Merge branch 'hotfix/5.5.2'
[cdmlib.git] / cdmlib-model / src / main / java / eu / etaxonomy / cdm / model / name / Rank.java
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.name;
11
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.commons.lang.StringUtils;
26 import org.apache.log4j.Logger;
27 import org.hibernate.annotations.Type;
28 import org.hibernate.envers.Audited;
29
30 import eu.etaxonomy.cdm.common.CdmUtils;
31 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
32 import eu.etaxonomy.cdm.model.common.Language;
33 import eu.etaxonomy.cdm.model.common.OrderedTermBase;
34 import eu.etaxonomy.cdm.model.common.Representation;
35 import eu.etaxonomy.cdm.model.common.TermType;
36 import eu.etaxonomy.cdm.model.common.TermVocabulary;
37 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
38
39 /**
40 * The class representing the taxonomical ranks (like "Family", "Genus" or
41 * "Species") used for {@link TaxonName taxon names} across all {@link NomenclaturalCode nomenclatural codes}
42 * for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
43 * cultivars (ICNCP) and animals (ICZN).
44 * <P>
45 * A standard (ordered) list of taxonomical rank instances will be automatically
46 * created as the project starts. But this class allows to extend this standard
47 * list by creating new instances of additional taxonomical ranks if needed.
48 * <P>
49 * This class corresponds to: <ul>
50 * <li> TaxonRankTerm according to the TDWG ontology
51 * <li> TaxonomicRankEnum according to the TCS
52 * <li> Rank according to the ABCD schema
53 * </ul>
54 *
55 * @author m.doering
56 * @since 08-Nov-2007 13:06:46
57 */
58 @XmlAccessorType(XmlAccessType.FIELD)
59 @XmlType(name = "Rank")
60 @Entity
61 //@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
62 //@Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
63 @Audited
64 public class Rank extends OrderedTermBase<Rank> {
65 private static final long serialVersionUID = -8648081681348758485L;
66 private static final Logger logger = Logger.getLogger(Rank.class);
67
68 private static final UUID uuidEmpire = UUID.fromString("ac470211-1586-4b24-95ca-1038050b618d");
69 private static final UUID uuidDomain = UUID.fromString("ffca6ec8-8b88-417b-a6a0-f7c992aac19b");
70 private static final UUID uuidSuperkingdom = UUID.fromString("64223610-7625-4cfd-83ad-b797bf7f0edd");
71 private static final UUID uuidKingdom = UUID.fromString("fbe7109d-66b3-498c-a697-c6c49c686162");
72 private static final UUID uuidSubkingdom = UUID.fromString("a71bd9d8-f3ab-4083-afb5-d89315d71655");
73 private static final UUID uuidInfrakingdom = UUID.fromString("1e37930c-86cf-44f6-90fd-7822928df260");
74 private static final UUID uuidSuperphylum = UUID.fromString("0d0cecb1-e254-4607-b210-6801e7ecbb04");
75 private static final UUID uuidPhylum = UUID.fromString("773430d2-76b4-438c-b817-97a543a33287");
76 private static final UUID uuidSubphylum = UUID.fromString("23a9b6ff-9408-49c9-bd9e-7a2ca5ab4725");
77 private static final UUID uuidInfraphylum = UUID.fromString("1701de3a-7693-42a5-a2d3-42697f944190");
78 private static final UUID uuidSuperdivision = UUID.fromString("a735a48f-4fc8-49a7-ae0c-6a984f658131");
79 private static final UUID uuidDivision = UUID.fromString("7e56f5cc-123a-4fd1-8cbb-6fd80358b581");
80 private static final UUID uuidSubdivision = UUID.fromString("931c840f-7a6b-4d76-ad38-bfdd77d7b2e8");
81 private static final UUID uuidInfradivision = UUID.fromString("c0ede273-be52-4dee-b411-66ee08d30c94");
82 private static final UUID uuidSuperclass = UUID.fromString("e65b4e1a-21ec-428d-9b9f-e87721ab967c");
83 private static final UUID uuidClass = UUID.fromString("f23d14c4-1d34-4ee6-8b4e-eee2eb9a3daf");
