553                     csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_DESCRIPTION)] = createMultilanguageString(textData.getMultilanguageText());
 554                 }
 555                 state.getProcessor().put(table, element, csvLine);
 556             } catch (Exception e) {
 557                 state.getResult().addException(e, "An unexpected error occurred when handling single specimen fact " +
 558                         cdmBaseStr(element) + ": " + e.getMessage());
 559             }
 560         }
 561     }
 562
 563     /**
 564      * @param multilanguageText
 565      * @return
 566      */
 567     private String createMultilanguageString(Map<Language, LanguageString> multilanguageText) {
 568        String text = "";
 569        int index = multilanguageText.size();
 570        for(LanguageString langString: multilanguageText.values()){
 571            text += langString.getText();
 572            if (index > 1){
 573                text += "; ";
 574            }
 575            index --;
 576        }
 577
 578         return text;
 579     }
 580
 581     /**
 582      * @param annotations
 583      * @return
 584      */
 585     private String createAnnotationsString(Set<Annotation> annotations) {
 586         StringBuffer strBuff = new StringBuffer();
 587
 588         for (Annotation ann:annotations){
 589             if (ann.getAnnotationType() == null ||!ann.getAnnotationType().equals(AnnotationType.TECHNICAL())){
 590                 strBuff.append(ann.getText());
 591                 strBuff.append("; ");
 592             }
 593         }
 594
 595         if (strBuff.length() > 2){
 596             return strBuff.substring(0, strBuff.length()-2);
 597         }else{
 598             return null;
 599         }
 600     }
 601
 602     /**
 603      * @param state
 604      * @param taxon
 605      * @param element
 606      */
 607     private void handleSource(CdmLightExportState state, DescriptionElementBase element, CdmLightExportTable factsTable) {
 608         CdmLightExportTable table = CdmLightExportTable.FACT_SOURCES;
 609         try {
 610         Set<DescriptionElementSource> sources = element.getSources();
 611
 612         for (DescriptionElementSource source: sources){
 613
 614                 String[] csvLine = new  String[table.getSize()];
 615                 Reference ref = source.getCitation();
 616                 if ((ref == null) && (source.getNameUsedInSource() == null)){
 617                     continue;
 618                 }
 619                 if (ref != null){
 620                     if (state.getReferenceFromStore(ref.getId()) == null){
 621                         handleReference(state, ref);
 622
 623                     }
 624                     csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, ref);
 625                 }
 626                 csvLine[table.getIndex(CdmLightExportTable.FACT_FK)] = getId(state, element);
 627
 628                 csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)] = getId(state, source.getNameUsedInSource());
 629                 csvLine[table.getIndex(CdmLightExportTable.FACT_TYPE)] = factsTable.getTableName();
 630                 if ( StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)])  && StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)])){
 631                     continue;
 632                 }
 633                 state.getProcessor().put(table, source, csvLine);
 634
 635         }
 636         } catch (Exception e) {
 637             state.getResult().addException(e, "An unexpected error occurred when handling single source " +
 638                     cdmBaseStr(element) + ": " + e.getMessage());
 639         }
 640
 641     }
 642
 643     /**
 644      * @param state
 645      * @param distributionFacts
 646      */
 647     private void handleDistributionFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> distributionFacts) {
 648         CdmLightExportTable table = CdmLightExportTable.GEOGRAPHIC_AREA_FACT;
 649
 650         for (DescriptionElementBase element: distributionFacts){
 651             try {
 652                 if (element instanceof Distribution){
 653                     String[] csvLine = new  String[table.getSize()];
 654                     Distribution distribution = (Distribution)element;
 655                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 656                     handleSource(state, element, table);
 657                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 658                     if (distribution.getArea() != null){
 659                         csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = distribution.getArea().getLabel();
 660                     }
 661                     if (distribution.getStatus() != null){
 662                         csvLine[table.getIndex(CdmLightExportTable.STATUS_LABEL)] = distribution.getStatus().getLabel();
 663                     }
 664                     state.getProcessor().put(table, distribution, csvLine);
 665                 } else{
 666                     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());
 667                 }
 668             } catch (Exception e) {
 669                 state.getResult().addException(e, "An unexpected error occurred when handling single distribution " +
 670                         cdmBaseStr(element) + ": " + e.getMessage());
 671             }
 672         }
 673     }
 674
 675     /**
 676      * @param state
 677      * @param commonNameFacts
 678      */
 679     private void handleCommonNameFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> commonNameFacts) {
 680         CdmLightExportTable table = CdmLightExportTable.COMMON_NAME_FACT;
 681
 682         for (DescriptionElementBase element: commonNameFacts){
 683             try {
 684                 if (element instanceof CommonTaxonName){
 685                     String[] csvLine = new  String[table.getSize()];
 686                     CommonTaxonName commonName = (CommonTaxonName)element;
 687                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 688                     handleSource(state, element, table);
 689                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 690                     if (commonName.getName() != null){csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = commonName.getName();}
 691                     if (commonName.getLanguage() != null){csvLine[table.getIndex(CdmLightExportTable.LANGUAGE)] = commonName.getLanguage().getLabel();}
 692                     if (commonName.getArea() != null){ csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = commonName.getArea().getLabel();}
 693                     state.getProcessor().put(table, commonName, csvLine);
 694                 } else{
 695                     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());
 696                 }
 697             } catch (Exception e) {
 698                 state.getResult().addException(e, "An unexpected error occurred when handling single common name " +
 699                         cdmBaseStr(element) + ": " + e.getMessage());
 700             }
 701         }
 702     }
 703
 704     /**
 705      * @param sec
 706      * @return
 707      */
 708     private String getTitleCache(IIdentifiableEntity identEntity) {
 709         if (identEntity == null){
 710             return "";
 711         }
 712         //TODO refresh?
