1
|
/**
|
2
|
* Copyright (C) 2007 EDIT
|
3
|
* European Distributed Institute of Taxonomy
|
4
|
* http://www.e-taxonomy.eu
|
5
|
*
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
8
|
*/
|
9
|
|
10
|
package eu.etaxonomy.cdm.model.occurrence;
|
11
|
|
12
|
import java.util.HashMap;
|
13
|
import java.util.HashSet;
|
14
|
import java.util.Map;
|
15
|
import java.util.Set;
|
16
|
|
17
|
import javax.persistence.Entity;
|
18
|
import javax.persistence.FetchType;
|
19
|
import javax.persistence.Inheritance;
|
20
|
import javax.persistence.InheritanceType;
|
21
|
import javax.persistence.ManyToMany;
|
22
|
import javax.persistence.ManyToOne;
|
23
|
import javax.persistence.OneToMany;
|
24
|
import javax.persistence.Transient;
|
25
|
import javax.validation.constraints.Min;
|
26
|
import javax.validation.constraints.NotNull;
|
27
|
import javax.xml.bind.annotation.XmlAccessType;
|
28
|
import javax.xml.bind.annotation.XmlAccessorType;
|
29
|
import javax.xml.bind.annotation.XmlElement;
|
30
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
31
|
import javax.xml.bind.annotation.XmlIDREF;
|
32
|
import javax.xml.bind.annotation.XmlRootElement;
|
33
|
import javax.xml.bind.annotation.XmlSchemaType;
|
34
|
import javax.xml.bind.annotation.XmlType;
|
35
|
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
|
36
|
|
37
|
import org.apache.log4j.Logger;
|
38
|
import org.hibernate.annotations.Cascade;
|
39
|
import org.hibernate.annotations.CascadeType;
|
40
|
import org.hibernate.annotations.Index;
|
41
|
import org.hibernate.annotations.Table;
|
42
|
import org.hibernate.envers.Audited;
|
43
|
import org.hibernate.search.annotations.Field;
|
44
|
import org.hibernate.search.annotations.IndexedEmbedded;
|
45
|
|
46
|
import eu.etaxonomy.cdm.jaxb.MultilanguageTextAdapter;
|
47
|
import eu.etaxonomy.cdm.model.common.Language;
|
48
|
import eu.etaxonomy.cdm.model.common.LanguageString;
|
49
|
import eu.etaxonomy.cdm.model.description.DescriptionBase;
|
50
|
import eu.etaxonomy.cdm.model.description.Sex;
|
51
|
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
|
52
|
import eu.etaxonomy.cdm.model.description.Stage;
|
53
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
54
|
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
|
55
|
import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
|
56
|
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
|
57
|
|
58
|
/**
|
59
|
* type figures are observations with at least a figure object in media
|
60
|
* @author m.doering
|
61
|
* @version 1.0
|
62
|
* @created 08-Nov-2007 13:06:41
|
63
|
*/
|
64
|
@XmlAccessorType(XmlAccessType.FIELD)
|
65
|
@XmlType(name = "SpecimenOrObservationBase", propOrder = {
|
66
|
"sex",
|
67
|
"individualCount",
|
68
|
"lifeStage",
|
69
|
"description",
|
70
|
"descriptions",
|
71
|
"determinations",
|
72
|
"derivationEvents"
|
73
|
})
|
74
|
@XmlRootElement(name = "SpecimenOrObservationBase")
|
75
|
@Entity
|
76
|
@Audited
|
77
|
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
|
78
|
@Table(appliesTo="SpecimenOrObservationBase", indexes = { @Index(name = "specimenOrObservationBaseTitleCacheIndex", columnNames = { "titleCache" }) })
|
79
|
public abstract class SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy> extends IdentifiableMediaEntity<S> {
|
80
|
|
81
|
private static final Logger logger = Logger.getLogger(SpecimenOrObservationBase.class);
