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.List;
  13 import java.util.Set;
  14 import java.util.UUID;
  15
  16 import org.eclipse.jface.viewers.ColumnLabelProvider;
  17 import org.eclipse.jface.viewers.TreeNode;
  18 import org.eclipse.swt.graphics.Image;
  19 import org.hibernate.LazyInitializationException;
  20
  21 import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
  22 import eu.etaxonomy.cdm.api.service.IOccurrenceService;
  23 import eu.etaxonomy.cdm.model.common.CdmBase;
  24 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  25 import eu.etaxonomy.cdm.model.common.Identifier;
  26 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  27 import eu.etaxonomy.cdm.model.molecular.Sequence;
  28 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  29 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  30 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  31 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
  32 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
  33 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  34 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  35 import eu.etaxonomy.taxeditor.model.ImageResources;
  36 import eu.etaxonomy.taxeditor.store.CdmStore;
  37
  38 /**
  39  * Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
  40  * <br>
  41  * <b>Note:</b> If you use this label provider you need to assure that you
  42  * created a {@link ConversationHolder} resp. have an open session because
  43  * the labels are generated from various fields of the derivate hierarchy which
  44  * are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
  45  * Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
  46  */
  47 public class DerivateLabelProvider extends ColumnLabelProvider {
  48
  49     private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
  50
  51     private Set<SingleRead> multiLinkSingleReads;
  52
  53     private ConversationHolder conversation;
  54
  55     private static DefinedTerm photoTerm = null;
  56     private static DefinedTerm drawingTerm = null;
  57     private static DefinedTerm specimenScanTerm = null;
  58     private static DefinedTerm detailImageTerm = null;
  59     private static DefinedTerm sampleDesignationTerm = null;
  60
  61     //FIXME: move static term getters to new singleton utility class
  62     private static void initializeTerms() {
  63         List<DefinedTerm> preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class);
  64         for (DefinedTerm definedTerm : preferredTerms) {
  65             if(definedTerm.getUuid().equals(UUID.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
  66                 photoTerm = definedTerm;
  67             }
  68             else if(definedTerm.getUuid().equals(UUID.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
  69                 drawingTerm = definedTerm;
  70             }
  71             else if(definedTerm.getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
  72                 specimenScanTerm = definedTerm;
  73             }
  74             else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
  75                 detailImageTerm = definedTerm;
  76             }
  77             else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
  78                 sampleDesignationTerm = definedTerm;
  79             }
  80         }
  81     }
  82
  83     public static DefinedTerm getLivingPlantPhotoTerm(){
  84         if(photoTerm==null){
  85             initializeTerms();
  86         }
  87         return photoTerm;
  88     }
  89
  90     public static DefinedTerm getArtworkTerm(){
  91         if(drawingTerm==null){
  92             initializeTerms();
  93         }
  94         return drawingTerm;
  95     }
  96
  97     public static DefinedTerm getSpecimenScanTerm(){
  98         if(specimenScanTerm==null){
  99             initializeTerms();
 100         }
 101         return specimenScanTerm;
 102     }
 103
 104     public static DefinedTerm getDetailImageTerm(){
 105         if(detailImageTerm==null){
 106             initializeTerms();
 107         }
 108         return detailImageTerm;
 109     }
 110
 111     public static DefinedTerm getSampleDesignationTerm(){
 112         if(sampleDesignationTerm==null){
 113             initializeTerms();
 114         }
 115         return sampleDesignationTerm;
 116     }
 117
 118
 119     /** {@inheritDoc} */
 120     @Override
 121     public String getText(Object element) {
 122         return getDerivateText(element);
 123     }
 124
 125     /** {@inheritDoc} */
 126     @Override
 127     public String getToolTipText(Object element) {
 128         return getDerivateText(element);
 129     }
 130
 131     /**
 132      * @param conversation the conversation to set
 133      */
 134     public void setConversation(ConversationHolder conversation) {
 135         this.conversation = conversation;
 136     }
 137
 138     public String getDerivateText(Object element){
 139         return getDerivateText(element, conversation);
 140     }
 141
 142     public static String getDerivateText(Object element, ConversationHolder conversation){
 143         //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
 144         TreeNode parentNode = null;
 145         TreeNode node = null;
 146         Object derivate = element;
 147         if(element instanceof TreeNode){
 148             node = (TreeNode) element;
 149             parentNode = node.getParent();
 150             //unwrap specimen from TreeNode
 151             derivate = node.getValue();
 152         }
 153
 154         conversation.bind();
 155
 156         final String emptyString = "";
 157         final String separator = ", ";
 158
 159         String label = emptyString;
 160
 161         //Field Unit
 162         if(derivate instanceof FieldUnit){
 163             FieldUnit fieldUnit = (FieldUnit)derivate;
 164             if(fieldUnit.getGatheringEvent()!=null){