 713         return identEntity.getTitleCache();
 714     }
 715
 716     /**
 717      * @param state
 718      * @param taxon
 719      * @return
 720      */
 721     private String getId(CdmLightExportState state, ICdmBase cdmBase) {
 722         if (cdmBase == null){
 723             return "";
 724         }
 725         //TODO make configurable
 726         return cdmBase.getUuid().toString();
 727     }
 728
 729     /**
 730      * @param state
 731      * @param synonym
 732      */
 733     private void handleSynonym(CdmLightExportState state, Synonym synonym) {
 734        try {
 735            if (isUnpublished(state.getConfig(), synonym)){
 736                return;
 737            }
 738            TaxonName name = synonym.getName();
 739            handleName(state, name);
 740
 741            CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 742            String[] csvLine = new String[table.getSize()];
 743
 744            csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, synonym);
 745            csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, synonym.getAcceptedTaxon());
 746            csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 747            csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, synonym.getSec());
 748            csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(synonym.getSec());
 749
 750            state.getProcessor().put(table, synonym, csvLine);
 751         } catch (Exception e) {
 752             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
 753                     cdmBaseStr(synonym) + ": " + e.getMessage());
 754         }
 755     }
 756
 757
 758     /**
 759      * Handles Misapplied names (including pro parte and partial as well as
 760      * pro parte and partial synonyms
 761      * @param state
 762      * @param rel
 763      */
 764     private void handleProPartePartialMisapplied(CdmLightExportState state, TaxonRelationship rel) {
 765         try {
 766             Taxon ppSyonym = rel.getFromTaxon();
 767             if (isUnpublished(state.getConfig(), ppSyonym)){
 768                 return;
 769             }
 770             TaxonName name = ppSyonym.getName();
 771             handleName(state, name);
 772
 773             CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 774             String[] csvLine = new String[table.getSize()];
 775
 776             csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, rel);
 777             csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, rel.getToTaxon());
 778             csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 779
 780             Reference secRef = ppSyonym.getSec();
 781             csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef);
 782             csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef);
 783             Reference synSecRef = rel.getCitation();
 784             csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, synSecRef);
 785             csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(synSecRef);
 786
 787             //pro parte type
 788             TaxonRelationshipType type = rel.getType();
 789             csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = type.isProParte()? "1":"0";
 790             csvLine[table.getIndex(CdmLightExportTable.IS_PARTIAL)] = type.isPartial()? "1":"0";
 791             csvLine[table.getIndex(CdmLightExportTable.IS_MISAPPLIED)] = type.isAnyMisappliedName()? "1":"0";
 792
 793             state.getProcessor().put(table, ppSyonym, csvLine);
 794          } catch (Exception e) {
 795              state.getResult().addException(e, "An unexpected error occurred when handling "
 796                      + "pro parte/partial synonym relationship " +
 797                      cdmBaseStr(rel) + ": " + e.getMessage());
 798          }
 799
 800     }
 801
 802
 803     /**
 804      * @param state
 805      * @param name
 806      */
 807     private void handleName(CdmLightExportState state, TaxonName name) {
 808         if (name == null){
 809             return;
 810         }
 811         try {
 812             Rank rank = name.getRank();
 813             CdmLightExportTable table = CdmLightExportTable.SCIENTIFIC_NAME;
 814             name = HibernateProxyHelper.deproxy(name);
 815             String[] csvLine = new String[table.getSize()];
 816
 817             csvLine[table.getIndex(CdmLightExportTable.NAME_ID)] = getId(state, name);
 818             if (name.getLsid() != null){
 819                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = name.getLsid().getLsid();
 820             }else{
 821                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = "";
 822             }
 823
 824             handleIdentifier(state, name);
 825             handleDescriptions(state, name);
 826
 827             csvLine[table.getIndex(CdmLightExportTable.RANK)] = getTitleCache(rank);
 828             if (rank != null){
 829                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
 830                 if (rank.isInfraGeneric()){
 831                     try {
 832                         csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
 833                     } catch (UnknownCdmTypeException e) {
 834                         state.getResult().addError("Infrageneric marker expected but not available for rank " + name.getRank().getTitleCache());
 835                     }
 836                 }
 837                 if (rank.isInfraSpecific()){
 838                     csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
 839                 }
 840             }else{
 841                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = "";
 842             }
 843             if (name.isProtectedTitleCache()){
 844                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] =name.getTitleCache();
 845             }else{
 846                 //TODO: adapt the tropicos titlecache creation
 847                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
 848             }
 849             csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
 850             csvLine[table.getIndex(CdmLightExportTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
 851
 852             csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
 853             csvLine[table.getIndex(CdmLightExportTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
 854
 855             csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
 856             csvLine[table.getIndex(CdmLightExportTable.BAS_AUTHORTEAM_FK)] = getId(state,name.getBasionymAuthorship());
