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

   1 /**
   2 * Copyright (C) 2017 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.io.cdmLight;
  10
  11 import java.io.File;
  12 import java.util.ArrayList;
  13 import java.util.Collections;
  14 import java.util.HashSet;
  15 import java.util.Iterator;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Set;
  19
  20 import org.apache.commons.lang3.StringUtils;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.common.CdmUtils;
  24 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  25 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  26 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  27 import eu.etaxonomy.cdm.io.common.CdmExportBase;
  28 import eu.etaxonomy.cdm.io.common.ExportResult.ExportResultState;
  29 import eu.etaxonomy.cdm.io.common.ICdmExport;
  30 import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
  31 import eu.etaxonomy.cdm.io.common.XmlExportState;
  32 import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
  33 import eu.etaxonomy.cdm.model.agent.AgentBase;
  34 import eu.etaxonomy.cdm.model.agent.Person;
  35 import eu.etaxonomy.cdm.model.agent.Team;
  36 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  37 import eu.etaxonomy.cdm.model.common.Annotation;
  38 import eu.etaxonomy.cdm.model.common.AnnotationType;
  39 import eu.etaxonomy.cdm.model.common.CdmBase;
  40 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  41 import eu.etaxonomy.cdm.model.common.ICdmBase;
  42 import eu.etaxonomy.cdm.model.common.IIdentifiableEntity;
  43 import eu.etaxonomy.cdm.model.common.Language;
  44 import eu.etaxonomy.cdm.model.common.LanguageString;
  45 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  46 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  47 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  48 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  49 import eu.etaxonomy.cdm.model.description.Distribution;
  50 import eu.etaxonomy.cdm.model.description.Feature;
  51 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  52 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  53 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  54 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  55 import eu.etaxonomy.cdm.model.description.TextData;
  56 import eu.etaxonomy.cdm.model.location.NamedArea;
  57 import eu.etaxonomy.cdm.model.media.Media;
  58 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  59 import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
  60 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  61 import eu.etaxonomy.cdm.model.name.HomotypicalGroupNameComparator;
  62 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  63 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  64 import eu.etaxonomy.cdm.model.name.Rank;
  65 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  66 import eu.etaxonomy.cdm.model.name.TaxonName;
  67 import eu.etaxonomy.cdm.model.name.TypeComparator;
  68 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  69 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  70 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  71 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  72 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  73 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  74 import eu.etaxonomy.cdm.model.reference.Reference;
  75 import eu.etaxonomy.cdm.model.reference.ReferenceType;
  76 import eu.etaxonomy.cdm.model.taxon.Synonym;
  77 import eu.etaxonomy.cdm.model.taxon.Taxon;
  78 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  79 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  80 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  81 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  82
  83 /**
  84  * @author k.luther
  85  * @since 15.03.2017
  86  */
  87 @Component
  88 public class CdmLightClassificationExport
  89             extends CdmExportBase<CdmLightExportConfigurator, CdmLightExportState, IExportTransformer, File>
  90             implements ICdmExport<CdmLightExportConfigurator, CdmLightExportState>{
  91
  92
  93     private static final long serialVersionUID = 2518643632756927053L;
  94     private static final String STD_TEAM_CONCATINATION = ", ";
  95     private static final String FINAL_TEAM_CONCATINATION = " & ";
  96
  97
  98     private static final String IPNI_NAME_IDENTIFIER = "Ipni Name Identifier";
  99     private static final String TROPICOS_NAME_IDENTIFIER = "Tropicos Name Identifier";
 100     private static final String WFO_NAME_IDENTIFIER = "WFO Name Identifier";
 101
 102     public CdmLightClassificationExport() {
 103         super();
 104         this.ioName = this.getClass().getSimpleName();
 105
 106     }
 107
 108     @Override
 109     public long countSteps(CdmLightExportState state) {
 110         TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
 111         return taxonNodeService.count(filter);
 112     }
 113
 114
 115     /**
 116      * {@inheritDoc}
 117      */
 118     @Override
 119     protected void doInvoke(CdmLightExportState state) {
 120         try {
 121
 122             IProgressMonitor monitor = state.getConfig().getProgressMonitor();
 123             CdmLightExportConfigurator config = state.getConfig();
 124             config.setFieldsTerminatedBy(",");
 125
 126 //            if (config.getTaxonNodeFilter().getTaxonNodesFilter().isEmpty() && config.getTaxonNodeFilter().getClassificationFilter().isEmpty()){
 127 //                //TODO
 128 //                state.setEmptyData();
 129 //                return;
 130 //            }
 131
 132
 133
 134 //            for (LogicFilter<Classification> classificationFilter : config.getTaxonNodeFilter().getClassificationFilter()){
 135 //                UUID classificationUuid = classificationFilter.getUuid();
 136 //                Classification classification = getClassificationService().find(classificationUuid);
 137 //                if (classification == null){
 138 //                    String message = String.format("Classification for given classification UUID not found. No data imported for %s", classificationUuid.toString());
 139 //                    state.getResult().addWarning(message);
 140 //                }else{
 141 //                    TaxonNode root = classification.getRootNode();
 142 //                    UUID uuid = root.getUuid();
 143 //                    root = getTaxonNodeService().load(uuid);
 144 //                    handleSingleClassification(state, root.getUuid());
 145 //                }
 146 //            }
 147
 148
 149             @SuppressWarnings("unchecked")
 150             TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
 151                   = TaxonNodeOutStreamPartitioner.NewInstance(
 152                           this, state, state.getConfig().getTaxonNodeFilter(),
 153                           100, monitor, null);
 154
 155
 156                 monitor.subTask("Start partitioning");
 157
 158                 TaxonNode node = partitioner.next();
 159                 while (node != null){
 160                     handleTaxonNode(state, node);
 161                     node = partitioner.next();
 162                 }
 163
 164
 165 //            for (LogicFilter<TaxonNode> taxonNodeFilter : config.getTaxonNodeFilter().getTaxonNodesFilter()){
 166 //                UUID nodeUuid = taxonNodeFilter.getUuid();
 167 //                handleSingleClassification(state, nodeUuid);
 168 //            }
 169             state.getProcessor().createFinalResult(state);
 170         } catch (Exception e) {
 171             state.getResult().addException(e, "An unexpected error occurred in main method doInvoke() " +
 172                     e.getMessage());
 173         }
 174     }
 175
 176     /**
 177      * @param state
 178      * @param classificationUuid
 179      */
 180     private void handleTaxonNode(CdmLightExportState state, TaxonNode taxonNode) {
 181
 182             if (taxonNode == null){
 183                 String message = "TaxonNode for given taxon node UUID not found. ";
 184                 //TODO
 185                 state.getResult().addWarning(message);
 186             }else{
 187                 try {
 188                     TaxonNode root = taxonNode;
 189                     if (root.hasTaxon()){
 190                         handleTaxon(state, root);
 191                     }else{
 192     //                    for (TaxonNode child : root.getChildNodes()){
 193     //                        handleTaxon(state, child);
 194     //                        //TODO progress monitor
 195     //                    }
 196                     }
 197                 } catch (Exception e) {
 198                     state.getResult().addException(e, "An unexpected error occurred when handling classification " +
 199                             taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace());
 200                 }
 201             }
 202     }
 203
 204     /**
 205      * @param state
 206      * @param taxon
 207      */
 208     private void handleTaxon(CdmLightExportState state, TaxonNode taxonNode) {
 209         try{
 210       //  Taxon taxon = taxonNode.getTaxon();
 211         if (taxonNode == null){
 212             state.getResult().addError ("The taxonNode was null.", "handleTaxon");
 213             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 214             return;
 215         }
 216         if (taxonNode.getTaxon() == null){
 217             state.getResult().addError ("There was a taxon node without a taxon: " + taxonNode.getUuid(), "handleTaxon");
 218             state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 219         }else{
 220             Taxon taxon = HibernateProxyHelper.deproxy(taxonNode.getTaxon(), Taxon.class);
 221
 222              try{
 223                 TaxonName name = taxon.getName();
 224                 handleName(state, name);
 225                 for (Synonym syn : taxon.getSynonyms()){
 226                     handleSynonym(state, syn);
 227                 }
 228                 for (TaxonRelationship rel : taxon.getProParteAndPartialSynonymRelations()){
 229                     handleProPartePartialMisapplied(state, rel);
 230                 }
 231                 for (TaxonRelationship rel : taxon.getMisappliedNameRelations()){
 232                     handleProPartePartialMisapplied(state, rel);
 233                 }
 234
 235                 CdmLightExportTable table = CdmLightExportTable.TAXON;
 236                 String[] csvLine = new String[table.getSize()];
 237
 238                 csvLine[table.getIndex(CdmLightExportTable.TAXON_ID)] = getId(state, taxon);
 239                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 240                 Taxon parent = (taxonNode.getParent()==null) ? null : taxonNode.getParent().getTaxon();
 241                 csvLine[table.getIndex(CdmLightExportTable.PARENT_FK)] = getId(state, parent);
 242                 csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, taxon.getSec());
 243                 if (taxon.getSec()!= null && taxon.getSec().getDatePublished() != null && taxon.getSec().getDatePublished().getFreeText() != null){
 244                     String sec_string = taxon.getSec().getTitleCache() + ". " + taxon.getSec().getDatePublished().getFreeText();
 245                     sec_string = sec_string.replace("..", ".");
 246                     csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = sec_string;
 247                 }else{
