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
|
package eu.etaxonomy.cdm.model.name;
|
10
|
|
11
|
import java.util.ArrayList;
|
12
|
import java.util.HashMap;
|
13
|
import java.util.List;
|
14
|
import java.util.Map;
|
15
|
import java.util.UUID;
|
16
|
|
17
|
import javax.persistence.Entity;
|
18
|
import javax.persistence.Transient;
|
19
|
import javax.validation.constraints.NotNull;
|
20
|
import javax.xml.bind.annotation.XmlAccessType;
|
21
|
import javax.xml.bind.annotation.XmlAccessorType;
|
22
|
import javax.xml.bind.annotation.XmlAttribute;
|
23
|
import javax.xml.bind.annotation.XmlType;
|
24
|
|
25
|
import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
|
26
|
import org.hibernate.annotations.Type;
|
27
|
import org.hibernate.envers.Audited;
|
28
|
|
29
|
import eu.etaxonomy.cdm.model.common.Language;
|
30
|
import eu.etaxonomy.cdm.model.term.DefinedTermBase;
|
31
|
import eu.etaxonomy.cdm.model.term.OrderedTermBase;
|
32
|
import eu.etaxonomy.cdm.model.term.Representation;
|
33
|
import eu.etaxonomy.cdm.model.term.TermType;
|
34
|
import eu.etaxonomy.cdm.model.term.TermVocabulary;
|
35
|
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
|
36
|
|
37
|
/**
|
38
|
* The class representing categories of nomenclatural status (like "invalid",
|
39
|
* "conserved" or "novum") to qualify the use of a particular taxon name string
|
40
|
* depending on its {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} (original publication),
|
41
|
* on its {@link NomenclaturalCode nomenclatural code} and on possible decisions of the corresponding
|
42
|
* competent authorities. Unfortunately the ICBN and the ICZN use sometimes
|
43
|
* different words for the same meaning or the same word for different meanings
|
44
|
* (for instance "valid" and "legitimate").
|
45
|
* <P>
|
46
|
* A standard (ordered) list of nomenclatural status type instances will be
|
47
|
* automatically created as the project starts. But this class allows to extend
|
48
|
* this standard list by creating new instances of additional nomenclatural
|
49
|
* status types if needed. The present standard list follows the ICBN
|
50
|
* terminology.
|
51
|
* <P>
|
52
|
* This class corresponds more or less to: <ul>
|
53
|
* <li> NomenclaturalNoteTypeTerm according to the TDWG ontology
|
54
|
* <li> NomenclaturalNoteType according to the TCS
|
55
|
* </ul>
|
56
|
*
|
57
|
* @author a.mueller
|
58
|
* @since 10.07.2008
|
59
|
*/
|
60
|
@XmlAccessorType(XmlAccessType.FIELD)
|
61
|
@XmlType(name = "NomenclaturalStatusType", propOrder = {
|
62
|
"nomenclaturalStanding"}
|
63
|
)
|
64
|
@Entity
|
65
|
//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
|
66
|
//@Indexed(index = "eu.etaxonomy.cdm.model.term.DefinedTermBase")
|
67
|
@Audited
|
68
|
public class NomenclaturalStatusType
|
69
|
extends OrderedTermBase<NomenclaturalStatusType>
|
70
|
implements INomenclaturalStanding {
|
71
|
|
72
|
private static final long serialVersionUID = 1337101678484153972L;
|
73
|
|
74
|
private static Logger logger = LogManager.getLogger(NomenclaturalStatusType.class);
|
75
|
|
76
|
//Botanical uuids
|
77
|
public static final UUID uuidIcnafpNomStatusVocabulary = UUID.fromString("bb28cdca-2f8a-4f11-9c21-517e9ae87f1f");
|
78
|
|
79
|
private static final UUID uuidAmbiguous = UUID.fromString("90f5012b-705b-4488-b4c6-002d2bc5198e");
|
80
|
private static final UUID uuidDoubtful = UUID.fromString("0ffeb39e-872e-4c0f-85ba-a4150d9f9e7d");
|
81
|
private static final UUID uuidConfusum = UUID.fromString("24955174-aa5c-4e71-a2fd-3efc79e885db");
|
82
|
private static final UUID uuidIllegitimate = UUID.fromString("b7c544cf-a375-4145-9d3e-4b97f3f18108");
|
83
|
private static final UUID uuidSuperfluous = UUID.fromString("6890483a-c6ba-4ae1-9ab1-9fbaa5736ce9");
|
84
|
private static final UUID uuidRejected = UUID.fromString("48107cc8-7a5b-482e-b438-efbba050b851");
|
85
|
private static final UUID uuidUtiqueRejected = UUID.fromString("04338fdd-c12a-402f-a1ca-68b4bf0be042");
|
86
|
private static final UUID uuidConservedProp = UUID.fromString("82bab006-5aed-4301-93ec-980deb30cbb1");
|
87
|
private static final UUID uuidOrthographyConservedProp = UUID.fromString("02f82bc5-1066-454b-a023-11967cba9092");
|
88
|
private static final UUID uuidLegitimate = UUID.fromString("51a3613c-b53b-4561-b0cd-9163d91c15aa");
|
89
|
private static final UUID uuidAlternative = UUID.fromString("3b8a8519-420f-4dfa-b050-b410cc257961");
|
90
|
private static final UUID uuidNovum = UUID.fromString("05fcb68f-af60-4851-b912-892512058897");
|
91
|
private static final UUID uuidUtiqueRejectedProp = UUID.fromString("643ee07f-026c-426c-b838-c778c8613383");
|
92
|
private static final UUID uuidOrthographyConserved = UUID.fromString("34a7d383-988b-4117-b8c0-52b947f8c711");
|
93
|
private static final UUID uuidRejectedProp = UUID.fromString("248e44c2-5436-4526-a352-f7467ecebd56");
|
94
|
private static final UUID uuidConserved = UUID.fromString("6330f719-e2bc-485f-892b-9f882058a966");
|
95
|
private static final UUID uuidSanctioned = UUID.fromString("1afe55c4-76aa-46c0-afce-4dc07f512733");
|
96
|
private static final UUID uuidInvalid = UUID.fromString("b09d4f51-8a77-442a-bbce-e7832aaf46b7");
|
97
|
private static final UUID uuidNudum = UUID.fromString("e0d733a8-7777-4b27-99a3-05ab50e9f312");
|
98
|
private static final UUID uuidCombinationInvalid = UUID.fromString("f858e619-7b7f-4225-913b-880a2143ec83");
|
99
|
private static final UUID uuidCombinationIllegitimate = UUID.fromString("d901d455-4e01-45cb-b653-01a840b97eed");
|
100
|
private static final UUID uuidProvisional = UUID.fromString("a277507e-ad93-4978-9419-077eb889c951");
|
101
|
private static final UUID uuidValid = UUID.fromString("bd036217-5499-4ccd-8f4c-72e06158db93");
|
102
|
private static final UUID uuidOpusUtiqueOppr = UUID.fromString("a5055d80-dbba-4660-b091-a1835d59fe7c");
|
103
|
private static final UUID uuidSubnudum = UUID.fromString("92a76bd0-6ea8-493f-98e0-4be0b98c092f");
|
104
|
private static final UUID uuidOrthographyRejected = UUID.fromString("39a25673-f716-4ec7-ae27-2498fce43166");
