eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/view/derivateSearch/DerivateLabelProvider.java

   1 /**
   2 * Copyright (C) 2013 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.taxeditor.view.derivateSearch;
  10
  11 import java.util.ArrayList;
  12 import java.util.Collection;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.Map.Entry;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.eclipse.jface.viewers.ColumnLabelProvider;
  22 import org.eclipse.jface.viewers.TreeNode;
  23 import org.eclipse.swt.graphics.Image;
  24 import org.hibernate.LazyInitializationException;
  25
  26 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  27 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  28 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  29 import eu.etaxonomy.cdm.common.CdmUtils;
  30 import eu.etaxonomy.cdm.format.CdmFormatterFactory;
  31 import eu.etaxonomy.cdm.format.ICdmFormatter.FormatKey;
  32 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  33 import eu.etaxonomy.cdm.model.common.CdmBase;
  34 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  35 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  36 import eu.etaxonomy.cdm.model.common.Identifier;
  37 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  38 import eu.etaxonomy.cdm.model.molecular.Sequence;
  39 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  40 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  41 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  42 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  43 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  44 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  45 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  46 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  47 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
  48 import eu.etaxonomy.taxeditor.model.ImageResources;
  49 import eu.etaxonomy.taxeditor.store.CdmStore;
  50
  51 /**
  52  * Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
  53  * <br>
  54  * <b>Note:</b> If you use this label provider you need to assure that you
  55  * created a {@link ConversationHolder} resp. have an open session because
  56  * the labels are generated from various fields of the derivate hierarchy which
  57  * are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
  58  * Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
  59  */
  60 public class DerivateLabelProvider extends ColumnLabelProvider {
  61
  62     private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
  63
  64     private static Set<SingleRead> multiLinkSingleReads;
  65
  66     private static Map<DerivedUnit, Collection<SpecimenTypeDesignation>> typeDesignations;
  67
  68     private ConversationHolder conversation;
  69
  70     private static DefinedTerm photoTerm = null;
  71     private static DefinedTerm drawingTerm = null;
  72     private static DefinedTerm specimenScanTerm = null;
  73     private static DefinedTerm detailImageTerm = null;
  74     private static DefinedTerm sampleDesignationTerm = null;
  75
  76     //FIXME: move static term getters to new singleton utility class
  77     private static void initializeTerms() {
  78         List<DefinedTerm> preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class);
  79         for (DefinedTerm definedTerm : preferredTerms) {
  80             if(definedTerm.getUuid().equals(UUID.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
  81                 photoTerm = definedTerm;
  82             }
  83             else if(definedTerm.getUuid().equals(UUID.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
  84                 drawingTerm = definedTerm;
  85             }
  86             else if(definedTerm.getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
  87                 specimenScanTerm = definedTerm;
  88             }
  89             else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
  90                 detailImageTerm = definedTerm;
  91             }
  92             else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
  93                 sampleDesignationTerm = definedTerm;
  94             }
  95         }
  96     }
  97
  98     public static DefinedTerm getLivingPlantPhotoTerm(){
  99         if(photoTerm==null){
 100             initializeTerms();
 101         }
 102         return photoTerm;
 103     }
 104
 105     public static DefinedTerm getArtworkTerm(){
 106         if(drawingTerm==null){
 107             initializeTerms();
 108         }
 109         return drawingTerm;
 110     }
 111
 112     public static DefinedTerm getSpecimenScanTerm(){
 113         if(specimenScanTerm==null){
 114             initializeTerms();
 115         }
 116         return specimenScanTerm;
 117     }
 118
 119     public static DefinedTerm getDetailImageTerm(){
 120         if(detailImageTerm==null){
 121             initializeTerms();
 122         }
 123         return detailImageTerm;
 124     }
 125
 126     public static DefinedTerm getSampleDesignationTerm(){
 127         if(sampleDesignationTerm==null){
 128             initializeTerms();
 129         }
 130         return sampleDesignationTerm;
 131     }
 132
 133
 134     /** {@inheritDoc} */
 135     @Override
 136     public String getText(Object element) {
 137         if(element instanceof TreeNode){
 138             element = ((TreeNode) element).getValue();
 139         }
 140         String text = null;
 141
 142         //check if collection code does not exist -> use collection name then
 143         FormatKey collectionKey = FormatKey.COLLECTION_CODE;
 144         text = CdmFormatterFactory.format(element,new FormatKey[]{FormatKey.COLLECTION_CODE});
 145         if(CdmUtils.isBlank(text)){
 146             collectionKey = FormatKey.COLLECTION_NAME;
 147         }
 148
 149         //Use titlecache for FieldUnits
 150         if(element instanceof FieldUnit){
 151             return ((FieldUnit) element).getTitleCache();