 857             if (name.getBasionymAuthorship() != null){
 858                 if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
 859                     handleAuthor(state, name.getBasionymAuthorship());
 860                 }
 861             }
 862             csvLine[table.getIndex(CdmLightExportTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
 863             if (name.getExBasionymAuthorship() != null){
 864                 if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
 865                     handleAuthor(state, name.getExBasionymAuthorship());
 866                 }
 867
 868             }
 869             csvLine[table.getIndex(CdmLightExportTable.COMB_AUTHORTEAM_FK)] = getId(state,name.getCombinationAuthorship());
 870             if (name.getCombinationAuthorship() != null){
 871                 if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
 872                     handleAuthor(state, name.getCombinationAuthorship());
 873                 }
 874             }
 875             csvLine[table.getIndex(CdmLightExportTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
 876             if (name.getExCombinationAuthorship() != null){
 877                 if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
 878                     handleAuthor(state, name.getExCombinationAuthorship());
 879                 }
 880
 881             }
 882
 883             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
 884
 885             Reference nomRef = name.getNomenclaturalReference();
 886
 887             if (nomRef != null){
 888                 if (state.getReferenceFromStore(nomRef.getId()) == null){
 889                     handleReference(state, nomRef);
 890                 }
 891                 csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, nomRef);
 892                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = nomRef.getType().name();
 893                 if (nomRef.getVolume() != null){
 894                     csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = nomRef.getVolume();
 895                     csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 896                 }
 897                 if (nomRef.getDatePublished() != null){
 898                     csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = nomRef.getTimePeriodPublishedString();
 899                     csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
 900                     csvLine[table.getIndex(CdmLightExportTable.VERBATIM_DATE)] = nomRef.getDatePublished().getVerbatimDate();
 901                 }
 902                 if (name.getNomenclaturalMicroReference() != null){
 903                     csvLine[table.getIndex(CdmLightExportTable.DETAIL)] = name.getNomenclaturalMicroReference();
 904                 }
 905                 nomRef = HibernateProxyHelper.deproxy(nomRef);
 906                 if (nomRef.getInReference() != null){
 907                     Reference inReference = nomRef.getInReference();
 908                     if (inReference.getDatePublished() != null && nomRef.getDatePublished() == null){
 909                         csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = inReference.getDatePublishedString();
 910                         csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = inReference.getDatePublished().getYear();
 911                     }
 912                     if (nomRef.getVolume() == null && inReference.getVolume() != null){
 913                         csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = inReference.getVolume();
 914                         csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 915                     }
 916                     if (inReference.getInReference() != null){
 917                         inReference = inReference.getInReference();
 918                     }
 919                     if (inReference.getAbbrevTitle() == null){
 920                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitleCache());
 921                     }else{
 922                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
 923                     }
 924                     if (inReference.getTitle() == null){
 925                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitleCache());
 926                     }else{
 927                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
 928                     }
 929
 930
 931                     TeamOrPersonBase<?> author = inReference.getAuthorship();
 932                     if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))){
 933                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
 934                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 935                     }else{
 936                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 937                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 938                     }
 939                 }else{
 940                     if (nomRef.getAbbrevTitle() == null){
 941                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitleCache());
 942                     }else{
 943                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle());
 944                     }
 945                     if (nomRef.getTitle() == null){
 946                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitleCache());
 947                     }else{
 948                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitle());
 949                     }
 950                     TeamOrPersonBase<?> author = nomRef.getAuthorship();
 951                     if (author != null ){
 952                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
 953                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 954                     }else{
 955                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 956                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 957                     }
 958
 959                 }
 960             }else{
 961                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = "";
 962             }
 963
 964
 965
 966             /*
 967             * Collation
 968
 969             Detail
 970
 971
 972             TitlePageYear
 973             */
 974             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 975             String protologueUriString = extractURIs(state, descriptions, Feature.PROTOLOGUE());
 976
 977             csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_URI)] = protologueUriString;
 978
 979             if (name.getStatus() == null || name.getStatus().isEmpty()){
