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
 154         else if(element instanceof MediaSpecimen){
 155             text = CdmFormatterFactory.format(element,
 156                     new FormatKey[]{
 157                             FormatKey.MEDIA_TITLE_CACHE, FormatKey.SPACE,
 158                             collectionKey, FormatKey.SPACE,
 159                             FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
 160                             FormatKey.MEDIA_TITLE, FormatKey.SPACE,
 161                             FormatKey.MEDIA_ARTIST, FormatKey.SPACE,
 162                             });
 163         }
 164         else if (element instanceof DnaSample) {
 165             text = CdmFormatterFactory.format(element,
 166                     new FormatKey[] {
 167                             collectionKey, FormatKey.SPACE,
 168                             FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
 169                             FormatKey.SAMPLE_DESIGNATION, FormatKey.SPACE
 170                             });
 171         }
 172         else if (element instanceof DerivedUnit) {
 173             text = CdmFormatterFactory.format(element,
 174                     new FormatKey[] {
 175                             collectionKey, FormatKey.SPACE,
 176                             FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE
 177                             });
 178         }
 179         else if (element instanceof Sequence) {
 180             text = CdmFormatterFactory.format(element,
 181                     new FormatKey[] {
 182                             FormatKey.SEQUENCE_DNA_MARKER, FormatKey.SPACE
 183                             });
 184         }
 185         else if (element instanceof SingleRead) {
 186             text = CdmFormatterFactory.format(element,
 187                     new FormatKey[] {
 188                             FormatKey.SINGLE_READ_PHEROGRAM_TITLE_CACHE, FormatKey.SPACE,
 189                             FormatKey.AMPLIFICATION_LABEL, FormatKey.SPACE,
 190             });
 191         }
 192         else if(element instanceof IdentifiableEntity){
 193
 194                 IdentifiableEntity identifiableEntity = (IdentifiableEntity) element;
 195                 if(identifiableEntity.isProtectedTitleCache()){
 196                         text = identifiableEntity.getTitleCache();
 197                 }
 198         }
 199         if(CdmUtils.isBlank(text) || text.equals(IdentifiableEntityDefaultCacheStrategy.TITLE_CACHE_GENERATION_NOT_IMPLEMENTED)){
 200             if(element instanceof CdmBase){
 201                 text = ((CdmBase) element).getUuid().toString();
 202             }
 203             else{
 204                 text = element.toString();
 205             }
 206         }
 207                 return text;
 208     }
 209
 210     /** {@inheritDoc} */
 211     @Override
 212     public String getToolTipText(Object element) {
 213         return getDerivateText(element);
 214     }
 215
 216     /**
 217      * @param conversation the conversation to set
 218      */
 219     public void setConversation(ConversationHolder conversation) {
 220         this.conversation = conversation;
 221     }
 222
 223     public String getDerivateText(Object element){
 224         return getDerivateText(element, conversation);
 225     }
 226
 227     public static String getDerivateText(Object element, ConversationHolder conversation){
 228         //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
 229         TreeNode parentNode = null;
 230         TreeNode node = null;
 231         Object derivate = element;
 232         if(element instanceof TreeNode){
 233             node = (TreeNode) element;
 234             parentNode = node.getParent();
 235             //unwrap specimen from TreeNode
 236             derivate = node.getValue();
 237         }
 238
 239         if(conversation!=null){
 240             conversation.bind();
 241         }
 242
 243         final String emptyString = "";
 244         final String separator = " ";
 245
 246         String label = emptyString;
 247
 248         //Field Unit
 249         if(derivate instanceof FieldUnit){
 250             FieldUnit fieldUnit = (FieldUnit)derivate;
 251             if(fieldUnit.getGatheringEvent()!=null){
 252                 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 253                 label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
 254                 label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
 255                 label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
 256                 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 257             }
 258             label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
 259         }
 260         //MediaSpecimen
 261         else if(derivate instanceof MediaSpecimen){
 262             MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
 263             if(mediaSpecimen.getMediaSpecimen()!=null){
 264                 label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
 265                 label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
 266             }
 267             eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
 268             if(collection!=null){
 269                 label += collection.getName()!=null?collection.getName()+" ":emptyString;
 270                 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 271             }
 272             label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
 273             label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
 274         }
 275         //TissueSample + DnaSample
 276         else if(derivate instanceof DnaSample){
 277             DnaSample dnaSample = (DnaSample)derivate;
 278             if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 279                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 280                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 281                     label += currentSampleDesignation.getIdentifier()+separator;
