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     private static void initializeTerms() {
  62         List<DefinedTerm> preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class);
  63         for (DefinedTerm definedTerm : preferredTerms) {
  64             if(definedTerm.getUuid().equals(UUID.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
  65                 photoTerm = definedTerm;
  66             }
  67             else if(definedTerm.getUuid().equals(UUID.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
  68                 drawingTerm = definedTerm;
  69             }
  70             else if(definedTerm.getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
  71                 specimenScanTerm = definedTerm;
  72             }
  73             else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
  74                 detailImageTerm = definedTerm;
  75             }
  76             else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
  77                 sampleDesignationTerm = definedTerm;
  78             }
  79         }
  80     }
  81
  82     public static DefinedTerm getLivingPlantPhotoTerm(){
  83         if(photoTerm==null){
  84             initializeTerms();
  85         }
  86         return photoTerm;
  87     }
  88
  89     public static DefinedTerm getArtworkTerm(){
  90         if(drawingTerm==null){
  91             initializeTerms();
  92         }
  93         return drawingTerm;
  94     }
  95
  96     public static DefinedTerm getSpecimenScanTerm(){
  97         if(specimenScanTerm==null){
  98             initializeTerms();
  99         }
 100         return specimenScanTerm;
 101     }
 102
 103     public static DefinedTerm getDetailImageTerm(){
 104         if(detailImageTerm==null){
 105             initializeTerms();
 106         }
 107         return detailImageTerm;
 108     }
 109
 110     public static DefinedTerm getSampleDesignationTerm(){
 111         if(sampleDesignationTerm==null){
 112             initializeTerms();
 113         }
 114         return sampleDesignationTerm;
 115     }
 116
 117
 118     /** {@inheritDoc} */
 119     @Override
 120     public String getText(Object element) {
 121         return getDerivateText(element);
 122     }
 123
 124     /** {@inheritDoc} */
 125     @Override
 126     public String getToolTipText(Object element) {
 127         return getDerivateText(element);
 128     }
 129
 130     /**
 131      * @param conversation the conversation to set
 132      */
 133     public void setConversation(ConversationHolder conversation) {
 134         this.conversation = conversation;
 135     }
 136
 137     /**
 138      *
 139      * @param derivate
 140      * @return
 141      */
 142     public String getDerivateText(Object element){
 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         }
 191         //TissueSample + DnaSample
 192         else if(derivate instanceof DnaSample){
 193             DnaSample dnaSample = (DnaSample)derivate;
 194             if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 195                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 196                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 197                     label += currentSampleDesignation.getIdentifier()+separator;
 198                 }
 199                 else{
 200                     label += NO_SAMPLE_DESIGNATION+separator;
 201                 }
 202             }
 203             else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
 204                 label += dnaSample.getKindOfUnit()+separator;
 205                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 206                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 207                     label += currentSampleDesignation.getIdentifier()+separator;
 208                 }
 209                 else{
 210                     label += NO_SAMPLE_DESIGNATION+separator;
 211                 }
 212             }
 213
 214         }
 215         //DerivedUnit + TissueSample
 216         else if(derivate instanceof DerivedUnit){
 217             DerivedUnit derivedUnit = (DerivedUnit)derivate;
 218             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 219                 java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
 220                 if(fieldUnits!=null && !fieldUnits.isEmpty()){
 221                     FieldUnit fieldUnit = fieldUnits.iterator().next();
 222                     GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 223 //                  gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
 224                     if(gatheringEvent!=null){
 225                         label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 226                     }
 227                     label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
 228                 }
 229                 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 230                 if(collection!=null){
 231                     label += collection.getName()!=null?collection.getName()+" ":emptyString;
 232                     label += collection.getCode()!=null?"("+collection.getCode()+"), ":emptyString;
 233                 }
 234                 label += derivedUnit.getAccessionNumber()!=null?derivedUnit.getAccessionNumber()+separator:emptyString;
 235                 label += derivedUnit.getBarcode()!=null?derivedUnit.getBarcode():emptyString;
 236             }
 237             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 238                 //TissueSample should only be created by using it's own class
 239                 //in future using only one class with different SpecimenOrObservationTypes is desired
 240 //                label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
 241             }
 242         }
 243         //Sequence