 248                     csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(taxon.getSec());
 249                 }
 250                 if (taxon.getSec() != null){
 251                     if (state.getReferenceFromStore(taxon.getSec().getId()) == null){
 252                         handleReference(state, taxon.getSec());
 253                     }
 254                 }
 255                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_ID)] = getId(state, taxonNode.getClassification());
 256                 csvLine[table.getIndex(CdmLightExportTable.CLASSIFICATION_TITLE)] = taxonNode.getClassification().getTitleCache();
 257
 258                 state.getProcessor().put(table, taxon, csvLine);
 259                 handleDescriptions(state, taxon);
 260              }catch(Exception e){
 261                  state.getResult().addException (e, "An unexpected problem occurred when trying to export "
 262                          + "taxon with id " + taxon.getId());
 263                  state.getResult().setState(ExportResultState.INCOMPLETE_WITH_ERROR);
 264              }
 265        }
 266
 267        taxonNode.removeNullValueFromChildren();
 268 //       for (TaxonNode child: taxonNode.getChildNodes()){
 269 //           handleTaxon(state, child);
 270 //       }
 271         }catch (Exception e){
 272             state.getResult().addException(e, "An unexpected error occurred when handling the taxon node of " +
 273                     cdmBaseStr(taxonNode.getTaxon()) + ": " + e.getMessage());
 274         }
 275     }
 276
 277
 278     /**
 279      * @param state
 280      * @param taxon
 281      */
 282     private void handleDescriptions(CdmLightExportState state, CdmBase cdmBase) {
 283         try{
 284         if (cdmBase instanceof Taxon){
 285             Taxon taxon = HibernateProxyHelper.deproxy(cdmBase, Taxon.class);
 286             Set<TaxonDescription> descriptions = taxon.getDescriptions();
 287             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 288             List<DescriptionElementBase> specimenFacts = new ArrayList<>();
 289             List<DescriptionElementBase> distributionFacts = new ArrayList<>();
 290             List<DescriptionElementBase> commonNameFacts = new ArrayList<>();
 291             List<DescriptionElementBase> usageFacts = new ArrayList<>();
 292             for (TaxonDescription description: descriptions){
 293                 if (description.getElements() != null){
 294                     for (DescriptionElementBase element: description.getElements()){
 295                         element = CdmBase.deproxy(element);
 296                         if (element.getFeature().equals(Feature.COMMON_NAME())){
 297                             commonNameFacts.add(element);
 298                         }else if (element.getFeature().equals(Feature.DISTRIBUTION())){
 299                             distributionFacts.add(element);
 300                         }else if (element instanceof IndividualsAssociation || isSpecimenFeature(element.getFeature())){
 301                             specimenFacts.add(element);
 302                         }else{
 303                             simpleFacts.add(element);
 304                         }
 305                     }
 306                 }
 307             }
 308             if (!commonNameFacts.isEmpty()){
 309                 handleCommonNameFacts(state, taxon, commonNameFacts);
 310             }
 311             if (!distributionFacts.isEmpty()){
 312                 handleDistributionFacts(state, taxon, distributionFacts);
 313             }
 314             if (!specimenFacts.isEmpty()){
 315                 handleSpecimenFacts(state, taxon, specimenFacts);
 316             }
 317             if (!simpleFacts.isEmpty()){
 318                 handleSimpleFacts(state, taxon, simpleFacts);
 319             }
 320         } else if (cdmBase instanceof TaxonName){
 321             TaxonName name = CdmBase.deproxy(cdmBase, TaxonName.class);
 322             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 323             List<DescriptionElementBase> simpleFacts = new ArrayList<>();
 324             for (TaxonNameDescription description: descriptions){
 325                 if (description.getElements() != null){
 326                     for (DescriptionElementBase element: description.getElements()){
 327                         if (!element.getFeature().equals(Feature.PROTOLOGUE())){
 328                             simpleFacts.add(element);
 329                         }
 330                     }
 331                 }
 332              }
 333             if (!simpleFacts.isEmpty()){
 334                 handleSimpleFacts(state, name, simpleFacts);
 335             }
 336         }
 337         }catch (Exception e){
 338             state.getResult().addException(e, "An unexpected error occurred when handling description of" +
 339                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 340         }
 341     }
 342
 343
 344     /**
 345      * @param feature
 346      * @return
 347      */
 348     private boolean isSpecimenFeature(Feature feature) {
 349         //TODO allow user defined specimen features
 350         if (feature == null){
 351             return false;
 352         }else if (feature.isSupportsIndividualAssociation()){
 353             return true;
 354         }else{
 355             return feature.equals(Feature.SPECIMEN()) || feature.equals(Feature.INDIVIDUALS_ASSOCIATION())
 356                     || feature.equals(Feature.MATERIALS_EXAMINED()) || feature.equals(Feature.OBSERVATION())
 357                     || feature.equals(Feature.OCCURRENCE())
 358                      ;
 359         }
 360     }
 361
 362     /**
 363      * @param state
 364      * @param taxon
 365      * @param simpleFacts
 366      */
 367     private void handleSimpleFacts(CdmLightExportState state, CdmBase cdmBase,
 368             List<DescriptionElementBase> simpleFacts) {
 369         try {
 370             CdmLightExportTable table = CdmLightExportTable.SIMPLE_FACT;
 371             CdmLightExportTable tableMedia = CdmLightExportTable.MEDIA;
 372             for (DescriptionElementBase element: simpleFacts){
 373                 if (element.getModifyingText().isEmpty() && !element.getMedia().isEmpty()){
 374                     handleSimpleMediaFact(state, cdmBase, tableMedia, element);
 375                 }else{
 376                     handleSingleSimpleFact(state, cdmBase, table, element);
 377                 }
 378             }
 379         } catch (Exception e) {
 380             state.getResult().addException(e, "An unexpected error occurred when handling simple facts for " +
 381                     cdmBaseStr(cdmBase) + ": " + e.getMessage());
 382         }
 383     }
 384
 385     /**
 386      * @param state
 387      * @param cdmBase
 388      * @param tableMedia
 389      * @param element
 390      */
 391     private void handleSimpleMediaFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 392             DescriptionElementBase element) {
 393         try {
 394             String[] csvLine;
 395             handleSource(state, element, CdmLightExportTable.MEDIA);
 396
 397             if (element instanceof TextData){
 398                TextData textData = (TextData)element;
 399                csvLine = new String[table.getSize()];
 400                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 401                if (cdmBase instanceof Taxon){
 402                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 403                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 404                }else if (cdmBase instanceof TaxonName){
 405                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 406                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 407                }
 408
 409
 410                String mediaUris = "";
 411                for (Media media: textData.getMedia()){
 412                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 413                    if (!StringUtils.isBlank(mediaString)){
 414                        mediaUris +=  mediaString + ";";
 415                    }
 416                    else{
 417                        state.getResult().addWarning("Empty Media object for "
 418                                + cdmBase.getUserFriendlyTypeName() + " " + cdmBase.getUuid()
 419                                + " (media: " + media.getUuid() + ")");
 420                    }
 421                }
 422                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 423
 424             }
 425         } catch (Exception e) {
 426             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 427                     cdmBaseStr(element) + ": " + e.getMessage());
 428         }
 429
 430     }
 431
 432     /**
 433      * @param state
 434      * @param cdmBase
 435      * @param table
 436      * @param element
 437      */
 438     private void handleSingleSimpleFact(CdmLightExportState state, CdmBase cdmBase, CdmLightExportTable table,
 439             DescriptionElementBase element) {
 440         try {
 441             String[] csvLine;
 442             handleSource(state, element, CdmLightExportTable.SIMPLE_FACT);
 443
 444             if (element instanceof TextData){
 445                TextData textData = (TextData)element;
 446                csvLine = new String[table.getSize()];
 447                csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 448                if (cdmBase instanceof Taxon){
 449                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 450                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = "";
 451                }else if (cdmBase instanceof TaxonName){
 452                    csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = "";
 453                    csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, cdmBase);
 454                }
 455                csvLine[table.getIndex(CdmLightExportTable.FACT_CATEGORY)] = textData.getFeature().getLabel();
 456
 457                String mediaUris = "";
 458                for (Media media: textData.getMedia()){
 459                    String mediaString = extractMediaUris(media.getRepresentations().iterator());
 460                    if (!StringUtils.isBlank(mediaString)){
 461                        mediaUris +=  mediaString + ";";
 462                    }
 463                    else{
 464                        state.getResult().addWarning("Empty Media object for uuid: " +
 465                                cdmBase.getUuid() + " uuid of media: " + media.getUuid());
 466                    }
 467                }
 468                csvLine[table.getIndex(CdmLightExportTable.MEDIA_URI)] = mediaUris;
 469                if (textData.getFeature().equals(Feature.CITATION())){
 470                   // csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, cdmBase);
 471                    state.getProcessor().put(table, textData, csvLine);
 472                }else if (!textData.getMultilanguageText().isEmpty()){
 473                    for (Language language: textData.getMultilanguageText().keySet()){
 474                        String[] csvLineLanguage = csvLine.clone();
 475                        LanguageString langString = textData.getLanguageText(language);
 476                        String text = langString.getText();
 477                        if (state.getConfig().isFilterIntextReferences()){
 478                            text = filterIntextReferences(langString.getText());