|
105
|
private static final UUID uuidConservedDesig = UUID.fromString("4e9c9702-a74d-4033-9d47-792ad123712c");
|
106
|
private static final UUID uuidIned = UUID.fromString("51429574-c6f9-4aa1-bab9-0bbc5b160ba1");
|
107
|
private static final UUID uuidProtected = UUID.fromString("d071187a-512d-4955-b75c-d1706702f098");
|
108
|
private static final UUID uuidScheda = UUID.fromString("f080cee4-6e0a-466f-986e-bad59e9f4ea7");
|
109
|
private static final UUID uuidProSynonymo = UUID.fromString("54900d07-a18f-4e11-b4be-3929bb78416a");
|
110
|
private static final UUID uuidOrthVar = UUID.fromString("6703745b-9834-42b5-8ddd-fcc6ce572372");
|
111
|
private static final UUID uuidCombIned = UUID.fromString("71c13910-19a4-46b2-9ec8-2a8dbd45cd83");
|
112
|
|
113
|
|
114
|
private static final UUID uuidCombNov = UUID.fromString("ed508710-deef-44b1-96f6-1ce6d2c9c884");
|
115
|
|
116
|
//zoological uuids
|
117
|
public static final UUID uuidIcznNomStatusVocabulary = UUID.fromString("5e3c08e9-13a9-498e-861e-b9b5656ab6ac");
|
118
|
|
119
|
private static final UUID uuidZooNotAvailable = UUID.fromString("6d9ed462-b761-4da3-9304-4749e883d4eb");
|
120
|
private static final UUID uuidZooInvalid = UUID.fromString("2bef7039-c129-410b-815e-2a1f7249127b");
|
121
|
private static final UUID uuidZooSuppressed = UUID.fromString("a61602c7-fbd4-4eb4-98a2-44919db8920b");
|
122
|
private static final UUID uuidZooOblitum = UUID.fromString("6a6f7a88-991f-4f76-8ce9-4110839fae8b");
|
123
|
|
124
|
|
125
|
public static NomenclaturalStatusType NewLatinInstance(String description, String label, String labelAbbrev) {
|
126
|
return new NomenclaturalStatusType(description, label, labelAbbrev, Language.LATIN());
|
127
|
}
|
128
|
|
129
|
public static NomenclaturalStatusType NewInstance(String description, String label, String labelAbbrev, Language language) {
|
130
|
return new NomenclaturalStatusType(description, label, labelAbbrev, language);
|
131
|
}
|
132
|
|
133
|
public static NomenclaturalStatusType NewInstance(String description, String label, String labelAbbrev) {
|
134
|
return new NomenclaturalStatusType(description, label, labelAbbrev);
|
135
|
}
|
136
|
|
137
|
protected static Map<UUID, NomenclaturalStatusType> termMap = null;
|
138
|
private static Map<String, UUID> abbrevMap = null;
|
139
|
private static Map<String, UUID> labelMap = null;
|
140
|
|
141
|
|
142
|
protected static Map<UUID, NomenclaturalStatusType> zooTermMap = null;
|
143
|
private static Map<String, UUID> zooAbbrevMap = null;
|
144
|
private static Map<String, UUID> zooLabelMap = null;
|
145
|
|
146
|
protected static NomenclaturalStatusType getTermByUuid(UUID uuid){
|
147
|
if ((termMap == null || termMap.isEmpty()) && (zooTermMap == null || zooTermMap.isEmpty())){
|
148
|
return getTermByClassAndUUID(NomenclaturalStatusType.class, uuid);
|
149
|
}
|
150
|
NomenclaturalStatusType result = null;
|
151
|
if (termMap != null){
|
152
|
result = termMap.get(uuid);
|
153
|
}
|
154
|
if (result == null && zooTermMap != null){
|
155
|
result = zooTermMap.get(uuid);
|
156
|
}
|
157
|
return result;
|
158
|
}
|
159
|
|
160
|
/**
|
161
|
* The {@link NomenclaturalStanding nomenclatural standing} of a name with a given
|
162
|
* nomenclatural status.
|
163
|
* It is usually needed for correct formatting of a name in a synonymy by e.g. using
|
164
|
* a dash instead of equal sign in front.
|
165
|
*/
|
166
|
@XmlAttribute(name ="NomenclaturalStanding")
|
167
|
@NotNull
|
168
|
@Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
|
169
|
parameters = {@org.hibernate.annotations.Parameter(name="enumClass", value="eu.etaxonomy.cdm.model.name.NomenclaturalStanding")}
|
170
|
)
|
171
|
@Audited
|
172
|
private NomenclaturalStanding nomenclaturalStanding;
|
173
|
|
174
|
|
175
|
//********************************** Constructor *********************************/
|
176
|
|
177
|
//for hibernate use only
|
178
|
@Deprecated
|
179
|
protected NomenclaturalStatusType() {
|
180
|
super(TermType.NomenclaturalStatusType);
|
181
|
}
|
182
|
|
183
|
/**
|
184
|
* Class constructor: creates an additional nomenclatural status type
|
185
|
* instance with a description (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label
|
186
|
* and a label abbreviation.
|
187
|
*
|
188
|
* @param term the string (in the default language) describing the
|
189
|
* new nomenclatural status type to be created
|
190
|
* @param label the string identifying the new nomenclatural status
|
191
|
* type to be created
|
192
|
* @param labelAbbrev the string identifying (in abbreviated form) the
|
193
|
* new nomenclatural status type to be created
|
194
|
* @see #NomenclaturalStatusType()
|
195
|
* @see #readCsvLine(List, Language)
|
196
|
* @see #readCsvLine(List)
|
197
|
*/
|
198
|
private NomenclaturalStatusType(String term, String label, String labelAbbrev) {
|
199
|
super(TermType.NomenclaturalStatusType, term, label, labelAbbrev);
|
200
|
}
|
201
|
|
202
|
private NomenclaturalStatusType(String term, String label, String labelAbbrev, Language language) {
|
203
|
super(TermType.NomenclaturalStatusType);
|
204
|
this.addRepresentation(new Representation(term, label, labelAbbrev, language));
|
205
|
}
|
206
|
|
207
|
// ************************ GETTER / SETTER ******************/
|
208
|
|
209
|
public NomenclaturalStanding getNomenclaturalStanding() {
|
210
|
return nomenclaturalStanding;
|
211
|
}
|
212
|
|
213
|
public void setNomenclaturalStanding(NomenclaturalStanding nomenclaturalStanding) {
|
214
|
this.nomenclaturalStanding = nomenclaturalStanding;
|
215
|
}
|
216
|
|
217
|
//********* METHODS **************************************
|
218
|
|
219
|
@Override
|
220
|
public void resetTerms(){
|
221
|
termMap = null;
|
222
|
zooTermMap = null;
|
223
|
}
|
224
|
|
225
|
@Override
|
226
|
@Transient
|
227
|
public boolean isDesignationOnly(){
|
228
|
//rejected, definitely rejected, confused, ined., comb. ined., ambigous, orth. var., orth. rej.
|
229
|
//cons. prop., orth. cons. prop.
