|
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.io.sdd;
|
|
11
|
|
|
12
|
import java.util.ArrayList;
|
|
13
|
import java.util.Collection;
|
|
14
|
import java.util.HashSet;
|
|
15
|
import java.util.List;
|
|
16
|
import java.util.Set;
|
|
17
|
|
|
18
|
import javassist.compiler.ast.Keyword;
|
|
19
|
|
|
20
|
import javax.xml.bind.annotation.XmlAccessType;
|
|
21
|
import javax.xml.bind.annotation.XmlAccessorType;
|
|
22
|
import javax.xml.bind.annotation.XmlElement;
|
|
23
|
import javax.xml.bind.annotation.XmlElementWrapper;
|
|
24
|
import javax.xml.bind.annotation.XmlElements;
|
|
25
|
import javax.xml.bind.annotation.XmlRootElement;
|
|
26
|
import javax.xml.bind.annotation.XmlType;
|
|
27
|
|
|
28
|
import eu.etaxonomy.cdm.model.agent.Address;
|
|
29
|
import eu.etaxonomy.cdm.model.agent.AgentBase;
|
|
30
|
import eu.etaxonomy.cdm.model.agent.Contact;
|
|
31
|
import eu.etaxonomy.cdm.model.agent.Institution;
|
|
32
|
import eu.etaxonomy.cdm.model.agent.InstitutionType;
|
|
33
|
import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
|
|
34
|
import eu.etaxonomy.cdm.model.agent.Person;
|
|
35
|
import eu.etaxonomy.cdm.model.agent.Team;
|
|
36
|
import eu.etaxonomy.cdm.model.common.AnnotationType;
|
|
37
|
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
|
|
38
|
import eu.etaxonomy.cdm.model.common.ExtensionType;
|
|
39
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
40
|
import eu.etaxonomy.cdm.model.common.LanguageString;
|
|
41
|
import eu.etaxonomy.cdm.model.common.LanguageStringBase;
|
|
42
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
|
43
|
import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
|
|
44
|
import eu.etaxonomy.cdm.model.common.RelationshipBase;
|
|
45
|
import eu.etaxonomy.cdm.model.common.Representation;
|
|
46
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
|
47
|
import eu.etaxonomy.cdm.model.common.VersionableEntity;
|
|
48
|
import eu.etaxonomy.cdm.model.description.AbsenceTerm;
|
|
49
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
50
|
import eu.etaxonomy.cdm.model.description.FeatureNode;
|
|
51
|
import eu.etaxonomy.cdm.model.description.FeatureTree;
|
|
52
|
import eu.etaxonomy.cdm.model.description.MeasurementUnit;
|
|
53
|
import eu.etaxonomy.cdm.model.description.Modifier;
|
|
54
|
import eu.etaxonomy.cdm.model.description.PresenceTerm;
|
|
55
|
import eu.etaxonomy.cdm.model.description.Scope;
|
|
56
|
import eu.etaxonomy.cdm.model.description.Sex;
|
|
57
|
import eu.etaxonomy.cdm.model.description.Stage;
|
|
58
|
import eu.etaxonomy.cdm.model.description.State;
|
|
59
|
import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
|
|
60
|
import eu.etaxonomy.cdm.model.description.TextFormat;
|
|
61
|
import eu.etaxonomy.cdm.model.location.Continent;
|
|
62
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
63
|
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
|
|
64
|
import eu.etaxonomy.cdm.model.location.NamedAreaType;
|
|
65
|
import eu.etaxonomy.cdm.model.location.ReferenceSystem;
|
|
66
|
import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
|
|
67
|
import eu.etaxonomy.cdm.model.media.RightsTerm;
|
|
68
|
import eu.etaxonomy.cdm.model.molecular.DnaSample;
|
|
69
|
import eu.etaxonomy.cdm.model.name.BacterialName;
|
|
70
|
import eu.etaxonomy.cdm.model.name.BotanicalName;
|
|
71
|
import eu.etaxonomy.cdm.model.name.CultivarPlantName;
|
|
72
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
|
73
|
import eu.etaxonomy.cdm.model.name.HybridRelationship;
|
|
74
|
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
|
|
75
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
|
76
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
|
77
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
|
|
78
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
|
79
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
|
|
80
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
|
|
81
|
import eu.etaxonomy.cdm.model.name.Rank;
|
|
82
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
|
|
83
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
|
|
84
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
85
|
import eu.etaxonomy.cdm.model.name.ViralName;
|
|
86
|
import eu.etaxonomy.cdm.model.name.ZoologicalName;
|
|
87
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
|
|
88
|
import eu.etaxonomy.cdm.model.occurrence.DeterminationModifier;
|
|
89
|
import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
|
|
90
|
import eu.etaxonomy.cdm.model.occurrence.Fossil;
|
|
91
|
import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
|
|
92
|
import eu.etaxonomy.cdm.model.occurrence.Observation;
|
|
93
|
import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
|
|
94
