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
.model
.common
.CdmBase
;
24 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTerm
;
25 import eu
.etaxonomy
.cdm
.model
.common
.Identifier
;
26 import eu
.etaxonomy
.cdm
.model
.molecular
.DnaSample
;
27 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
28 import eu
.etaxonomy
.cdm
.model
.molecular
.SingleRead
;
29 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivedUnit
;
30 import eu
.etaxonomy
.cdm
.model
.occurrence
.FieldUnit
;
31 import eu
.etaxonomy
.cdm
.model
.occurrence
.GatheringEvent
;
32 import eu
.etaxonomy
.cdm
.model
.occurrence
.MediaSpecimen
;
33 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationBase
;
34 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationType
;
35 import eu
.etaxonomy
.taxeditor
.model
.ImageResources
;
36 import eu
.etaxonomy
.taxeditor
.store
.CdmStore
;
39 * Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
41 * <b>Note:</b> If you use this label provider you need to assure that you
42 * created a {@link ConversationHolder} resp. have an open session because
43 * the labels are generated from various fields of the derivate hierarchy which
44 * are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
45 * Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
47 public class DerivateLabelProvider
extends ColumnLabelProvider
{
49 private static final String NO_SAMPLE_DESIGNATION
= "[no sample designation]";
51 private Set
<SingleRead
> multiLinkSingleReads
;
53 private ConversationHolder conversation
;
55 private static DefinedTerm photoTerm
= null;
56 private static DefinedTerm drawingTerm
= null;
57 private static DefinedTerm specimenScanTerm
= null;
58 private static DefinedTerm detailImageTerm
= null;
59 private static DefinedTerm sampleDesignationTerm
= null;
61 //FIXME: move static term getters to new singleton utility class
62 private static void initializeTerms() {
63 List
<DefinedTerm
> preferredTerms
= CdmStore
.getTermManager().getPreferredTerms(DefinedTerm
.class);
64 for (DefinedTerm definedTerm
: preferredTerms
) {
65 if(definedTerm
.getUuid().equals(UUID
.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
66 photoTerm
= definedTerm
;
68 else if(definedTerm
.getUuid().equals(UUID
.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
69 drawingTerm
= definedTerm
;
71 else if(definedTerm
.getUuid().equals(UUID
.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
72 specimenScanTerm
= definedTerm
;
74 else if(definedTerm
.getUuid().equals(UUID
.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
75 detailImageTerm
= definedTerm
;
77 else if(definedTerm
.getUuid().equals(UUID
.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
78 sampleDesignationTerm
= definedTerm
;
83 public static DefinedTerm
getLivingPlantPhotoTerm(){
90 public static DefinedTerm
getArtworkTerm(){
91 if(drawingTerm
==null){
97 public static DefinedTerm
getSpecimenScanTerm(){
98 if(specimenScanTerm
==null){
101 return specimenScanTerm
;
104 public static DefinedTerm
getDetailImageTerm(){
105 if(detailImageTerm
==null){
108 return detailImageTerm
;
111 public static DefinedTerm
getSampleDesignationTerm(){
112 if(sampleDesignationTerm
==null){
115 return sampleDesignationTerm
;
121 public String
getText(Object element
) {
122 return getDerivateText(element
);
127 public String
getToolTipText(Object element
) {
128 return getDerivateText(element
);
132 * @param conversation the conversation to set
134 public void setConversation(ConversationHolder conversation
) {
135 this.conversation
= conversation
;
138 public String
getDerivateText(Object element
){
139 return getDerivateText(element
, conversation
);
142 public static String
getDerivateText(Object element
, ConversationHolder conversation
){
143 //TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
144 TreeNode parentNode
= null;
145 TreeNode node
= null;
146 Object derivate
= element
;
147 if(element
instanceof TreeNode
){
148 node
= (TreeNode
) element
;
149 parentNode
= node
.getParent();
150 //unwrap specimen from TreeNode
151 derivate
= node
.getValue();