 152         }
 153         else if(element instanceof MediaSpecimen){
 154             text = CdmFormatterFactory.format(element,
 155                     new FormatKey[]{
 156                             FormatKey.MEDIA_TITLE_CACHE, FormatKey.SPACE,
 157                             collectionKey, FormatKey.SPACE,
 158                             FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
 159                             FormatKey.MEDIA_TITLE, FormatKey.SPACE,
 160                             FormatKey.MEDIA_ARTIST, FormatKey.SPACE,
 161                             });
 162         }
 163         else if (element instanceof DnaSample) {
 164             text = CdmFormatterFactory.format(element,
 165                     new FormatKey[] {
 166                             collectionKey, FormatKey.SPACE,
 167                             FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
 168                             FormatKey.SAMPLE_DESIGNATION, FormatKey.SPACE
 169                             });
 170         }
 171         else if (element instanceof DerivedUnit) {
 172             text = CdmFormatterFactory.format(element,
 173                     new FormatKey[] {
 174                             collectionKey, FormatKey.SPACE,
 175                             FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE
 176                             });
 177         }
 178         else if (element instanceof Sequence) {
 179             text = CdmFormatterFactory.format(element,
 180                     new FormatKey[] {
 181                             FormatKey.SEQUENCE_DNA_MARKER, FormatKey.SPACE
 182                             });
 183         }
 184         else if (element instanceof SingleRead) {
 185             text = CdmFormatterFactory.format(element,
 186                     new FormatKey[] {
 187                             FormatKey.SINGLE_READ_PHEROGRAM_TITLE_CACHE, FormatKey.SPACE,
 188                             FormatKey.AMPLIFICATION_LABEL, FormatKey.SPACE,
 189             });
 190         }
 191         else if(element instanceof IdentifiableEntity){
 192                 IdentifiableEntity identifiableEntity = (IdentifiableEntity) element;
 193                 if(identifiableEntity.isProtectedTitleCache()){
 194                         text = identifiableEntity.getTitleCache();
 195                 }
 196         }
 197         if(CdmUtils.isBlank(text) || text.equals(IdentifiableEntityDefaultCacheStrategy.TITLE_CACHE_GENERATION_NOT_IMPLEMENTED)){
 198             if(element instanceof CdmBase){
 199                 text = ((CdmBase) element).getUuid().toString();
 200             }
 201             else{
 202                 text = element.toString();
 203             }
 204         }
 205                 return text;
 206     }
 207
 208     /** {@inheritDoc} */
 209     @Override
 210     public String getToolTipText(Object element) {
 211         return getDerivateText(element);
 212     }
 213
 214     /**
 215      * @param conversation the conversation to set
 216      */
 217     public void setConversation(ConversationHolder conversation) {
 218         this.conversation = conversation;
 219     }
 220
 221     public String getDerivateText(Object element){
 222         return getDerivateText(element, conversation);
 223     }
 224
 225     public static String getDerivateText(Object element, ConversationHolder conversation){
 226         //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
 227         TreeNode parentNode = null;
 228         TreeNode node = null;
 229         Object derivate = element;
 230         if(element instanceof TreeNode){
 231             node = (TreeNode) element;
 232             parentNode = node.getParent();
 233             //unwrap specimen from TreeNode
 234             derivate = node.getValue();
 235         }
 236
 237         if(conversation!=null){
 238             conversation.bind();
 239         }
 240
 241         final String emptyString = "";
 242         final String separator = " ";
 243
 244         String label = emptyString;
 245
 246         //Field Unit
 247         if(derivate instanceof FieldUnit){
 248             FieldUnit fieldUnit = (FieldUnit)derivate;
 249             if(fieldUnit.getGatheringEvent()!=null){
 250                 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 251                 label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
 252                 label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
 253                 label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
 254                 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 255             }
 256             label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
 257         }
 258         //MediaSpecimen
 259         else if(derivate instanceof MediaSpecimen){
 260             MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
 261             if(mediaSpecimen.getMediaSpecimen()!=null){
 262                 label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
 263                 label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
 264             }
 265             eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
 266             if(collection!=null){
 267                 label += collection.getName()!=null?collection.getName()+" ":emptyString;
 268                 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 269             }
 270             label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
 271             label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
 272         }
 273         //TissueSample + DnaSample
 274         else if(derivate instanceof DnaSample){
 275             DnaSample dnaSample = (DnaSample)derivate;
 276             if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 277                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 278                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 279                     label += currentSampleDesignation.getIdentifier()+separator;