 479                        }
 480                        csvLineLanguage[table.getIndex(CdmLightExportTable.FACT_TEXT)] = text;
 481                        csvLineLanguage[table.getIndex(CdmLightExportTable.LANGUAGE)] = language.getLabel();
 482                        state.getProcessor().put(table, textData, csvLineLanguage);
 483                    }
 484                } else{
 485                    state.getProcessor().put(table, textData, csvLine);
 486                }
 487             }
 488         } catch (Exception e) {
 489             state.getResult().addException(e, "An unexpected error occurred when handling single simple fact " +
 490                     cdmBaseStr(element) + ": " + e.getMessage());
 491         }
 492     }
 493
 494
 495     /**
 496      * @param text
 497      * @return
 498      */
 499     private String filterIntextReferences(String text) {
 500         /*
 501          * (<cdm:reference cdmId='fbd19251-efee-4ded-b780-915000f66d41' intextId='1352d42c-e201-4155-a02a-55360d3b563e'>Ridley in Fl. Malay Pen. 3 (1924) 22</cdm:reference>)
 502          */
 503
 504        String newText = text.replaceAll("<cdm:reference cdmId='[a-z0-9\\-]*' intextId='[a-z0-9\\-]*'>","");
 505        newText = newText.replaceAll("</cdm:reference>","");
 506
 507        newText = newText.replaceAll("<cdm:key cdmId='[a-z0-9\\-]*' intextId='[a-z0-9\\-]*'>","");
 508        newText = newText.replaceAll("</cdm:key>","");
 509        return newText;
 510     }
 511
 512     /**
 513      * @param state
 514      * @param specimenFacts
 515      */
 516     private void handleSpecimenFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> specimenFacts) {
 517         CdmLightExportTable table = CdmLightExportTable.SPECIMEN_FACT;
 518
 519         for (DescriptionElementBase element: specimenFacts){
 520             try {
 521                 String[] csvLine = new String[table.getSize()];
 522                 csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 523                 csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 524                 handleSource(state, element, table);
 525                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_NOTES)] = createAnnotationsString(element.getAnnotations());
 526
 527                 if (element instanceof IndividualsAssociation){
 528
 529                     IndividualsAssociation indAssociation = (IndividualsAssociation)element;
 530                     if (indAssociation.getAssociatedSpecimenOrObservation() == null){
 531                         state.getResult().addWarning("There is an individual association with no specimen associated (Taxon "+ taxon.getTitleCache() + "(" + taxon.getUuid() +"). Could not be exported.");
 532                         continue;
 533                     }else{
 534                         if (state.getSpecimenFromStore(indAssociation.getAssociatedSpecimenOrObservation().getId()) == null){
 535                             SpecimenOrObservationBase<?> specimenBase = HibernateProxyHelper.deproxy(indAssociation.getAssociatedSpecimenOrObservation());
 536
 537                             if (specimenBase instanceof SpecimenOrObservationBase){
 538                                 SpecimenOrObservationBase derivedUnit = specimenBase;
 539                                 handleSpecimen(state, derivedUnit);
 540                                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, indAssociation.getAssociatedSpecimenOrObservation());
 541                             }else{
 542                                 //field units are not supported
 543                                 state.getResult().addError("The associated Specimen of taxon " + taxon.getUuid() + " is not an DerivedUnit. Could not be exported.");
 544
 545                             }
 546                         }
 547                     }
 548                 } else if (element instanceof TextData){
 549                     TextData textData = HibernateProxyHelper.deproxy(element, TextData.class);
 550                     csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_DESCRIPTION)] = createMultilanguageString(textData.getMultilanguageText());
 551                 }
 552                 state.getProcessor().put(table, element, csvLine);
 553             } catch (Exception e) {
 554                 state.getResult().addException(e, "An unexpected error occurred when handling single specimen fact " +
 555                         cdmBaseStr(element) + ": " + e.getMessage());
 556             }
 557         }
 558     }
 559
 560     /**
 561      * @param multilanguageText
 562      * @return
 563      */
 564     private String createMultilanguageString(Map<Language, LanguageString> multilanguageText) {
 565        String text = "";
 566        int index = multilanguageText.size();
 567        for(LanguageString langString: multilanguageText.values()){
 568            text += langString.getText();
 569            if (index > 1){
 570                text += "; ";
 571            }
 572            index --;
 573        }
 574
 575         return text;
 576     }
 577
 578     /**
 579      * @param annotations
 580      * @return
 581      */
 582     private String createAnnotationsString(Set<Annotation> annotations) {
 583         StringBuffer strBuff = new StringBuffer();
 584
 585         for (Annotation ann:annotations){
 586             if (ann.getAnnotationType() == null ||!ann.getAnnotationType().equals(AnnotationType.TECHNICAL())){
 587                 strBuff.append(ann.getText());
 588                 strBuff.append("; ");
 589             }
 590         }
 591
 592         if (strBuff.length() > 2){
 593             return strBuff.substring(0, strBuff.length()-2);
 594         }else{
 595             return null;
 596         }
 597     }
 598
 599     /**
 600      * @param state
 601      * @param taxon
 602      * @param element
 603      */
 604     private void handleSource(CdmLightExportState state, DescriptionElementBase element, CdmLightExportTable factsTable) {
 605         CdmLightExportTable table = CdmLightExportTable.FACT_SOURCES;
 606         try {
 607         Set<DescriptionElementSource> sources = element.getSources();
 608
 609         for (DescriptionElementSource source: sources){
 610
 611                 String[] csvLine = new  String[table.getSize()];
 612                 Reference ref = source.getCitation();
 613                 if ((ref == null) && (source.getNameUsedInSource() == null)){
 614                     continue;
 615                 }
 616                 if (ref != null){
 617                     if (state.getReferenceFromStore(ref.getId()) == null){
 618                         handleReference(state, ref);
 619
 620                     }
 621                     csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, ref);
 622                 }
 623                 csvLine[table.getIndex(CdmLightExportTable.FACT_FK)] = getId(state, element);
 624
 625                 csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)] = getId(state, source.getNameUsedInSource());
 626                 csvLine[table.getIndex(CdmLightExportTable.FACT_TYPE)] = factsTable.getTableName();
 627                 if ( StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)])  && StringUtils.isBlank(csvLine[table.getIndex(CdmLightExportTable.NAME_IN_SOURCE_FK)])){
 628                     continue;
 629                 }
 630                 state.getProcessor().put(table, source, csvLine);
 631
 632         }
 633         } catch (Exception e) {
 634             state.getResult().addException(e, "An unexpected error occurred when handling single source " +
 635                     cdmBaseStr(element) + ": " + e.getMessage());
 636         }
 637
 638     }
 639
 640     /**
 641      * @param state
 642      * @param distributionFacts
 643      */
 644     private void handleDistributionFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> distributionFacts) {
 645         CdmLightExportTable table = CdmLightExportTable.GEOGRAPHIC_AREA_FACT;
 646
 647         for (DescriptionElementBase element: distributionFacts){
 648             try {
 649                 if (element instanceof Distribution){
 650                     String[] csvLine = new  String[table.getSize()];
 651                     Distribution distribution = (Distribution)element;
 652                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 653                     handleSource(state, element, table);
 654                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 655                     if (distribution.getArea() != null){
 656                         csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = distribution.getArea().getLabel();
 657                     }
 658                     if (distribution.getStatus() != null){
 659                         csvLine[table.getIndex(CdmLightExportTable.STATUS_LABEL)] = distribution.getStatus().getLabel();
 660                     }
 661                     state.getProcessor().put(table, distribution, csvLine);
 662                 } else{
 663                     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());
 664                 }
 665             } catch (Exception e) {
 666                 state.getResult().addException(e, "An unexpected error occurred when handling single distribution " +
 667                         cdmBaseStr(element) + ": " + e.getMessage());
 668             }
 669         }
 670     }
 671
 672     /**
 673      * @param state
 674      * @param commonNameFacts
 675      */
 676     private void handleCommonNameFacts(CdmLightExportState state, Taxon taxon, List<DescriptionElementBase> commonNameFacts) {
 677         CdmLightExportTable table = CdmLightExportTable.COMMON_NAME_FACT;
 678
 679         for (DescriptionElementBase element: commonNameFacts){
 680             try {
 681                 if (element instanceof CommonTaxonName){
 682                     String[] csvLine = new  String[table.getSize()];
 683                     CommonTaxonName commonName = (CommonTaxonName)element;
 684                     csvLine[table.getIndex(CdmLightExportTable.FACT_ID)] = getId(state, element);
 685                     handleSource(state, element, table);
 686                     csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, taxon);
 687                     if (commonName.getName() != null){csvLine[table.getIndex(CdmLightExportTable.FACT_TEXT)] = commonName.getName();}
 688                     if (commonName.getLanguage() != null){csvLine[table.getIndex(CdmLightExportTable.LANGUAGE)] = commonName.getLanguage().getLabel();}
 689                     if (commonName.getArea() != null){ csvLine[table.getIndex(CdmLightExportTable.AREA_LABEL)] = commonName.getArea().getLabel();}
 690                     state.getProcessor().put(table, commonName, csvLine);
 691                 } else{
 692                     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());
 693                 }
 694             } catch (Exception e) {
 695                 state.getResult().addException(e, "An unexpected error occurred when handling single common name " +
 696                         cdmBaseStr(element) + ": " + e.getMessage());
 697             }
 698         }
 699     }
 700
 701     /**
 702      * @param sec
 703      * @return
 704      */
 705     private String getTitleCache(IIdentifiableEntity identEntity) {
 706         if (identEntity == null){
 707             return "";
 708         }
 709         //TODO refresh?