|
230
|
return this.getNomenclaturalStanding() == NomenclaturalStanding.OTHER_DESIGNATION;
|
231
|
}
|
232
|
|
233
|
@Override
|
234
|
@Transient
|
235
|
public boolean isInvalid(){
|
236
|
return this.getNomenclaturalStanding().isInvalid();
|
237
|
}
|
238
|
|
239
|
@Override
|
240
|
@Transient
|
241
|
public boolean isValid(){
|
242
|
return this.getNomenclaturalStanding().isValid();
|
243
|
}
|
244
|
|
245
|
@Override
|
246
|
@Transient
|
247
|
public boolean isValidExplicit(){
|
248
|
//valid: valid, legitimate, conserved, sanctioned, protected, orth. cons., alternative
|
249
|
// rej. prop, utique rej prop, nom. cons. des.
|
250
|
return this.getNomenclaturalStanding().isValidExplicit();
|
251
|
}
|
252
|
|
253
|
@Override
|
254
|
@Transient
|
255
|
public boolean isNoStatus(){
|
256
|
//nom. dub., novum, comb. nov., nom. cons. prop., nom. orth. cons. prop., nom. subnud.
|
257
|
return this.getNomenclaturalStanding().isNoStatus();
|
258
|
}
|
259
|
|
260
|
@Override
|
261
|
@Transient
|
262
|
public boolean isInvalidExplicit(){
|
263
|
//nom. inval., comb. inval., nom. nud., nom. prov., op. utique oppr., in sched.
|
264
|
//pro syn., "published with alternative name" (TODO)
|
265
|
return this.getNomenclaturalStanding() == NomenclaturalStanding.INVALID;
|
266
|
}
|
267
|
|
268
|
/**
|
269
|
* Returns the boolean value indicating whether <i>this</i> nomenclatural status
|
270
|
* type is itself "legitimate" or a kind of "legitimate" (true)
|
271
|
* or not (false). Corresponds to "valid" for {@link IZoologicalName zoological names}.<BR>
|
272
|
* Returns false if <i>this</i> nomenclatural status type is null.<BR>
|
273
|
* A "valid" (zool.: "available") {@link TaxonName taxon name}, unless "rejected",
|
274
|
* is "legitimate" if it was not "superfluous" when published
|
275
|
* or has been later "conserved".<BR>
|
276
|
*
|
277
|
* @see #isInvalid()
|
278
|
* @see #isIllegitimate()
|
279
|
* @see eu.etaxonomy.cdm.model.term.DefinedTermBase#getKindOf()
|
280
|
*/
|
281
|
@Override
|
282
|
@Transient
|
283
|
public boolean isLegitimate(){
|
284
|
return this.nomenclaturalStanding.isLegitimate();
|
285
|
}
|
286
|
|
287
|
/**
|
288
|
* Returns the boolean value indicating whether <i>this</i> nomenclatural status
|
289
|
* type is itself "illegitimate" or a kind of "illegitimate" (true)
|
290
|
* or not (false) - this corresponds to "invalid" for {@link IZoologicalName zoological names} -.
|
291
|
* Returns false if <i>this</i> nomenclatural status type is null.<BR>
|
292
|
* A "valid" ("available") {@link TaxonName taxon name}, unless "conserved" or
|
293
|
* "sanctioned", is "illegitimate" if it was "superfluous" when published
|
294
|
* or has been later "rejected".
|
295
|
*
|
296
|
* @see #VALID()
|
297
|
* @see #isInvalid()
|
298
|
* @see #ILLEGITIMATE()
|
299
|
* @see #CONSERVED()
|
300
|
* @see #SANCTIONED()
|
301
|
* @see eu.etaxonomy.cdm.model.term.DefinedTermBase#getKindOf()
|
302
|
*/
|
303
|
@Override
|
304
|
@Transient
|
305
|
public boolean isIllegitimate(){
|
306
|
//nom. illeg., comb. illeg., nom. superfl.,
|
307
|
//zoo nom. inval., zoo suppressed,
|
308
|
return this.nomenclaturalStanding.isIllegitimate();
|
309
|
}
|
310
|
|
311
|
/**
|
312
|
* Returns the nomenclatural status type "ambiguous". A "valid"
|
313
|
* ("available") {@link TaxonName taxon name} is "ambiguous" if it has been used so long
|
314
|
* by different authors in different senses (other than the originally
|
315
|
* intended) that it has become a persistent cause of error and confusion.<BR>
|
316
|
* An "ambiguous" taxon name is treated as if "rejected" and is therefore
|
317
|
* also "illegitimate" ("invalid" for {@link IZoologicalName zoological names}).
|
318
|
*
|
319
|
* @see #VALID()
|
320
|
* @see #REJECTED()
|
321
|
* @see #isIllegitimate()
|
322
|
*/
|
323
|
public static final NomenclaturalStatusType AMBIGUOUS(){
|
324
|
return getTermByUuid(uuidAmbiguous);
|
325
|
}
|
326
|
|
327
|
/**
|
328
|
* Returns the nomenclatural status type "doubtful" (dubious). A "valid"
|
329
|
* ("available") {@link TaxonName taxon name} is "doubtful" if its
|
330
|
* application is uncertain; the confusion being derived from an incomplete
|
331
|
* or confusing description.<BR>
|
332
|
* A "doubtful" taxon name is treated as if "rejected" and is therefore
|
333
|
* also "illegitimate" (("invalid" for {@link IZoologicalName zoological names}).
|
334
|
*
|
335
|
* @see #VALID()
|
336
|
* @see #REJECTED()
|
337
|
* @see #isIllegitimate()
|
338
|
*/
|
339
|
public static final NomenclaturalStatusType DOUBTFUL(){
|
340
|
return getTermByUuid(uuidDoubtful);
|
341
|
}
|
342
|
|
343
|
/**
|
344
|
* Returns the nomenclatural status type "confusum". A "valid" ("available")
|
345
|
* {@link TaxonName taxon name} is "confusum" if it has been widely
|
346
|
* and persistently used for a taxon or taxa not including its type.<BR>
|
347
|
* A "confusum" taxon name is treated as if "rejected" and is therefore
|
348
|
* also "illegitimate" ("invalid" for {@link IZoologicalName zoological names}).
|
349
|
*
|
350
|
* @see #VALID()
|
351
|
* @see #REJECTED()
|
352
|
* @see #isIllegitimate()
|
353
|
*/
|
354
|
public static final NomenclaturalStatusType CONFUSUM(){
|
355
|
return getTermByUuid(uuidConfusum);
|
356
|
}
|
357
|
|
358
|
/**
|
359
|
* Returns the nomenclatural status type "illegitimate" ("invalid" for
|
360
|
* {@link IZoologicalName zoological names}). A "valid" ("available")
|
361
|
* {@link TaxonName taxon name}, unless "conserved" or "sanctioned", is "illegitimate"
|
362
|
* if it was "superfluous" when published or has been later "rejected".<BR>
|
363
|
*
|
364
|
* @see #VALID()
|
365
|
* @see #SUPERFLUOUS()
|
366
|
* @see #REJECTED()
|
367
|
*/
|
368
|
public static final NomenclaturalStatusType ILLEGITIMATE(){
|
369
|
return getTermByUuid(uuidIllegitimate);
|
370
|
}
|
371
|
|
372
|
/**
|
373
|
* Returns the nomenclatural status type "superfluous". A "valid"
|
374
|
* ("available") {@link TaxonName taxon name} is "superfluous" if, when published,
|
375
|
* the taxon to which it was applied, as circumscribed by its {@link NonViralName#getCombinationAuthorship() author},
|
376
|
* definitely included the type of a name which ought to have been adopted,
|
377
|
* or of which the epithet ought to have been adopted, under the rules of
|
378
|
* the {@link NomenclaturalCode nomenclature code}, and if it has not been later declared
|
379
|
* "conserved" or "sanctioned" by the competent authorities.<BR>
|
380
|
* A "superfluous" taxon name is therefore also "illegitimate" ("invalid" for
|
381
|
* {@link IZoologicalName zoological names}).