 244         else if(derivate instanceof Sequence){
 245             Sequence sequence = (Sequence)derivate;
 246             Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 247             if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 248                 label += currentSampleDesignation.getIdentifier()+separator;
 249             }
 250             else{
 251                 label += NO_SAMPLE_DESIGNATION+separator;
 252             }
 253             label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 254         }
 255         //SingleRead
 256         else if(derivate instanceof SingleRead){
 257             SingleRead singleRead = (SingleRead)derivate;
 258             if(parentNode!=null && parentNode.getValue() instanceof Sequence){
 259                 Sequence sequence = (Sequence) parentNode.getValue();
 260                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 261                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 262                     label = currentSampleDesignation.getIdentifier()+separator;
 263                 }
 264                 else{
 265                     label += NO_SAMPLE_DESIGNATION+separator;
 266                 }
 267                 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
 268                 if(sequence!=null){
 269                     label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 270                 }
 271             }
 272         }
 273         //SOOB
 274         else if(derivate instanceof SpecimenOrObservationBase){
 275             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
 276             SpecimenOrObservationType type = specimen.getRecordBasis();
 277             return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
 278         }
 279         if(label.isEmpty()){
 280             label = derivate.toString();
 281         }
 282         //remove last comma
 283         else if(label.endsWith(separator)){
 284             label = label.substring(0, label.length()-separator.length());
 285         }
 286         return label;
 287     }
 288
 289     /* (non-Javadoc)
 290      * @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object)
 291      */
 292     @Override
 293     public Image getImage(Object element) {
 294         if(element instanceof TreeNode){
 295             element = ((TreeNode) element).getValue();
 296         }
 297         if(element instanceof FieldUnit){
 298             return ImageResources.getImage(ImageResources.FIELD_UNIT);
 299         }
 300         else if(element instanceof DerivedUnit){
 301             DerivedUnit derivedUnit = (DerivedUnit)element;
 302             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
 303                 return ImageResources.getImage(ImageResources.FIELD_UNIT);
 304             }
 305             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 306                 return ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
 307             }
 308             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 309                 return ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
 310             }
 311             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 312                 return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
 313             }
 314             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
 315                 if(derivedUnit.getKindOfUnit()!=null){
 316                     if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
 317                         return ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
 318                     }
 319                     else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
 320                         return ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
 321                     }
 322                     else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
 323                         return ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
 324                     }
 325                     else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
 326                         return ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
 327                     }
 328                 }
 329             }
 330         }
 331         else if(element instanceof Sequence){
 332             return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
 333         }
 334
 335         else if(element instanceof SingleRead){
 336             if(multiLinkSingleReads.contains(element)){
 337                 return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
 338             }
 339             else{
 340                 return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
 341             }
 342         }
 343         return super.getImage(element);
 344     }
 345
 346     public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
 347         if(entity instanceof DnaSample){
 348             DnaSample dnaSample = (DnaSample)entity;
 349             for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
 350                 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
 351                     //first sample designation is the current
 352                     return identifier;
 353                 }
 354             }
 355         }
 356         else if(entity instanceof Sequence){
 357             Sequence sequence = (Sequence)entity;
 358             if(sequence.getDnaSample()!=null){
 359                 return getCurrentSampleDesignation(sequence.getDnaSample());
 360             }
 361         }
 362         return null;
 363     }
 364
 365     /**
 366      * @param multiLinkSingleReads2
 367      */
 368     public void setMultiLinkSingleReads(Set<SingleRead> multiLinkSingleReads) {
 369         this.multiLinkSingleReads = multiLinkSingleReads;
 370     }
 371
 372 }