|
import eu.etaxonomy.cdm.model.occurrence.Specimen;
|
|
95
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
|
|
96
|
/*import eu.etaxonomy.cdm.model.reference.Article;
|
|
97
|
import eu.etaxonomy.cdm.model.reference.Book;
|
|
98
|
import eu.etaxonomy.cdm.model.reference.BookSection;
|
|
99
|
import eu.etaxonomy.cdm.model.reference.CdDvd;
|
|
100
|
import eu.etaxonomy.cdm.model.reference.Database;
|
|
101
|
import eu.etaxonomy.cdm.model.reference.Generic;
|
|
102
|
import eu.etaxonomy.cdm.model.reference.InProceedings;
|
|
103
|
import eu.etaxonomy.cdm.model.reference.Journal;
|
|
104
|
import eu.etaxonomy.cdm.model.reference.Map;
|
|
105
|
import eu.etaxonomy.cdm.model.reference.Patent;
|
|
106
|
import eu.etaxonomy.cdm.model.reference.PersonalCommunication;
|
|
107
|
import eu.etaxonomy.cdm.model.reference.PrintSeries;
|
|
108
|
import eu.etaxonomy.cdm.model.reference.Proceedings;*/
|
|
109
|
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
|
|
110
|
/*import eu.etaxonomy.cdm.model.reference.Report;
|
|
111
|
import eu.etaxonomy.cdm.model.reference.Thesis;
|
|
112
|
import eu.etaxonomy.cdm.model.reference.WebPage;*/
|
|
113
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
114
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
|
|
115
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
116
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
117
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
118
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
|
119
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
|
120
|
|
|
121
|
/**
|
|
122
|
* @author a.babadshanjan
|
|
123
|
*/
|
|
124
|
@XmlAccessorType(XmlAccessType.FIELD)
|
|
125
|
@XmlType(name = "", propOrder = {
|
|
126
|
"terms",
|
|
127
|
"termVocabularies",
|
|
128
|
"agents",
|
|
129
|
"agentData",
|
|
130
|
"occurrences",
|
|
131
|
"references",
|
|
132
|
"referencedEntities",
|
|
133
|
"featureData",
|
|
134
|
"languageData",
|
|
135
|
"taxonomicNames",
|
|
136
|
"homotypicalGroups",
|
|
137
|
"taxa",
|
|
138
|
"synonyms",
|
|
139
|
"relationships",
|
|
140
|
"media"
|
|
141
|
})
|
|
142
|
@XmlRootElement(name = "DataSet", namespace = "http://etaxonomy.eu/cdm/model/1.0")
|
|
143
|
public class SDDDataSet {
|
|
144
|
|
|
145
|
// Some fields are of type List and some are of type Set.
|
|
146
|
// This is mainly because
|
|
147
|
// the service classes return lists, i.e.
|
|
148
|
// TaxonServiceImpl.getRootTaxa() returns List<Taxon>
|
|
149
|
// and the Taxon methods return sets, i.e.
|
|
150
|
// Taxon.getTaxonomicChildren() returns Set<Taxon>.
|
|
151
|
|
|
152
|
@XmlElementWrapper(name = "Agents")
|
|
153
|
@XmlElements({
|
|
154
|
@XmlElement(name = "Team", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Team.class),
|
|
155
|
@XmlElement(name = "Institution", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Institution.class),
|
|
156
|
@XmlElement(name = "Person", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Person.class)
|
|
157
|
})
|
|
158
|
protected List<? extends AgentBase> agents;
|
|
159
|
|
|
160
|
@XmlElementWrapper(name = "AgentData")
|
|
161
|
@XmlElements({
|
|
162
|
@XmlElement(name = "Address", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Address.class),
|
|
163
|
@XmlElement(name = "Contact", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Contact.class),
|
|
164
|
@XmlElement(name = "InstitutionalMembership", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionalMembership.class)
|
|
165
|
})
|
|
166
|
protected List<VersionableEntity> agentData;
|
|
167
|
|
|
168
|
@XmlElementWrapper(name = "FeatureData")
|
|
169
|
@XmlElements({
|
|
170
|
@XmlElement(name = "FeatureNode", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureNode.class),
|
|
171
|
@XmlElement(name = "FeatureTree", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = FeatureTree.class)
|
|
172
|
})
|
|
173
|
// protected List<VersionableEntity> featureData;
|
|
174
|
protected List<VersionableEntity> featureData;
|
|
175
|
|
|
176
|
@XmlElementWrapper(name = "LanguageData")
|
|
177
|
@XmlElements({
|
|
178
|
@XmlElement(name = "Representation", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Representation.class),
|
|
179
|
@XmlElement(name = "LanguageString", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = LanguageString.class)
|
|
180
|
})
|
|
181
|
protected List<LanguageStringBase> languageData;
|
|
182
|
|
|
183
|
@XmlElementWrapper(name = "Terms")
|
|
184
|
@XmlElements({
|
|
185
|
@XmlElement(name = "AbsenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = AbsenceTerm.class),
|
|
186
|
@XmlElement(name = "AnnotationType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = AnnotationType.class),
|
|
187
|