 980                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = "";
 981                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = "";
 982             }else{
 983
 984                 String statusStringAbbrev = extractStatusString(state, name, true);
 985                 String statusString = extractStatusString(state, name, false);
 986
 987                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = statusString.trim();
 988                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
 989             }
 990
 991             HomotypicalGroup group =name.getHomotypicalGroup();
 992
 993             if (state.getHomotypicalGroupFromStore(group.getId()) == null){
 994                 handleHomotypicalGroup(state, HibernateProxyHelper.deproxy(group, HomotypicalGroup.class));
 995             }
 996             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
 997             List<TaxonName> typifiedNames = new ArrayList<>();
 998             typifiedNames.addAll(group.getTypifiedNames());
 999             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
1000             Integer  seqNumber= typifiedNames.indexOf(name);
1001             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
1002             state.getProcessor().put(table, name, csvLine);
1003
1004             /*
1005              *
1006             Tropicos_ID
1007             IPNI_ID
1008
1009
1010             InfragenericRank
1011
1012
1013             InfraspecificRank
1014             Collation
1015             Volume (Issue)
1016             Detail
1017             DatePublished
1018             YearPublished
1019             TitlePageYear
1020
1021
1022
1023             HomotypicGroupSequenceNumber
1024
1025
1026              *
1027              */
1028         } catch (Exception e) {
1029             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
1030                     cdmBaseStr(name) + ": " + e.getMessage());
1031         }
1032     }
1033
1034     /**
1035      * @return
1036      */
1037     private String createCollatation(TaxonName name) {
1038         String collation = "";
1039         if (name.getNomenclaturalReference() != null){
1040             Reference ref = name.getNomenclaturalReference();
1041             collation = getVolume(ref);
1042         }
1043         if (name.getNomenclaturalMicroReference() != null){
1044             if (!StringUtils.isBlank(collation)){
1045                 collation += ":";
1046             }
1047             collation +=name.getNomenclaturalMicroReference();
1048         }
1049
1050         return collation;
1051     }
1052
1053     /**
1054      * @param nomenclaturalReference
1055      * @return
1056      */
1057     private String getVolume(Reference reference) {
1058         if (reference.getVolume() != null){
1059             return reference.getVolume();
1060         }else if (reference.getInReference() != null){
1061             if (reference.getInReference().getVolume() != null){
1062                 return reference.getInReference().getVolume();
1063             }
1064         }
1065         return null;
1066     }
1067
1068     /**
1069      * @param state
1070      * @param name
1071      */
1072     private void handleIdentifier(CdmLightExportState state, TaxonName name) {
1073         CdmLightExportTable table = CdmLightExportTable.IDENTIFIER;
1074         String[] csvLine;
1075         try {
1076             Set<String>  IPNIidentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_IPNI());
1077             Set<String>  tropicosIdentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_TROPICOS());
1078             Set<String>  WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
1079             if (!IPNIidentifiers.isEmpty()){
1080                 csvLine = new String[table.getSize()];
1081                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1082                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
1083                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(IPNIidentifiers);
1084                 state.getProcessor().put(table, name, csvLine);
1085             }
1086             if (!tropicosIdentifiers.isEmpty()){
1087                 csvLine = new String[table.getSize()];
1088                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1089                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = TROPICOS_NAME_IDENTIFIER;
1090                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(tropicosIdentifiers);
1091                 state.getProcessor().put(table, name, csvLine);
1092             }
1093             if (!WFOIdentifiers.isEmpty()){
1094                 csvLine = new String[table.getSize()];
1095                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1096                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
1097                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(WFOIdentifiers);
1098                 state.getProcessor().put(table, name, csvLine);
1099             }
1100         } catch (Exception e) {
1101             state.getResult().addException(e, "An unexpected error occurred when handling identifiers for " +
1102                     cdmBaseStr(name) + ": " + e.getMessage());
1103
1104         }
1105     }
1106
1107     /**
1108      * @param tropicosIdentifiers
1109      */
1110     private String extractIdentifier(Set<String> identifierSet) {
1111
1112         String identifierString = "";
1113         for (String identifier: identifierSet){
1114             if (!StringUtils.isBlank(identifierString)){
1115                 identifierString += ", ";
1116             }
1117             identifierString += identifier;
1118         }
1119
1120         return identifierString;
1121     }
1122
1123     /**
1124      * @param state
1125      * @param descriptions
1126      * @return
1127      */
1128     private String extractURIs(CdmLightExportState state,
1129             Set<? extends DescriptionBase<?>> descriptionsSet, Feature feature) {
1130         String mediaUriString = "";
1131         SpecimenDescription specimenDescription;
1132         TaxonDescription taxonDescription;
1133         TaxonNameDescription nameDescription;
1134         Set<DescriptionElementBase> elements = new HashSet<>();
1135         for (DescriptionBase<?> description : descriptionsSet){
1136             try {
1137                 if (!description.getElements().isEmpty()){
1138                     if (description instanceof SpecimenDescription){
1139                         specimenDescription = (SpecimenDescription)description;
