3 * Copyright (C) 2013 EDIT
4 * European Distributed Institute of Taxonomy
5 * http://www.e-taxonomy.eu
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.
10 package eu
.etaxonomy
.taxeditor
.view
.derivateSearch
;
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
;
18 import java
.util
.Map
.Entry
;
20 import java
.util
.UUID
;
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
;
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
.hibernate
.HibernateProxyHelper
;
31 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
32 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTerm
;
33 import eu
.etaxonomy
.cdm
.model
.common
.Identifier
;
34 import eu
.etaxonomy
.cdm
.model
.molecular
.DnaSample
;
35 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
36 import eu
.etaxonomy
.cdm
.model
.molecular
.SingleRead
;
37 import eu
.etaxonomy
.cdm
.model
.name
.SpecimenTypeDesignation
;
38 import eu
.etaxonomy
.cdm
.model
.name
.TaxonNameBase
;
39 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivedUnit
;
40 import eu
.etaxonomy
.cdm
.model
.occurrence
.DeterminationEvent
;
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
;
50 * Label provider for the views to show {@link SpecimenOrObservationBase}s.<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.
58 public class DerivateLabelProvider
extends ColumnLabelProvider
{
60 private static final String NO_SAMPLE_DESIGNATION
= "[no sample designation]";
62 private static Set
<SingleRead
> multiLinkSingleReads
;
64 private static Map
<DerivedUnit
, List
<DeterminationEvent
>> determinationEvents
;
66 private static Map
<DerivedUnit
, List
<SpecimenTypeDesignation
>> typeDesignations
;
68 private ConversationHolder conversation
;
70 private static DefinedTerm photoTerm
= null;
71 private static DefinedTerm drawingTerm
= null;
72 private static DefinedTerm specimenScanTerm
= null;
73 private static DefinedTerm detailImageTerm
= null;
74 private static DefinedTerm sampleDesignationTerm
= null;
76 //FIXME: move static term getters to new singleton utility class
77 private static void initializeTerms() {
78 List
<DefinedTerm
> preferredTerms
= CdmStore
.getTermManager().getPreferredTerms(DefinedTerm
.class);
79 for (DefinedTerm definedTerm
: preferredTerms
) {
80 if(definedTerm
.getUuid().equals(UUID
.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
81 photoTerm
= definedTerm
;
83 else if(definedTerm
.getUuid().equals(UUID
.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
84 drawingTerm
= definedTerm
;
86 else if(definedTerm
.getUuid().equals(UUID
.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
87 specimenScanTerm
= definedTerm
;
89 else if(definedTerm
.getUuid().equals(UUID
.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
90 detailImageTerm
= definedTerm
;
92 else if(definedTerm
.getUuid().equals(UUID
.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
93 sampleDesignationTerm
= definedTerm
;
98 public static DefinedTerm
getLivingPlantPhotoTerm(){
105 public static DefinedTerm
getArtworkTerm(){
106 if(drawingTerm
==null){
112 public static DefinedTerm
getSpecimenScanTerm(){
113 if(specimenScanTerm
==null){
116 return specimenScanTerm
;
119 public static DefinedTerm
getDetailImageTerm(){
120 if(detailImageTerm
==null){
123 return detailImageTerm
;
126 public static DefinedTerm
getSampleDesignationTerm(){
127 if(sampleDesignationTerm
==null){
130 return sampleDesignationTerm
;
136 public String
getText(Object element
) {
137 return getDerivateText(element
);
142 public String
getToolTipText(Object element
) {
143 return getDerivateText(element
);
147 * @param conversation the conversation to set
149 public void setConversation(ConversationHolder conversation
) {
150 this.conversation
= conversation
;
153 public String
getDerivateText(Object element
){
154 return getDerivateText(element
, conversation
);
157 public static String
getDerivateText(Object element
, ConversationHolder conversation
){
158 //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
159 TreeNode parentNode
= null;
160 TreeNode node
= null;
161 Object derivate
= element
;
162 if(element
instanceof TreeNode
){
163 node
= (TreeNode
) element
;
164 parentNode
= node
.getParent();
165 //unwrap specimen from TreeNode
166 derivate
= node
.getValue();
169 if(conversation
!=null){
173 final String emptyString
= "";