@XmlElement(name = "Continent", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = Continent.class),
|
|
188
|
@XmlElement(name = "DerivationEventType", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DerivationEventType.class),
|
|
189
|
@XmlElement(name = "DeterminationModifier", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DeterminationModifier.class),
|
|
190
|
@XmlElement(name = "ExtensionType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = ExtensionType.class),
|
|
191
|
@XmlElement(name = "Feature", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Feature.class),
|
|
192
|
@XmlElement(name = "HybridRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationshipType.class),
|
|
193
|
@XmlElement(name = "InstitutionType", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionType.class),
|
|
194
|
@XmlElement(name = "Language", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Language.class),
|
|
195
|
@XmlElement(name = "MarkerType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = MarkerType.class),
|
|
196
|
@XmlElement(name = "MeasurementUnit", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = MeasurementUnit.class),
|
|
197
|
@XmlElement(name = "Modifier", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Modifier.class),
|
|
198
|
@XmlElement(name = "NamedArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
|
|
199
|
@XmlElement(name = "NamedAreaLevel", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaLevel.class),
|
|
200
|
@XmlElement(name = "NamedAreaType", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaType.class),
|
|
201
|
@XmlElement(name = "NameRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationshipType.class),
|
|
202
|
@XmlElement(name = "NomenclaturalCode", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalCode.class),
|
|
203
|
@XmlElement(name = "NomenclaturalStatusType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatusType.class),
|
|
204
|
@XmlElement(name = "PresenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = PresenceTerm.class),
|
|
205
|
@XmlElement(name = "PreservationMethod", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = PreservationMethod.class),
|
|
206
|
@XmlElement(name = "Rank", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = Rank.class),
|
|
207
|
@XmlElement(name = "ReferenceSystem", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = ReferenceSystem.class),
|
|
208
|
@XmlElement(name = "RightsTerm", namespace = "http://etaxonomy.eu/cdm/model/media/1.0", type = RightsTerm.class),
|
|
209
|
@XmlElement(name = "Scope", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Scope.class),
|
|
210
|
@XmlElement(name = "Sex", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Sex.class),
|
|
211
|
@XmlElement(name = "Stage", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Stage.class),
|
|
212
|
@XmlElement(name = "State", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = State.class),
|
|
213
|
@XmlElement(name = "StatisticalMeasure", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = StatisticalMeasure.class),
|
|
214
|
@XmlElement(name = "SynonymRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationshipType.class),
|
|
215
|
@XmlElement(name = "TaxonRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationshipType.class),
|
|
216
|
@XmlElement(name = "TextFormat", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TextFormat.class),
|
|
217
|
@XmlElement(name = "TypeDesignationStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignationStatus.class),
|
|
218
|
@XmlElement(name = "WaterbodyOrCountry", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = WaterbodyOrCountry.class)
|
|
219
|
})
|
|
220
|
protected List<DefinedTermBase> terms;
|
|
221
|
|
|
222
|
@XmlElementWrapper(name = "TermVocabularies")
|
|
223
|
@XmlElement(name = "TermVocabulary", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
|
|
224
|
protected List<TermVocabulary<DefinedTermBase>> termVocabularies;
|
|
225
|
|
|
226
|
@XmlElementWrapper(name = "Occurrences")
|
|
227
|
@XmlElements({
|
|
228
|
@XmlElement(name = "DnaSample", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DnaSample.class),
|
|
229
|
@XmlElement(name = "FieldObservation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = FieldObservation.class),
|
|
230
|
@XmlElement(name = "Fossil", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Fossil.class),
|
|
231
|
@XmlElement(name = "LivingBeing", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = LivingBeing.class),
|
|
232
|
@XmlElement(name = "Observation", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Observation.class),
|
|
233
|
@XmlElement(name = "Specimen", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = Specimen.class)
|
|
234
|
})
|
|
235
|
