Add type specimen icon to derivate editor
[taxeditor.git] / 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, Collection<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 return formatter.format(element);
155 }
156
157 /** {@inheritDoc} */
158 @Override
159 public String getToolTipText(Object element) {
160 return getDerivateText(element);
161 }
162
163 /**
164 * @param conversation the conversation to set
165 */
166 public void setConversation(ConversationHolder conversation) {
167 this.conversation = conversation;
168 }
169
170 public String getDerivateText(Object element){
171 return getDerivateText(element, conversation);
172 }
173
174 public static String getDerivateText(Object element, ConversationHolder conversation){
175 //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
176 TreeNode parentNode = null;
177 TreeNode node = null;
178 Object derivate = element;
179 if(element instanceof TreeNode){
180 node = (TreeNode) element;
181 parentNode = node.getParent();
182 //unwrap specimen from TreeNode
183 derivate = node.getValue();
184 }
185
186 if(conversation!=null){
187 conversation.bind();
188 }
189
190 final String emptyString = "";
191 final String separator = " ";
192
193 String label = emptyString;
194
195 //Field Unit
196 if(derivate instanceof FieldUnit){
197 FieldUnit fieldUnit = (FieldUnit)derivate;
198 if(fieldUnit.getGatheringEvent()!=null){
199 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
200 label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
201 label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
202 label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
203 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
204 }
205 label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
206 }
207 //MediaSpecimen
208 else if(derivate instanceof MediaSpecimen){
209 MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
210 if(mediaSpecimen.getMediaSpecimen()!=null){
211 label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
212 label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
213 }
214 eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
215 if(collection!=null){
216 label += collection.getName()!=null?collection.getName()+" ":emptyString;
217 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
218 }
219 label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
220 label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
221 }
222 //TissueSample + DnaSample
223 else if(derivate instanceof DnaSample){
224 DnaSample dnaSample = (DnaSample)derivate;
225 if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
226 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
227 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
228 label += currentSampleDesignation.getIdentifier()+separator;
229 }
230 else{
231 label += NO_SAMPLE_DESIGNATION+separator;
232 }
233 }
234 else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
235 if(dnaSample.getKindOfUnit()!=null){
236 label += dnaSample.getKindOfUnit()+separator;
237 }
238 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
239 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
240 label += currentSampleDesignation.getIdentifier()+separator;
241 }
242 else{
243 label += NO_SAMPLE_DESIGNATION+separator;
244 }
245 }
246
247 }
248 //DerivedUnit + TissueSample
249 else if(derivate instanceof DerivedUnit){
250 DerivedUnit derivedUnit = (DerivedUnit)derivate;
251 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
252 //check for type designation
253 if(typeDesignations.get(derivedUnit)==null){
254 for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
255 addTypeDesignation(derivedUnit, specimenTypeDesignation);
256 }
257 }
258 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
259 //TODO : This is not generic anymore for performance reasons
260 Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
261 if(originals!=null && originals.size() ==1) {
262 SpecimenOrObservationBase specimen = originals.iterator().next();
263 if(specimen instanceof FieldUnit) {
264 FieldUnit fieldUnit = (FieldUnit)specimen;
265 GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
266 if(gatheringEvent!=null){
267 label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
268 }
269 label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
270 }
271 }
272
273 eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
274 if(collection!=null){
275 label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
276 }
277 String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
278 label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
279 }
280 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
281 //TissueSample should only be created by using it's own class
282 //in future using only one class with different SpecimenOrObservationTypes is desired
283 // label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
284 }
285 }
286 //Sequence
287 else if(derivate instanceof Sequence){
288 Sequence sequence = (Sequence)derivate;
289 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
290 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
291 label += currentSampleDesignation.getIdentifier()+separator;
292 }
293 else{
294 label += NO_SAMPLE_DESIGNATION+separator;
295 }
296 label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
297 }
298 //SingleRead
299 else if(derivate instanceof SingleRead){
300 SingleRead singleRead = (SingleRead)derivate;
301 if(parentNode!=null && parentNode.getValue() instanceof Sequence){
302 Sequence sequence = (Sequence) parentNode.getValue();