 165                 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 166                 if(CdmStore.getService(IOccurrenceService.class).exists(fieldUnit.getUuid()) && !conversation.getSession().contains(gatheringEvent)){
 167                     fieldUnit = (FieldUnit) CdmStore.getService(IOccurrenceService.class).load(fieldUnit.getUuid());
 168                     gatheringEvent = fieldUnit.getGatheringEvent();
 169                 }
 170                 label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
 171                 label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
 172                 label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
 173                 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 174             }
 175             label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
 176         }
 177         //MediaSpecimen
 178         else if(derivate instanceof MediaSpecimen){
 179             MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
 180             if(mediaSpecimen.getMediaSpecimen()!=null){
 181                 label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
 182                 label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
 183             }
 184             eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
 185             if(collection!=null){
 186                 label += collection.getName()!=null?collection.getName()+" ":emptyString;
 187                 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 188             }
 189             label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
 190             label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
 191         }
 192         //TissueSample + DnaSample
 193         else if(derivate instanceof DnaSample){
 194             DnaSample dnaSample = (DnaSample)derivate;
 195             if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 196                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 197                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 198                     label += currentSampleDesignation.getIdentifier()+separator;
 199                 }
 200                 else{
 201                     label += NO_SAMPLE_DESIGNATION+separator;
 202                 }
 203             }
 204             else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
 205                 if(dnaSample.getKindOfUnit()!=null){
 206                     label += dnaSample.getKindOfUnit()+separator;
 207                 }
 208                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 209                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 210                     label += currentSampleDesignation.getIdentifier()+separator;
 211                 }
 212                 else{
 213                     label += NO_SAMPLE_DESIGNATION+separator;
 214                 }
 215             }
 216
 217         }
 218         //DerivedUnit + TissueSample
 219         else if(derivate instanceof DerivedUnit){
 220             DerivedUnit derivedUnit = (DerivedUnit)derivate;
 221             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 222                 java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
 223                 if(fieldUnits!=null && !fieldUnits.isEmpty()){
 224                     FieldUnit fieldUnit = fieldUnits.iterator().next();
 225                     GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 226 //                  gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
 227                     if(gatheringEvent!=null){
 228                         label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 229                     }
 230                     label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
 231                 }
 232                 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 233                 if(collection!=null){
 234                     label += collection.getName()!=null?collection.getName()+" ":emptyString;
 235                     label += collection.getCode()!=null?"("+collection.getCode()+"), ":emptyString;
 236                 }
 237                 String mostSignificantIdentifier = CdmStore.getService(IOccurrenceService.class).getMostSignificantIdentifier(derivedUnit);
 238                 label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
 239                 label += derivedUnit.getBarcode()!=null?derivedUnit.getBarcode():emptyString;
 240             }
 241             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 242                 //TissueSample should only be created by using it's own class
 243                 //in future using only one class with different SpecimenOrObservationTypes is desired
 244 //                label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
 245             }
 246         }
 247         //Sequence
 248         else if(derivate instanceof Sequence){
 249             Sequence sequence = (Sequence)derivate;
 250             Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 251             if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 252                 label += currentSampleDesignation.getIdentifier()+separator;
 253             }
 254             else{
 255                 label += NO_SAMPLE_DESIGNATION+separator;
 256             }
 257             label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 258         }
 259         //SingleRead
 260         else if(derivate instanceof SingleRead){
 261             SingleRead singleRead = (SingleRead)derivate;
 262             if(parentNode!=null && parentNode.getValue() instanceof Sequence){
 263                 Sequence sequence = (Sequence) parentNode.getValue();
 264                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 265                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 266                     label = currentSampleDesignation.getIdentifier()+separator;