 280                 }
 281                 else{
 282                     label += NO_SAMPLE_DESIGNATION+separator;
 283                 }
 284             }
 285             else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
 286                 if(dnaSample.getKindOfUnit()!=null){
 287                     label += dnaSample.getKindOfUnit()+separator;
 288                 }
 289                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 290                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 291                     label += currentSampleDesignation.getIdentifier()+separator;
 292                 }
 293                 else{
 294                     label += NO_SAMPLE_DESIGNATION+separator;
 295                 }
 296             }
 297
 298         }
 299         //DerivedUnit + TissueSample
 300         else if(derivate instanceof DerivedUnit){
 301             DerivedUnit derivedUnit = (DerivedUnit)derivate;
 302             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 303                 //check for type designation
 304                 if(typeDesignations.get(derivedUnit)==null){
 305                     for (SpecimenTypeDesignation specimenTypeDesignation : derivedUnit.getSpecimenTypeDesignations()) {
 306                         addTypeDesignation(derivedUnit, specimenTypeDesignation);
 307                     }
 308                 }
 309                 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
 310                 //TODO : This is not generic anymore for performance reasons
 311                 Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 312                 if(originals!=null && originals.size() ==1) {
 313                     SpecimenOrObservationBase specimen = originals.iterator().next();
 314                     if(specimen instanceof FieldUnit) {
 315                         FieldUnit fieldUnit = (FieldUnit)specimen;
 316                         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 317                         if(gatheringEvent!=null){
 318                             label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 319                         }
 320                         label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
 321                     }
 322                 }
 323
 324                 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 325                 if(collection!=null){
 326                     label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 327                 }
 328                 String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
 329                 label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
 330             }
 331             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 332                 //TissueSample should only be created by using it's own class
 333                 //in future using only one class with different SpecimenOrObservationTypes is desired
 334 //                label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
 335             }
 336         }
 337         //Sequence
 338         else if(derivate instanceof Sequence){
 339             Sequence sequence = (Sequence)derivate;
 340             Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 341             if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 342                 label += currentSampleDesignation.getIdentifier()+separator;
 343             }
 344             else{
 345                 label += NO_SAMPLE_DESIGNATION+separator;
 346             }
 347             label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 348         }
 349         //SingleRead
 350         else if(derivate instanceof SingleRead){
 351             SingleRead singleRead = (SingleRead)derivate;
 352             if(parentNode!=null && parentNode.getValue() instanceof Sequence){
 353                 Sequence sequence = (Sequence) parentNode.getValue();
 354                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 355                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 356                     label = currentSampleDesignation.getIdentifier()+separator;
 357                 }
 358                 else{
 359                     label += NO_SAMPLE_DESIGNATION+separator;
 360                 }
 361                 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
 362                 if(sequence!=null && sequence.getDnaMarker()!=null){
 363                     label += sequence.getDnaMarker()+separator;
 364                 }
 365                 if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
 366                     label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
 367                 }
 368             }
 369         }
 370         //SOOB
 371         else if(derivate instanceof SpecimenOrObservationBase){
 372             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
 373             SpecimenOrObservationType type = specimen.getRecordBasis();
 374             return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
 375         }
 376         if(label.isEmpty()){
 377             label = derivate.toString();
 378         }
 379         //remove last comma
 380         else if(label.endsWith(separator)){
 381             label = label.substring(0, label.length()-separator.length());
 382         }
 383         return label;
 384     }
 385
 386     @Override
 387     public Image getImage(Object element) {
 388         if(element instanceof TreeNode){
 389             element = ((TreeNode) element).getValue();
 390         }
 391         if(element instanceof CdmBase){
 392             CdmBase cdmBase = (CdmBase)element;
 393             boolean hasCharacterData = false;
 394             if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