303 Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
304 if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
305 label = currentSampleDesignation.getIdentifier()+separator;
306 }
307 else{
308 label += NO_SAMPLE_DESIGNATION+separator;
309 }
310 label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
311 if(sequence!=null && sequence.getDnaMarker()!=null){
312 label += sequence.getDnaMarker()+separator;
313 }
314 if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
315 label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
316 }
317 }
318 }
319 //SOOB
320 else if(derivate instanceof SpecimenOrObservationBase){
321 SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
322 SpecimenOrObservationType type = specimen.getRecordBasis();
323 return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
324 }
325 if(label.isEmpty()){
326 label = derivate.toString();
327 }
328 //remove last comma
329 else if(label.endsWith(separator)){
330 label = label.substring(0, label.length()-separator.length());
331 }
332 return label;
333 }
334
335 @Override
336 public Image getImage(Object element) {
337 if(element instanceof TreeNode){
338 element = ((TreeNode) element).getValue();
339 }
340 if(element instanceof CdmBase){
341 CdmBase cdmBase = (CdmBase)element;
342 boolean hasCharacterData = false;
343 if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
344 SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
345 if(specimen.hasCharacterData()){
346 hasCharacterData = true;
347 }
348 }
349 if(cdmBase.isInstanceOf(FieldUnit.class)){
350 return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
351 }
352 else if(cdmBase.isInstanceOf(DerivedUnit.class)){
353 DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
354
355 if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
356 return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
357 }
358 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
359 return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
360 }
361 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
362 return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
363 }
364 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
365 if(typeDesignations.get(derivedUnit)!=null && !typeDesignations.get(derivedUnit).isEmpty()){
366 return ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_TYPE);
367 }
368 return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
369 }
370 else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
371 if(derivedUnit.getKindOfUnit()!=null){
372 if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
373 return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
374 }
375 else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
376 return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
377 }
378 else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
379 return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
380 }
381 else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
382 return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
383 }
384 }
385 }
386 }
387 else if(cdmBase.isInstanceOf(Sequence.class)){
388 return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
389 }
390
391 else if(cdmBase.isInstanceOf(SingleRead.class)){
392 if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
393 return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
394 }
395 else{
396 return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
397 }
398 }
399 }
400 return super.getImage(element);
401 }
402
403 public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
404 if(entity.isInstanceOf(DnaSample.class)){
405 DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
406 for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
407 if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
408 //first sample designation is the current
409 return identifier;
410 }
411 }
412 }
413 else if(entity.isInstanceOf(Sequence.class)){
414 Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
415 if(sequence.getDnaSample()!=null){
416 return getCurrentSampleDesignation(sequence.getDnaSample());
417 }
418 }
419 return null;
420 }
421
422 private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
423 Collection<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
424 if(list==null){
425 list = new ArrayList<SpecimenTypeDesignation>();
426 }
427 list.add(typeDesignation);
428 typeDesignations.put(derivedUnit, list);
429 }
430
431 public static Set<SingleRead> getMultiLinkSingleReads() {
432 return multiLinkSingleReads;
433 }
434
435 public void initCache(Collection<SpecimenOrObservationBase<?>> rootElements) {
436 DerivateLabelProvider.multiLinkSingleReads = new HashSet<SingleRead>();
437 DerivateLabelProvider.typeDesignations = new HashMap<DerivedUnit, Collection<SpecimenTypeDesignation>>();
438 for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
439 if(entry.getValue().size()>1){
440 multiLinkSingleReads.add(entry.getKey());
441 }
442 }
443 if(rootElements!=null){
444 Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
445 for (SpecimenOrObservationBase specimenOrObservationBase : rootElements) {
446 derivedUnits.addAll(CdmStore.getService(IOccurrenceService.class).getAllChildDerivatives(specimenOrObservationBase.getUuid()));
447 if(specimenOrObservationBase.isInstanceOf(DerivedUnit.class)){
448 derivedUnits.add(HibernateProxyHelper.deproxy(specimenOrObservationBase, DerivedUnit.class));
449 }
450 }
451 typeDesignations = CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnits, null, null, null, null);
452 }
453 }
454
455 }