174 final String separator
= " ";
176 String label
= emptyString
;
179 if(derivate
instanceof FieldUnit
){
180 FieldUnit fieldUnit
= (FieldUnit
)derivate
;
181 if(fieldUnit
.getGatheringEvent()!=null){
182 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
183 label
+= gatheringEvent
.getCountry()!=null?gatheringEvent
.getCountry().getLabel()+separator
:emptyString
;
184 label
+= gatheringEvent
.getLocality()!=null?gatheringEvent
.getLocality().getText()+separator
:emptyString
;
185 label
+= gatheringEvent
.getGatheringDate()!=null?gatheringEvent
.getGatheringDate()+separator
:emptyString
;
186 label
+= gatheringEvent
.getCollector()!=null?gatheringEvent
.getCollector()+separator
:emptyString
;
188 label
+= fieldUnit
.getFieldNumber()!=null?fieldUnit
.getFieldNumber():emptyString
;
191 else if(derivate
instanceof MediaSpecimen
){
192 MediaSpecimen mediaSpecimen
= (MediaSpecimen
)derivate
;
193 if(mediaSpecimen
.getMediaSpecimen()!=null){
194 label
+= mediaSpecimen
.getMediaSpecimen().getTitle()!=null?mediaSpecimen
.getMediaSpecimen().getTitle().getText()+separator
:"[no motif]";
195 label
+= mediaSpecimen
.getMediaSpecimen().getArtist()!=null?mediaSpecimen
.getMediaSpecimen().getArtist()+separator
:emptyString
;
197 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= mediaSpecimen
.getCollection();
198 if(collection
!=null){
199 label
+= collection
.getName()!=null?collection
.getName()+" ":emptyString
;
200 label
+= collection
.getCode()!=null?
"("+collection
.getCode()+")"+separator
:emptyString
;
202 label
+= mediaSpecimen
.getAccessionNumber()!=null?mediaSpecimen
.getAccessionNumber()+separator
:emptyString
;
203 label
+= mediaSpecimen
.getBarcode()!=null?mediaSpecimen
.getBarcode()+separator
:emptyString
;
205 //TissueSample + DnaSample
206 else if(derivate
instanceof DnaSample
){
207 DnaSample dnaSample
= (DnaSample
)derivate
;
208 if(((DnaSample
) derivate
).getRecordBasis()==SpecimenOrObservationType
.DnaSample
){
209 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(dnaSample
);
210 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
211 label
+= currentSampleDesignation
.getIdentifier()+separator
;
214 label
+= NO_SAMPLE_DESIGNATION
+separator
;
217 else if(((DnaSample
) derivate
).getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
218 if(dnaSample
.getKindOfUnit()!=null){
219 label
+= dnaSample
.getKindOfUnit()+separator
;
221 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(dnaSample
);
222 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
223 label
+= currentSampleDesignation
.getIdentifier()+separator
;
226 label
+= NO_SAMPLE_DESIGNATION
+separator
;
231 //DerivedUnit + TissueSample
232 else if(derivate
instanceof DerivedUnit
){
233 DerivedUnit derivedUnit
= (DerivedUnit
)derivate
;
234 if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
235 //check for type designation
236 if(typeDesignations
.get(derivedUnit
)==null){
237 for (SpecimenTypeDesignation specimenTypeDesignation
: CdmStore
.getService(IOccurrenceService
.class).listTypeDesignations(derivedUnit
, null, null, null, null)) {
238 addTypeDesignation(derivedUnit
, specimenTypeDesignation
);
241 //check for determination events
242 if(determinationEvents
.get(derivedUnit
)==null){
243 for (DeterminationEvent determinationEvent
: CdmStore
.getService(IOccurrenceService
.class).listDeterminationEvents(derivedUnit
, null, null, null, null)) {
244 addDeterminationEvent(derivedUnit
, determinationEvent
);
247 //java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
248 //TODO : This is not generic anymore for performance reasons
249 Set
<SpecimenOrObservationBase
> originals
= derivedUnit
.getOriginals();
250 if(originals
!=null && originals
.size() ==1) {
251 SpecimenOrObservationBase specimen
= originals
.iterator().next();
252 if(specimen
instanceof FieldUnit
) {
253 FieldUnit fieldUnit
= (FieldUnit
)specimen
;
254 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
255 if(gatheringEvent
!=null){
256 label
+= gatheringEvent
.getCollector()!=null?gatheringEvent
.getCollector()+separator
:emptyString
;
258 label
+= fieldUnit
.getFieldNumber()!=null?fieldUnit
.getFieldNumber()+separator
:emptyString
;
262 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= derivedUnit
.getCollection();
263 if(collection
!=null){
264 label
+= collection
.getCode()!=null?
