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
.List
;
14 import java
.util
.UUID
;
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
;
21 import eu
.etaxonomy
.cdm
.api
.conversation
.ConversationHolder
;
22 import eu
.etaxonomy
.cdm
.api
.service
.IOccurrenceService
;
23 import eu
.etaxonomy
.cdm
.hibernate
.HibernateProxyHelper
;
24 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
25 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTerm
;
26 import eu
.etaxonomy
.cdm
.model
.common
.Identifier
;
27 import eu
.etaxonomy
.cdm
.model
.molecular
.DnaSample
;
28 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
29 import eu
.etaxonomy
.cdm
.model
.molecular
.SingleRead
;
30 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivedUnit
;
31 import eu
.etaxonomy
.cdm
.model
.occurrence
.FieldUnit
;
32 import eu
.etaxonomy
.cdm
.model
.occurrence
.GatheringEvent
;
33 import eu
.etaxonomy
.cdm
.model
.occurrence
.MediaSpecimen
;
34 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationBase
;
35 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationType
;
36 import eu
.etaxonomy
.taxeditor
.model
.ImageResources
;
37 import eu
.etaxonomy
.taxeditor
.store
.CdmStore
;
40 * Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
42 * <b>Note:</b> If you use this label provider you need to assure that you
43 * created a {@link ConversationHolder} resp. have an open session because
44 * the labels are generated from various fields of the derivate hierarchy which
45 * are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
46 * Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
48 public class DerivateLabelProvider
extends ColumnLabelProvider
{
50 private static final String NO_SAMPLE_DESIGNATION
= "[no sample designation]";
52 private Set
<SingleRead
> multiLinkSingleReads
;
54 private ConversationHolder conversation
;
56 private static DefinedTerm photoTerm
= null;
57 private static DefinedTerm drawingTerm
= null;
58 private static DefinedTerm specimenScanTerm
= null;
59 private static DefinedTerm detailImageTerm
= null;
60 private static DefinedTerm sampleDesignationTerm
= null;
62 //FIXME: move static term getters to new singleton utility class
63 private static void initializeTerms() {
64 List
<DefinedTerm
> preferredTerms
= CdmStore
.getTermManager().getPreferredTerms(DefinedTerm
.class);
65 for (DefinedTerm definedTerm
: preferredTerms
) {
66 if(definedTerm
.getUuid().equals(UUID
.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
67 photoTerm
= definedTerm
;
69 else if(definedTerm
.getUuid().equals(UUID
.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
70 drawingTerm
= definedTerm
;
72 else if(definedTerm
.getUuid().equals(UUID
.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
73 specimenScanTerm
= definedTerm
;
75 else if(definedTerm
.getUuid().equals(UUID
.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
76 detailImageTerm
= definedTerm
;
78 else if(definedTerm
.getUuid().equals(UUID
.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
79 sampleDesignationTerm
= definedTerm
;
84 public static DefinedTerm
getLivingPlantPhotoTerm(){
91 public static DefinedTerm
getArtworkTerm(){
92 if(drawingTerm
==null){
98 public static DefinedTerm
getSpecimenScanTerm(){
99 if(specimenScanTerm
==null){
102 return specimenScanTerm
;
105 public static DefinedTerm
getDetailImageTerm(){
106 if(detailImageTerm
==null){
109 return detailImageTerm
;
112 public static DefinedTerm
getSampleDesignationTerm(){
113 if(sampleDesignationTerm
==null){
116 return sampleDesignationTerm
;
122 public String
getText(Object element
) {
123 return getDerivateText(element
);
128 public String
getToolTipText(Object element
) {
129 return getDerivateText(element
);
133 * @param conversation the conversation to set
135 public void setConversation(ConversationHolder conversation
) {
136 this.conversation
= conversation
;
139 public String
getDerivateText(Object element
){
140 return getDerivateText(element
, conversation
);
143 public static String
getDerivateText(Object element
, ConversationHolder conversation
){
144 //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
145 TreeNode parentNode
= null;
146 TreeNode node
= null;
147 Object derivate
= element
;
148 if(element
instanceof TreeNode
){
149 node
= (TreeNode
) element
;
150 parentNode
= node
.getParent();
151 //unwrap specimen from TreeNode
152 derivate
= node
.getValue();
157 final String emptyString
= "";
158 final String separator
= " ";
160 String label
= emptyString
;
163 if(derivate
instanceof FieldUnit
){
164 FieldUnit fieldUnit
= (FieldUnit
)derivate
;
165 if(fieldUnit
.getGatheringEvent()!=null){
166 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
167 if(CdmStore
.getService(IOccurrenceService
.class).exists(fieldUnit
.getUuid())){
168 fieldUnit
= (FieldUnit
) CdmStore
.getService(IOccurrenceService
.class).load(fieldUnit
.getUuid());
169 gatheringEvent
= fieldUnit
.getGatheringEvent();
171 label
+= gatheringEvent
.getCountry()!=null?gatheringEvent
.getCountry().getLabel()+separator
:emptyString
;
172 label
+= gatheringEvent
.getLocality()!=null?gatheringEvent
.getLocality().getText()+separator
:emptyString
;
173 label
+= gatheringEvent
.getGatheringDate()!=null?gatheringEvent
.getGatheringDate()+separator
:emptyString
;
174 label
+= gatheringEvent
.getCollector()!=null?gatheringEvent
.getCollector()+separator
:emptyString
;
176 label
+= fieldUnit
.getFieldNumber()!=null?fieldUnit
.getFieldNumber():emptyString
;
179 else if(derivate
instanceof MediaSpecimen
){
180 MediaSpecimen mediaSpecimen
= (MediaSpecimen
)derivate
;
181 if(mediaSpecimen
.getMediaSpecimen()!=null){
182 label
+= mediaSpecimen
.getMediaSpecimen().getTitle()!=null?mediaSpecimen
.getMediaSpecimen().getTitle().getText()+separator
:"[no motif]";
183 label
+= mediaSpecimen
.getMediaSpecimen().getArtist()!=null?mediaSpecimen
.getMediaSpecimen().getArtist()+separator
:emptyString
;
185 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= mediaSpecimen
.getCollection();
186 if(collection
!=null){
187 label
+= collection
.getName()!=null?collection
.getName()+" ":emptyString
;
188 label
+= collection
.getCode()!=null?