protected List<SpecimenOrObservationBase> occurrences;
|
|
236
|
|
|
237
|
@XmlElementWrapper(name = "References")
|
|
238
|
@XmlElement(name = "Reference", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = ReferenceBase.class)
|
|
239
|
|
|
240
|
protected List<ReferenceBase> references;
|
|
241
|
|
|
242
|
@XmlElementWrapper(name = "ReferencedEntities")
|
|
243
|
@XmlElements({
|
|
244
|
@XmlElement(name = "NomenclaturalStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatus.class),
|
|
245
|
@XmlElement(name = "NameTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameTypeDesignation.class),
|
|
246
|
@XmlElement(name = "SpecimenTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignation.class)
|
|
247
|
})
|
|
248
|
protected List<ReferencedEntityBase> referencedEntities;
|
|
249
|
|
|
250
|
|
|
251
|
@XmlElementWrapper(name = "TaxonomicNames")
|
|
252
|
@XmlElements({
|
|
253
|
@XmlElement(name = "BacterialName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BacterialName.class),
|
|
254
|
@XmlElement(name = "BotanicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = BotanicalName.class),
|
|
255
|
@XmlElement(name = "CultivarPlantName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = CultivarPlantName.class),
|
|
256
|
@XmlElement(name = "ViralName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = ViralName.class),
|
|
257
|
@XmlElement(name = "ZoologicalName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = ZoologicalName.class)
|
|
258
|
})
|
|
259
|
protected List<TaxonNameBase> taxonomicNames;
|
|
260
|
|
|
261
|
@XmlElementWrapper(name = "Taxa")
|
|
262
|
@XmlElement(name = "Taxon", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
|
|
263
|
protected List<Taxon> taxa;
|
|
264
|
|
|
265
|
@XmlElementWrapper(name = "Synonyms")
|
|
266
|
@XmlElement(name = "Synonym", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
|
|
267
|
protected List<Synonym> synonyms;
|
|
268
|
|
|
269
|
@XmlElementWrapper(name = "Relationships")
|
|
270
|
@XmlElements({
|
|
271
|
@XmlElement(name = "TaxonRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationship.class),
|
|
272
|
@XmlElement(name = "SynonymRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymRelationship.class),
|
|
273
|
@XmlElement(name = "NameRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationship.class),
|
|
274
|
@XmlElement(name = "HybridRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationship.class)
|
|
275
|
})
|
|
276
|
protected Set<RelationshipBase> relationships;
|
|
277
|
|
|
278
|
@XmlElementWrapper(name = "Media_")
|
|
279
|
@XmlElement(name = "Media", namespace = "http://etaxonomy.eu/cdm/model/media/1.0")
|
|
280
|
protected List<VersionableEntity> media;
|
|
281
|
|
|
282
|
@XmlElementWrapper(name = "HomotypicalGroups")
|
|
283
|
@XmlElement(name = "HomotypicalGroup", namespace = "http://etaxonomy.eu/cdm/model/name/1.0")
|
|
284
|
protected List<HomotypicalGroup> homotypicalGroups;
|
|
285
|
|
|
286
|
// @XmlElement(name = "TdwgArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = TdwgArea.class),
|
|
287
|
|
|
288
|
public SDDDataSet () {
|
|
289
|
|
|
290
|
agents = new ArrayList<AgentBase>();
|
|
291
|
agentData = new ArrayList<VersionableEntity>();
|
|
292
|
// featureData = new ArrayList<VersionableEntity>();
|
|
293
|
featureData = new ArrayList<VersionableEntity>();
|
|
294
|
languageData = new ArrayList<LanguageStringBase>();
|
|
295
|
terms = new ArrayList<DefinedTermBase>();
|
|
296
|
termVocabularies = new ArrayList<TermVocabulary<DefinedTermBase>>();
|
|
297
|
occurrences = new ArrayList<SpecimenOrObservationBase>();
|
|
298
|
references = new ArrayList<ReferenceBase>();
|
|
299
|
referencedEntities = new ArrayList<ReferencedEntityBase>();
|
|
300
|
taxonomicNames = new ArrayList<TaxonNameBase>();
|
|
301
|
taxa = new ArrayList<Taxon>();
|
|
302
|
synonyms = new ArrayList<Synonym>();
|
|
303
|
relationships = new HashSet<RelationshipBase>();
|
|
304
|
media = new ArrayList<VersionableEntity>();
|
|
305
|
homotypicalGroups = new ArrayList<HomotypicalGroup>();
|
|
306
|
}
|
|
307
|
|
|
308
|
/**
|
|
309
|
* Gets the value of the agents property.
|
|
310
|
*
|
|
311
|
* @return
|
|
312
|
* possible object is
|
|
313
|
* {@link List<Agent> }
|
|
314
|
*
|
|
315
|
*/
|
|
316
|
public List<? extends AgentBase> getAgents() {
|
|
317
|
return agents;
|
|
318
|
}
|
|
319
|
|
|
320
|
/**
|
|
321
|
* Sets the value of the agents property.
|
|
322
|
*
|
|
323
|
* @param value
|
|
324
|
* allowed object is
|
|
325
|
* {@link List<Agent> }
|
|
326
|
*
|
|
327
|
*/
|
|
328
|
public void setAgents(List<? extends AgentBase> value) {
|
|
329
|
this.agents = value;
|
|
330
|
}
|
|
331
|
|
|
332
|
/**
|
|
333
|
* Gets the value of the agentData property.