"("+collection
.getCode()+")"+separator
:emptyString
;
266 String mostSignificantIdentifier
= derivedUnit
.getMostSignificantIdentifier();
267 label
+= mostSignificantIdentifier
!=null?mostSignificantIdentifier
+separator
:emptyString
;
268 //type designation extension
269 List
<SpecimenTypeDesignation
> typeDesignationList
= typeDesignations
.get(derivedUnit
);
270 if(typeDesignationList
!=null){
271 for (SpecimenTypeDesignation specimenTypeDesignation
: typeDesignationList
) {
272 label
+= "("+specimenTypeDesignation
.getTypeStatus()+" of ";
273 for (TaxonNameBase taxonNameBase
: specimenTypeDesignation
.getTypifiedNames()) {
274 label
+= taxonNameBase
+separator
;
276 if(label
.endsWith(separator
)){
277 label
= label
.substring(0, label
.length()-separator
.length());
282 //determination event extension
283 List
<DeterminationEvent
> determinationEventList
= determinationEvents
.get(derivedUnit
);
284 if(determinationEventList
!=null){
285 for (DeterminationEvent determinationEvent
: determinationEventList
) {
287 if(determinationEvent
.getTaxon()!=null){
288 label
+= "Determined as "+determinationEvent
.getTaxon();
291 if(label
.endsWith(separator
)){
292 label
= label
.substring(0, label
.length()-separator
.length());
298 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
299 //TissueSample should only be created by using it's own class
300 //in future using only one class with different SpecimenOrObservationTypes is desired
301 // label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
305 else if(derivate
instanceof Sequence
){
306 Sequence sequence
= (Sequence
)derivate
;
307 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(sequence
);
308 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
309 label
+= currentSampleDesignation
.getIdentifier()+separator
;
312 label
+= NO_SAMPLE_DESIGNATION
+separator
;
314 label
+= sequence
.getDnaMarker()!=null?sequence
.getDnaMarker():emptyString
;
317 else if(derivate
instanceof SingleRead
){
318 SingleRead singleRead
= (SingleRead
)derivate
;
319 if(parentNode
!=null && parentNode
.getValue() instanceof Sequence
){
320 Sequence sequence
= (Sequence
) parentNode
.getValue();
321 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(sequence
);
322 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
323 label
= currentSampleDesignation
.getIdentifier()+separator
;
326 label
+= NO_SAMPLE_DESIGNATION
+separator
;
328 label
+= singleRead
.getPrimer()!=null?singleRead
.getPrimer().getLabel()+separator
:emptyString
;
329 if(sequence
!=null && sequence
.getDnaMarker()!=null){
330 label
+= sequence
.getDnaMarker()+separator
;
332 if(singleRead
.getAmplificationResult()!=null && singleRead
.getAmplificationResult().getAmplification()!=null){
333 label
+= singleRead
.getAmplificationResult().getAmplification().getLabelCache()+separator
;
338 else if(derivate
instanceof SpecimenOrObservationBase
){
339 SpecimenOrObservationBase
<?
> specimen
= (SpecimenOrObservationBase
<?
>) derivate
;
340 SpecimenOrObservationType type
= specimen
.getRecordBasis();
341 return specimen
.getTitleCache() + (type
!=null?
" ["+type
.toString()+"]":emptyString
);
344 label
= derivate
.toString();
347 else if(label
.endsWith(separator
)){
348 label
= label
.substring(0, label
.length()-separator
.length());
354 public Image
getImage(Object element
) {
355 if(element
instanceof TreeNode
){
356 element
= ((TreeNode
) element
).getValue();
358 if(element
instanceof CdmBase
){
359 CdmBase cdmBase
= (CdmBase
)element
;
360 boolean hasCharacterData
= false;
361 if(cdmBase
.isInstanceOf(SpecimenOrObservationBase
.class)){
362 SpecimenOrObservationBase
<?
