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