 710         return identEntity.getTitleCache();
 711     }
 712
 713     /**
 714      * @param state
 715      * @param taxon
 716      * @return
 717      */
 718     private String getId(CdmLightExportState state, ICdmBase cdmBase) {
 719         if (cdmBase == null){
 720             return "";
 721         }
 722         //TODO make configurable
 723         return cdmBase.getUuid().toString();
 724     }
 725
 726     /**
 727      * @param state
 728      * @param synonym
 729      */
 730     private void handleSynonym(CdmLightExportState state, Synonym synonym) {
 731        try {
 732            if (isUnpublished(state.getConfig(), synonym)){
 733                return;
 734            }
 735            TaxonName name = synonym.getName();
 736            handleName(state, name);
 737
 738            CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 739            String[] csvLine = new String[table.getSize()];
 740
 741            csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, synonym);
 742            csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, synonym.getAcceptedTaxon());
 743            csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 744            csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, synonym.getSec());
 745            csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(synonym.getSec());
 746
 747            state.getProcessor().put(table, synonym, csvLine);
 748         } catch (Exception e) {
 749             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
 750                     cdmBaseStr(synonym) + ": " + e.getMessage());
 751         }
 752     }
 753
 754
 755     /**
 756      * Handles Misapplied names (including pro parte and partial as well as
 757      * pro parte and partial synonyms
 758      * @param state
 759      * @param rel
 760      */
 761     private void handleProPartePartialMisapplied(CdmLightExportState state, TaxonRelationship rel) {
 762         try {
 763             Taxon ppSyonym = rel.getFromTaxon();
 764             if (isUnpublished(state.getConfig(), ppSyonym)){
 765                 return;
 766             }
 767             TaxonName name = ppSyonym.getName();
 768             handleName(state, name);
 769
 770             CdmLightExportTable table = CdmLightExportTable.SYNONYM;
 771             String[] csvLine = new String[table.getSize()];
 772
 773             csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, rel);
 774             csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, rel.getToTaxon());
 775             csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name);
 776
 777             Reference secRef = ppSyonym.getSec();
 778             csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef);
 779             csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef);
 780             Reference synSecRef = rel.getCitation();
 781             csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, synSecRef);
 782             csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(synSecRef);
 783
 784             //pro parte type
 785             TaxonRelationshipType type = rel.getType();
 786             csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = type.isProParte()? "1":"0";
 787             csvLine[table.getIndex(CdmLightExportTable.IS_PARTIAL)] = type.isPartial()? "1":"0";
 788             csvLine[table.getIndex(CdmLightExportTable.IS_MISAPPLIED)] = type.isAnyMisappliedName()? "1":"0";
 789
 790             state.getProcessor().put(table, ppSyonym, csvLine);
 791          } catch (Exception e) {
 792              state.getResult().addException(e, "An unexpected error occurred when handling "
 793                      + "pro parte/partial synonym relationship " +
 794                      cdmBaseStr(rel) + ": " + e.getMessage());
 795          }
 796
 797     }
 798
 799
 800     /**
 801      * @param state
 802      * @param name
 803      */
 804     private void handleName(CdmLightExportState state, TaxonName name) {
 805         if (name == null){
 806             return;
 807         }
 808         try {
 809             Rank rank = name.getRank();
 810             CdmLightExportTable table = CdmLightExportTable.SCIENTIFIC_NAME;
 811             name = HibernateProxyHelper.deproxy(name);
 812             String[] csvLine = new String[table.getSize()];
 813
 814             csvLine[table.getIndex(CdmLightExportTable.NAME_ID)] = getId(state, name);
 815             if (name.getLsid() != null){
 816                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = name.getLsid().getLsid();
 817             }else{
 818                 csvLine[table.getIndex(CdmLightExportTable.LSID)] = "";
 819             }
 820
 821             handleIdentifier(state, name);
 822             handleDescriptions(state, name);
 823
 824             csvLine[table.getIndex(CdmLightExportTable.RANK)] = getTitleCache(rank);
 825             if (rank != null){
 826                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());
 827                 if (rank.isInfraGeneric()){
 828                     try {
 829                         csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_RANK)] = name.getRank().getInfraGenericMarker();
 830                     } catch (UnknownCdmTypeException e) {
 831                         state.getResult().addError("Infrageneric marker expected but not available for rank " + name.getRank().getTitleCache());
 832                     }
 833                 }
 834                 if (rank.isInfraSpecific()){
 835                     csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_RANK)] = name.getRank().getAbbreviation();
 836                 }
 837             }else{
 838                 csvLine[table.getIndex(CdmLightExportTable.RANK_SEQUENCE)] = "";
 839             }
 840             if (name.isProtectedTitleCache()){
 841                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] =name.getTitleCache();
 842             }else{
 843                 //TODO: adapt the tropicos titlecache creation
 844                 csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_WITH_AUTHORS)] = name.getTitleCache();
 845             }
 846             csvLine[table.getIndex(CdmLightExportTable.FULL_NAME_NO_AUTHORS)] = name.getNameCache();
 847             csvLine[table.getIndex(CdmLightExportTable.GENUS_UNINOMIAL)] = name.getGenusOrUninomial();
 848
 849             csvLine[table.getIndex(CdmLightExportTable.INFRAGENERIC_EPITHET)] = name.getInfraGenericEpithet();
 850             csvLine[table.getIndex(CdmLightExportTable.SPECIFIC_EPITHET)] = name.getSpecificEpithet();
 851
 852             csvLine[table.getIndex(CdmLightExportTable.INFRASPECIFIC_EPITHET)] = name.getInfraSpecificEpithet();
 853             csvLine[table.getIndex(CdmLightExportTable.BAS_AUTHORTEAM_FK)] = getId(state,name.getBasionymAuthorship());
 854             if (name.getBasionymAuthorship() != null){
 855                 if (state.getAuthorFromStore(name.getBasionymAuthorship().getId()) == null) {
 856                     handleAuthor(state, name.getBasionymAuthorship());
 857                 }
 858             }
 859             csvLine[table.getIndex(CdmLightExportTable.BAS_EX_AUTHORTEAM_FK)] = getId(state, name.getExBasionymAuthorship());
 860             if (name.getExBasionymAuthorship() != null){
 861                 if (state.getAuthorFromStore(name.getExBasionymAuthorship().getId()) == null) {
 862                     handleAuthor(state, name.getExBasionymAuthorship());
 863                 }
 864
 865             }
 866             csvLine[table.getIndex(CdmLightExportTable.COMB_AUTHORTEAM_FK)] = getId(state,name.getCombinationAuthorship());
 867             if (name.getCombinationAuthorship() != null){
 868                 if (state.getAuthorFromStore(name.getCombinationAuthorship().getId()) == null) {
 869                     handleAuthor(state, name.getCombinationAuthorship());
 870                 }
 871             }
 872             csvLine[table.getIndex(CdmLightExportTable.COMB_EX_AUTHORTEAM_FK)] = getId(state, name.getExCombinationAuthorship());
 873             if (name.getExCombinationAuthorship() != null){
 874                 if (state.getAuthorFromStore(name.getExCombinationAuthorship().getId()) == null) {
 875                     handleAuthor(state, name.getExCombinationAuthorship());
 876                 }
 877
 878             }
 879
 880             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TEAM_STRING)] = name.getAuthorshipCache();
 881
 882             Reference nomRef = name.getNomenclaturalReference();
 883
 884             if (nomRef != null){
 885                 if (state.getReferenceFromStore(nomRef.getId()) == null){
 886                     handleReference(state, nomRef);
 887                 }
 888                 csvLine[table.getIndex(CdmLightExportTable.REFERENCE_FK)] = getId(state, nomRef);
 889                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = nomRef.getType().name();
 890                 if (nomRef.getVolume() != null){
 891                     csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = nomRef.getVolume();
 892                     csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 893                 }
 894                 if (nomRef.getDatePublished() != null){
 895                     csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = nomRef.getTimePeriodPublishedString();
 896                     csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = nomRef.getDatePublished().getYear();
 897                     csvLine[table.getIndex(CdmLightExportTable.VERBATIM_DATE)] = nomRef.getDatePublished().getVerbatimDate();
 898                 }
 899                 if (name.getNomenclaturalMicroReference() != null){
 900                     csvLine[table.getIndex(CdmLightExportTable.DETAIL)] = name.getNomenclaturalMicroReference();
 901                 }
 902                 nomRef = HibernateProxyHelper.deproxy(nomRef);
 903                 if (nomRef.getInReference() != null){
 904                     Reference inReference = nomRef.getInReference();
 905                     if (inReference.getDatePublished() != null && nomRef.getDatePublished() == null){
 906                         csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = inReference.getDatePublishedString();
 907                         csvLine[table.getIndex(CdmLightExportTable.YEAR_PUBLISHED)] = inReference.getDatePublished().getYear();
 908                     }
 909                     if (nomRef.getVolume() == null && inReference.getVolume() != null){
 910                         csvLine[table.getIndex(CdmLightExportTable.VOLUME_ISSUE)] = inReference.getVolume();
 911                         csvLine[table.getIndex(CdmLightExportTable.COLLATION)] = createCollatation(name);
 912                     }
 913                     if (inReference.getInReference() != null){
 914                         inReference = inReference.getInReference();
 915                     }
 916                     if (inReference.getAbbrevTitle() == null){
 917                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitleCache());
 918                     }else{
 919                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(inReference.getAbbrevTitle());
 920                     }
 921                     if (inReference.getTitle() == null){
 922                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitleCache());
 923                     }else{
 924                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(inReference.getTitle());
 925                     }
 926
 927
 928                     TeamOrPersonBase<?> author = inReference.getAuthorship();
 929                     if (author != null && (nomRef.isOfType(ReferenceType.BookSection) || nomRef.isOfType(ReferenceType.Section))){