 395                 SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
 396                 if(specimen.hasCharacterData()){
 397                     hasCharacterData = true;
 398                 }
 399             }
 400             if(cdmBase.isInstanceOf(FieldUnit.class)){
 401                 return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 402             }
 403             else if(cdmBase.isInstanceOf(DerivedUnit.class)){
 404                 DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
 405
 406                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
 407                     return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 408                 }
 409                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 410                     return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
 411                 }
 412                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 413                     return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
 414                 }
 415                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 416                     if(typeDesignations.get(derivedUnit)!=null && !typeDesignations.get(derivedUnit).isEmpty()){
 417                         return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_TYPE);
 418                     }
 419                     return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
 420                 }
 421                 else if(derivedUnit.getRecordBasis().isMedia()
 422                         || derivedUnit.getRecordBasis().isKindOf(SpecimenOrObservationType.Media)){
 423                     if(derivedUnit.getKindOfUnit()!=null){
 424                         if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
 425                             return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
 426                         }
 427                         else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
 428                             return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
 429                         }
 430                         else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
 431                             return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
 432                         }
 433                         else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
 434                             return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
 435                         }
 436                     }
 437                 }
 438             }
 439             else if(cdmBase.isInstanceOf(Sequence.class)){
 440                 return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
 441             }
 442
 443             else if(cdmBase.isInstanceOf(SingleRead.class)){
 444                 if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
 445                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
 446                 }
 447                 else{
 448                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
 449                 }
 450             }
 451         }
 452         return ImageResources.getImage(ImageResources.DEFAULT_DERIVATIVE);
 453     }
 454
 455     public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
 456         if(entity.isInstanceOf(DnaSample.class)){
 457             DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
 458             for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
 459                 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
 460                     //first sample designation is the current
 461                     return identifier;
 462                 }
 463             }
 464         }
 465         else if(entity.isInstanceOf(Sequence.class)){
 466             Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
 467             if(sequence.getDnaSample()!=null){
 468                 return getCurrentSampleDesignation(sequence.getDnaSample());
 469             }
 470         }
 471         return null;
 472     }
 473
 474     private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
 475         Collection<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
 476         if(list==null){
 477             list = new ArrayList<SpecimenTypeDesignation>();
 478         }
 479         list.add(typeDesignation);
 480         typeDesignations.put(derivedUnit, list);
 481     }
 482
 483     public static Set<SingleRead> getMultiLinkSingleReads() {
 484         return multiLinkSingleReads;
 485     }
 486
 487     public void updateLabelCache(Collection<SpecimenOrObservationBase<?>> rootElements) {
 488         multiLinkSingleReads = new HashSet<SingleRead>();
 489         typeDesignations = new HashMap<DerivedUnit, Collection<SpecimenTypeDesignation>>();
 490         for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
 491             if(entry.getValue().size()>1){
 492                 multiLinkSingleReads.add(entry.getKey());
 493             }
 494         }
 495         if(rootElements!=null){
 496             Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 497             for (SpecimenOrObservationBase specimenOrObservationBase : rootElements) {
 498                 derivedUnits.addAll(CdmStore.getService(IOccurrenceService.class).getAllChildDerivatives(specimenOrObservationBase.getUuid()));
 499                 if(specimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
 500                     derivedUnits.add(HibernateProxyHelper.deproxy(specimenOrObservationBase, DerivedUnit.class));
 501                 }
 502             }
 503             for (DerivedUnit derivedUnit : derivedUnits) {
 504                 if(!derivedUnit.getSpecimenTypeDesignations().isEmpty()){
 505                     typeDesignations.put(derivedUnit, derivedUnit.getSpecimenTypeDesignations());
 506                 }
 507             }
 508         }
 509     }
 510
 511 }