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