|
82
|
|
83
|
@XmlElementWrapper(name = "Descriptions")
|
84
|
@XmlElement(name = "Description")
|
85
|
@ManyToMany(fetch = FetchType.LAZY,mappedBy="describedSpecimenOrObservations",targetEntity=DescriptionBase.class)
|
86
|
@Cascade(CascadeType.SAVE_UPDATE)
|
87
|
@NotNull
|
88
|
private Set<DescriptionBase> descriptions = new HashSet<DescriptionBase>();
|
89
|
|
90
|
@XmlElementWrapper(name = "Determinations")
|
91
|
@XmlElement(name = "Determination")
|
92
|
@OneToMany(mappedBy="identifiedUnit")
|
93
|
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
|
94
|
@IndexedEmbedded(depth = 2)
|
95
|
@NotNull
|
96
|
private Set<DeterminationEvent> determinations = new HashSet<DeterminationEvent>();
|
97
|
|
98
|
@XmlElement(name = "Sex")
|
99
|
@XmlIDREF
|
100
|
@XmlSchemaType(name = "IDREF")
|
101
|
@ManyToOne(fetch = FetchType.LAZY)
|
102
|
private Sex sex;
|
103
|
|
104
|
@XmlElement(name = "LifeStage")
|
105
|
@XmlIDREF
|
106
|
@XmlSchemaType(name = "IDREF")
|
107
|
@ManyToOne(fetch = FetchType.LAZY)
|
108
|
private Stage lifeStage;
|
109
|
|
110
|
@XmlElement(name = "IndividualCount")
|
111
|
@Field(index=org.hibernate.search.annotations.Index.UN_TOKENIZED)
|
112
|
@Min(0)
|
113
|
private Integer individualCount;
|
114
|
|
115
|
// the verbatim description of this occurrence. Free text usable when no atomised data is available.
|
116
|
// in conjunction with titleCache which serves as the "citation" string for this object
|
117
|
@XmlElement(name = "Description")
|
118
|
@XmlJavaTypeAdapter(MultilanguageTextAdapter.class)
|
119
|
@OneToMany(fetch = FetchType.LAZY)
|
120
|
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
|
121
|
@IndexedEmbedded
|
122
|
@NotNull
|
123
|
protected Map<Language,LanguageString> description = new HashMap<Language,LanguageString>();
|
124
|
|
125
|
// events that created derivedUnits from this unit
|
126
|
@XmlElementWrapper(name = "DerivationEvents")
|
127
|
@XmlElement(name = "DerivationEvent")
|
128
|
@XmlIDREF
|
129
|
@XmlSchemaType(name = "IDREF")
|
130
|
@ManyToMany(fetch=FetchType.LAZY)
|
131
|
@Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
|
132
|
@NotNull
|
133
|
protected Set<DerivationEvent> derivationEvents = new HashSet<DerivationEvent>();
|
134
|
|
135
|
/**
|
136
|
* Constructor
|
137
|
*/
|
138
|
protected SpecimenOrObservationBase(){
|
139
|
super();
|
140
|
}
|
141
|
|
142
|
/**
|
143
|
* The descriptions this specimen or observation is part of.<BR>
|
144
|
* A specimen can not only have it's own {@link SpecimenDescription specimen description }
|
145
|
* but can also be part of a {@link TaxonDescription taxon description} or a
|
146
|
* {@link TaxonNameDescription taxon name description}.<BR>
|
147
|
* @see #getSpecimenDescriptions()
|
148
|
* @return
|
149
|
*/
|
150
|
public Set<DescriptionBase> getDescriptions() {
|
151
|
if(descriptions == null) {
|
152
|
this.descriptions = new HashSet<DescriptionBase>();
|
153
|
}
|
154
|
return this.descriptions;
|
155
|
}
|
156
|
|
157
|
/**
|
158
|
* Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
|
159
|
* @see #getDescriptions()
|
160
|
* @return
|
161
|
*/
|
162
|
public Set<SpecimenDescription> getSpecimenDescriptions() {
|
163
|
return getSpecimenDescriptions(true);
|
164
|
}
|
165
|
|
166
|
/**
|
167
|
* Returns the {@link SpecimenDescription specimen descriptions} this specimen is part of.