 282                 }
 283                 else{
 284                     label += NO_SAMPLE_DESIGNATION+separator;
 285                 }
 286             }
 287             else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
 288                 if(dnaSample.getKindOfUnit()!=null){
 289                     label += dnaSample.getKindOfUnit()+separator;
 290                 }
 291                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 292                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 293                     label += currentSampleDesignation.getIdentifier()+separator;
 294                 }
 295                 else{
 296                     label += NO_SAMPLE_DESIGNATION+separator;
 297                 }
 298             }
 299
 300         }
 301         //DerivedUnit + TissueSample
 302         else if(derivate instanceof DerivedUnit){
 303             DerivedUnit derivedUnit = (DerivedUnit)derivate;
 304             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 305                 //check for type designation
 306                 if(typeDesignations.get(derivedUnit)==null){
 307                     for (SpecimenTypeDesignation specimenTypeDesignation : derivedUnit.getSpecimenTypeDesignations()) {
 308                         addTypeDesignation(derivedUnit, specimenTypeDesignation);
 309                     }
 310                 }
 311                 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
 312                 //TODO : This is not generic anymore for performance reasons
 313                 Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 314                 if(originals!=null && originals.size() ==1) {
 315                     SpecimenOrObservationBase specimen = originals.iterator().next();
 316                     if(specimen instanceof FieldUnit) {
 317                         FieldUnit fieldUnit = (FieldUnit)specimen;
 318                         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 319                         if(gatheringEvent!=null){
 320                             label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 321                         }
 322                         label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
 323                     }
 324                 }
 325
 326                 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 327                 if(collection!=null){
 328                     label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 329                 }
 330                 String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
 331                 label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
 332             }
 333             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 334                 //TissueSample should only be created by using it's own class
 335                 //in future using only one class with different SpecimenOrObservationTypes is desired
 336 //                label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
 337             }
 338         }
 339         //Sequence
 340         else if(derivate instanceof Sequence){
 341             Sequence sequence = (Sequence)derivate;
 342             Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 343             if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 344                 label += currentSampleDesignation.getIdentifier()+separator;
 345             }
 346             else{
 347                 label += NO_SAMPLE_DESIGNATION+separator;
 348             }
 349             label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 350         }
 351         //SingleRead
 352         else if(derivate instanceof SingleRead){
 353             SingleRead singleRead = (SingleRead)derivate;
 354             if(parentNode!=null && parentNode.getValue() instanceof Sequence){
 355                 Sequence sequence = (Sequence) parentNode.getValue();
 356                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 357                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 358                     label = currentSampleDesignation.getIdentifier()+separator;
 359                 }
 360                 else{
 361                     label += NO_SAMPLE_DESIGNATION+separator;
 362                 }
 363                 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
 364                 if(sequence!=null && sequence.getDnaMarker()!=null){
 365                     label += sequence.getDnaMarker()+separator;
 366                 }
 367                 if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
 368                     label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
 369                 }
 370             }
 371         }
 372         //SOOB
 373         else if(derivate instanceof SpecimenOrObservationBase){
 374             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
 375             SpecimenOrObservationType type = specimen.getRecordBasis();
 376             return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
 377         }
 378         if(label.isEmpty()){
 379             label = derivate.toString();
 380         }
 381         //remove last comma
 382         else if(label.endsWith(separator)){
 383             label = label.substring(0, label.length()-separator.length());
 384         }
 385         return label;
 386     }
 387
 388     @Override
 389     public Image getImage(Object element) {
 390         if(element instanceof TreeNode){
 391             element = ((TreeNode) element).getValue();
 392         }
 393         if(element instanceof CdmBase){
 394             CdmBase cdmBase = (CdmBase)element;
 395             boolean hasCharacterData = false;
 396             if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
 397                 SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
 398                 if(specimen.hasCharacterData()){
 399                     hasCharacterData = true;
 400                 }
 401             }
 402             if(cdmBase.isInstanceOf(FieldUnit.class)){