156 final String emptyString
= "";
157 final String separator
= ", ";
159 String label
= emptyString
;
162 if(derivate
instanceof FieldUnit
){
163 FieldUnit fieldUnit
= (FieldUnit
)derivate
;
164 if(fieldUnit
.getGatheringEvent()!=null){
165 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
166 if(CdmStore
.getService(IOccurrenceService
.class).exists(fieldUnit
.getUuid()) && !conversation
.getSession().contains(gatheringEvent
)){
167 fieldUnit
= (FieldUnit
) CdmStore
.getService(IOccurrenceService
.class).load(fieldUnit
.getUuid());
168 gatheringEvent
= fieldUnit
.getGatheringEvent();
170 label
+= gatheringEvent
.getCountry()!=null?gatheringEvent
.getCountry().getLabel()+separator
:emptyString
;
171 label
+= gatheringEvent
.getLocality()!=null?gatheringEvent
.getLocality().getText()+separator
:emptyString
;
172 label
+= gatheringEvent
.getGatheringDate()!=null?gatheringEvent
.getGatheringDate()+separator
:emptyString
;
173 label
+= gatheringEvent
.getCollector()!=null?gatheringEvent
.getCollector()+separator
:emptyString
;
175 label
+= fieldUnit
.getFieldNumber()!=null?fieldUnit
.getFieldNumber():emptyString
;
178 else if(derivate
instanceof MediaSpecimen
){
179 MediaSpecimen mediaSpecimen
= (MediaSpecimen
)derivate
;
180 if(mediaSpecimen
.getMediaSpecimen()!=null){
181 label
+= mediaSpecimen
.getMediaSpecimen().getTitle()!=null?mediaSpecimen
.getMediaSpecimen().getTitle().getText()+separator
:"[no motif]";
182 label
+= mediaSpecimen
.getMediaSpecimen().getArtist()!=null?mediaSpecimen
.getMediaSpecimen().getArtist()+separator
:emptyString
;
184 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= mediaSpecimen
.getCollection();
185 if(collection
!=null){
186 label
+= collection
.getName()!=null?collection
.getName()+" ":emptyString
;
187 label
+= collection
.getCode()!=null?
"("+collection
.getCode()+")"+separator
:emptyString
;
189 label
+= mediaSpecimen
.getAccessionNumber()!=null?mediaSpecimen
.getAccessionNumber()+separator
:emptyString
;
190 label
+= mediaSpecimen
.getBarcode()!=null?mediaSpecimen
.getBarcode()+separator
:emptyString
;
192 //TissueSample + DnaSample
193 else if(derivate
instanceof DnaSample
){
194 DnaSample dnaSample
= (DnaSample
)derivate
;
195 if(((DnaSample
) derivate
).getRecordBasis()==SpecimenOrObservationType
.DnaSample
){
196 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(dnaSample
);
197 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
198 label
+= currentSampleDesignation
.getIdentifier()+separator
;
201 label
+= NO_SAMPLE_DESIGNATION
+separator
;
204 else if(((DnaSample
) derivate
).getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
205 if(dnaSample
.getKindOfUnit()!=null){
206 label
+= dnaSample
.getKindOfUnit()+separator
;
208 Identifier
<DnaSample
> currentSampleDesignation
= getCurrentSampleDesignation(dnaSample
);
209 if(currentSampleDesignation
!=null && currentSampleDesignation
.getIdentifier()!=null){
210 label
+= currentSampleDesignation
.getIdentifier()+separator
;
213 label
+= NO_SAMPLE_DESIGNATION
+separator
;
218 //DerivedUnit + TissueSample
219 else if(derivate
instanceof DerivedUnit
){
220 DerivedUnit derivedUnit
= (DerivedUnit
)derivate
;
221 if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
222 java
.util
.Collection
<FieldUnit
> fieldUnits
= CdmStore
.getService(IOccurrenceService
.class).getFieldUnits(derivedUnit
.getUuid());
223 if(fieldUnits
!=null && !fieldUnits
.isEmpty()){
224 FieldUnit fieldUnit
= fieldUnits
.iterator().next();
225 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
226 // gatheringEvent = HibernateProxyHelper.deproxy(gatheringEvent, GatheringEvent.class);
227 if(gatheringEvent
!=null){
228 label
+= gatheringEvent
.getCollector()!=null?gatheringEvent
.getCollector()+separator
:emptyString
;
230 label
+= fieldUnit
.getFieldNumber()!=null?fieldUnit
.getFieldNumber()+separator
:emptyString
;
232 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= derivedUnit
.getCollection();
233 if(collection
!=null){
234 label
+= collection
.getName()!=null?collection
.getName()+" ":emptyString
;
235 label
+= collection
.getCode()!=null?