|
382
|
*
|
383
|
* @see #VALID()
|
384
|
* @see #CONSERVED()
|
385
|
* @see #SANCTIONED()
|
386
|
* @see #isIllegitimate()
|
387
|
*/
|
388
|
public static final NomenclaturalStatusType SUPERFLUOUS(){
|
389
|
return getTermByUuid(uuidSuperfluous);
|
390
|
}
|
391
|
|
392
|
/**
|
393
|
* Returns the nomenclatural status type "rejected". A "valid" ("available")
|
394
|
* {@link TaxonName taxon name} is "rejected" if, even though by the strict
|
395
|
* application of the rules of the {@link NomenclaturalCode nomenclature code}, and especially
|
396
|
* of the principle of priority, it should be "legitimate" ("valid" for
|
397
|
* {@link IZoologicalName zoological names}), competent authorities decided to handle
|
398
|
* it as "illegitimate".<BR>
|
399
|
* A "rejected" taxon name is therefore also "illegitimate" ("invalid" for
|
400
|
* zoological names). A "rejected" taxon name is always rejected in favour
|
401
|
* of a "conserved" taxon name.
|
402
|
*
|
403
|
* @see #VALID()
|
404
|
* @see #isLegitimate()
|
405
|
* @see #isIllegitimate()
|
406
|
* @see #CONSERVED()
|
407
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
408
|
*/
|
409
|
public static final NomenclaturalStatusType REJECTED(){
|
410
|
return getTermByUuid(uuidRejected);
|
411
|
}
|
412
|
|
413
|
/**
|
414
|
* Returns the nomenclatural status type "utique rejected". A "valid"
|
415
|
* ("available") {@link TaxonName taxon name} is "utique rejected" if it is rejected
|
416
|
* outright (without being rejected in favour of a "conserved" taxon name).<BR>
|
417
|
* An "utique rejected" taxon name is therefore also "illegitimate"
|
418
|
* ("invalid" for zoological names).
|
419
|
*
|
420
|
* @see #REJECTED()
|
421
|
* @see #VALID()
|
422
|
* @see #isIllegitimate()
|
423
|
* @see #CONSERVED()
|
424
|
*/
|
425
|
public static final NomenclaturalStatusType UTIQUE_REJECTED(){
|
426
|
return getTermByUuid(uuidUtiqueRejected);
|
427
|
}
|
428
|
|
429
|
/**
|
430
|
* Returns the nomenclatural status type "proposed to be conserved". A
|
431
|
* "valid" ("available") {@link TaxonName taxon name} is "proposed to be conserved"
|
432
|
* if, even though by the strict application of the rules of
|
433
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
434
|
* it is "illegitimate" ("invalid" for {@link IZoologicalName zoological names}),
|
435
|
* it has been submitted to competent authorities in order to decide whether
|
436
|
* it should be handled as "legitimate".<BR>
|
437
|
* A "proposed to be conserved" taxon name is therefore still "illegitimate"
|
438
|
* ("invalid" for zoological names).
|
439
|
*
|
440
|
* {@link https://dev.e-taxonomy.eu/redmine/issues/5662}
|
441
|
*
|
442
|
* @see #VALID()
|
443
|
* @see #isIllegitimate()
|
444
|
* @see #isLegitimate()
|
445
|
* @see #CONSERVED()
|
446
|
* @see #CONSERVED_DESIG()
|
447
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
448
|
*/
|
449
|
public static final NomenclaturalStatusType CONSERVED_PROP(){
|
450
|
return getTermByUuid(uuidConservedProp);
|
451
|
}
|
452
|
|
453
|
/**
|
454
|
* Returns the nomenclatural status type "designated to be conserved". A
|
455
|
* "valid" ("available") {@link TaxonName taxon name} is "designated to be conserved".
|
456
|
* The name is considered to be legitimate as it has been decided by the General Committee
|
457
|
* though not yet ratified by the Int. Bot./Zool. Congr.
|
458
|
*
|
459
|
* NOTE: This interpretation needs further clarification.
|
460
|
*
|
461
|
* {@link https://dev.e-taxonomy.eu/redmine/issues/5662}
|
462
|
*
|
463
|
* @see #VALID()
|
464
|
* @see #isIllegitimate()
|
465
|
* @see #isLegitimate()
|
466
|
* @see #CONSERVED()
|
467
|
* @see #CONSERVED_PROP()()
|
468
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
469
|
*/
|
470
|
public static final NomenclaturalStatusType CONSERVED_DESIG(){
|
471
|
return getTermByUuid(uuidConservedDesig);
|
472
|
}
|
473
|
|
474
|
/**
|
475
|
* Returns the nomenclatural status type "proposed to be conserved
|
476
|
* (orthography)". A {@link TaxonName taxon name} is "proposed to be conserved
|
477
|
* (orthography)" if, even though originally published with another
|
478
|
* spelling, it has been submitted to competent authorities in order to
|
479
|
* decide whether the proposed alternative spelling should be "conserved".<BR>
|
480
|
* A "proposed to be conserved (orthography)" taxon name is therefore still
|
481
|
* "illegitimate" ("invalid" for {@link IZoologicalName zoological names}).
|
482
|
*
|
483
|
* @see #isIllegitimate()
|
484
|
* @see #CONSERVED_PROP()
|
485
|
* @see #CONSERVED()
|
486
|
* @see NameRelationshipType#ORTHOGRAPHIC_VARIANT()
|
487
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
488
|
*/
|
489
|
public static final NomenclaturalStatusType ORTHOGRAPHY_CONSERVED_PROP(){
|
490
|
return getTermByUuid(uuidOrthographyConservedProp);
|
491
|
}
|
492
|
|
493
|
/**
|
494
|
* Returns the nomenclatural status type "legitimate" ("valid" for
|
495
|
* {@link IZoologicalName zoological names}). A "valid" ("available")
|
496
|
* {@link TaxonName taxon name}, unless "rejected", is "legitimate" if it was not
|
497
|
* "superfluous" when published or has been later "conserved".<BR>
|
498
|
*
|
499
|
* @see #VALID()
|
500
|
* @see #SUPERFLUOUS()
|
501
|
* @see #CONSERVED()
|
502
|
*/
|
503
|
public static final NomenclaturalStatusType LEGITIMATE(){
|
504
|
return getTermByUuid(uuidLegitimate);
|
505
|
}
|
506
|
|
507
|
/**
|
508
|
* Returns the nomenclatural status type "alternative". A family
|
509
|
* {@link BotanicalName botanical name} is "alternative" if it is a classical name
|
510
|
* long in use, in some cases even before 1753, and is considered as
|
511
|
* {@link NomenclaturalStatusType#VALID() "valid"} although it does not follow the rules for
|
512
|
* family names (see Article 18 of the ICBN).<BR>
|
513
|
* An "alternative" taxon name is treated as if "conserved" and is therefore
|
514
|
* also "legitimate".