|
|
334
|
*
|
|
335
|
* @return
|
|
336
|
* possible object is
|
|
337
|
* {@link List<VersionableEntity> }
|
|
338
|
*
|
|
339
|
*/
|
|
340
|
public List<VersionableEntity> getAgentData() {
|
|
341
|
return agentData;
|
|
342
|
}
|
|
343
|
|
|
344
|
/**
|
|
345
|
* Sets the value of the agentData property.
|
|
346
|
*
|
|
347
|
* @param value
|
|
348
|
* allowed object is
|
|
349
|
* {@link List<VersionableEntity> }
|
|
350
|
*
|
|
351
|
*/
|
|
352
|
public void setAgentData(List<VersionableEntity> value) {
|
|
353
|
this.agentData = value;
|
|
354
|
}
|
|
355
|
|
|
356
|
/**
|
|
357
|
* Gets the value of the terms property.
|
|
358
|
*
|
|
359
|
* @return
|
|
360
|
* possible object is
|
|
361
|
* {@link List<TermBase> }
|
|
362
|
*
|
|
363
|
*/
|
|
364
|
|
|
365
|
//public List<? extends TermBase> getTerms() {
|
|
366
|
public List<DefinedTermBase> getTerms() {
|
|
367
|
return terms;
|
|
368
|
}
|
|
369
|
|
|
370
|
/**
|
|
371
|
* Sets the value of the terms property.
|
|
372
|
*
|
|
373
|
* @param value
|
|
374
|
* allowed object is
|
|
375
|
* {@link List<TermBase> }
|
|
376
|
*
|
|
377
|
*/
|
|
378
|
//public void setTerms(List<? extends TermBase> value) {
|
|
379
|
public void setTerms(List<DefinedTermBase> value) {
|
|
380
|
this.terms = value;
|
|
381
|
}
|
|
382
|
|
|
383
|
/**
|
|
384
|
* Gets the value of the term vocabularies property.
|
|
385
|
*
|
|
386
|
* @return
|
|
387
|
* possible object is
|
|
388
|
* {@link List<TermVocabulary> }
|
|
389
|
*
|
|
390
|
*/
|
|
391
|
|
|
392
|
public List<TermVocabulary<DefinedTermBase>> getTermVocabularies() {
|
|
393
|
return termVocabularies;
|
|
394
|
}
|
|
395
|
|
|
396
|
/**
|
|
397
|
* Sets the value of the term vocabularies property.
|
|
398
|
*
|
|
399
|
* @param value
|
|
400
|
* allowed object is
|
|
401
|
* {@link List<TermVocabulary> }
|
|
402
|
*
|
|
403
|
*/
|
|
404
|
public void setTermVocabularies(List<TermVocabulary<DefinedTermBase>> value) {
|
|
405
|
this.termVocabularies = value;
|
|
406
|
}
|
|
407
|
|
|
408
|
/**
|
|
409
|
* Gets the value of the taxonomicNames property.
|
|
410
|
*
|
|
411
|
* @return
|
|
412
|
* possible object is
|
|
413
|
* {@link List<axonNameBase> }
|
|
414
|
*
|
|
415
|
*/
|
|
416
|
public List<TaxonNameBase> getTaxonomicNames() {
|
|
417
|
return taxonomicNames;
|
|
418
|
}
|
|
419
|
|
|
420
|
/**
|
|
421
|
* Sets the value of the taxonomicNames property.
|
|
422
|
*
|
|
423
|
* @param value
|
|
424
|
* allowed object is
|
|
425
|
* {@link List<TaxonNameBase> }
|
|
426
|
*
|
|
427
|
*/
|
|
428
|
public void setTaxonomicNames(List<TaxonNameBase> value) {
|
|
429
|
this.taxonomicNames = value;
|
|
430
|
}
|
|
431
|
|
|
432
|
/**
|
|
433
|
* Gets the value of the references property.
|
|
434
|
*
|
|
435
|
* @return
|
|
436
|
* possible object is
|
|
437
|
* {@link List<SpecimenOrObservationBase> }
|
|
438
|
*
|
|
439
|
*/
|
|
440
|
public List<SpecimenOrObservationBase> getOccurrences() {
|
|
441
|
return occurrences;
|
|
442
|
}
|
|
443
|
|
|
444
|
/**
|
|
445
|
* Sets the value of the references property.
|
|
446
|
*
|
|
447
|
* @param value
|
|
448
|
* allowed object is
|
|
449
|
* {@link List<SpecimenOrObservationBase> }
|
|
450
|
*
|
|
451
|
*/
|
|
452
|
public void setOccurrences(List<SpecimenOrObservationBase> value) {
|
|
453
|
this.occurrences = value;
|
|
454
|
}
|
|
455
|
|
|
456
|
/**
|
|
457
|
* Gets the value of the references property.
|
|
458
|
*
|
|
459
|
* @return
|
|
460
|
* possible object is
|
|
461
|
* {@link List<ReferenceBase> }
|
|
462
|
*
|
|
463
|
*/
|
|
464
|
public List<ReferenceBase> getReferences() {
|
|
465
|
return references;
|
|
466
|
}
|
|
467
|
|
|
468
|
/**
|
|
469
|
* Sets the value of the references property.