"("+collection
.getCode()+"), ":emptyString
;
237 label
+= derivedUnit
.getAccessionNumber()!=null?derivedUnit
.getAccessionNumber()+separator
:emptyString
;
238 label
+= derivedUnit
.getBarcode()!=null?derivedUnit
.getBarcode():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 FieldUnit
){
304 return ImageResources
.getImage(ImageResources
.FIELD_UNIT
);
306 else if(element
instanceof DerivedUnit
){
307 DerivedUnit derivedUnit
= (DerivedUnit
)element
;
308 if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.FieldUnit
){
309 return ImageResources
.getImage(ImageResources
.FIELD_UNIT
);
311 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.DnaSample
){
312 return ImageResources
.getImage(ImageResources
.DNA_SAMPLE_DERIVATE
);
314 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.TissueSample
){
315 return ImageResources
.getImage(ImageResources
.TISSUE_SAMPLE_DERIVATE
);
317 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
318 return ImageResources
.getImage(ImageResources
.SPECIMEN_DERIVATE
);
320 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.Media
){
321 if(derivedUnit
.getKindOfUnit()!=null){
322 if(derivedUnit
.getKindOfUnit().equals(getArtworkTerm())){
323 return ImageResources
.getImage(ImageResources
.ARTWORK_DERIVATE
);
325 else if(derivedUnit
.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
326 return ImageResources
.getImage(ImageResources
.LIVING_PLANT_PHOTO_DERIVATE
);
328 else if(derivedUnit
.getKindOfUnit().equals(getSpecimenScanTerm())){
329 return ImageResources
.getImage(ImageResources
.SPECIMEN_SCAN_DERIVATE
);
331 else if(derivedUnit
.getKindOfUnit().equals(getDetailImageTerm())){
332 return ImageResources
.getImage(ImageResources
.DETAIL_IMAGE_DERIVATE
);
337 else if(element
instanceof Sequence
){
338 return ImageResources
.getImage(ImageResources
.SEQUENCE_DERIVATE
);
341 else if(element
instanceof SingleRead
){
342 if(multiLinkSingleReads
.contains(element
)){
343 return ImageResources
.getImage(ImageResources
.SINGLE_READ_DERIVATE_MULTILINK
);
346 return ImageResources
.getImage(ImageResources
.SINGLE_READ_DERIVATE
);
349 return super.getImage(element
);
352 public static Identifier
<DnaSample
> getCurrentSampleDesignation(CdmBase entity
) {
353 if(entity
instanceof DnaSample
){
354 DnaSample dnaSample
= (DnaSample
)entity
;
355 for (Identifier
<DnaSample
> identifier
: dnaSample
.getIdentifiers()) {
356 if(identifier
.getType()!=null && identifier
.getType().equals(DerivateLabelProvider
.getSampleDesignationTerm())){
357 //first sample designation is the current
362 else if(entity
instanceof Sequence
){
363 Sequence sequence
= (Sequence
)entity
;
364 if(sequence
.getDnaSample()!=null){
365 return getCurrentSampleDesignation(sequence
.getDnaSample());
372 * @param multiLinkSingleReads2
374 public void setMultiLinkSingleReads(Set
<SingleRead
> multiLinkSingleReads
) {
375 this.multiLinkSingleReads
= multiLinkSingleReads
;