|
515
|
*
|
516
|
* @see #VALID()
|
517
|
* @see #CONSERVED()
|
518
|
* @see #isLegitimate()
|
519
|
* @see NameRelationshipType#ALTERNATIVE_NAME()
|
520
|
*/
|
521
|
public static final NomenclaturalStatusType ALTERNATIVE(){
|
522
|
return getTermByUuid(uuidAlternative);
|
523
|
}
|
524
|
|
525
|
/**
|
526
|
* Returns the nomenclatural status type "novum". A "valid"
|
527
|
* ("available") {@link TaxonName taxon name} is "novum" if it has been created
|
528
|
* in order either to replace an earlier name that is "illegitimate" or to
|
529
|
* avoid the building of a "later homonym".<BR>
|
530
|
* A "novum" taxon name is therefore also "legitimate" ("valid" for
|
531
|
* {@link IZoologicalName zoological names}).
|
532
|
*
|
533
|
* @see #VALID()
|
534
|
* @see #isIllegitimate()
|
535
|
* @see NameRelationshipType#REPLACED_SYNONYM()
|
536
|
* @see NameRelationshipType#BLOCKING_NAME_FOR()
|
537
|
*/
|
538
|
public static final NomenclaturalStatusType NOVUM(){
|
539
|
return getTermByUuid(uuidNovum);
|
540
|
}
|
541
|
|
542
|
/**
|
543
|
* Returns the nomenclatural status type "proposed to be utique rejected". A
|
544
|
* "valid" ("available") {@link TaxonName taxon name} is "proposed to be utique rejected"
|
545
|
* if, even though by the strict application of the rules of
|
546
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
547
|
* it is "legitimate" ("valid" for {@link IZoologicalName zoological names}),
|
548
|
* it has been submitted to competent authorities in order to decide whether
|
549
|
* it should be handled as "illegitimate" (without to be rejected in favour
|
550
|
* of a "conserved" taxon name).<BR>
|
551
|
* A "proposed to be utique rejected" taxon name is therefore still "legitimate"
|
552
|
* ("valid" for zoological names).
|
553
|
*
|
554
|
* @see #VALID()
|
555
|
* @see #isLegitimate()
|
556
|
* @see #isIllegitimate()
|
557
|
* @see #REJECTED()
|
558
|
* @see #REJECTED_PROP()
|
559
|
*/
|
560
|
public static final NomenclaturalStatusType UTIQUE_REJECTED_PROP(){
|
561
|
return getTermByUuid(uuidUtiqueRejectedProp);
|
562
|
}
|
563
|
|
564
|
/**
|
565
|
* Returns the nomenclatural status type "conserved (orthography)". A
|
566
|
* {@link TaxonName taxon name} is "conserved (orthography)" if competent authorities
|
567
|
* decided to conserve a different spelling to the one published originally.<BR>
|
568
|
* A "conserved (orthography)" taxon name is "conserved" and hence
|
569
|
* "legitimate" ("valid" for {@link IZoologicalName zoological names}).
|
570
|
*
|
571
|
* @see #isLegitimate()
|
572
|
* @see #CONSERVED()
|
573
|
* @see #ORTHOGRAPHY_CONSERVED_PROP()
|
574
|
* @see NameRelationshipType#ORTHOGRAPHIC_VARIANT()
|
575
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
576
|
*/
|
577
|
public static final NomenclaturalStatusType ORTHOGRAPHY_CONSERVED(){
|
578
|
return getTermByUuid(uuidOrthographyConserved);
|
579
|
}
|
580
|
|
581
|
/**
|
582
|
* Returns the nomenclatural status type "orthography rejected". <BR>
|
583
|
* TBC.
|
584
|
* See also {@link https://dev.e-taxonomy.eu/redmine/issues/5649}
|
585
|
*
|
586
|
* @see #ORTHOGRAPHY_CONSERVED()
|
587
|
* @see #REJECTED()
|
588
|
* @see #isIllegitimate()
|
589
|
*/
|
590
|
public static final NomenclaturalStatusType ORTHOGRAPHY_REJECTED(){
|
591
|
return getTermByUuid(uuidOrthographyRejected);
|
592
|
}
|
593
|
|
594
|
/**
|
595
|
* Returns the nomenclatural status type "proposed to be rejected". A
|
596
|
* "valid" ("available") {@link TaxonName taxon name} is "proposed to be rejected"
|
597
|
* if, even though by the strict application of the rules of
|
598
|
* the {@link NomenclaturalCode nomenclature code}, and especially of the principle of priority,
|
599
|
* it should be "legitimate" ("valid" for {@link IZoologicalName zoological names}),
|
600
|
* it has been submitted to competent authorities in order to decide whether
|
601
|
* it should be handled as "illegitimate".<BR>
|
602
|
* A "proposed to be rejected" taxon name is therefore still "legitimate"
|
603
|
* ("valid" for zoological names). A "proposed to be rejected" taxon name is always
|
604
|
* to be rejected in favour of a "proposed to be conserved" taxon name.
|
605
|
*
|
606
|
* @see #VALID()
|
607
|
* @see #isLegitimate()
|
608
|
* @see #isIllegitimate()
|
609
|
* @see #REJECTED()
|
610
|
* @see #CONSERVED_PROP()
|
611
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
612
|
*/
|
613
|
public static final NomenclaturalStatusType REJECTED_PROP(){
|
614
|
return getTermByUuid(uuidRejectedProp);
|
615
|
}
|
616
|
|
617
|
|
618
|
/**
|
619
|
* Returns the nomenclatural status type "conserved". A "valid"
|
620
|
* ("available") {@link TaxonName taxon name} is "conserved" if, even though by the strict
|
621
|
* application of the rules of the {@link NomenclaturalCode nomenclature code}, and especially of
|
622
|
* the principle of priority, it should be "illegitimate" ("invalid" for
|
623
|
* {@link IZoologicalName zoological names}), competent authorities decided to handle
|
624
|
* it as "legitimate".<BR>
|
625
|
* A "conserved" taxon name is therefore also "legitimate" ("valid" for
|
626
|
* zoological names).
|
627
|
*
|
628
|
* @see #VALID()
|
629
|
* @see #isIllegitimate()
|
630
|
* @see #isLegitimate()
|
631
|
* @see NameRelationshipType#CONSERVED_AGAINST()
|
632
|
*/
|
633
|
public static final NomenclaturalStatusType CONSERVED(){
|
634
|
return getTermByUuid(uuidConserved);
|
635
|
}
|
636
|
|
637
|
/**
|
638
|
* Returns the nomenclatural status type "sanctioned". {@link BotanicalName Botanical names}
|
639
|
* for fungi are "sanctioned" if they were published in the opera mentioned
|
640
|
* in Article 13.1d of the {@link NomenclaturalCode#ICBN() ICBN}.<BR>
|
641
|
* A "sanctioned" taxon name is treated as if "conserved" and is therefore
|
642
|
* also "legitimate".
