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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2013 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.taxeditor.view.derivateSearch;
  11
  12 import java.util.ArrayList;
  13 import java.util.Collection;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Map.Entry;
  19 import java.util.Set;
  20 import java.util.UUID;
  21
  22 import org.eclipse.jface.viewers.ColumnLabelProvider;
  23 import org.eclipse.jface.viewers.TreeNode;
  24 import org.eclipse.swt.graphics.Image;
  25 import org.hibernate.LazyInitializationException;
  26
  27 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  28 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  29 import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
  30 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  31 import eu.etaxonomy.cdm.model.common.CdmBase;
  32 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  33 import eu.etaxonomy.cdm.model.common.Identifier;
  34 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  35 import eu.etaxonomy.cdm.model.molecular.Sequence;
  36 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  37 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  38 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  39 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  40 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  41 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  42 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  43 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  44 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  45 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  46 import eu.etaxonomy.taxeditor.model.ImageResources;
  47 import eu.etaxonomy.taxeditor.store.CdmStore;
  48
  49 /**
  50  * Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
  51  * <br>
  52  * <b>Note:</b> If you use this label provider you need to assure that you
  53  * created a {@link ConversationHolder} resp. have an open session because
  54  * the labels are generated from various fields of the derivate hierarchy which
  55  * are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
  56  * Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
  57  */
  58 public class DerivateLabelProvider extends ColumnLabelProvider {
  59
  60     private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
  61
  62     private static Set<SingleRead> multiLinkSingleReads;
  63
  64     private static Map<DerivedUnit, List<DeterminationEvent>> determinationEvents;
  65
  66     private static Map<DerivedUnit, List<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         return getDerivateText(element);
 138     }
 139
 140     /** {@inheritDoc} */
 141     @Override
 142     public String getToolTipText(Object element) {
 143         return getDerivateText(element);
 144     }
 145
 146     /**
 147      * @param conversation the conversation to set
 148      */
 149     public void setConversation(ConversationHolder conversation) {
 150         this.conversation = conversation;
 151     }
 152
 153     public String getDerivateText(Object element){
 154         return getDerivateText(element, conversation);
 155     }
 156
 157     public static String getDerivateText(Object element, ConversationHolder conversation){
 158         //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
 159         TreeNode parentNode = null;
 160         TreeNode node = null;
 161         Object derivate = element;
 162         if(element instanceof TreeNode){
 163             node = (TreeNode) element;
 164             parentNode = node.getParent();
 165             //unwrap specimen from TreeNode
 166             derivate = node.getValue();
 167         }
 168
 169         if(conversation!=null){
 170             conversation.bind();
 171         }
 172
 173         final String emptyString = "";
 174         final String separator = " ";
 175
 176         String label = emptyString;
 177
 178         //Field Unit
 179         if(derivate instanceof FieldUnit){
 180             FieldUnit fieldUnit = (FieldUnit)derivate;
 181             if(fieldUnit.getGatheringEvent()!=null){
 182                 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 183                 label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
 184                 label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
 185                 label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
 186                 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 187             }
 188             label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
 189         }
 190         //MediaSpecimen
 191         else if(derivate instanceof MediaSpecimen){
 192             MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
 193             if(mediaSpecimen.getMediaSpecimen()!=null){
 194                 label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
 195                 label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
 196             }
 197             eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
 198             if(collection!=null){
 199                 label += collection.getName()!=null?collection.getName()+" ":emptyString;
 200                 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 201             }
 202             label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
 203             label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
 204         }
 205         //TissueSample + DnaSample
 206         else if(derivate instanceof DnaSample){
 207             DnaSample dnaSample = (DnaSample)derivate;
 208             if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 209                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 210                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 211                     label += currentSampleDesignation.getIdentifier()+separator;
 212                 }
 213                 else{
 214                     label += NO_SAMPLE_DESIGNATION+separator;
 215                 }
 216             }
 217             else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
 218                 if(dnaSample.getKindOfUnit()!=null){
 219                     label += dnaSample.getKindOfUnit()+separator;
 220                 }