 267                 }
 268                 else{
 269                     label += NO_SAMPLE_DESIGNATION+separator;
 270                 }
 271                 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
 272                 if(sequence!=null && sequence.getDnaMarker()!=null){
 273                     label += sequence.getDnaMarker()+separator;
 274                 }
 275                 if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
 276                     label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
 277                 }
 278             }
 279         }
 280         //SOOB
 281         else if(derivate instanceof SpecimenOrObservationBase){
 282             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
 283             SpecimenOrObservationType type = specimen.getRecordBasis();
 284             return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
 285         }
 286         if(label.isEmpty()){
 287             label = derivate.toString();
 288         }
 289         //remove last comma
 290         else if(label.endsWith(separator)){
 291             label = label.substring(0, label.length()-separator.length());
 292         }
 293         return label;
 294     }
 295
 296     /* (non-Javadoc)
 297      * @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object)
 298      */
 299     @Override
 300     public Image getImage(Object element) {
 301         if(element instanceof TreeNode){
 302             element = ((TreeNode) element).getValue();
 303         }
 304         if(element instanceof CdmBase){
 305             CdmBase cdmBase = (CdmBase)element;
 306 //            boolean hasCharacterData = false;
 307 //            if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
 308 //                SpecimenOrObservationBase specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
 309 //                if(!CdmStore.getService(IOccurrenceService.class).getCharacterDataForSpecimen(specimen).isEmpty()){
 310 //                    hasCharacterData = true;
 311 //                    return ImageResources.getImage(ImageResources.CHARACTER_DATA_DERIVATE);
 312 //                }
 313 //            }
 314             if(cdmBase.isInstanceOf(FieldUnit.class)){
 315                 return ImageResources.getImage(ImageResources.FIELD_UNIT);
 316             }
 317             else if(cdmBase.isInstanceOf(DerivedUnit.class)){
 318                 DerivedUnit derivedUnit = (DerivedUnit)element;
 319                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
 320                     return ImageResources.getImage(ImageResources.FIELD_UNIT);
 321                 }
 322                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 323                     return ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
 324                 }
 325                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 326                     return ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
 327                 }
 328                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 329                     return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
 330                 }
 331                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
 332                     if(derivedUnit.getKindOfUnit()!=null){
 333                         if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
 334                             return ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
 335                         }
 336                         else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
 337                             return ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
 338                         }
 339                         else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
 340                             return ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
 341                         }
 342                         else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
 343                             return ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
 344                         }
 345                     }
 346                 }
 347             }
 348             else if(cdmBase.isInstanceOf(Sequence.class)){
 349                 return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
 350             }
 351
 352             else if(cdmBase.isInstanceOf(SingleRead.class)){
 353                 if(multiLinkSingleReads.contains(element)){
 354                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
 355                 }
 356                 else{
 357                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
 358                 }
 359             }
 360         }
 361         return super.getImage(element);
 362     }
 363
 364     public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
 365         if(entity instanceof DnaSample){
 366             DnaSample dnaSample = (DnaSample)entity;
 367             for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
 368                 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
 369                     //first sample designation is the current
 370                     return identifier;
 371                 }
 372             }
 373         }
 374         else if(entity instanceof Sequence){
 375             Sequence sequence = (Sequence)entity;
 376             if(sequence.getDnaSample()!=null){
 377                 return getCurrentSampleDesignation(sequence.getDnaSample());
 378             }
 379         }
 380         return null;
 381     }
 382
 383     /**
 384      * @param multiLinkSingleReads2
 385      */
 386     public void setMultiLinkSingleReads(Set<SingleRead> multiLinkSingleReads) {
 387         this.multiLinkSingleReads = multiLinkSingleReads;
 388     }
 389
 390 }