|
643
|
*
|
644
|
* @see #VALID()
|
645
|
* @see #CONSERVED()
|
646
|
* @see #isLegitimate()
|
647
|
*/
|
648
|
public static final NomenclaturalStatusType SANCTIONED(){
|
649
|
return getTermByUuid(uuidSanctioned);
|
650
|
}
|
651
|
|
652
|
/**
|
653
|
* Returns the nomenclatural status type "invalid" (this corresponds to
|
654
|
* "not available" for {@link IZoologicalName zoological names}). The use of "invalid"
|
655
|
* {@link TaxonName taxon names} should be avoided.<BR>
|
656
|
* A taxon name is "invalid" if it is not "valid"; this means that
|
657
|
* the taxon name:<ul>
|
658
|
* <li>has not been effectively published or
|
659
|
* <li>has a form which does not comply with the rules of the
|
660
|
* {@link NomenclaturalCode nomenclature code} or
|
661
|
* <li>is not accompanied by a description or diagnosis or by a reference to
|
662
|
* such a previously published description or diagnosis
|
663
|
* </ul>
|
664
|
*
|
665
|
* @see #VALID()
|
666
|
* @see #isInvalid()
|
667
|
* @see #ILLEGITIMATE()
|
668
|
*/
|
669
|
public static final NomenclaturalStatusType INVALID(){
|
670
|
return getTermByUuid(uuidInvalid);
|
671
|
}
|
672
|
|
673
|
/**
|
674
|
* Returns the nomenclatural status type "nudum". A {@link TaxonName taxon name} is "nudum"
|
675
|
* if its publication is not accompanied by a description or diagnosis or
|
676
|
* by a reference to such a previously published description or diagnosis.<BR>
|
677
|
* A "nudum" taxon name is therefore also "invalid" ("not available" for
|
678
|
* {@link IZoologicalName zoological names}).
|
679
|
*
|
680
|
* @see #isInvalid()
|
681
|
*/
|
682
|
public static final NomenclaturalStatusType NUDUM(){
|
683
|
return getTermByUuid(uuidNudum);
|
684
|
}
|
685
|
|
686
|
/**
|
687
|
* Returns the nomenclatural status type "invalid combination". A
|
688
|
* {@link TaxonName bi- or trinomial} is an "invalid combination" if its
|
689
|
* {@link NonViralName#getCombinationAuthorship() author} did not definitely associate the final
|
690
|
* epithet with the name of the genus or species, or with its abbreviation.<BR>
|
691
|
* An "invalid combination" taxon name is therefore also "invalid"
|
692
|
* ("not available" for {@link IZoologicalName zoological names}).
|
693
|
*
|
694
|
* @see #isInvalid()
|
695
|
*/
|
696
|
public static final NomenclaturalStatusType COMBINATION_INVALID(){
|
697
|
return getTermByUuid(uuidCombinationInvalid);
|
698
|
}
|
699
|
|
700
|
/**
|
701
|
* Returns the nomenclatural status type "illegitimate combination".
|
702
|
* TODO explanation
|
703
|
*
|
704
|
* @see #isInvalid()
|
705
|
*/
|
706
|
public static final NomenclaturalStatusType COMBINATION_ILLEGITIMATE(){
|
707
|
return getTermByUuid(uuidCombinationIllegitimate);
|
708
|
}
|
709
|
|
710
|
/**
|
711
|
* Returns the nomenclatural status type "provisional". A {@link TaxonName taxon name} is
|
712
|
* "provisional" if it is not validly published, because not finally accepted by the author<BR>
|
713
|
* Some people use it in the same way as {@link #INED() ined.}
|
714
|
*
|
715
|
* @see #INED()
|
716
|
* @see #isInvalid()
|
717
|
*/
|
718
|
public static final NomenclaturalStatusType PROVISIONAL(){
|
719
|
return getTermByUuid(uuidProvisional);
|
720
|
}
|
721
|
|
722
|
/**
|
723
|
* Returns the nomenclatural status type "ined.". A {@link TaxonName taxon name} is
|
724
|
* "inedited" if it it has not yet been published.<BR>
|
725
|
* An inedited taxon name is therefore also "invalid" (bot.) / "not available (zool.)
|
726
|
*<BR>
|
727
|
* see also https://dev.e-taxonomy.eu/redmine/issues/5896
|
728
|
*
|
729
|
* @see #PROVISIONAL()
|
730
|
* @see #isInvalid()
|
731
|
* @return
|
732
|
*/
|
733
|
public static final NomenclaturalStatusType INED(){
|
734
|
return getTermByUuid(uuidIned);
|
735
|
}
|
736
|
|
737
|
/**
|
738
|
* Returns the nomenclatural status type "valid" (this corresponds to
|
739
|
* "available" for {@link IZoologicalName zoological names}).<BR>
|
740
|
* A {@link TaxonName taxon name} is "valid" if it:<ul>
|
741
|
* <li>has been effectively published and
|
742
|
* <li>has a form which complies with the rules of the
|
743
|
* {@link NomenclaturalCode nomenclature code} and
|
744
|
* <li>is accompanied by a description or diagnosis or by a reference to
|
745
|
* such a previously published description or diagnosis
|
746
|
* </ul>
|
747
|
*
|
748
|
* @see #INVALID()
|
749
|
* @see #LEGITIMATE()
|
750
|
*/
|
751
|
public static final NomenclaturalStatusType VALID(){
|
752
|
return getTermByUuid(uuidValid);
|
753
|
}
|
754
|
|
755
|
/**
|
756
|
* Returns the nomenclatural status type "subnudum". This type is not
|
757
|
* covered by {@link NomenclaturalCode nomenclature codes}. It appears
|
758
|
* sometimes in literature and represents the opinion of the author who
|
759
|
* considers the {@link TaxonName taxon name} to be unusable for an unambiguous
|
760
|
* taxonomic use.
|
761
|
*
|
762
|
* As the name is not explicitly invalid we handle it as valid name.
|
763
|
* For discussion see #3046#comment:4
|
764
|
*
|
765
|
* @see #AMBIGUOUS()
|
766
|
* @see #CONFUSUM()
|
767
|
*
|
768
|
*/
|
769
|
public static final NomenclaturalStatusType SUBNUDUM(){
|
770
|
return getTermByUuid(uuidSubnudum);
|
771
|
}
|
772
|
|
773
|
/**
|
774
|
* Returns the nomenclatural status type "comb. nov.". No further information available for now.
|
775
|
* @return
|
776
|
*/
|
777
|
//TODO javadoc. this term was added for Flore du Gabon
|
778
|
public static final NomenclaturalStatusType COMB_NOV(){
|
779
|
return getTermByUuid(uuidCombNov);
|
780
|
}
|
781
|
|
782
|
/**
|
783
|
* Returns the nomenclatural status type "opus utique oppressum". This type
|
784
|
* relates to article 32.7 (old ICBN) and article 32.9 as well as App. 6
|
785
|
* (new {@link NomenclaturalCode#ICBN() ICBN}). This is a reference list of botanical opera, in which all
|
786
|
* {@link BotanicalName taxon names} (or names of a certain rank) are oppressed. Such a name has the
|
787
|
* status "invalid" but in contrary to "rejected" not a single name
|
788
|
* is rejected by the commission but an opus with regard to the validity of
|
789
|
* all taxon names occurring in it.<BR>
|
790
|
* An "opus utique oppressum" taxon name is therefore also "invalid"
|
791
|
* ("not available" for {@link IZoologicalName zoological names}).