 930                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
 931                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 932                     }else{
 933                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 934                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 935                     }
 936                 }else{
 937                     if (nomRef.getAbbrevTitle() == null){
 938                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitleCache());
 939                     }else{
 940                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_TITLE)] = CdmUtils.Nz(nomRef.getAbbrevTitle());
 941                     }
 942                     if (nomRef.getTitle() == null){
 943                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitleCache());
 944                     }else{
 945                         csvLine[table.getIndex(CdmLightExportTable.FULL_TITLE)] = CdmUtils.Nz(nomRef.getTitle());
 946                     }
 947                     TeamOrPersonBase<?> author = nomRef.getAuthorship();
 948                     if (author != null ){
 949                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = CdmUtils.Nz(author.getNomenclaturalTitle());
 950                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = CdmUtils.Nz(author.getTitleCache());
 951                     }else{
 952                         csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_AUTHOR)] = "";
 953                         csvLine[table.getIndex(CdmLightExportTable.FULL_REF_AUTHOR)] = "";
 954                     }
 955
 956                 }
 957             }else{
 958                 csvLine[table.getIndex(CdmLightExportTable.PUBLICATION_TYPE)] = "";
 959             }
 960
 961
 962
 963             /*
 964             * Collation
 965
 966             Detail
 967
 968
 969             TitlePageYear
 970             */
 971             Set<TaxonNameDescription> descriptions = name.getDescriptions();
 972             String protologueUriString = extractURIs(state, descriptions, Feature.PROTOLOGUE());
 973
 974             csvLine[table.getIndex(CdmLightExportTable.PROTOLOGUE_URI)] = protologueUriString;
 975
 976             if (name.getStatus() == null || name.getStatus().isEmpty()){
 977                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = "";
 978                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = "";
 979             }else{
 980
 981                 String statusStringAbbrev = extractStatusString(state, name, true);
 982                 String statusString = extractStatusString(state, name, false);
 983
 984                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS)] = statusString.trim();
 985                 csvLine[table.getIndex(CdmLightExportTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();
 986             }
 987
 988             HomotypicalGroup group =name.getHomotypicalGroup();
 989
 990             if (state.getHomotypicalGroupFromStore(group.getId()) == null){
 991                 handleHomotypicalGroup(state, group);
 992             }
 993             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_FK)] = getId(state, group);
 994             List<TaxonName> typifiedNames = new ArrayList<>();
 995             typifiedNames.addAll(group.getTypifiedNames());
 996             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
 997             Integer  seqNumber= typifiedNames.indexOf(name);
 998             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_SEQ)] = String.valueOf(seqNumber);
 999             state.getProcessor().put(table, name, csvLine);
1000
1001             /*
1002              *
1003             Tropicos_ID
1004             IPNI_ID
1005
1006
1007             InfragenericRank
1008
1009
1010             InfraspecificRank
1011             Collation
1012             Volume (Issue)
1013             Detail
1014             DatePublished
1015             YearPublished
1016             TitlePageYear
1017
1018
1019
1020             HomotypicGroupSequenceNumber
1021
1022
1023              *
1024              */
1025         } catch (Exception e) {
1026             state.getResult().addException(e, "An unexpected error occurred when handling synonym " +
1027                     cdmBaseStr(name) + ": " + e.getMessage());
1028         }
1029     }
1030
1031     /**
1032      * @return
1033      */
1034     private String createCollatation(TaxonName name) {
1035         String collation = "";
1036         if (name.getNomenclaturalReference() != null){
1037             Reference ref = name.getNomenclaturalReference();
1038             collation = getVolume(ref);
1039         }
1040         if (name.getNomenclaturalMicroReference() != null){
1041             if (!StringUtils.isBlank(collation)){
1042                 collation += ":";
1043             }
1044             collation +=name.getNomenclaturalMicroReference();
1045         }
1046
1047         return collation;
1048     }
1049
1050     /**
1051      * @param nomenclaturalReference
1052      * @return
1053      */
1054     private String getVolume(Reference reference) {
1055         if (reference.getVolume() != null){
1056             return reference.getVolume();
1057         }else if (reference.getInReference() != null){
1058             if (reference.getInReference().getVolume() != null){
1059                 return reference.getInReference().getVolume();
1060             }
1061         }
1062         return null;
1063     }
1064
1065     /**
1066      * @param state
1067      * @param name
1068      */
1069     private void handleIdentifier(CdmLightExportState state, TaxonName name) {
1070         CdmLightExportTable table = CdmLightExportTable.IDENTIFIER;
1071         String[] csvLine;
1072         try {
1073             Set<String>  IPNIidentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_IPNI());
1074             Set<String>  tropicosIdentifiers = name.getIdentifiers(DefinedTerm.IDENTIFIER_NAME_TROPICOS());
1075             Set<String>  WFOIdentifiers = name.getIdentifiers(DefinedTerm.uuidWfoNameIdentifier);
1076             if (!IPNIidentifiers.isEmpty()){
1077                 csvLine = new String[table.getSize()];
1078                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1079                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = IPNI_NAME_IDENTIFIER;
1080                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(IPNIidentifiers);
1081                 state.getProcessor().put(table, name, csvLine);
1082             }
1083             if (!tropicosIdentifiers.isEmpty()){
1084                 csvLine = new String[table.getSize()];
1085                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1086                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = TROPICOS_NAME_IDENTIFIER;
1087                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(tropicosIdentifiers);
1088                 state.getProcessor().put(table, name, csvLine);
1089             }
1090             if (!WFOIdentifiers.isEmpty()){
1091                 csvLine = new String[table.getSize()];
1092                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId( state, name);
1093                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_TYPE)] = WFO_NAME_IDENTIFIER;
1094                 csvLine[table.getIndex(CdmLightExportTable.IDENTIFIER_IDS)] = extractIdentifier(WFOIdentifiers);
1095                 state.getProcessor().put(table, name, csvLine);
1096             }
1097         } catch (Exception e) {
1098             state.getResult().addException(e, "An unexpected error occurred when handling identifiers for " +
1099                     cdmBaseStr(name) + ": " + e.getMessage());
1100
1101         }
1102     }
1103
1104     /**
1105      * @param tropicosIdentifiers
1106      */
1107     private String extractIdentifier(Set<String> identifierSet) {
1108
1109         String identifierString = "";
1110         for (String identifier: identifierSet){
1111             if (!StringUtils.isBlank(identifierString)){
1112                 identifierString += ", ";
1113             }
1114             identifierString += identifier;
1115         }
1116
1117         return identifierString;
1118     }
1119
1120     /**
1121      * @param state
1122      * @param descriptions
1123      * @return
1124      */
1125     private String extractURIs(CdmLightExportState state,
1126             Set<? extends DescriptionBase<?>> descriptionsSet, Feature feature) {
1127         String mediaUriString = "";
1128         SpecimenDescription specimenDescription;
1129         TaxonDescription taxonDescription;
1130         TaxonNameDescription nameDescription;
1131         Set<DescriptionElementBase> elements = new HashSet<>();
1132         for (DescriptionBase<?> description : descriptionsSet){
1133             try {
1134                 if (!description.getElements().isEmpty()){
1135                     if (description instanceof SpecimenDescription){
1136                         specimenDescription = (SpecimenDescription)description;
1137                         elements = specimenDescription.getElements();
1138                     }else if (description instanceof TaxonDescription){
1139                         taxonDescription = (TaxonDescription) description;
1140                         elements = taxonDescription.getElements();
1141                     } else if (description instanceof TaxonNameDescription){
1142                         nameDescription = (TaxonNameDescription) description;
1143                         elements = nameDescription.getElements();
1144                     }
1145
1146                     for (DescriptionElementBase element : elements){
1147                         Feature entityFeature = HibernateProxyHelper.deproxy(element.getFeature());
1148                         if (entityFeature.equals(feature)){
1149                             if (!element.getMedia().isEmpty()){
1150                                 List<Media> media = element.getMedia();
1151                                 for (Media mediaElement: media){
1152                                     Iterator<MediaRepresentation> it =  mediaElement.getRepresentations().iterator();
1153                                     mediaUriString = extractMediaUris(it);
1154                                 }
1155                             }
1156                         }
1157                     }
1158                 }
1159             } catch (Exception e) {
1160                 state.getResult().addException(e, "An unexpected error occurred when extracting media URIs for " +
1161                         cdmBaseStr(description) + ": " + e.getMessage());
1162             }
1163         }
1164         return mediaUriString;
1165     }
1166
1167     /**
1168      * @param state
1169      * @param basionymAuthorship
1170      */
1171     private void handleAuthor(CdmLightExportState state, TeamOrPersonBase<?> author) {
1172         try {
1173             if (state.getAuthorFromStore(author.getId()) != null){
1174                 return;
1175             }
1176             state.addAuthorToStore(author);
1177             CdmLightExportTable table = CdmLightExportTable.NOMENCLATURAL_AUTHOR;
1178             String[] csvLine = new String[table.getSize()];
1179             CdmLightExportTable tableAuthorRel = CdmLightExportTable.NOMENCLATURAL_AUTHOR_TEAM_RELATION;
1180             String[] csvLineRel = new String[tableAuthorRel.getSize()];
1181             String[] csvLineMember = new String[table.getSize()];
1182             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, author);
1183             csvLine[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = author.getNomenclaturalTitle();