1140                         elements = specimenDescription.getElements();
1141                     }else if (description instanceof TaxonDescription){
1142                         taxonDescription = (TaxonDescription) description;
1143                         elements = taxonDescription.getElements();
1144                     } else if (description instanceof TaxonNameDescription){
1145                         nameDescription = (TaxonNameDescription) description;
1146                         elements = nameDescription.getElements();
1147                     }
1148
1149                     for (DescriptionElementBase element : elements){
1150                         Feature entityFeature = HibernateProxyHelper.deproxy(element.getFeature());
1151                         if (entityFeature.equals(feature)){
1152                             if (!element.getMedia().isEmpty()){
1153                                 List<Media> media = element.getMedia();
1154                                 for (Media mediaElement: media){
1155                                     Iterator<MediaRepresentation> it =  mediaElement.getRepresentations().iterator();
1156                                     mediaUriString = extractMediaUris(it);
1157                                 }
1158                             }
1159                         }
1160                     }
1161                 }
1162             } catch (Exception e) {
1163                 state.getResult().addException(e, "An unexpected error occurred when extracting media URIs for " +
1164                         cdmBaseStr(description) + ": " + e.getMessage());
1165             }
1166         }
1167         return mediaUriString;
1168     }
1169
1170     /**
1171      * @param state
1172      * @param basionymAuthorship
1173      */
1174     private void handleAuthor(CdmLightExportState state, TeamOrPersonBase<?> author) {
1175         try {
1176             if (state.getAuthorFromStore(author.getId()) != null){
1177                 return;
1178             }
1179             state.addAuthorToStore(author);
1180             CdmLightExportTable table = CdmLightExportTable.NOMENCLATURAL_AUTHOR;
1181             String[] csvLine = new String[table.getSize()];
1182             CdmLightExportTable tableAuthorRel = CdmLightExportTable.NOMENCLATURAL_AUTHOR_TEAM_RELATION;
1183             String[] csvLineRel = new String[tableAuthorRel.getSize()];
1184             String[] csvLineMember = new String[table.getSize()];
1185             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, author);
1186             csvLine[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = author.getNomenclaturalTitle();
1187             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = author.getTitleCache();
1188             author = HibernateProxyHelper.deproxy(author);
1189             if (author instanceof Person){
1190                 Person authorPerson = (Person)author;
1191                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_GIVEN_NAME)] = authorPerson.getGivenName();
1192                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FAMILY_NAME)] = authorPerson.getFamilyName();
1193                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = authorPerson.getPrefix();
1194                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = authorPerson.getSuffix();
1195             } else{
1196                 // create an entry in rel table and all members in author table, check whether the team members already in author table
1197
1198                 Team authorTeam = (Team)author;
1199                 int index = 0;
1200                 for (Person member: authorTeam.getTeamMembers()){
1201                     csvLineRel = new String[tableAuthorRel.getSize()];
1202                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_FK)] = getId(state, authorTeam);
1203                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state, member);
1204                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_SEQ_NUMBER)] = String.valueOf(index);
1205                     state.getProcessor().put(tableAuthorRel, authorTeam.getId() +":" +member.getId(), csvLineRel);
1206
1207                     if (state.getAuthorFromStore(member.getId()) == null){
1208                         state.addAuthorToStore(member);
1209                         csvLineMember = new String[table.getSize()];
1210                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, member);
1211                         csvLineMember[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = member.getNomenclaturalTitle();
1212                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = member.getTitleCache();
1213                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_GIVEN_NAME)] = member.getGivenName();
1214                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_FAMILY_NAME)] = member.getFamilyName();
1215                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = member.getPrefix();
1216                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = member.getSuffix();
1217                         state.getProcessor().put(table, member, csvLineMember);
1218                     }
1219                     index++;
1220
1221                 }
1222             }
1223             state.getProcessor().put(table, author, csvLine);
1224         } catch (Exception e) {
1225             state.getResult().addException(e, "An unexpected error occurred when handling author " +
1226                     cdmBaseStr(author) + ": " + e.getMessage());
1227         }
1228     }
1229
1230     /**
1231      * @param state
1232      * @param name
1233      * @param statusString
1234      * @return
1235      */
1236     private String extractStatusString(CdmLightExportState state, TaxonName name, boolean abbrev) {
1237         try {
1238             Set<NomenclaturalStatus> status = name.getStatus();
1239             if (status.isEmpty()){
1240                 return "";
1241             }
1242             String statusString = "";
1243             for (NomenclaturalStatus nameStatus: status){
1244                 if (nameStatus != null){
1245                     if (abbrev){
1246                         if (nameStatus.getType() != null){
1247                             statusString += nameStatus.getType().getIdInVocabulary();
1248                         }
1249                     }else{
1250                         if (nameStatus.getType() != null){
1251                             statusString += nameStatus.getType().getTitleCache();
1252                         }