"("+collection
.getCode()+")"+separator
:emptyString
;
190 label
+= mediaSpecimen
.getAccessionNumber()!=null?mediaSpecimen
.getAccessionNumber()+separator
:emptyString
;
191 label
+= mediaSpecimen
.getBarcode()!=null?mediaSpecimen
.getBarcode()+separator
:emptyString
;
193 //TissueSample + DnaSample
194 else if(derivate
instanceof DnaSample
){
195 DnaSample dnaSample
= (DnaSample
)derivate
;
196 if(((DnaSample
) derivate
).getRecordBasis()==SpecimenOrObservationType
.DnaSample
){
197 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(dnaSample
);
198 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
199 label
+= currentSampleDesignation
.getIdentifier()+separator
;
202 label
+= NO_SAMPLE_DESIGNATION
+separator
;
205 else if(((DnaSample
) derivate
).getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
206 if(dnaSample
.getKindOfUnit()!=null){
207 label
+= dnaSample
.getKindOfUnit()+separator
;
209 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(dnaSample
);
210 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
211 label
+= currentSampleDesignation
.getIdentifier()+separator
;
214 label
+= NO_SAMPLE_DESIGNATION
+separator
;
219 //DerivedUnit + TissueSample
220 else if(derivate
instanceof DerivedUnit
){
221 DerivedUnit derivedUnit
= (DerivedUnit
)derivate
;
222 if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
223 java
.util
.Collection
<FieldUnit
> fieldUnits
= CdmStore
.getService(IOccurrenceService
.class).getFieldUnits(derivedUnit
.getUuid());
224 if(fieldUnits
!=null && !fieldUnits
.isEmpty()){
225 FieldUnit fieldUnit
= fieldUnits
.iterator().next();
226 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
227 // gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
228 if(gatheringEvent
!=null){
229 label
+= gatheringEvent
.getCollector()!=null?gatheringEvent
.getCollector()+separator
:emptyString
;
231 label
+= fieldUnit
.getFieldNumber()!=null?fieldUnit
.getFieldNumber()+separator
:emptyString
;
233 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= derivedUnit
.getCollection();
234 if(collection
!=null){
235 label
+= collection
.getCode()!=null?
"("+collection
.getCode()+")"+separator
:emptyString
;
237 String mostSignificantIdentifier
= CdmStore
.getService(IOccurrenceService
.class).getMostSignificantIdentifier(derivedUnit
);
238 label
+= mostSignificantIdentifier
!=null?mostSignificantIdentifier
+separator
:emptyString
;
240 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
241 //TissueSample should only be created by using it's own class
242 //in future using only one class with different SpecimenOrObservationTypes is desired
243 // label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
247 else if(derivate
instanceof Sequence
){
248 Sequence sequence
= (Sequence
)derivate
;
249 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(sequence
);
250 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
251 label
+= currentSampleDesignation
.getIdentifier()+separator
;
254 label
+= NO_SAMPLE_DESIGNATION
+separator
;
256 label
+= sequence
.getDnaMarker()!=null?sequence
.getDnaMarker():emptyString
;
259 else if(derivate
instanceof SingleRead
){
260 SingleRead singleRead
= (SingleRead
)derivate
;
261 if(parentNode
!=null && parentNode
.getValue() instanceof Sequence
){
262 Sequence sequence
= (Sequence
) parentNode
.getValue();
263 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(sequence
);
264 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
265 label
= currentSampleDesignation
.getIdentifier()+separator
;
268 label
+= NO_SAMPLE_DESIGNATION
+separator
;
270 label
+= singleRead
.getPrimer()!=null?singleRead
.getPrimer().getLabel()+separator
:emptyString
;
271 if(sequence
!=null && sequence
.getDnaMarker()!=null){
272 label
+= sequence
.getDnaMarker()+separator
;
274 if(singleRead
.getAmplificationResult()!=null && singleRead
.getAmplificationResult().getAmplification()!=null){
275 label
+= singleRead
.getAmplificationResult().getAmplification().getLabelCache()+separator
;
280 else if(derivate
instanceof SpecimenOrObservationBase
){
281 SpecimenOrObservationBase
<?