1184             csvLine[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = author.getTitleCache();
1185             author = HibernateProxyHelper.deproxy(author);
1186             if (author instanceof Person){
1187                 Person authorPerson = (Person)author;
1188                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_GIVEN_NAME)] = authorPerson.getGivenName();
1189                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FAMILY_NAME)] = authorPerson.getFamilyName();
1190                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = authorPerson.getPrefix();
1191                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = authorPerson.getSuffix();
1192             } else{
1193                 // create an entry in rel table and all members in author table, check whether the team members already in author table
1194
1195                 Team authorTeam = (Team)author;
1196                 int index = 0;
1197                 for (Person member: authorTeam.getTeamMembers()){
1198                     csvLineRel = new String[tableAuthorRel.getSize()];
1199                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_FK)] = getId(state, authorTeam);
1200                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state, member);
1201                     csvLineRel[tableAuthorRel.getIndex(CdmLightExportTable.AUTHOR_TEAM_SEQ_NUMBER)] = String.valueOf(index);
1202                     state.getProcessor().put(tableAuthorRel, authorTeam.getId() +":" +member.getId(), csvLineRel);
1203
1204                     if (state.getAuthorFromStore(member.getId()) == null){
1205                         state.addAuthorToStore(member);
1206                         csvLineMember = new String[table.getSize()];
1207                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_ID)] = getId(state, member);
1208                         csvLineMember[table.getIndex(CdmLightExportTable.ABBREV_AUTHOR)] = member.getNomenclaturalTitle();
1209                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_TITLE)] = member.getTitleCache();
1210                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_GIVEN_NAME)] = member.getGivenName();
1211                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_FAMILY_NAME)] = member.getFamilyName();
1212                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_PREFIX)] = member.getPrefix();
1213                         csvLineMember[table.getIndex(CdmLightExportTable.AUTHOR_SUFFIX)] = member.getSuffix();
1214                         state.getProcessor().put(table, member, csvLineMember);
1215                     }
1216                     index++;
1217
1218                 }
1219             }
1220             state.getProcessor().put(table, author, csvLine);
1221         } catch (Exception e) {
1222             state.getResult().addException(e, "An unexpected error occurred when handling author " +
1223                     cdmBaseStr(author) + ": " + e.getMessage());
1224         }
1225     }
1226
1227     /**
1228      * @param state
1229      * @param name
1230      * @param statusString
1231      * @return
1232      */
1233     private String extractStatusString(CdmLightExportState state, TaxonName name, boolean abbrev) {
1234         try {
1235             Set<NomenclaturalStatus> status = name.getStatus();
1236             if (status.isEmpty()){
1237                 return "";
1238             }
1239             String statusString = "";
1240             for (NomenclaturalStatus nameStatus: status){
1241                 if (nameStatus != null){
1242                     if (abbrev){
1243                         if (nameStatus.getType() != null){
1244                             statusString += nameStatus.getType().getIdInVocabulary();
1245                         }
1246                     }else{
1247                         if (nameStatus.getType() != null){
1248                             statusString += nameStatus.getType().getTitleCache();
1249                         }
1250                     }
1251                     if (!abbrev){
1252
1253                         if (nameStatus.getRuleConsidered() != null && !StringUtils.isBlank(nameStatus.getRuleConsidered())){
1254                             statusString += " " + nameStatus.getRuleConsidered();
1255                         }
1256                         if (nameStatus.getCitation() != null){
1257                             statusString += " " + nameStatus.getCitation().getTitleCache();
1258                         }
1259                         if (nameStatus.getCitationMicroReference() != null && !StringUtils.isBlank(nameStatus.getCitationMicroReference())){
1260                             statusString += " " + nameStatus.getCitationMicroReference();
1261                         }
1262                     }
1263                     statusString += " ";
1264                 }
1265             }
1266             return statusString;
1267         } catch (Exception e) {
1268             state.getResult().addException(e, "An unexpected error occurred when extracting status string for " +
1269                     cdmBaseStr(name) + ": " + e.getMessage());
1270             return "";
1271         }
1272     }
1273
1274     /**
1275      * @param group
1276      */
1277     private void handleHomotypicalGroup(CdmLightExportState state, HomotypicalGroup group) {
1278         try {
1279             state.addHomotypicalGroupToStore(group);
1280             CdmLightExportTable table = CdmLightExportTable.HOMOTYPIC_GROUP;
1281             String[] csvLine = new String[table.getSize()];
1282
1283             csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_ID)] = getId(state, group);
1284             List<TaxonName> typifiedNames = new ArrayList<>();
1285             typifiedNames.addAll(group.getTypifiedNames());
1286             Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));
1287             String typifiedNamesString = "";
1288             for (TaxonName name: typifiedNames){
1289                 //Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)
1290                 //TODO: nameRelations, which and how to display
1291
1292
1293                 typifiedNamesString += name.getTitleCache()+ extractStatusString(state, name, true) + "; ";
1294             }
1295             typifiedNamesString = typifiedNamesString.substring(0, typifiedNamesString.length()-2);
1296             if (typifiedNamesString != null){
1297                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = typifiedNamesString.trim();
1298             }else{
1299                 csvLine[table.getIndex(CdmLightExportTable.HOMOTYPIC_GROUP_STRING)] = "";
1300             }
1301             Set<TypeDesignationBase> typeDesigantions = group.getTypeDesignations();
1302             List<TypeDesignationBase> designationList = new ArrayList<>();
1303             designationList.addAll(typeDesigantions);
1304             Collections.sort(designationList, new TypeComparator());
1305             StringBuffer typeDesignationString = new StringBuffer();
1306             for (TypeDesignationBase typeDesignation: typeDesigantions){
1307                 if (typeDesignation != null && typeDesignation.getTypeStatus() != null){
1308                     typeDesignationString.append(typeDesignation.getTypeStatus().getTitleCache() + ": ");
1309                 }
1310                 if (typeDesignation instanceof SpecimenTypeDesignation){
1311                     if (((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen() != null){
1312                         typeDesignationString.append(((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen().getTitleCache());
1313                         handleSpecimen(state, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
1314                     }
1315                 }else{
1316                     if (((NameTypeDesignation)typeDesignation).getTypeName() != null){
1317                         typeDesignationString.append(((NameTypeDesignation)typeDesignation).getTypeName().getTitleCache());
1318                     }
1319                 }
1320                 if(typeDesignation.getCitation() != null ){
1321                     typeDesignationString.append(", "+typeDesignation.getCitation().getTitleCache());
1322                 }
1323                 //TODO...
1324                 /*
1325                  * Sortierung:
1326                 1.  Status der Typen: a) holo, lecto, neo, syn, b) epi, paralecto, c) para (wenn überhaupt) – die jeweiligen iso immer direct mit dazu
1327                 2.  Land
1328                 3.  Sammler
1329                 4.  Nummer
1330
1331                 Aufbau der Typusinformationen:
1332                 Land: Lokalität mit Höhe und Koordinaten; Datum; Sammler Nummer (Herbar/Barcode, Typusart; Herbar/Barcode, Typusart …)
1333
1334                  */
1335             }
1336             String typeDesignations = typeDesignationString.toString();
1337             if (typeDesignations != null){
1338                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = typeDesignations;
1339             }else{
1340                 csvLine[table.getIndex(CdmLightExportTable.TYPE_STRING)] = "";
1341             }
1342             state.getProcessor().put(table, String.valueOf(group.getId()), csvLine);
1343         } catch (Exception e) {
1344             state.getResult().addException(e, "An unexpected error occurred when handling homotypic group " +
1345                     cdmBaseStr(group) + ": " + e.getMessage());
1346         }
1347     }
1348
1349     /**
1350      * @param name
1351      * @return
1352      */
1353     private String getTropicosTitleCache(CdmLightExportState state, TaxonName name) {
1354         try {
1355             String basionymStart = "(";
1356             String basionymEnd = ") ";
1357             String exAuthorSeperator = " ex ";
1358             TeamOrPersonBase<?> combinationAuthor = name.getCombinationAuthorship();
1359             TeamOrPersonBase<?> exCombinationAuthor = name.getExCombinationAuthorship();
1360             TeamOrPersonBase<?> basionymAuthor = name.getBasionymAuthorship();
1361             TeamOrPersonBase<?> exBasionymAuthor = name.getExBasionymAuthorship();
1362
1363             String combinationAuthorString = "";
1364             if (combinationAuthor != null){
1365                 combinationAuthor = HibernateProxyHelper.deproxy(combinationAuthor);
1366                 if (combinationAuthor instanceof Team){
1367                     combinationAuthorString = createTropicosTeamTitle(combinationAuthor);
1368                 }else{
1369                     Person person = HibernateProxyHelper.deproxy(combinationAuthor, Person.class);
1370                     combinationAuthorString = createTropicosAuthorString(person);
1371                 }
1372             }
1373             String exCombinationAuthorString = "";
1374             if (exCombinationAuthor != null){
1375                 exCombinationAuthor = HibernateProxyHelper.deproxy(exCombinationAuthor);
1376                 if (exCombinationAuthor instanceof Team){
1377                    exCombinationAuthorString = createTropicosTeamTitle(exCombinationAuthor);
1378                 }else{
1379                     Person person = HibernateProxyHelper.deproxy(exCombinationAuthor, Person.class);
1380                     exCombinationAuthorString = createTropicosAuthorString(person);
1381                 }
1382             }
1383
1384             String basionymAuthorString = "";
1385             if (basionymAuthor != null){
1386                 basionymAuthor = HibernateProxyHelper.deproxy(basionymAuthor);
1387                 if (basionymAuthor instanceof Team){
1388                     basionymAuthorString =  createTropicosTeamTitle(basionymAuthor);
1389                 }else{
1390                     Person person = HibernateProxyHelper.deproxy(basionymAuthor, Person.class);