> specimen
= HibernateProxyHelper
.deproxy(cdmBase
, SpecimenOrObservationBase
.class);
363 if(specimen
.hasCharacterData()){
364 hasCharacterData
= true;
367 if(cdmBase
.isInstanceOf(FieldUnit
.class)){
368 return hasCharacterData?ImageResources
.getImage(ImageResources
.FIELD_UNIT_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.FIELD_UNIT
);
370 else if(cdmBase
.isInstanceOf(DerivedUnit
.class)){
371 DerivedUnit derivedUnit
= HibernateProxyHelper
.deproxy(element
, DerivedUnit
.class);
372 if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.FieldUnit
){
373 return hasCharacterData?ImageResources
.getImage(ImageResources
.FIELD_UNIT_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.FIELD_UNIT
);
375 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.DnaSample
){
376 return hasCharacterData?ImageResources
.getImage(ImageResources
.DNA_SAMPLE_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.DNA_SAMPLE_DERIVATE
);
378 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
379 return hasCharacterData?ImageResources
.getImage(ImageResources
.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.TISSUE_SAMPLE_DERIVATE
);
381 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
382 return hasCharacterData?ImageResources
.getImage(ImageResources
.SPECIMEN_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.SPECIMEN_DERIVATE
);
384 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.Media
){
385 if(derivedUnit
.getKindOfUnit()!=null){
386 if(derivedUnit
.getKindOfUnit().equals(getArtworkTerm())){
387 return hasCharacterData?ImageResources
.getImage(ImageResources
.ARTWORK_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.ARTWORK_DERIVATE
);
389 else if(derivedUnit
.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
390 return hasCharacterData?ImageResources
.getImage(ImageResources
.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.LIVING_PLANT_PHOTO_DERIVATE
);
392 else if(derivedUnit
.getKindOfUnit().equals(getSpecimenScanTerm())){
393 return hasCharacterData?ImageResources
.getImage(ImageResources
.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.SPECIMEN_SCAN_DERIVATE
);
395 else if(derivedUnit
.getKindOfUnit().equals(getDetailImageTerm())){
396 return hasCharacterData?ImageResources
.getImage(ImageResources
.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.DETAIL_IMAGE_DERIVATE
);
401 else if(cdmBase
.isInstanceOf(Sequence
.class)){
402 return ImageResources
.getImage(ImageResources
.SEQUENCE_DERIVATE
);
405 else if(cdmBase
.isInstanceOf(SingleRead
.class)){
406 if(multiLinkSingleReads
!=null && multiLinkSingleReads
.contains(element
)){
407 return ImageResources
.getImage(ImageResources
.SINGLE_READ_DERIVATE_MULTILINK
);
410 return ImageResources
.getImage(ImageResources
.SINGLE_READ_DERIVATE
);
414 return super.getImage(element
);
417 public static Identifier
<DnaSample
> getCurrentSampleDesignation(CdmBase entity
) {
418 if(entity
.isInstanceOf(DnaSample
.class)){
419 DnaSample dnaSample
= HibernateProxyHelper
.deproxy(entity
, DnaSample
.class);
420 for (Identifier
<DnaSample
> identifier
: dnaSample
.getIdentifiers()) {
421 if(identifier
.getType()!=null && identifier
.getType().equals(DerivateLabelProvider
.getSampleDesignationTerm())){
422 //first sample designation is the current
427 else if(entity
.isInstanceOf(Sequence
.class)){
428 Sequence sequence
= HibernateProxyHelper
.deproxy(entity
, Sequence
.class);
429 if(sequence
.getDnaSample()!=null){
430 return getCurrentSampleDesignation(sequence
.getDnaSample());
437 * Refreshes cached label extensions
438 * @param multiLinkSingleReads
440 public void refresh() {
441 DerivateLabelProvider
.multiLinkSingleReads
= new HashSet
<SingleRead
>();
442 for(Entry
<SingleRead
, Collection
<Sequence
>> entry
:CdmStore
.getService(ISequenceService
.class).getSingleReadSequencesMap().entrySet()){
443 if(entry
.getValue().size()>1){
444 multiLinkSingleReads
.add(entry
.getKey());
447 DerivateLabelProvider
.typeDesignations
= new HashMap
<DerivedUnit
, List
<SpecimenTypeDesignation
>>();
448 DerivateLabelProvider
.determinationEvents
= new HashMap
<DerivedUnit
, List
<DeterminationEvent
>>();
451 private static void addDeterminationEvent(DerivedUnit derivedUnit
, DeterminationEvent determinationEvent
){
452 List
<DeterminationEvent
> list
= determinationEvents
.get(derivedUnit
);
454 list
= new ArrayList
<DeterminationEvent
>();
456 list
.add(determinationEvent
);
457 determinationEvents
.put(derivedUnit
, list
);
460 private static void addTypeDesignation(DerivedUnit derivedUnit
, SpecimenTypeDesignation typeDesignation
){
461 List
<SpecimenTypeDesignation
> list
= typeDesignations
.get(derivedUnit
);
463 list
= new ArrayList
<SpecimenTypeDesignation
>();
465 list
.add(typeDesignation
);
466 typeDesignations
.put(derivedUnit
, list
);
469 public static Set
<SingleRead
> getMultiLinkSingleReads() {
470 return multiLinkSingleReads
;