|
|
470
|
*
|
|
471
|
* @param value
|
|
472
|
* allowed object is
|
|
473
|
* {@link List<ReferenceBase> }
|
|
474
|
*
|
|
475
|
*/
|
|
476
|
public void setReferences(List<ReferenceBase> value) {
|
|
477
|
this.references = value;
|
|
478
|
}
|
|
479
|
|
|
480
|
/**
|
|
481
|
* Adds the referenced entities in value to the referenced entity property list.
|
|
482
|
*
|
|
483
|
* @param value
|
|
484
|
* allowed object is
|
|
485
|
* {@link Collection<ReferencedEntityBase> }
|
|
486
|
*
|
|
487
|
*/
|
|
488
|
public <T extends ReferencedEntityBase> void addReferencedEntities(Collection<T> value) {
|
|
489
|
for (T referencedEntity: value) {
|
|
490
|
this.referencedEntities.add(referencedEntity);
|
|
491
|
}
|
|
492
|
}
|
|
493
|
|
|
494
|
/**
|
|
495
|
* Gets the value of the property.
|
|
496
|
*
|
|
497
|
* @return
|
|
498
|
* possible object is
|
|
499
|
* {@link List<ReferencedEntityBase> }
|
|
500
|
*
|
|
501
|
*/
|
|
502
|
public List<ReferencedEntityBase> getReferencedEntities() {
|
|
503
|
return referencedEntities;
|
|
504
|
}
|
|
505
|
|
|
506
|
/**
|
|
507
|
* Sets the value of the referencedEntities property.
|
|
508
|
*
|
|
509
|
* @param value
|
|
510
|
* allowed object is
|
|
511
|
* {@link List<ReferencedEntityBase> }
|
|
512
|
*
|
|
513
|
*/
|
|
514
|
public void setReferencedEntities(List<? extends ReferencedEntityBase> value) {
|
|
515
|
this.referencedEntities = new ArrayList<ReferencedEntityBase>();
|
|
516
|
referencedEntities.addAll(value);
|
|
517
|
}
|
|
518
|
|
|
519
|
/**
|
|
520
|
* Adds the features in value to the feature data property list.
|
|
521
|
*
|
|
522
|
* @param value
|
|
523
|
* allowed object is
|
|
524
|
* {@link Collection<VersionableEntity> }
|
|
525
|
*
|
|
526
|
*/
|
|
527
|
public <T extends VersionableEntity> void addFeatureData(Collection<T> value) {
|
|
528
|
for (T featureItem: value) {
|
|
529
|
this.featureData.add(featureItem);
|
|
530
|
}
|
|
531
|
}
|
|
532
|
|
|
533
|
/**
|
|
534
|
* Gets the value of the feature data property.
|
|
535
|
*
|
|
536
|
* @return
|
|
537
|
* possible object is
|
|
538
|
* {@link List<VersionableEntity> }
|
|
539
|
*
|
|
540
|
*/
|
|
541
|
// public List<VersionableEntity> getFeatureData() {
|
|
542
|
public List<VersionableEntity> getFeatureData() {
|
|
543
|
return featureData;
|
|
544
|
}
|
|
545
|
|
|
546
|
/**
|
|
547
|
* Sets the value of the feature data property.
|
|
548
|
*
|
|
549
|
* @param value
|
|
550
|
* allowed object is
|
|
551
|
* {@link List<VersionableEntity> }
|
|
552
|
*
|
|
553
|
*/
|
|
554
|
public <T extends VersionableEntity> void setFeatureData(List<T> value) {
|
|
555
|
featureData = new ArrayList<VersionableEntity>();
|
|
556
|
for (T featureItem: value) {
|
|
557
|
this.featureData.add(featureItem);
|
|
558
|
}
|
|
559
|
}
|
|
560
|
|
|
561
|
// public void setFeatureData(List<? extends VersionableEntity> value) {
|
|
562
|
//public void setFeatureData(List<? extends VersionableEntity<?>> value) {
|
|
563
|
// this.featureData = new ArrayList<VersionableEntity>();
|
|
564
|
// this.featureData = new ArrayList<VersionableEntity<?>>();
|
|
565
|
// featureData.addAll(value);
|
|
566
|
//}
|
|
567
|
|
|
568
|
/**
|
|
569
|
* Adds the features in value to the language data property list.
|
|
570
|
*
|
|
571
|
* @param value
|
|
572
|
* allowed object is
|
|
573
|
* {@link Collection<LanguageStringBase> }
|
|
574
|
*
|
|
575
|
*/
|
|
576
|
public <T extends LanguageStringBase> void addLanguageData(Collection<T> value) {
|
|
577
|
for (T languageItem: value) {
|
|
578
|
this.languageData.add(languageItem);
|
|
579
|
}
|
|
580
|
}
|
|
581
|
|
|
582
|
/**
|
|
583
|
* Gets the value of the language data property.