1391                     basionymAuthorString = createTropicosAuthorString(person);
1392                 }
1393             }
1394
1395             String exBasionymAuthorString = "";
1396
1397             if (exBasionymAuthor != null){
1398                 exBasionymAuthor = HibernateProxyHelper.deproxy(exBasionymAuthor);
1399                 if (exBasionymAuthor instanceof Team){
1400                     exBasionymAuthorString = createTropicosTeamTitle(exBasionymAuthor);
1401
1402                 }else{
1403                     Person person = HibernateProxyHelper.deproxy(exBasionymAuthor, Person.class);
1404                     exBasionymAuthorString = createTropicosAuthorString(person);
1405                 }
1406             }
1407             String completeAuthorString =  name.getNameCache() + " ";
1408
1409             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ? basionymStart: "";
1410             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString)) ? (CdmUtils.Nz(exBasionymAuthorString) + exAuthorSeperator): "" ;
1411             completeAuthorString += (!CdmUtils.isBlank(basionymAuthorString))? CdmUtils.Nz(basionymAuthorString):"";
1412             completeAuthorString += (!CdmUtils.isBlank(exBasionymAuthorString) || !CdmUtils.isBlank(basionymAuthorString)) ?  basionymEnd:"";
1413             completeAuthorString += (!CdmUtils.isBlank(exCombinationAuthorString)) ? (CdmUtils.Nz(exCombinationAuthorString) + exAuthorSeperator): "" ;
1414             completeAuthorString += (!CdmUtils.isBlank(combinationAuthorString))? CdmUtils.Nz(combinationAuthorString):"";
1415
1416
1417             return completeAuthorString;
1418         } catch (Exception e) {
1419             state.getResult().addException(e, "An unexpected error occurred when handling tropicos title cache for " +
1420                     cdmBaseStr(name) + ": " + e.getMessage());
1421             return null;
1422         }
1423     }
1424
1425     /**
1426      * @param combinationAuthor
1427      * @return
1428      */
1429     private String createTropicosTeamTitle(TeamOrPersonBase<?> combinationAuthor) {
1430         String combinationAuthorString;
1431         Team team = HibernateProxyHelper.deproxy(combinationAuthor, Team.class);
1432         Team tempTeam = Team.NewInstance();
1433         for (Person teamMember:team.getTeamMembers()){
1434             combinationAuthorString = createTropicosAuthorString(teamMember);
1435             Person tempPerson = Person.NewTitledInstance(combinationAuthorString);
1436             tempTeam.addTeamMember(tempPerson);
1437         }
1438         combinationAuthorString = tempTeam.generateTitle();
1439         return combinationAuthorString;
1440     }
1441
1442     /**
1443      * @param teamMember
1444      */
1445     private String createTropicosAuthorString(Person teamMember) {
1446         String nomAuthorString = "";
1447         String[] splittedAuthorString = null;
1448         if (teamMember == null){
1449             return nomAuthorString;
1450         }
1451
1452         if (teamMember.getGivenName() != null){
1453             String givenNameString = teamMember.getGivenName().replaceAll("\\.", "\\. ");
1454             splittedAuthorString = givenNameString.split("\\s");
1455             for (String split: splittedAuthorString){
1456                 if (!StringUtils.isBlank(split)){
1457                     nomAuthorString += split.substring(0, 1);
1458                     nomAuthorString += ".";
1459                 }
1460             }
1461         }
1462         if (teamMember.getFamilyName() != null){
1463             String familyNameString = teamMember.getFamilyName().replaceAll("\\.", "\\. ");
1464             splittedAuthorString = familyNameString.split("\\s");
1465             for (String split: splittedAuthorString){
1466                 nomAuthorString += " " +split;
1467             }
1468         }
1469         if (StringUtils.isBlank(nomAuthorString.trim())){
1470             if (teamMember.getTitleCache() != null) {
1471                 String titleCacheString = teamMember.getTitleCache().replaceAll("\\.", "\\. ");
1472                 splittedAuthorString = titleCacheString.split("\\s");
1473             }
1474
1475
1476             int index = 0;
1477             for (String split: splittedAuthorString){
1478                 if ( index < splittedAuthorString.length-1 && (split.length()==1 || split.endsWith("."))){
1479                     nomAuthorString += split;
1480                 }else{
1481                     nomAuthorString = nomAuthorString +" "+ split;
1482                 }
1483                 index++;
1484             }
1485         }
1486         return nomAuthorString.trim();
1487     }
1488
1489     /**
1490      * @param state
1491      * @param name
1492      */
1493     private void handleReference(CdmLightExportState state, Reference reference) {
1494         try {
1495             state.addReferenceToStore(reference);
1496             CdmLightExportTable table = CdmLightExportTable.REFERENCE;
1497
1498             String[] csvLine = new String[table.getSize()];
1499             csvLine[table.getIndex(CdmLightExportTable.REFERENCE_ID)] = getId(state, reference);
1500             //TODO short citations correctly
1501             String shortCitation = createShortCitation(reference);  //Should be Author(year) like in Taxon.sec
1502             csvLine[table.getIndex(CdmLightExportTable.BIBLIO_SHORT_CITATION)] = shortCitation;
1503             //TODO get preferred title
1504             csvLine[table.getIndex(CdmLightExportTable.REF_TITLE)] = reference.getTitle();
1505             csvLine[table.getIndex(CdmLightExportTable.ABBREV_REF_TITLE)] = reference.getAbbrevTitle();
1506             csvLine[table.getIndex(CdmLightExportTable.DATE_PUBLISHED)] = reference.getDatePublishedString();
1507             //TBC
1508             csvLine[table.getIndex(CdmLightExportTable.EDITION)] = reference.getEdition();
1509             csvLine[table.getIndex(CdmLightExportTable.EDITOR)] = reference.getEditor();
1510             csvLine[table.getIndex(CdmLightExportTable.ISBN)] = reference.getIsbn();
1511             csvLine[table.getIndex(CdmLightExportTable.ISSN)] = reference.getIssn();
1512             csvLine[table.getIndex(CdmLightExportTable.ORGANISATION)] = reference.getOrganization();
1513             csvLine[table.getIndex(CdmLightExportTable.PAGES)] = reference.getPages();
1514             csvLine[table.getIndex(CdmLightExportTable.PLACE_PUBLISHED)] = reference.getPlacePublished();
1515             csvLine[table.getIndex(CdmLightExportTable.PUBLISHER)] = reference.getPublisher();
1516             csvLine[table.getIndex(CdmLightExportTable.REF_ABSTRACT)] = reference.getReferenceAbstract();
1517             csvLine[table.getIndex(CdmLightExportTable.SERIES_PART)] = reference.getSeriesPart();
1518             csvLine[table.getIndex(CdmLightExportTable.VOLUME)] = reference.getVolume();
1519             csvLine[table.getIndex(CdmLightExportTable.YEAR)] = reference.getYear();
1520
1521             if ( reference.getAuthorship() != null){
1522                 csvLine[table.getIndex(CdmLightExportTable.AUTHORSHIP_TITLE)] = createFullAuthorship(reference);
1523                 csvLine[table.getIndex(CdmLightExportTable.AUTHOR_FK)] = getId(state,reference.getAuthorship());
1524             }
1525
1526             csvLine[table.getIndex(CdmLightExportTable.IN_REFERENCE)] = getId(state, reference.getInReference());
1527             if (reference.getInReference() != null && state.getReferenceFromStore(reference.getInReference().getId()) == null){
1528                 handleReference(state, reference.getInReference());
1529             }
1530             if ( reference.getInstitution() != null){ csvLine[table.getIndex(CdmLightExportTable.INSTITUTION)] = reference.getInstitution().getTitleCache();}
1531             if ( reference.getLsid() != null){ csvLine[table.getIndex(CdmLightExportTable.LSID)] = reference.getLsid().getLsid();}
1532             if ( reference.getSchool() != null){ csvLine[table.getIndex(CdmLightExportTable.SCHOOL)] = reference.getSchool().getTitleCache();}
1533             if ( reference.getUri() != null){ csvLine[table.getIndex(CdmLightExportTable.URI)] = reference.getUri().toString();}
1534             csvLine[table.getIndex(CdmLightExportTable.REF_TYPE)] = reference.getType().getKey();
1535
1536             state.getProcessor().put(table, reference, csvLine);
1537         } catch (Exception e) {
1538             state.getResult().addException(e, "An unexpected error occurred when handling reference " +
1539                     cdmBaseStr(reference) + ": " + e.getMessage());
1540         }
1541
1542     }
1543
1544
1545     /**
1546      * @param reference
1547      * @return
1548      */
1549     private String createShortCitation(Reference reference) {
1550         TeamOrPersonBase<?> authorship = reference.getAuthorship();
1551         String shortCitation = "";
1552         if (authorship == null) {
1553             return null;
1554         }
1555         authorship = HibernateProxyHelper.deproxy(authorship);
1556         if (authorship instanceof Person){
1557             shortCitation = ((Person)authorship).getFamilyName();
1558             if (StringUtils.isBlank(shortCitation) ){
1559                 shortCitation = ((Person)authorship).getTitleCache();
1560             }
1561         }
1562         else if (authorship instanceof Team){
1563
1564             Team authorTeam = HibernateProxyHelper.deproxy(authorship, Team.class);
1565             int index = 0;
1566
1567             for (Person teamMember : authorTeam.getTeamMembers()){
1568                 index++;
1569                 if (index == 3){
1570                     shortCitation += " & al.";
1571                     break;
1572                 }
1573                 String concat = concatString(authorTeam, authorTeam.getTeamMembers(), index);
1574                 if (teamMember.getFamilyName() != null){
1575                     shortCitation += concat + teamMember.getFamilyName();
1576                 }else{
1577                     shortCitation += concat + teamMember.getTitleCache();
1578                 }
1579
1580             }
1581             if (StringUtils.isBlank(shortCitation)){
1582                 shortCitation = authorTeam.getTitleCache();
1583             }
1584
1585         }
1586         if (!StringUtils.isBlank(reference.getDatePublished().getFreeText())){
1587             shortCitation = shortCitation + " (" + reference.getDatePublished().getFreeText() + ")";
1588         }else if (!StringUtils.isBlank(reference.getYear()) ){
1589             shortCitation = shortCitation + " (" + reference.getYear() + ")";
1590         }
1591         return shortCitation;
1592     }
1593
1594     /**
1595      * @param reference
1596      * @return
1597      */
1598     private String createFullAuthorship(Reference reference) {
1599         TeamOrPersonBase<?> authorship = reference.getAuthorship();
1600         String fullAuthorship = "";
1601         if (authorship == null) {
1602             return null;
1603         }
1604         authorship = HibernateProxyHelper.deproxy(authorship);
1605         if (authorship instanceof Person){
1606             fullAuthorship = ((Person)authorship).getTitleCache();
1607
1608         }
1609         else if (authorship instanceof Team){
1610
1611             Team authorTeam = HibernateProxyHelper.deproxy(authorship, Team.class);
1612             int index = 0;
1613
1614             for (Person teamMember : authorTeam.getTeamMembers()){
1615                 index++;
1616                 String concat = concatString(authorTeam, authorTeam.getTeamMembers(), index);
1617                 fullAuthorship += concat + teamMember.getTitleCache();
1618             }
1619
1620         }
1621
1622         return fullAuthorship;