 403                 return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 404             }
 405             else if(cdmBase.isInstanceOf(DerivedUnit.class)){
 406                 DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
 407
 408                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
 409                     return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 410                 }
 411                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 412                     return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
 413                 }
 414                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 415                     return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
 416                 }
 417                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 418                     if(typeDesignations.get(derivedUnit)!=null && !typeDesignations.get(derivedUnit).isEmpty()){
 419                         return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_TYPE);
 420                     }
 421                     return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
 422                 }
 423                 else if(derivedUnit.getRecordBasis().isMedia()
 424                         || derivedUnit.getRecordBasis().isKindOf(SpecimenOrObservationType.Media)){
 425                     if(derivedUnit.getKindOfUnit()!=null){
 426                         if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
 427                             return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
 428                         }
 429                         else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
 430                             return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
 431                         }
 432                         else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
 433                             return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
 434                         }
 435                         else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
 436                             return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
 437                         }
 438                     }
 439                 }
 440             }
 441             else if(cdmBase.isInstanceOf(Sequence.class)){
 442                 return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
 443             }
 444
 445             else if(cdmBase.isInstanceOf(SingleRead.class)){
 446                 if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
 447                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
 448                 }
 449                 else{
 450                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
 451                 }
 452             }
 453         }
 454         return ImageResources.getImage(ImageResources.DEFAULT_DERIVATIVE);
 455     }
 456
 457     public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
 458         if(entity.isInstanceOf(DnaSample.class)){
 459             DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
 460             for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
 461                 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
 462                     //first sample designation is the current
 463                     return identifier;
 464                 }
 465             }
 466         }
 467         else if(entity.isInstanceOf(Sequence.class)){
 468             Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
 469             if(sequence.getDnaSample()!=null){
 470                 return getCurrentSampleDesignation(sequence.getDnaSample());
 471             }
 472         }
 473         return null;
 474     }
 475
 476     private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
 477         Collection<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
 478         if(list==null){
 479             list = new ArrayList<SpecimenTypeDesignation>();
 480         }
 481         list.add(typeDesignation);
 482         typeDesignations.put(derivedUnit, list);
 483     }
 484
 485     public static Set<SingleRead> getMultiLinkSingleReads() {
 486         return multiLinkSingleReads;
 487     }
 488
 489     public void updateLabelCache(Collection<SpecimenOrObservationBase<?>> rootElements) {
 490         multiLinkSingleReads = new HashSet<SingleRead>();
 491         typeDesignations = new HashMap<DerivedUnit, Collection<SpecimenTypeDesignation>>();
 492         for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
 493             if(entry.getValue().size()>1){
 494                 multiLinkSingleReads.add(entry.getKey());
 495             }
 496         }
 497         if(rootElements!=null){
 498             Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
 499             for (SpecimenOrObservationBase specimenOrObservationBase : rootElements) {
 500                 List<DerivedUnit> childUnits = CdmStore.getService(IOccurrenceService.class).getAllChildDerivatives(specimenOrObservationBase.getUuid());
 501                 if (childUnits != null){
 502                     derivedUnits.addAll(childUnits);
 503                 }
 504                 if(specimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
 505                     specimenOrObservationBase = CdmStore.getService(IOccurrenceService.class).load(specimenOrObservationBase.getUuid());
 506                     if (specimenOrObservationBase != null){
 507                         derivedUnits.add(HibernateProxyHelper.deproxy(specimenOrObservationBase, DerivedUnit.class));
 508                     }
 509                 }
 510             }
 511             for (DerivedUnit derivedUnit : derivedUnits) {
 512                 if(!derivedUnit.getSpecimenTypeDesignations().isEmpty()){
 513                     typeDesignations.put(derivedUnit, derivedUnit.getSpecimenTypeDesignations());
 514                 }
 515             }
 516         }
 517     }
 518
 519 }