|
|
584
|
*
|
|
585
|
* @return
|
|
586
|
* possible object is
|
|
587
|
* {@link List<LanguageStringBase> }
|
|
588
|
*
|
|
589
|
*/
|
|
590
|
public List<LanguageStringBase> getLanguageData() {
|
|
591
|
return languageData;
|
|
592
|
}
|
|
593
|
|
|
594
|
/**
|
|
595
|
* Sets the value of the feature data property.
|
|
596
|
*
|
|
597
|
* @param value
|
|
598
|
* allowed object is
|
|
599
|
* {@link List<LanguageStringBase> }
|
|
600
|
*
|
|
601
|
*/
|
|
602
|
public void setLanguageData(List<? extends LanguageStringBase> value) {
|
|
603
|
this.languageData = new ArrayList<LanguageStringBase>();
|
|
604
|
languageData.addAll(value);
|
|
605
|
}
|
|
606
|
|
|
607
|
/**
|
|
608
|
* Adds the taxa in value to the taxa property list.
|
|
609
|
*
|
|
610
|
* @param value
|
|
611
|
* allowed object is
|
|
612
|
* {@link Collection<Taxon> }
|
|
613
|
*
|
|
614
|
*/
|
|
615
|
public void addTaxa(Collection<Taxon> value) {
|
|
616
|
for (Taxon taxon: value) {
|
|
617
|
this.taxa.add(taxon);
|
|
618
|
}
|
|
619
|
}
|
|
620
|
|
|
621
|
/**
|
|
622
|
* Gets the value of the taxa property.
|
|
623
|
*
|
|
624
|
* @return
|
|
625
|
* possible object is
|
|
626
|
* {@link List<Taxon> }
|
|
627
|
*
|
|
628
|
*/
|
|
629
|
// public List<Taxon> getTaxa() {
|
|
630
|
// return taxa;
|
|
631
|
// }
|
|
632
|
|
|
633
|
/**
|
|
634
|
* Gets the value of the taxa property as {@link Collection<TaxonBase> }
|
|
635
|
*
|
|
636
|
* @return
|
|
637
|
* possible object is
|
|
638
|
* {@link Collection<TaxonBase> }
|
|
639
|
*
|
|
640
|
*/
|
|
641
|
public Collection<? extends TaxonBase> getTaxa() {
|
|
642
|
|
|
643
|
//TODO can be deleted when everything works
|
|
644
|
//Object obj = taxa;
|
|
645
|
//Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;
|
|
646
|
List<Taxon> list = taxa;
|
|
647
|
return list;
|
|
648
|
}
|
|
649
|
|
|
650
|
public Collection<TaxonBase> getTaxonBases() {
|
|
651
|
|
|
652
|
Collection<TaxonBase> result = new HashSet<TaxonBase>();;
|
|
653
|
if (taxa != null) {
|
|
654
|
result.addAll(taxa);
|
|
655
|
}
|
|
656
|
if (synonyms != null) {
|
|
657
|
result.addAll(synonyms);
|
|
658
|
}
|
|
659
|
return result;
|
|
660
|
}
|
|
661
|
|
|
662
|
/**
|
|
663
|
* Sets the value of the taxa property.
|
|
664
|
*
|
|
665
|
* @param value
|
|
666
|
* allowed object is
|
|
667
|
* {@link List<Taxon> }
|
|
668
|
*
|
|
669
|
*/
|
|
670
|
public void setTaxa(List<Taxon> value) {
|
|
671
|
this.taxa = value;
|
|
672
|
}
|
|
673
|
|
|
674
|
/**
|
|
675
|
* Adds the taxon in value to the taxa property list.
|
|
676
|
*
|
|
677
|
* @param value
|
|
678
|
*
|
|
679
|
*/
|
|
680
|
public void addTaxon(Taxon value) {
|
|
681
|
this.taxa.add(value);
|
|
682
|
}
|
|
683
|
|
|
684
|
|
|
685
|
/**
|
|
686
|
* Gets the value of the synonyms property.
|
|
687
|
*
|
|
688
|
* @return
|
|
689
|
* possible object is
|
|
690
|
* {@link List<Synonym> }
|
|
691
|
*
|
|
692
|
*/
|
|
693
|
public List<Synonym> getSynonyms() {
|
|
694
|
return synonyms;
|
|
695
|
}
|
|
696
|
|
|
697
|
/**
|
|
698
|
* Sets the value of the synonyms property.
|
|
699
|
*
|
|
700
|
* @param value
|
|
701
|
* allowed object is
|
|
702
|
* {@link List<Synonym> }
|
|
703
|
*
|
|
704
|
*/
|
|
705
|
public void setSynonyms(List<Synonym> value) {
|
|
706
|
this.synonyms = value;
|
|
707
|
}
|
|
708
|
|
|
709
|
/**
|
|
710
|
* Adds the synonym in value to the taxa property list.
