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(
 139                 FormatKey.GATHERING_COUNTRY, FormatKey.SPACE,
 140                 FormatKey.GATHERING_LOCALITY_TEXT, FormatKey.SPACE,
 141                 FormatKey.GATHERING_DATE, FormatKey.SPACE,
 142                 FormatKey.GATHERING_COLLECTOR, FormatKey.SPACE,
 143                 FormatKey.FIELD_NUMBER, FormatKey.SPACE,
 144                 FormatKey.COLLECTION_CODE, FormatKey.SPACE,
 145                 FormatKey.MOST_SIGNIFICANT_IDENTIFIER, FormatKey.SPACE,
 146                 FormatKey.KIND_OF_UNIT, FormatKey.SPACE,
 147                 FormatKey.SAMPLE_DESIGNATION, FormatKey.SPACE,
 148                 FormatKey.SINGLE_READ_PRIMER, FormatKey.SPACE,
 149                 FormatKey.SEQUENCE_DNA_MARKER, FormatKey.SPACE,
 150                 FormatKey.AMPLIFICATION_LABEL, FormatKey.SPACE,
 151                 FormatKey.MEDIA_TITLE, FormatKey.SPACE,
 152                 FormatKey.MEDIA_ARTIST, FormatKey.SPACE
 153                 );
 154         System.out.println(formatter.format(element));
 155         return formatter.format(element);
 156 //        return getDerivateText(element);
 157     }
 158
 159     /** {@inheritDoc} */
 160     @Override
 161     public String getToolTipText(Object element) {
 162         return getDerivateText(element);
 163     }
 164
 165     /**
 166      * @param conversation the conversation to set
 167      */
 168     public void setConversation(ConversationHolder conversation) {
 169         this.conversation = conversation;
 170     }
 171
 172     public String getDerivateText(Object element){
 173         return getDerivateText(element, conversation);
 174     }
 175
 176     public static String getDerivateText(Object element, ConversationHolder conversation){
 177         //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
 178         TreeNode parentNode = null;
 179         TreeNode node = null;
 180         Object derivate = element;
 181         if(element instanceof TreeNode){
 182             node = (TreeNode) element;
 183             parentNode = node.getParent();
 184             //unwrap specimen from TreeNode
 185             derivate = node.getValue();
 186         }
 187
 188         if(conversation!=null){
 189             conversation.bind();
 190         }
 191
 192         final String emptyString = "";
 193         final String separator = " ";
 194
 195         String label = emptyString;
 196
 197         //Field Unit
 198         if(derivate instanceof FieldUnit){
 199             FieldUnit fieldUnit = (FieldUnit)derivate;
 200             if(fieldUnit.getGatheringEvent()!=null){
 201                 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 202                 label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
 203                 label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
 204                 label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
 205                 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 206             }
 207             label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
 208         }
 209         //MediaSpecimen
 210         else if(derivate instanceof MediaSpecimen){
 211             MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
 212             if(mediaSpecimen.getMediaSpecimen()!=null){
 213                 label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
 214                 label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
 215             }
 216             eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
 217             if(collection!=null){
 218                 label += collection.getName()!=null?collection.getName()+" ":emptyString;
 219                 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 220             }
 221             label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
 222             label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
 223         }
 224         //TissueSample + DnaSample
 225         else if(derivate instanceof DnaSample){
 226             DnaSample dnaSample = (DnaSample)derivate;
 227             if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
 228                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 229                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 230                     label += currentSampleDesignation.getIdentifier()+separator;
 231                 }
 232                 else{
 233                     label += NO_SAMPLE_DESIGNATION+separator;
 234                 }
 235             }
 236             else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
 237                 if(dnaSample.getKindOfUnit()!=null){
 238                     label += dnaSample.getKindOfUnit()+separator;
 239                 }
 240                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
 241                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 242                     label += currentSampleDesignation.getIdentifier()+separator;
 243                 }
 244                 else{
 245                     label += NO_SAMPLE_DESIGNATION+separator;
 246                 }
 247             }
 248
 249         }
 250         //DerivedUnit + TissueSample
 251         else if(derivate instanceof DerivedUnit){
 252             DerivedUnit derivedUnit = (DerivedUnit)derivate;
 253             if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 254                 //check for type designation
 255                 if(typeDesignations.get(derivedUnit)==null){
 256                     for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
 257                         addTypeDesignation(derivedUnit, specimenTypeDesignation);
 258                     }
 259                 }
 260                 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
 261                 //TODO : This is not generic anymore for performance reasons
 262                 Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
 263                 if(originals!=null && originals.size() ==1) {
 264                     SpecimenOrObservationBase specimen = originals.iterator().next();
 265                     if(specimen instanceof FieldUnit) {
 266                         FieldUnit fieldUnit = (FieldUnit)specimen;
 267                         GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
 268                         if(gatheringEvent!=null){
 269                             label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
 270                         }
 271                         label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
 272                     }
 273                 }
 274
 275                 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
 276                 if(collection!=null){
 277                     label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
 278                 }
 279                 String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
 280                 label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
 281             }
 282             else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 283                 //TissueSample should only be created by using it's own class
 284                 //in future using only one class with different SpecimenOrObservationTypes is desired
 285 //                label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
 286             }
 287         }
 288         //Sequence
 289         else if(derivate instanceof Sequence){
 290             Sequence sequence = (Sequence)derivate;