> specimen
= (SpecimenOrObservationBase
<?
>) derivate
;
282 SpecimenOrObservationType type
= specimen
.getRecordBasis();
283 return specimen
.getTitleCache() + (type
!=null?
" ["+type
.toString()+"]":emptyString
);
286 label
= derivate
.toString();
289 else if(label
.endsWith(separator
)){
290 label
= label
.substring(0, label
.length()-separator
.length());
296 * @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object)
299 public Image
getImage(Object element
) {
300 if(element
instanceof TreeNode
){
301 element
= ((TreeNode
) element
).getValue();
303 if(element
instanceof CdmBase
){
304 CdmBase cdmBase
= (CdmBase
)element
;
305 boolean hasCharacterData
= false;
306 if(cdmBase
.isInstanceOf(SpecimenOrObservationBase
.class)){
307 SpecimenOrObservationBase
<?
> specimen
= HibernateProxyHelper
.deproxy(cdmBase
, SpecimenOrObservationBase
.class);
308 if(!CdmStore
.getService(IOccurrenceService
.class).getCharacterDataForSpecimen(specimen
.getUuid()).isEmpty()){
309 hasCharacterData
= true;
312 if(cdmBase
.isInstanceOf(FieldUnit
.class)){
313 return hasCharacterData?ImageResources
.getImage(ImageResources
.FIELD_UNIT_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.FIELD_UNIT
);
315 else if(cdmBase
.isInstanceOf(DerivedUnit
.class)){
316 DerivedUnit derivedUnit
= HibernateProxyHelper
.deproxy(element
, DerivedUnit
.class);
317 if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.FieldUnit
){
318 return hasCharacterData?ImageResources
.getImage(ImageResources
.FIELD_UNIT_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.FIELD_UNIT
);
320 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.DnaSample
){
321 return hasCharacterData?ImageResources
.getImage(ImageResources
.DNA_SAMPLE_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.DNA_SAMPLE_DERIVATE
);
323 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
324 return hasCharacterData?ImageResources
.getImage(ImageResources
.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.TISSUE_SAMPLE_DERIVATE
);
326 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
327 return hasCharacterData?ImageResources
.getImage(ImageResources
.SPECIMEN_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.SPECIMEN_DERIVATE
);
329 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.Media
){
330 if(derivedUnit
.getKindOfUnit()!=null){
331 if(derivedUnit
.getKindOfUnit().equals(getArtworkTerm())){
332 return hasCharacterData?ImageResources
.getImage(ImageResources
.ARTWORK_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.ARTWORK_DERIVATE
);
334 else if(derivedUnit
.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
335 return hasCharacterData?ImageResources
.getImage(ImageResources
.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.LIVING_PLANT_PHOTO_DERIVATE
);
337 else if(derivedUnit
.getKindOfUnit().equals(getSpecimenScanTerm())){
338 return hasCharacterData?ImageResources
.getImage(ImageResources
.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.SPECIMEN_SCAN_DERIVATE
);
340 else if(derivedUnit
.getKindOfUnit().equals(getDetailImageTerm())){
341 return hasCharacterData?ImageResources
.getImage(ImageResources
.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA
):ImageResources
.getImage(ImageResources
.DETAIL_IMAGE_DERIVATE
);
346 else if(cdmBase
.isInstanceOf(Sequence
.class)){
347 return ImageResources
.getImage(ImageResources
.SEQUENCE_DERIVATE
);
350 else if(cdmBase
.isInstanceOf(SingleRead
.class)){
351 if(multiLinkSingleReads
.contains(element
)){
352 return ImageResources
.getImage(ImageResources
.SINGLE_READ_DERIVATE_MULTILINK
);
355 return ImageResources
.getImage(ImageResources
.SINGLE_READ_DERIVATE
);
359 return super.getImage(element
);
362 public static Identifier
<DnaSample
> getCurrentSampleDesignation(CdmBase entity
) {
363 if(entity
.isInstanceOf(DnaSample
.class)){
364 DnaSample dnaSample
= HibernateProxyHelper
.deproxy(entity
, DnaSample
.class);
365 for (Identifier
<DnaSample
> identifier
: dnaSample
.getIdentifiers()) {
366 if(identifier
.getType()!=null && identifier
.getType().equals(DerivateLabelProvider
.getSampleDesignationTerm())){
367 //first sample designation is the current
372 else if(entity
.isInstanceOf(Sequence
.class)){
373 Sequence sequence
= HibernateProxyHelper
.deproxy(entity
, Sequence
.class);
374 if(sequence
.getDnaSample()!=null){
375 return getCurrentSampleDesignation(sequence
.getDnaSample());
382 * @param multiLinkSingleReads2
384 public void setMultiLinkSingleReads(Set
<SingleRead
> multiLinkSingleReads
) {
385 this.multiLinkSingleReads
= multiLinkSingleReads
;