1253                     }
1254                     if (!abbrev){
1255
1256                         if (nameStatus.getRuleConsidered() != null && !StringUtils.isBlank(nameStatus.getRuleConsidered())){
1257                             statusString += " " + nameStatus.getRuleConsidered();
1258                         }
1259                         if (nameStatus.getCitation() != null){
1260                             statusString += " " + nameStatus.getCitation().getTitleCache();
1261                         }
1262                         if (nameStatus.getCitationMicroReference() != null && !StringUtils.isBlank(nameStatus.getCitationMicroReference())){
1263                             statusString += " " + nameStatus.getCitationMicroReference();
1264                         }
1265                     }
1266                     statusString += " ";
1267                 }
1268             }
1269             return statusString;
1270         } catch (Exception e) {
1271             state.getResult().addException(e, "An unexpected error occurred when extracting status string for " +
1272                     cdmBaseStr(name) + ": " + e.getMessage());
1273             return "";
1274         }
1275     }
1276
1277     /**
1278      * @param group
1279      */
1280     private void handleHomotypicalGroup(CdmLightExportState state, HomotypicalGroup group) {
1281         try {
1282            state.addHomotypicalGroupToStore(group);
1283             CdmLightExportTable table = CdmLightExportTable.HOMOTYPIC_GROUP;
1284             String[] csvLine = new String[table.getSize()];
1285
1286             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_ID)] = getId(state, group);
1287             List<TaxonName> typifiedNames = new ArrayList<>();
1288             typifiedNames.addAll(group.getTypifiedNames());
1289             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
1290             String typifiedNamesString = "";
1291             for (TaxonName name: typifiedNames){
1292                 //Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)
1293                 //TODO: nameRelations, which and how to display
1294
1295
1296                 typifiedNamesString += name.getTitleCache()+ extractStatusString(state, name, true) + "; ";
1297             }
1298             typifiedNamesString = typifiedNamesString.substring(0, typifiedNamesString.length()-2);
1299             if (typifiedNamesString != null){
1300                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = typifiedNamesString.trim();
1301             }else{
1302                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = "";
1303             }
1304             Set<TypeDesignationBase> typeDesigantionSet = group.getTypeDesignations();
1305             List<TypeDesignationBase> designationList = new ArrayList<>();
1306             designationList.addAll(typeDesigantionSet);
1307             Collections.sort(designationList, new TypeComparator());
1308             StringBuffer typeDesignationString = new StringBuffer();
1309             List<TaggedText> list = new ArrayList<TaggedText>();
1310             if (!designationList.isEmpty()){
1311                 TypeDesignationSetManager manager = new TypeDesignationSetManager(group);
1312
1313                 list.addAll( manager.toTaggedTextWithCitation());
1314                 System.err.println(list.toString());
1315             }
1316             StringBuffer homotypicalGroupTypeDesignationString = new StringBuffer();
1317
1318             for (TaggedText text:list){
1319                 if (text != null && text.getText() != null && (text.getText().equals("Type:") || text.getText().equals("NameType:"))){
1320                   //do nothing
1321                 } else if (text.getType().equals(TagEnum.reference)){
1322                     homotypicalGroupTypeDesignationString.append(" [fide "+ text.getText() + "]");
1323                 }else if (text.getType().equals(TagEnum.typeDesignation)){
1324                     homotypicalGroupTypeDesignationString.append(text.getText().replace(").", "").replace("(", "").replace(")", "") );
1325                 } else{
1326                     homotypicalGroupTypeDesignationString.append(text.getText());
1327                 }
1328             }
1329
1330
1331             String typeDesignations= homotypicalGroupTypeDesignationString.toString();
1332             typeDesignations = typeDesignations.trim();
1333
1334             typeDesignations += ".";
1335             typeDesignations = typeDesignations.replace("..", ".");
1336             typeDesignations = typeDesignations.replace(". .", ".");
1337             if (typeDesignations.equals(".")){
1338                 typeDesignations = null;
1339             }
1340             System.err.println(typeDesignations);
1341        /*     for (TypeDesignationBase typeDesignation: designationList){
1342                 //[Vorschlag Soll:]
1343                // Sumatra Utara, Kab. Karo, around Sidikalang areas, 1000─1500 m, Dec 11, 2003, Nepenthes Team (Hernawati, P. Akhriadi & I. Petra), NP 354 (‘ANDA’–Holo, BO–Iso) [fide Akhriadi & al. 2004]
1344                 if (typeDesignation != null && typeDesignation.getTypeStatus() != null){
1345                     typeDesignationString.append(typeDesignation.getTypeStatus().getTitleCache() + ":");
1346                 }
1347                 if (typeDesignation instanceof SpecimenTypeDesignation){
1348                     if (((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen() != null){
1349                         typeDesignationString.append(" "+((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen().getTitleCache());
1350                         if (typeDesignationString.lastIndexOf(".") == typeDesignationString.length()){
1351                             typeDesignationString.deleteCharAt(typeDesignationString.lastIndexOf("."));
1352                         }
1353                         handleSpecimen(state, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
1354                     }
1355                 }else{
1356                     if (((NameTypeDesignation)typeDesignation).getTypeName() != null){
1357                         typeDesignationString.append(((NameTypeDesignation)typeDesignation).getTypeName().getTitleCache());
1358                     }
1359                 }
1360                 if(typeDesignation.getCitation() != null ){
1361                     typeDesignationString.append(" [fide " + ((DefaultReferenceCacheStrategy)typeDesignation.getCitation().getCacheStrategy()).createShortCitation(typeDesignation.getCitation()) +"]");
1362                 }
1363                 //TODO...