 291             Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 292             if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 293                 label += currentSampleDesignation.getIdentifier()+separator;
 294             }
 295             else{
 296                 label += NO_SAMPLE_DESIGNATION+separator;
 297             }
 298             label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
 299         }
 300         //SingleRead
 301         else if(derivate instanceof SingleRead){
 302             SingleRead singleRead = (SingleRead)derivate;
 303             if(parentNode!=null && parentNode.getValue() instanceof Sequence){
 304                 Sequence sequence = (Sequence) parentNode.getValue();
 305                 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
 306                 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
 307                     label = currentSampleDesignation.getIdentifier()+separator;
 308                 }
 309                 else{
 310                     label += NO_SAMPLE_DESIGNATION+separator;
 311                 }
 312                 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
 313                 if(sequence!=null && sequence.getDnaMarker()!=null){
 314                     label += sequence.getDnaMarker()+separator;
 315                 }
 316                 if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
 317                     label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
 318                 }
 319             }
 320         }
 321         //SOOB
 322         else if(derivate instanceof SpecimenOrObservationBase){
 323             SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
 324             SpecimenOrObservationType type = specimen.getRecordBasis();
 325             return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
 326         }
 327         if(label.isEmpty()){
 328             label = derivate.toString();
 329         }
 330         //remove last comma
 331         else if(label.endsWith(separator)){
 332             label = label.substring(0, label.length()-separator.length());
 333         }
 334         return label;
 335     }
 336
 337     @Override
 338     public Image getImage(Object element) {
 339         if(element instanceof TreeNode){
 340             element = ((TreeNode) element).getValue();
 341         }
 342         if(element instanceof CdmBase){
 343             CdmBase cdmBase = (CdmBase)element;
 344             boolean hasCharacterData = false;
 345             if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
 346                 SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
 347                 if(specimen.hasCharacterData()){
 348                     hasCharacterData = true;
 349                 }
 350             }
 351             if(cdmBase.isInstanceOf(FieldUnit.class)){
 352                 return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 353             }
 354             else if(cdmBase.isInstanceOf(DerivedUnit.class)){
 355                 DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
 356
 357                 boolean isType = false;
 358                 //type designation extension
 359                 if(typeDesignations.get(derivedUnit)!=null){
 360                     isType = true;
 361                 }
 362                 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
 363                     return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
 364                 }
 365                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
 366                     return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
 367                 }
 368                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
 369                     return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
 370                 }
 371                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
 372                     return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
 373                 }
 374                 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
 375                     if(derivedUnit.getKindOfUnit()!=null){
 376                         if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
 377                             return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
 378                         }
 379                         else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
 380                             return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
 381                         }
 382                         else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
 383                             return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
 384                         }
 385                         else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
 386                             return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
 387                         }
 388                     }
 389                 }
 390             }
 391             else if(cdmBase.isInstanceOf(Sequence.class)){
 392                 return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
 393             }
 394
 395             else if(cdmBase.isInstanceOf(SingleRead.class)){
 396                 if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
 397                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
 398                 }
 399                 else{
 400                     return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
 401                 }
 402             }
 403         }
 404         return super.getImage(element);
 405     }
 406
 407     public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
 408         if(entity.isInstanceOf(DnaSample.class)){
 409             DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
 410             for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
 411                 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
 412                     //first sample designation is the current
 413                     return identifier;
 414                 }
 415             }
 416         }
 417         else if(entity.isInstanceOf(Sequence.class)){
 418             Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
 419             if(sequence.getDnaSample()!=null){
 420                 return getCurrentSampleDesignation(sequence.getDnaSample());
 421             }
 422         }
 423         return null;
 424     }
 425
 426     /**
 427      * Refreshes cached label extensions
 428      * @param multiLinkSingleReads
 429      */
 430     public void refresh() {
 431         DerivateLabelProvider.multiLinkSingleReads = new HashSet<SingleRead>();
 432         for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
 433             if(entry.getValue().size()>1){
 434                 multiLinkSingleReads.add(entry.getKey());
 435             }
 436         }
 437         DerivateLabelProvider.typeDesignations = new HashMap<DerivedUnit, List<SpecimenTypeDesignation>>();
 438     }
 439
 440     private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
 441         List<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
 442         if(list==null){
 443             list = new ArrayList<SpecimenTypeDesignation>();
 444         }
 445         list.add(typeDesignation);
 446         typeDesignations.put(derivedUnit, list);
 447     }
 448
 449     public static Set<SingleRead> getMultiLinkSingleReads() {
 450         return multiLinkSingleReads;
 451     }
 452
 453 }