 221                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 222                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 223                     label += currentSampleDesignation.getIdentifier()+separator;
 224                 }
 225                 else{
 226                     label += NO_SAMPLE_DESIGNATION+separator;
 227                 }
 228             }
 229
 230         }
 231         //DerivedUnit + TissueSample
 232         else if(derivate instanceof DerivedUnit){
 233             DerivedUnit derivedUnit = (DerivedUnit)derivate;
 234             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 235                 //check for type designation
 236                 if(typeDesignations.get(derivedUnit)==null){
 237                     for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
 238                         addTypeDesignation(derivedUnit, specimenTypeDesignation);
 239                     }
 240                 }
 241                 //check for determination events
 242                 if(determinationEvents.get(derivedUnit)==null){
 243                     for (DeterminationEvent determinationEvent : CdmStore.getService(IOccurrenceService.class).listDeterminationEvents(derivedUnit, null, null, null, null)) {
 244                         addDeterminationEvent(derivedUnit, determinationEvent);
 245                     }
 246                 }
 247                 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
 248                 //TODO : This is not generic anymore for performance reasons
 249                 Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 250                 if(originals!=null && originals.size() ==1) {
 251                     SpecimenOrObservationBase specimen = originals.iterator().next();
 252                     if(specimen instanceof FieldUnit) {
 253                         FieldUnit fieldUnit = (FieldUnit)specimen;
 254                         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 255                         if(gatheringEvent!=null){
 256                             label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 257                         }
 258                         label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
 259                     }
 260                 }
 261
 262                 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 263                 if(collection!=null){
 264                     label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 265                 }
 266                 String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
 267                 label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
 268                 //type designation extension
 269                 List<SpecimenTypeDesignation> typeDesignationList = typeDesignations.get(derivedUnit);
 270                 if(typeDesignationList!=null){
 271                     for (SpecimenTypeDesignation specimenTypeDesignation : typeDesignationList) {
 272                         label += "("+specimenTypeDesignation.getTypeStatus()+" of ";
 273                         for (TaxonNameBase taxonNameBase : specimenTypeDesignation.getTypifiedNames()) {
 274                             label += taxonNameBase+separator;
 275                         }
 276                         if(label.endsWith(separator)){
 277                             label = label.substring(0, label.length()-separator.length());
 278                         }
 279                         label += ")";
 280                     }
 281                 }
 282                 //determination event extension
 283                 List<DeterminationEvent> determinationEventList = determinationEvents.get(derivedUnit);
 284                 if(determinationEventList!=null){
 285                     for (DeterminationEvent determinationEvent : determinationEventList) {
 286                         label += "(";
 287                         if(determinationEvent.getTaxon()!=null){
 288                             label += "Determined as "+determinationEvent.getTaxon();
 289                         }
 290
 291                         if(label.endsWith(separator)){
 292                             label = label.substring(0, label.length()-separator.length());
 293                         }
 294                         label += ")";
 295                     }
 296                 }
 297             }
 298             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 299                 //TissueSample should only be created by using it's own class
 300                 //in future using only one class with different SpecimenOrObservationTypes is desired
 301 //                label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
 302             }
 303         }
 304         //Sequence
 305         else if(derivate instanceof Sequence){
 306             Sequence sequence = (Sequence)derivate;
 307             Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 308             if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 309                 label += currentSampleDesignation.getIdentifier()+separator;
 310             }
 311             else{
 312                 label += NO_SAMPLE_DESIGNATION+separator;
 313             }
 314             label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 315         }
 316         //SingleRead
 317         else if(derivate instanceof SingleRead){
 318             SingleRead singleRead = (SingleRead)derivate;
 319             if(parentNode!=null && parentNode.getValue() instanceof Sequence){
 320                 Sequence sequence = (Sequence) parentNode.getValue();
 321                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 322                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 323                     label = currentSampleDesignation.getIdentifier()+separator;
 324                 }
 325                 else{
 326                     label += NO_SAMPLE_DESIGNATION+separator;
 327                 }
 328                 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
 329                 if(sequence!=null && sequence.getDnaMarker()!=null){
 330                     label += sequence.getDnaMarker()+separator;
 331                 }
 332                 if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
 333                     label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
 334                 }