1364                 /*
1365                  * Sortierung:
1366                 1.  Status der Typen: a) holo, lecto, neo, syn, b) epi, paralecto, c) para (wenn überhaupt) – die jeweiligen iso immer direct mit dazu
1367                 2.  Land
1368                 3.  Sammler
1369                 4.  Nummer
1370
1371                 Aufbau der Typusinformationen:
1372                 Land: Lokalität mit Höhe und Koordinaten; Datum; Sammler Nummer (Herbar/Barcode, Typusart; Herbar/Barcode, Typusart …)
1373
1374
1375             }*/
1376            // typeDesignations = typeDesignationString.toString();
1377             if (typeDesignations != null){
1378                 if (!typeDesignations.endsWith(".") ){
1379                     typeDesignations =typeDesignations + ".";
1380                 }
1381                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = typeDesignations;
1382
1383             }else{
1384                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = "";
1385             }
1386             state.getProcessor().put(table, String.valueOf(group.getId()), csvLine);
1387         } catch (Exception e) {
1388             e.printStackTrace();
1389             state.getResult().addException(e, "An unexpected error occurred when handling homotypic group " +
1390                     cdmBaseStr(group) + ": " + e.getMessage());
1391         }
1392     }
1393
1394     /**
1395      * @param name
1396      * @return
1397      */
1398     private String getTropicosTitleCache(CdmLightExportState state, TaxonName name) {
1399         try {
1400             String basionymStart = "(";
1401             String basionymEnd = ") ";
1402             String exAuthorSeperator = " ex ";
1403             TeamOrPersonBase<?> combinationAuthor = name.getCombinationAuthorship();
1404             TeamOrPersonBase<?> exCombinationAuthor = name.getExCombinationAuthorship();
1405             TeamOrPersonBase<?> basionymAuthor = name.getBasionymAuthorship();
1406             TeamOrPersonBase<?> exBasionymAuthor = name.getExBasionymAuthorship();
1407
1408             String combinationAuthorString = "";
1409             if (combinationAuthor != null){
1410                 combinationAuthor = HibernateProxyHelper.deproxy(combinationAuthor);
1411                 if (combinationAuthor instanceof Team){
1412                     combinationAuthorString = createTropicosTeamTitle(combinationAuthor);
1413                 }else{
1414                     Person person = HibernateProxyHelper.deproxy(combinationAuthor, Person.class);
1415                     combinationAuthorString = createTropicosAuthorString(person);
1416                 }
1417             }
1418             String exCombinationAuthorString = "";
1419             if (exCombinationAuthor != null){
1420                 exCombinationAuthor = HibernateProxyHelper.deproxy(exCombinationAuthor);
1421                 if (exCombinationAuthor instanceof Team){
1422                    exCombinationAuthorString = createTropicosTeamTitle(exCombinationAuthor);
1423                 }else{
1424                     Person person = HibernateProxyHelper.deproxy(exCombinationAuthor, Person.class);
1425                     exCombinationAuthorString = createTropicosAuthorString(person);
1426                 }
1427             }
1428
1429             String basionymAuthorString = "";
1430             if (basionymAuthor != null){
1431                 basionymAuthor = HibernateProxyHelper.deproxy(basionymAuthor);
1432                 if (basionymAuthor instanceof Team){
1433                     basionymAuthorString =  createTropicosTeamTitle(basionymAuthor);
1434                 }else{
1435                     Person person = HibernateProxyHelper.deproxy(basionymAuthor, Person.class);
1436                     basionymAuthorString = createTropicosAuthorString(person);
1437                 }
1438             }
1439
1440             String exBasionymAuthorString = "";
1441
1442             if (exBasionymAuthor != null){
1443                 exBasionymAuthor = HibernateProxyHelper.deproxy(exBasionymAuthor);
1444                 if (exBasionymAuthor instanceof Team){
1445                     exBasionymAuthorString = createTropicosTeamTitle(exBasionymAuthor);
1446
1447                 }else{
1448                     Person person = HibernateProxyHelper.deproxy(exBasionymAuthor, Person.class);
1449                     exBasionymAuthorString = createTropicosAuthorString(person);
1450                 }
1451             }
1452             String completeAuthorString =  name.getNameCache() + " ";
1453
1454             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymStart: "";
1455             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString)) ? (CdmUtils.Nz(exBasionymAuthorString) + exAuthorSeperator): "" ;
1456             completeAuthorString += (!CdmUtils.isBlank(basionymAuthorString))? CdmUtils.Nz(basionymAuthorString):"";
1457             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ?  basionymEnd:"";
1458             completeAuthorString += (!CdmUtils.isBlank(exCombinationAuthorString)) ? (CdmUtils.Nz(exCombinationAuthorString) + exAuthorSeperator): "" ;
1459             completeAuthorString += (!CdmUtils.isBlank(combinationAuthorString))? CdmUtils.Nz(combinationAuthorString):"";
1460
1461
1462             return completeAuthorString;
1463         } catch (Exception e) {
1464             state.getResult().addException(e, "An unexpected error occurred when handling tropicos title cache for " +
1465                     cdmBaseStr(name) + ": " + e.getMessage());
1466             return null;
1467         }
1468     }
1469
1470     /**
1471      * @param combinationAuthor
1472      * @return
1473      */
1474     private String createTropicosTeamTitle(TeamOrPersonBase<?> combinationAuthor) {
1475         String combinationAuthorString;
1476         Team team = HibernateProxyHelper.deproxy(combinationAuthor, Team.class);
1477         Team tempTeam = Team.NewInstance();
1478         for (Person teamMember:team.getTeamMembers()){
1479             combinationAuthorString = createTropicosAuthorString(teamMember);
1480             Person tempPerson = Person.NewTitledInstance(combinationAuthorString);