|
792
|
*
|
793
|
* @see #isInvalid()
|
794
|
*/
|
795
|
public static final NomenclaturalStatusType OPUS_UTIQUE_OPPR(){
|
796
|
return getTermByUuid(uuidOpusUtiqueOppr);
|
797
|
}
|
798
|
|
799
|
/**
|
800
|
* Returns the nomenclatural status type "protected name".
|
801
|
* It indicates a valid name.
|
802
|
* "The name of an organism treated as a fungus listed (in App. IIA, III, and IV)
|
803
|
* with its type and treated as conserved against any competing listed or unlisted
|
804
|
* synonyms or homonyms (including sanctioned names), although conservation
|
805
|
* under Art. 14 overrides this protection (Art. F.2.1)."
|
806
|
*
|
807
|
* See also #9272.
|
808
|
*
|
809
|
* @return the nomenclatural status type "protected name"
|
810
|
*/
|
811
|
public static final NomenclaturalStatusType PROTECTED_NAME(){
|
812
|
return getTermByUuid(uuidProtected);
|
813
|
}
|
814
|
|
815
|
/**
|
816
|
* Returns the nomenclatural status type "herbarium designation".
|
817
|
* It indicates an invalid designation (invalid name).
|
818
|
*
|
819
|
* See also #9272.
|
820
|
*
|
821
|
* @return the nomenclatural status type "herbarium designation"
|
822
|
*/
|
823
|
public static final NomenclaturalStatusType IN_SCHEDA(){
|
824
|
return getTermByUuid(uuidScheda);
|
825
|
}
|
826
|
|
827
|
/**
|
828
|
* Returns the nomenclatural status type "published in synonymy".
|
829
|
* It indicates an invalid designation (invalid name).
|
830
|
*
|
831
|
* See also #9272.
|
832
|
*
|
833
|
* @return the nomenclatural status type "published in synonymy"
|
834
|
*/
|
835
|
public static final NomenclaturalStatusType PRO_SYNONYMO(){
|
836
|
return getTermByUuid(uuidProSynonymo);
|
837
|
}
|
838
|
|
839
|
/**
|
840
|
* Returns the nomenclatural status type "orthographical variant".
|
841
|
* This status should only be used if the other name this name is
|
842
|
* an orth. var. for is not known for some reason.
|
843
|
* Otherwise use name relationship {@link NameRelationshipType#ORTHOGRAPHIC_VARIANT()}.
|
844
|
* These 2 types may be unified in future (#9273).
|
845
|
*
|
846
|
* See also #9272.
|
847
|
*
|
848
|
* @return the nomenclatural status type "orthographical variant"
|
849
|
*/
|
850
|
public static final NomenclaturalStatusType ORTH_VAR(){
|
851
|
return getTermByUuid(uuidOrthVar);
|
852
|
}
|
853
|
|
854
|
/**
|
855
|
* Returns the nomenclatural status type "unpublished combination".
|
856
|
* A {@link TaxonName combination} is "inedited" if it it has not yet been published.<BR>
|
857
|
* An inedited taxon name is therefore also "invalid" (bot.) / "not available (zool.)
|
858
|
* <BR><BR>
|
859
|
* {@link https://dev.e-taxonomy.eu/redmine/issues/5795}
|
860
|
*
|
861
|
* @see #INED()
|
862
|
* @see #PROVISIONAL()
|
863
|
* @see #isInvalid()
|
864
|
* @return the nomenclatural status type "comb. ined."
|
865
|
*/
|
866
|
public static final NomenclaturalStatusType COMB_INED(){
|
867
|
return getTermByUuid(uuidCombIned);
|
868
|
}
|
869
|
|
870
|
/**
|
871
|
* TODO
|
872
|
* @return
|
873
|
*/
|
874
|
public static final NomenclaturalStatusType ZOO_NOT_AVAILABLE (){
|
875
|
return getTermByUuid(uuidZooNotAvailable);
|
876
|
}
|
877
|
|
878
|
/**
|
879
|
* TODO
|
880
|
* @return
|
881
|
*/
|
882
|
public static final NomenclaturalStatusType ZOO_INVALID (){
|
883
|
return getTermByUuid(uuidZooInvalid);
|
884
|
}
|
885
|
|
886
|
/**
|
887
|
* TODO
|
888
|
* @return
|
889
|
*/
|
890
|
public static final NomenclaturalStatusType ZOO_SUPPRESSED (){
|
891
|
return getTermByUuid(uuidZooSuppressed);
|
892
|
}
|
893
|
|
894
|
/**
|
895
|
* TODO
|
896
|
* @return
|
897
|
*/
|
898
|
public static final NomenclaturalStatusType ZOO_OBLITUM (){
|
899
|
return getTermByUuid(uuidZooOblitum);
|
900
|
}
|
901
|
|
902
|
//TODO further Zoological status
|
903
|
|
904
|
// TODO
|
905
|
// Preliminary implementation for BotanicalNameParser.
|
906
|
// not yet complete
|
907
|
/**
|
908
|
* Returns the nomenclatural status type identified through its label
|
909
|
* abbreviation. Preliminary implementation for BotanicalNameParser.
|
910
|
*
|
911
|
* @param statusAbbreviation the label abbreviation
|
912
|
* @param name the taxon name
|
913
|
* @return the nomenclatural status type
|
914
|
*
|
915
|
*/
|
916
|
public static NomenclaturalStatusType getNomenclaturalStatusTypeByAbbreviation(String statusAbbreviation, ITaxonNameBase name) throws UnknownCdmTypeException{
|
917
|
if (statusAbbreviation == null){
|
918
|
throw new NullPointerException("Abbreviation is NULL in getNomenclaturalStatusTypeByAbbreviation");
|
919
|
}
|
920
|
NomenclaturalStatusType result = null;
|
921
|
statusAbbreviation = normalizeStatusAbbrev(statusAbbreviation);
|
922
|
|
923
|
//TODO handle undefined names correctly
|
924
|
boolean isZooname = name == null? false : name.getNameType().equals(NomenclaturalCode.ICZN);
|
925
|
|
926
|
Map<String, UUID> map = isZooname ? zooAbbrevMap : abbrevMap;
|
927
|
if (map == null ){
|
928
|
return null;
|
929
|
}
|
930
|
//non unique abbrev
|
931
|
if (! isZooname && statusAbbreviation.equalsIgnoreCase("nom. alternativ.")){
|
932
|
return NomenclaturalStatusType.ALTERNATIVE();
|
933
|
}
|
934
|
UUID uuid = map.get(statusAbbreviation);
|
935
|
if (uuid != null ){
|
936
|
result = getTermByUuid(uuid);
|
937
|
}
|
938
|
if (result != null){
|
939
|
return result;
|
940
|
}else {
|
941
|
throw new UnknownCdmTypeException("Unknown nom. status abbreviation: " + statusAbbreviation);
|
942
|
}
|
943
|
}
|
944
|
|
945
|
private static String normalizeStatusAbbrev(String statusAbbreviation) {
|
946
|
//#7109 should not happen anymore
|
947
|
if (statusAbbreviation.equalsIgnoreCase("nom. valid")){
|
948
|
statusAbbreviation = "nom. val.";
|
949
|
}
|
950
|
return statusAbbreviation;
|
951
|
}
|
952
|
|
953
|
/**
|
954
|
* Returns the nomenclatural status type identified through its label.