 335             }
 336         }
 337         //SOOB
 338         else if(derivate instanceof SpecimenOrObservationBase){
 339             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
 340             SpecimenOrObservationType type = specimen.getRecordBasis();
 341             return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
 342         }
 343         if(label.isEmpty()){
 344             label = derivate.toString();
 345         }
 346         //remove last comma
 347         else if(label.endsWith(separator)){
 348             label = label.substring(0, label.length()-separator.length());
 349         }
 350         return label;
 351     }
 352
 353     @Override
 354     public Image getImage(Object element) {
 355         if(element instanceof TreeNode){
 356             element = ((TreeNode) element).getValue();
 357         }
 358         if(element instanceof CdmBase){
 359             CdmBase cdmBase = (CdmBase)element;
 360             boolean hasCharacterData = false;
 361             if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
 362                 SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
 363                 if(specimen.hasCharacterData()){
 364                     hasCharacterData = true;
 365                 }
 366             }
 367             if(cdmBase.isInstanceOf(FieldUnit.class)){
 368                 return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 369             }
 370             else if(cdmBase.isInstanceOf(DerivedUnit.class)){
 371                 DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
 372                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
 373                     return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 374                 }
 375                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 376                     return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
 377                 }
 378                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 379                     return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
 380                 }
 381                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 382                     return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
 383                 }
 384                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
 385                     if(derivedUnit.getKindOfUnit()!=null){
 386                         if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
 387                             return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
 388                         }
 389                         else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
 390                             return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
 391                         }
 392                         else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
 393                             return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
 394                         }
 395                         else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
 396                             return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
 397                         }
 398                     }
 399                 }
 400             }
 401             else if(cdmBase.isInstanceOf(Sequence.class)){
 402                 return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
 403             }
 404
 405             else if(cdmBase.isInstanceOf(SingleRead.class)){
 406                 if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
 407                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
 408                 }
 409                 else{
 410                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
 411                 }
 412             }
 413         }
 414         return super.getImage(element);
 415     }
 416
 417     public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
 418         if(entity.isInstanceOf(DnaSample.class)){
 419             DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
 420             for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
 421                 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
 422                     //first sample designation is the current
 423                     return identifier;
 424                 }
 425             }
 426         }
 427         else if(entity.isInstanceOf(Sequence.class)){
 428             Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
 429             if(sequence.getDnaSample()!=null){
 430                 return getCurrentSampleDesignation(sequence.getDnaSample());
 431             }
 432         }
 433         return null;
 434     }
 435
 436     /**
 437      * Refreshes cached label extensions
 438      * @param multiLinkSingleReads
 439      */
 440     public void refresh() {
 441         DerivateLabelProvider.multiLinkSingleReads = new HashSet<SingleRead>();
 442         for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
 443             if(entry.getValue().size()>1){
 444                 multiLinkSingleReads.add(entry.getKey());
 445             }
 446         }
 447         DerivateLabelProvider.typeDesignations = new HashMap<DerivedUnit, List<SpecimenTypeDesignation>>();
 448         DerivateLabelProvider.determinationEvents = new HashMap<DerivedUnit, List<DeterminationEvent>>();
 449     }
 450
 451     private static void addDeterminationEvent(DerivedUnit derivedUnit, DeterminationEvent determinationEvent){
 452         List<DeterminationEvent> list = determinationEvents.get(derivedUnit);
 453         if(list==null){
 454             list = new ArrayList<DeterminationEvent>();
 455         }
 456         list.add(determinationEvent);
 457         determinationEvents.put(derivedUnit, list);
 458     }
 459
 460     private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
 461         List<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
 462         if(list==null){
 463             list = new ArrayList<SpecimenTypeDesignation>();
 464         }
 465         list.add(typeDesignation);
 466         typeDesignations.put(derivedUnit, list);
 467     }
 468
 469     public static Set<SingleRead> getMultiLinkSingleReads() {
 470         return multiLinkSingleReads;
 471     }
 472
 473 }