1481             tempTeam.addTeamMember(tempPerson);
1482         }
1483         combinationAuthorString = tempTeam.generateTitle();
1484         return combinationAuthorString;
1485     }
1486
1487     /**
1488      * @param teamMember
1489      */
1490     private String createTropicosAuthorString(Person teamMember) {
1491         String nomAuthorString = "";
1492         String[] splittedAuthorString = null;
1493         if (teamMember == null){
1494             return nomAuthorString;
1495         }
1496
1497         if (teamMember.getGivenName() != null){
1498             String givenNameString = teamMember.getGivenName().replaceAll("\\.", "\\. ");
1499             splittedAuthorString = givenNameString.split("\\s");
1500             for (String split: splittedAuthorString){
1501                 if (!StringUtils.isBlank(split)){
1502                     nomAuthorString += split.substring(0, 1);
1503                     nomAuthorString += ".";
1504                 }
1505             }
1506         }
1507         if (teamMember.getFamilyName() != null){
1508             String familyNameString = teamMember.getFamilyName().replaceAll("\\.", "\\. ");
1509             splittedAuthorString = familyNameString.split("\\s");
1510             for (String split: splittedAuthorString){
1511                 nomAuthorString += " " +split;
1512             }
1513         }
1514         if (StringUtils.isBlank(nomAuthorString.trim())){
1515             if (teamMember.getTitleCache() != null) {
1516                 String titleCacheString = teamMember.getTitleCache().replaceAll("\\.", "\\. ");
1517                 splittedAuthorString = titleCacheString.split("\\s");
1518             }
1519
1520
1521             int index = 0;
1522             for (String split: splittedAuthorString){
1523                 if ( index < splittedAuthorString.length-1 && (split.length()==1 || split.endsWith("."))){
1524                     nomAuthorString += split;
1525                 }else{
1526                     nomAuthorString = nomAuthorString +" "+ split;
1527                 }
1528                 index++;
1529             }
1530         }
1531         return nomAuthorString.trim();
1532     }
1533
1534     /**
1535      * @param state
1536      * @param name
1537      */
1538     private void handleReference(CdmLightExportState state, Reference reference) {
1539         try {
1540             state.addReferenceToStore(reference);
1541             CdmLightExportTable table = CdmLightExportTable.REFERENCE;
1542
1543             String[] csvLine = new String[table.getSize()];
1544             csvLine[table.getIndex(CdmLightExportTable.REFERENCE_ID)] = getId(state, reference);
1545             //TODO short citations correctly
1546             String shortCitation = ((DefaultReferenceCacheStrategy)reference.getCacheStrategy()).createShortCitation(reference);  //Should be Author(year) like in Taxon.sec
1547             csvLine[table.getIndex(CdmLightExportTable.BIBLIO_SHORT_CITATION)] = shortCitation;
1548             //TODO get preferred title
1549             csvLine[table.getIndex(CdmLightExportTable.REF_TITLE)] = reference.getTitle();
1550             csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_TITLE)] = reference.getAbbrevTitle();
1551             csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = reference.getDatePublishedString();
1552             //TBC
1553             csvLine[table.getIndex(CdmLightExportTable.EDITION)] = reference.getEdition();
1554             csvLine[table.getIndex(CdmLightExportTable.EDITOR)] = reference.getEditor();
1555             csvLine[table.getIndex(CdmLightExportTable.ISBN)] = reference.getIsbn();
1556             csvLine[table.getIndex(CdmLightExportTable.ISSN)] = reference.getIssn();
1557             csvLine[table.getIndex(CdmLightExportTable.ORGANISATION)] = reference.getOrganization();
1558             csvLine[table.getIndex(CdmLightExportTable.PAGES)] = reference.getPages();
1559             csvLine[table.getIndex(CdmLightExportTable.PLACE_PUBLISHED)] = reference.getPlacePublished();
1560             csvLine[table.getIndex(CdmLightExportTable.PUBLISHER)] = reference.getPublisher();
1561             csvLine[table.getIndex(CdmLightExportTable.REF_ABSTRACT)] = reference.getReferenceAbstract();
1562             csvLine[table.getIndex(CdmLightExportTable.SERIES_PART)] = reference.getSeriesPart();
1563             csvLine[table.getIndex(CdmLightExportTable.VOLUME)] = reference.getVolume();
1564             csvLine[table.getIndex(CdmLightExportTable.YEAR)] = reference.getYear();
1565
1566             if ( reference.getAuthorship() != null){
1567                 csvLine[table.getIndex(CdmLightExportTable.AUTHORSHIP_TITLE)] = createFullAuthorship(reference);
1568                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state,reference.getAuthorship());
1569             }
1570
1571             csvLine[table.getIndex(CdmLightExportTable.IN_REFERENCE)] = getId(state, reference.getInReference());
1572             if (reference.getInReference() != null && state.getReferenceFromStore(reference.getInReference().getId()) == null){
1573                 handleReference(state, reference.getInReference());
1574             }
1575             if ( reference.getInstitution() != null){ csvLine[table.getIndex(CdmLightExportTable.INSTITUTION)] = reference.getInstitution().getTitleCache();}
1576             if ( reference.getLsid() != null){ csvLine[table.getIndex(CdmLightExportTable.LSID)] = reference.getLsid().getLsid();}
1577             if ( reference.getSchool() != null){ csvLine[table.getIndex(CdmLightExportTable.SCHOOL)] = reference.getSchool().getTitleCache();}
1578             if ( reference.getUri() != null){ csvLine[table.getIndex(CdmLightExportTable.URI)] = reference.getUri().toString();}
1579             csvLine[table.getIndex(CdmLightExportTable.REF_TYPE)] = reference.getType().getKey();
1580
1581             state.getProcessor().put(table, reference, csvLine);
1582         } catch (Exception e) {
1583             state.getResult().addException(e, "An unexpected error occurred when handling reference " +
1584                     cdmBaseStr(reference) + ": " + e.getMessage());
1585         }
1586
1587     }
1588
1589
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 }