|
168
|
* @see #getDescriptions()
|
169
|
* @return
|
170
|
*/
|
171
|
public Set<SpecimenDescription> getSpecimenDescriptions(boolean includeImageGallery) {
|
172
|
Set<SpecimenDescription> specimenDescriptions = new HashSet<SpecimenDescription>();
|
173
|
for (DescriptionBase descriptionBase : getDescriptions()){
|
174
|
if (descriptionBase.isInstanceOf(SpecimenDescription.class)){
|
175
|
if (includeImageGallery || descriptionBase.isImageGallery() == false){
|
176
|
specimenDescriptions.add(descriptionBase.deproxy(descriptionBase, SpecimenDescription.class));
|
177
|
}
|
178
|
|
179
|
}
|
180
|
}
|
181
|
return specimenDescriptions;
|
182
|
}
|
183
|
|
184
|
/**
|
185
|
* Adds a new description to this specimen or observation
|
186
|
* @param description
|
187
|
*/
|
188
|
public void addDescription(DescriptionBase description) {
|
189
|
this.descriptions.add(description);
|
190
|
if (! description.getDescribedSpecimenOrObservations().contains(this)){
|
191
|
description.addDescribedSpecimenOrObservation(this);
|
192
|
}
|
193
|
// Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "addDescribedSpecimenOrObservation", new Class[] {SpecimenOrObservationBase.class});
|
194
|
// ReflectionUtils.makeAccessible(method);
|
195
|
// ReflectionUtils.invokeMethod(method, description, new Object[] {this});
|
196
|
}
|
197
|
|
198
|
/**
|
199
|
* Removes a specimen from a description (removes a description from this specimen)
|
200
|
* @param description
|
201
|
*/
|
202
|
public void removeDescription(DescriptionBase description) {
|
203
|
this.descriptions.remove(description);
|
204
|
if (description.getDescribedSpecimenOrObservations().contains(this)){
|
205
|
description.removeDescribedSpecimenOrObservation(this);
|
206
|
}
|
207
|
// Method method = ReflectionUtils.findMethod(SpecimenDescription.class, "removeDescribedSpecimenOrObservations", new Class[] {SpecimenOrObservationBase.class});
|
208
|
// ReflectionUtils.makeAccessible(method);
|
209
|
// ReflectionUtils.invokeMethod(method, description, new Object[] {this});
|
210
|
}
|
211
|
|
212
|
public Set<DerivationEvent> getDerivationEvents() {
|
213
|
if(derivationEvents == null) {
|
214
|
this.derivationEvents = new HashSet<DerivationEvent>();
|
215
|
}
|
216
|
return this.derivationEvents;
|
217
|
}
|
218
|
|
219
|
public void addDerivationEvent(DerivationEvent derivationEvent) {
|
220
|
if (! this.derivationEvents.contains(derivationEvent)){
|
221
|
this.derivationEvents.add(derivationEvent);
|
222
|
derivationEvent.addOriginal(this);
|
223
|
}
|
224
|
}
|
225
|
|
226
|
public void removeDerivationEvent(DerivationEvent derivationEvent) {
|
227
|
this.derivationEvents.remove(derivationEvent);
|
228
|
}
|
229
|
|
230
|
public Set<DeterminationEvent> getDeterminations() {
|
231
|
if(determinations == null) {
|
232
|
this.determinations = new HashSet<DeterminationEvent>();
|
233
|
}
|
234
|
return this.determinations;
|
235
|
}
|
236
|
|
237
|
public void addDetermination(DeterminationEvent determination) {
|
238
|
// FIXME bidirectional integrity. Use protected Determination setter
|
239
|
this.determinations.add(determination);
|
240
|
}
|
241
|
|
242
|
public void removeDetermination(DeterminationEvent determination) {
|
243
|
// FIXME bidirectional integrity. Use protected Determination setter
|
244
|
this.determinations.remove(determination);