|
955
|
*
|
956
|
* @param statusLabel the nomenclatural status label
|
957
|
* @return the nomenclatural status type
|
958
|
*
|
959
|
*/
|
960
|
public static NomenclaturalStatusType getNomenclaturalStatusTypeByLabel(String statusLabel) throws UnknownCdmTypeException{
|
961
|
if (statusLabel == null){
|
962
|
throw new NullPointerException("Status label is NULL in getNomenclaturalStatusTypeBylabel");
|
963
|
}
|
964
|
NomenclaturalStatusType result = null;
|
965
|
if (labelMap == null){
|
966
|
return null;
|
967
|
}
|
968
|
statusLabel = statusLabel.toLowerCase();
|
969
|
UUID uuid = labelMap.get(statusLabel);
|
970
|
if (uuid != null ){
|
971
|
result = getTermByUuid(uuid);
|
972
|
}
|
973
|
if (result != null){
|
974
|
return result;
|
975
|
}else {
|
976
|
if (statusLabel == null){
|
977
|
statusLabel = "(null)";
|
978
|
}
|
979
|
throw new UnknownCdmTypeException("Unknown nom. status label: " + statusLabel);
|
980
|
}
|
981
|
}
|
982
|
|
983
|
/**
|
984
|
* Fills <i>this</i> nomenclatural status type with contents (uuid, uri,
|
985
|
* description text, label and label abbreviation) coming from a csv line.
|
986
|
* The implicit language for the description text is "latin".
|
987
|
* This method overrides the method of {@link eu.etaxonomy.cdm.model.term.DefinedTermBase DefinedTermBase}.
|
988
|
*
|
989
|
* @param csvLine the (ordered) list of substrings from a csv string
|
990
|
* to be used to fill <i>this</i> nomenclatural status type
|
991
|
* @see #NomenclaturalStatusType(String, String, String)
|
992
|
* @see #readCsvLine(List, Language)
|
993
|
* @see eu.etaxonomy.cdm.model.term.DefinedTermBase#readCsvLine(List)
|
994
|
*/
|
995
|
|
996
|
@Override
|
997
|
public NomenclaturalStatusType readCsvLine(Class<NomenclaturalStatusType> termClass, List<String> csvLine, TermType termType,
|
998
|
Map<UUID,DefinedTermBase> terms, boolean abbrevAsId) { //TODO should be List<String> but makes error for some strange reason
|
999
|
try {
|
1000
|
NomenclaturalStatusType newInstance = termClass.newInstance();
|
1001
|
newInstance.setTermType(termType);
|
1002
|
DefinedTermBase.readCsvLine(newInstance, csvLine, Language.LATIN(), abbrevAsId);
|
1003
|
String nomenclaturalStanding = csvLine.get(5).trim(); //not in use yet?
|
1004
|
newInstance.setNomenclaturalStanding(NomenclaturalStanding.getByKey(nomenclaturalStanding));
|
1005
|
|
1006
|
return newInstance;
|
1007
|
} catch (Exception e) {
|
1008
|
e.printStackTrace();
|
1009
|
throw new RuntimeException(e);
|
1010
|
}
|
1011
|
}
|
1012
|
|
1013
|
@Override
|
1014
|
protected void setDefaultTerms(TermVocabulary<NomenclaturalStatusType> termVocabulary) {
|
1015
|
if (termVocabulary.getUuid().equals(uuidIcnafpNomStatusVocabulary)){
|
1016
|
termMap = new HashMap<>();
|
1017
|
abbrevMap = new HashMap<>();
|
1018
|
labelMap = new HashMap<>();
|
1019
|
for (NomenclaturalStatusType term : termVocabulary.getTerms()){
|
1020
|
termMap.put(term.getUuid(), term);
|
1021
|
addStatusType(term, abbrevMap, labelMap);
|
1022
|
}
|
1023
|
}else if (termVocabulary.getUuid().equals(uuidIcznNomStatusVocabulary)){
|
1024
|
zooTermMap = new HashMap<>();
|
1025
|
zooAbbrevMap = new HashMap<>();
|
1026
|
zooLabelMap = new HashMap<>();
|
1027
|
for (NomenclaturalStatusType term : termVocabulary.getTerms()){
|
1028
|
zooTermMap.put(term.getUuid(), term);
|
1029
|
addStatusType(term, zooAbbrevMap, zooLabelMap);
|
1030
|
}
|
1031
|
}else{
|
1032
|
throw new IllegalArgumentException("Unknown Nom.Status Vocabulary");
|
1033
|
}
|
1034
|
}
|
1035
|
|
1036
|
public static void initDefaultTerms() {
|
1037
|
TermVocabulary<NomenclaturalStatusType> vocabulary = getTermByUuid(uuidDoubtful).getVocabulary();
|
1038
|
(new NomenclaturalStatusType()).setDefaultTerms(vocabulary);
|
1039
|
}
|
1040
|
|
1041
|
/**
|
1042
|
* Adds the status type to the (abbreviated) label maps
|
1043
|
* @param term
|
1044
|
*/
|
1045
|
private void addStatusType(NomenclaturalStatusType statusType, Map<String, UUID> abbrevMap, Map<String, UUID> labelMap ) {
|
1046
|
if (statusType == null){
|
1047
|
logger.warn("statusType is NULL");
|
1048
|
return;
|
1049
|
}
|
1050
|
List<Language> list = new ArrayList<>();
|
1051
|
list.add(Language.LATIN());
|
1052
|
list.add(Language.ENGLISH());
|
1053
|
list.add(Language.DEFAULT());
|
1054
|
|
1055
|
Representation representation = statusType.getPreferredRepresentation(list);
|
1056
|
if (representation != null){
|
1057
|
|
1058
|
String abbrevLabel = representation.getAbbreviatedLabel();
|
1059
|
String label = representation.getLabel();
|
1060
|
if (abbrevLabel == null){
|
1061
|
logger.warn("label is NULL");
|
1062
|
return;
|
1063
|
}
|
1064
|
|
1065
|
//add to map
|
1066
|
abbrevMap.put(abbrevLabel, statusType.getUuid());
|
1067
|
labelMap.put(label.toLowerCase(), statusType.getUuid());
|
1068
|
}
|
1069
|
|
1070
|
}
|
1071
|
|
1072
|
/**
|
1073
|
* NomenclaturalStatusType should always be shown in latin, therefore the only existing representation
|
1074
|
* is the latin one. In case we pass in another Language to this method it will return a <code>null</code> representation.
|
1075
|
*
|
1076
|
* In case the representation becomes null, we fall back to the latin representation.
|
1077
|
*
|
1078
|
*/
|
1079
|
@Override
|
1080
|
public Representation getRepresentation(Language lang) {
|
1081
|
Representation representation = super.getRepresentation(lang);
|
1082
|
|
1083
|
if(representation == null){
|
1084
|
representation = super.getRepresentation(Language.LATIN());
|
1085
|
}
|
1086
|
|
1087
|
return representation;
|
1088
|
}
|
1089
|
}
|