|
|
711
|
*
|
|
712
|
* @param value
|
|
713
|
*
|
|
714
|
*/
|
|
715
|
public void addSynonym(Synonym value) {
|
|
716
|
this.synonyms.add(value);
|
|
717
|
}
|
|
718
|
|
|
719
|
/**
|
|
720
|
* Adds the synonym in value to the synonyms property list.
|
|
721
|
*
|
|
722
|
* @param value
|
|
723
|
* allowed object is
|
|
724
|
* {@link Collection<Synonym> }
|
|
725
|
*
|
|
726
|
*/
|
|
727
|
public void addSynonyms(Collection<Synonym> value) {
|
|
728
|
for (Synonym synonym: value) {
|
|
729
|
this.synonyms.add(synonym);
|
|
730
|
}
|
|
731
|
}
|
|
732
|
|
|
733
|
/**
|
|
734
|
* Gets the value of the relationships property.
|
|
735
|
*
|
|
736
|
* @return
|
|
737
|
* possible object is
|
|
738
|
* {@link Set<RelationshipBase> }
|
|
739
|
*
|
|
740
|
*/
|
|
741
|
public Set<RelationshipBase> getRelationships() {
|
|
742
|
return relationships;
|
|
743
|
}
|
|
744
|
|
|
745
|
/**
|
|
746
|
* Sets the value of the relationships property.
|
|
747
|
*
|
|
748
|
* @param value
|
|
749
|
* allowed object is
|
|
750
|
* {@link Set<RelationshipBase> }
|
|
751
|
*
|
|
752
|
*/
|
|
753
|
public void setRelationships(Set<RelationshipBase> value) {
|
|
754
|
this.relationships = value;
|
|
755
|
}
|
|
756
|
|
|
757
|
/**
|
|
758
|
* Adds the relationship in value to the relationships property list.
|
|
759
|
*
|
|
760
|
* @param value
|
|
761
|
* allowed object is
|
|
762
|
* {@link Collection<RelationshipBase> }
|
|
763
|
*
|
|
764
|
*/
|
|
765
|
public void addRelationships(Collection<? extends RelationshipBase> value) {
|
|
766
|
for (RelationshipBase relationship: value) {
|
|
767
|
this.relationships.add(relationship);
|
|
768
|
}
|
|
769
|
}
|
|
770
|
|
|
771
|
/**
|
|
772
|
* Adds the media in value to the media property list.
|
|
773
|
*
|
|
774
|
* @param value
|
|
775
|
* allowed object is
|
|
776
|
* {@link Collection<VersionableEntity> }
|
|
777
|
*
|
|
778
|
*/
|
|
779
|
public <T extends VersionableEntity> void addMedia(Collection<T> value) {
|
|
780
|
for (T medium: value) {
|
|
781
|
this.media.add(medium);
|
|
782
|
}
|
|
783
|
}
|
|
784
|
|
|
785
|
/**
|
|
786
|
* Gets the value of the property.
|
|
787
|
*
|
|
788
|
* @return
|
|
789
|
* possible object is
|
|
790
|
* {@link List<ReferencedEntityBase> }
|
|
791
|
*
|
|
792
|
*/
|
|
793
|
public List<VersionableEntity> getMedia() {
|
|
794
|
return media;
|
|
795
|
}
|
|
796
|
|
|
797
|
/**
|
|
798
|
* Sets the value of the referencedEntities property.
|
|
799
|
*
|
|
800
|
* @param value
|
|
801
|
* allowed object is
|
|
802
|
* {@link List<ReferencedEntityBase> }
|
|
803
|
*
|
|
804
|
*/
|
|
805
|
public void setMedia(List<? extends VersionableEntity> value) {
|
|
806
|
this.media = new ArrayList<VersionableEntity>();
|
|
807
|
media.addAll(value);
|
|
808
|
}
|
|
809
|
|
|
810
|
/**
|
|
811
|
* Gets the value of the synonyms property.
|
|
812
|
*
|
|
813
|
* @return
|
|
814
|
* possible object is
|
|
815
|
* {@link List<Synonym> }
|
|
816
|
*
|
|
817
|
*/
|
|
818
|
public List<HomotypicalGroup> getHomotypicalGroups() {
|
|
819
|
return homotypicalGroups;
|
|
820
|
}
|
|
821
|
|
|
822
|
/**
|
|
823
|
* Sets the value of the synonyms property.
|
|
824
|
*
|
|
825
|
* @param value
|
|
826
|
* allowed object is
|
|
827
|
* {@link List<Synonym> }
|
|
828
|
*
|
|
829
|
*/
|
|
830
|
public void setHomotypicalGroups(List<HomotypicalGroup> value) {
|
|
831
|
this.homotypicalGroups = value;
|
|
832
|
}
|
|
833
|
|
|
834
|
}
|