1623     }
1624
1625     private static String concatString(Team team, List<Person> teamMembers, int i) {
1626         String concat;
1627         if (i <= 1){
1628             concat = "";
1629         }else if (i < teamMembers.size() || ( team.isHasMoreMembers() && i == teamMembers.size())){
1630             concat = STD_TEAM_CONCATINATION;
1631         }else{
1632             concat = FINAL_TEAM_CONCATINATION;
1633         }
1634         return concat;
1635     }
1636
1637     /*
1638      * TypeDesignation table
1639      * Specimen_Fk
1640      *  EditName_Fk
1641      *   TypeVerbatimCitation
1642      *   TypeCategory
1643      *   TypeDesignatedByString
1644      *   TypeDesignatedByRef_Fk
1645      */
1646
1647     private void handleSpecimenTypeDesignations(CdmLightExportState state, TaxonName name){
1648        try {
1649            Set<SpecimenTypeDesignation> typeDesignations = name.getSpecimenTypeDesignations();
1650            CdmLightExportTable table = CdmLightExportTable.TYPE_DESIGNATION;
1651            String nameId = getId(state, name);
1652            String[] csvLine = new String[table.getSize()];
1653             for (SpecimenTypeDesignation specimenType: typeDesignations){
1654                 csvLine = new String[table.getSize()];
1655                 DerivedUnit specimen = specimenType.getTypeSpecimen();
1656                 if (state.getSpecimenFromStore(specimen.getId()) == null){
1657                     handleSpecimen(state, specimen);
1658                 }
1659                 csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_FK)] = getId(state, specimenType.getTypeSpecimen());
1660                 csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = nameId;
1661                 csvLine[table.getIndex(CdmLightExportTable.TYPE_VERBATIM_CITATION)] = specimenType.getTypeSpecimen().generateTitle();
1662                 //TODO: add link to existing Vorcabulary
1663                 csvLine[table.getIndex(CdmLightExportTable.TYPE_CATEGORY)] = "";
1664                 csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_STRING)] = specimenType.getCitation().getTitleCache();
1665                 csvLine[table.getIndex(CdmLightExportTable.TYPE_DESIGNATED_BY_REF_FK)] = getId(state, specimenType.getCitation());
1666             }
1667         } catch (Exception e) {
1668             state.getResult().addException(e, "An unexpected error occurred when handling specimen type designations for " +
1669                     cdmBaseStr(name) + ": " + e.getMessage());
1670         }
1671     }
1672
1673     /**
1674      * @param state
1675      * @param specimen
1676      */
1677     private void handleSpecimen(CdmLightExportState state, SpecimenOrObservationBase specimen) {
1678         try {
1679             state.addSpecimenToStore(specimen);
1680             CdmLightExportTable table = CdmLightExportTable.SPECIMEN;
1681             String specimenId = getId(state, specimen);
1682             String[] csvLine = new String[table.getSize()];
1683
1684             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_ID)] = specimenId;
1685             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_CITATION)] = specimen.getTitleCache();
1686             csvLine[table.getIndex(CdmLightExportTable.SPECIMEN_IMAGE_URIS)] = extractURIs(state, specimen.getDescriptions(), Feature.IMAGE());
1687             if (specimen instanceof DerivedUnit){
1688                     DerivedUnit derivedUnit = (DerivedUnit)specimen;
1689                     if (derivedUnit.getCollection() != null){ csvLine[table.getIndex(CdmLightExportTable.HERBARIUM_ABBREV)] = derivedUnit.getCollection().getCode();}
1690
1691                 if (specimen instanceof MediaSpecimen){
1692                     MediaSpecimen mediaSpecimen = (MediaSpecimen) specimen;
1693                     Iterator<MediaRepresentation> it = mediaSpecimen.getMediaSpecimen().getRepresentations().iterator();
1694                     String mediaUris = extractMediaUris(it);
1695                     csvLine[table.getIndex(CdmLightExportTable.MEDIA_SPECIMEN_URL)] = mediaUris;
1696
1697                 }
1698
1699                 if (derivedUnit.getDerivedFrom() != null){
1700                     for (SpecimenOrObservationBase<?> original: derivedUnit.getDerivedFrom().getOriginals()){
1701                         //TODO: What to do if there are more then one FieldUnit??
1702                         if (original instanceof FieldUnit){
1703                             FieldUnit fieldUnit = (FieldUnit)original;
1704                             csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_NUMBER)] = fieldUnit.getFieldNumber();
1705
1706                             GatheringEvent gathering = fieldUnit.getGatheringEvent();
1707                             if (gathering != null){
1708                                 if (gathering.getLocality() != null){ csvLine[table.getIndex(CdmLightExportTable.LOCALITY)] = gathering.getLocality().getText();}
1709                                 if (gathering.getCountry() != null){csvLine[table.getIndex(CdmLightExportTable.COUNTRY)] = gathering.getCountry().getLabel();}
1710                                 csvLine[table.getIndex(CdmLightExportTable.COLLECTOR_STRING)] = createCollectorString(state, gathering, fieldUnit);
1711                                 addCollectingAreas(state, gathering);
1712                                 if (gathering.getGatheringDate() != null){csvLine[table.getIndex(CdmLightExportTable.COLLECTION_DATE)] = gathering.getGatheringDate().toString();}
1713                                 if (!gathering.getCollectingAreas().isEmpty()){
1714                                     int index = 0;
1715                                     csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "0";
1716                                     for (NamedArea area: gathering.getCollectingAreas()){
1717                                         if (index == 0){
1718                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY1)] = area.getTermType().getKey();
1719                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME1)] = area.getLabel();
1720                                         }
1721                                         if (index == 1){
1722                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY2)] = area.getTermType().getKey();
1723                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME2)] = area.getLabel();
1724                                         }
1725                                         if (index == 2){
1726                                             csvLine[table.getIndex(CdmLightExportTable.AREA_CATEGORY3)] = area.getTermType().getKey();
1727                                             csvLine[table.getIndex(CdmLightExportTable.AREA_NAME3)] = area.getLabel();
1728                                         }
1729                                         if (index == 3){
1730                                             csvLine[table.getIndex(CdmLightExportTable.FURTHER_AREAS)] = "1";
1731                                             break;
1732                                         }
1733                                         index++;
1734                                     }
1735                                 }
1736                             }
1737                         }
1738                     }
1739                 }
1740             }
1741
1742             state.getProcessor().put(table, specimen, csvLine);
1743         } catch (Exception e) {
1744             state.getResult().addException(e, "An unexpected error occurred when handling specimen " +
1745                     cdmBaseStr(specimen) + ": " + e.getMessage());
1746         }
1747     }
1748
1749     /**
1750      * @param it
1751      */
1752     private String extractMediaUris(Iterator<MediaRepresentation> it) {
1753
1754         String mediaUriString = "";
1755         boolean first = true;
1756         while(it.hasNext()){
1757             MediaRepresentation rep = it.next();
1758             List<MediaRepresentationPart> parts = rep.getParts();
1759             for (MediaRepresentationPart part: parts){
1760                 if (first){
1761                     if (part.getUri() != null){
1762                         mediaUriString += part.getUri().toString();
1763                         first = false;
1764                     }
1765                 }else{
1766                     if (part.getUri() != null){
1767                         mediaUriString += ", " +part.getUri().toString();
1768                     }
1769                 }
1770             }
1771         }
1772
1773         return mediaUriString;
1774     }
1775
1776     /**
1777      * @param state
1778      * @param gathering
1779      */
1780     private void addCollectingAreas(CdmLightExportState state, GatheringEvent gathering) {
1781         // TODO implement !!!
1782
1783         if (!gathering.getCollectingAreas().isEmpty()){
1784             state.getResult().addWarning("Collecting areas not yet implemented but gathering " +
1785                     cdmBaseStr(gathering) + " has collecting areas.");
1786         }
1787
1788     }
1789
1790     /**
1791      * @param gathering
1792      * @return
1793      */
1794     private String createCollectorString(CdmLightExportState state, GatheringEvent gathering, FieldUnit fieldUnit) {
1795         try {
1796             String collectorString = "";
1797             AgentBase<?> collectorA = CdmBase.deproxy(gathering.getCollector());
1798             if (gathering.getCollector() != null){
1799                if (collectorA instanceof TeamOrPersonBase
1800                        && state.getConfig().isHighLightPrimaryCollector()){
1801
1802                    Person primaryCollector = fieldUnit.getPrimaryCollector();
1803                    if (collectorA instanceof Team){
1804                        Team collectorTeam = (Team)collectorA;
1805                        boolean isFirst = true;
1806                        for (Person member: collectorTeam.getTeamMembers()){
1807                            if (!isFirst){
1808                                collectorString += "; ";
1809                            }
1810                            if (member.equals(primaryCollector)){
1811                                //highlight
1812                                collectorString += "<b>" + member.getTitleCache() + "</b>";
1813                            }else{
1814                                collectorString += member.getTitleCache();
1815                            }
1816                        }
1817                    }
1818                } else{
1819                    collectorString = collectorA.getTitleCache();
1820                }
1821            }
1822            return collectorString;
1823         } catch (Exception e) {
1824             state.getResult().addException(e, "An unexpected error occurred when creating collector string for " +
1825                     cdmBaseStr(fieldUnit) + ": " + e.getMessage());
1826             return "";
1827         }
1828     }
1829
1830
1831     /**
1832      * Returns a string representation of the {@link CdmBase cdmBase} object
1833      * for result messages.
1834      */
1835     private String cdmBaseStr(CdmBase cdmBase) {
1836         if (cdmBase == null){
1837             return "-no object available-";
1838         }else{
1839             return cdmBase.getClass().getSimpleName() + ": " + cdmBase.getUuid();
1840         }
1841     }
1842
1843     /**
1844      * {@inheritDoc}
1845      */
1846     @Override
1847     protected boolean doCheck(CdmLightExportState state) {
1848         return false;
1849     }
1850
1851     /**
1852      * {@inheritDoc}
1853      */
1854     @Override
1855     protected boolean isIgnore(CdmLightExportState state) {
1856         return false;
1857     }
1858
1859 }