|
245
|
}
|
246
|
|
247
|
public Sex getSex() {
|
248
|
return sex;
|
249
|
}
|
250
|
|
251
|
public void setSex(Sex sex) {
|
252
|
this.sex = sex;
|
253
|
}
|
254
|
|
255
|
public Stage getLifeStage() {
|
256
|
return lifeStage;
|
257
|
}
|
258
|
|
259
|
public void setLifeStage(Stage lifeStage) {
|
260
|
this.lifeStage = lifeStage;
|
261
|
}
|
262
|
|
263
|
@Override
|
264
|
public String generateTitle(){
|
265
|
return getCacheStrategy().getTitleCache(this);
|
266
|
}
|
267
|
|
268
|
public Integer getIndividualCount() {
|
269
|
return individualCount;
|
270
|
}
|
271
|
|
272
|
public void setIndividualCount(Integer individualCount) {
|
273
|
this.individualCount = individualCount;
|
274
|
}
|
275
|
|
276
|
public Map<Language,LanguageString> getDefinition(){
|
277
|
return this.description;
|
278
|
}
|
279
|
|
280
|
public void addDefinition(LanguageString description){
|
281
|
this.description.put(description.getLanguage(),description);
|
282
|
}
|
283
|
|
284
|
public void addDefinition(String text, Language language){
|
285
|
this.description.put(language, LanguageString.NewInstance(text, language));
|
286
|
}
|
287
|
public void removeDefinition(Language lang){
|
288
|
this.description.remove(lang);
|
289
|
}
|
290
|
|
291
|
/**
|
292
|
* for derived units get the single next higher parental/original unit.
|
293
|
* If multiple original units exist throw error
|
294
|
* @return
|
295
|
*/
|
296
|
@Transient
|
297
|
public SpecimenOrObservationBase getOriginalUnit(){
|
298
|
logger.warn("GetOriginalUnit not yet implemented");
|
299
|
return null;
|
300
|
}
|
301
|
|
302
|
@Transient
|
303
|
public abstract GatheringEvent getGatheringEvent();
|
304
|
|
305
|
|
306
|
//******************** CLONE **********************************************/
|
307
|
|
308
|
/* (non-Javadoc)
|
309
|
* @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
|
310
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()
|
311
|
* @see java.lang.Object#clone()
|
312
|
*/
|
313
|
@Override
|
314
|
public Object clone() throws CloneNotSupportedException {
|
315
|
SpecimenOrObservationBase result = null;
|
316
|
result = (SpecimenOrObservationBase)super.clone();
|
317
|
|
318
|
//defininion (description, languageString)
|
319
|
result.description = new HashMap<Language,LanguageString>();
|
320
|
for(LanguageString languageString : this.description.values()) {
|
321
|
LanguageString newLanguageString = (LanguageString)languageString.clone();
|
322
|
result.addDefinition(newLanguageString);
|
323
|
}
|
324
|
|
325
|
//sex
|
326
|
result.setSex(this.sex);
|
327
|
//life stage
|
328
|
result.setLifeStage(this.lifeStage);
|
329
|
|
330
|
//Descriptions
|
331
|
for(DescriptionBase description : this.descriptions) {
|
332
|
result.addDescription((SpecimenDescription)description);
|
333
|
}
|
334
|
|
335
|
//DeterminationEvent FIXME should clone() the determination
|
336
|
// as the relationship is OneToMany
|
337
|
for(DeterminationEvent determination : this.determinations) {
|
338
|
result.addDetermination(determination);
|
339
|
}
|
340
|
|
341
|
//DerivationEvent
|
342
|
for(DerivationEvent derivationEvent : this.derivationEvents) {
|
343
|
result.addDerivationEvent(derivationEvent);
|
344
|
}
|
345
|
|
346
|
//no changes to: individualCount
|
347
|
return result;
|
348
|
}
|
349
|
}
|