84 private static final UUID uuidSubclass = UUID.fromString("8cb26733-e2f5-46cb-ab5c-f99254f877aa");
85 private static final UUID uuidInfraclass = UUID.fromString("ad23cfda-879a-4021-8629-c54d27caf717");
86 private static final UUID uuidSuperorder = UUID.fromString("c8c67a22-301a-4219-b882-4a49121232ff");
87 private static final UUID uuidOrder = UUID.fromString("b0785a65-c1c1-4eb4-88c7-dbd3df5aaad1");
88 private static final UUID uuidSuborder = UUID.fromString("768ad378-fa85-42ab-b668-763225832f57");
89 private static final UUID uuidInfraorder = UUID.fromString("84099182-a6f5-47d7-8586-33c9e9955a10");
90 private static final UUID uuidSectionZoology = UUID.fromString("691d371e-10d7-43f0-93db-3d7fa1a62c54");
91 private static final UUID uuidSubsectionZoology = UUID.fromString("0ed32d28-adc4-4303-a9ca-68e2acd67e33");
92 private static final UUID uuidSuperfamily = UUID.fromString("2cfa510a-dcea-4a03-b66a-b1528f9b0796");
93 private static final UUID uuidFamily = UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6");
94 private static final UUID uuidSubfamily = UUID.fromString("862526ee-7592-4760-a23a-4ff3641541c5");
95 private static final UUID uuidInfrafamily = UUID.fromString("c3f2e3bb-6eef-4a26-9fb7-b14f4c8c5e4f");
96 private static final UUID uuidSupertribe = UUID.fromString("11e94828-8c61-499b-87d6-1de35ce2c51c");
97 private static final UUID uuidTribe = UUID.fromString("4aa6890b-0363-4899-8d7c-ee0cb78e6166");
98 private static final UUID uuidSubtribe = UUID.fromString("ae41ecc5-5165-4126-9d24-79939ae5d822");
99 private static final UUID uuidInfratribe = UUID.fromString("1ec02e8f-f2b7-4c65-af9f-b436b34c79a3");
100 private static final UUID uuidSupragenericTaxon = UUID.fromString("1fdc0b93-c354-441a-8406-091e0303ff5c");
101 public static final UUID uuidGenus = UUID.fromString("1b11c34c-48a8-4efa-98d5-84f7f66ef43a");
102 private static final UUID uuidSubgenus = UUID.fromString("78786e16-2a70-48af-a608-494023b91904");
103 private static final UUID uuidInfragenus = UUID.fromString("a9972969-82cd-4d54-b693-a096422f13fa");
104 private static final UUID uuidSectionBotany = UUID.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
105 private static final UUID uuidSubsectionBotany = UUID.fromString("d20f5b61-d463-4448-8f8a-c1ff1f262f59");
106 private static final UUID uuidSeries = UUID.fromString("d7381ecf-48f8-429b-9c54-f461656978cd");
107 private static final UUID uuidSubseries = UUID.fromString("80c9a263-f4db-4a13-b6c2-b7fec1aa1200");
108 private static final UUID uuidSpeciesAggregate = UUID.fromString("1ecae058-4217-4f75-9c27-6d8ba099ac7a");
109 private static final UUID uuidSpeciesGroup = UUID.fromString("d1988a11-292b-46fa-8fb7-bc64ea6d8fc6");
110 public static final UUID uuidInfragenericTaxon = UUID.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
111 public static final UUID uuidSpecies = UUID.fromString("b301f787-f319-4ccc-a10f-b4ed3b99a86d");
112 private static final UUID uuidSubspecificAggregate = UUID.fromString("72c248b9-027d-4402-b375-dd4f0850c9ad");
113 private static final UUID uuidSubspecies = UUID.fromString("462a7819-8b00-4190-8313-88b5be81fad5");
114 private static final UUID uuidInfraspecies = UUID.fromString("f28ebc9e-bd50-4194-9af1-42f5cb971a2c");
115 private static final UUID uuidNatio = UUID.fromString("965f2f38-7f97-4270-ab5a-1999bf050a22");
116 private static final UUID uuidVariety = UUID.fromString("d5feb6a5-af5c-45ef-9878-bb4f36aaf490");
117 private static final UUID uuidBioVariety = UUID.fromString("a3a364cb-1a92-43fc-a717-3c44980a0991");
118 private static final UUID uuidPathoVariety = UUID.fromString("2f4f4303-a099-47e3-9048-d749d735423b");
119 private static final UUID uuidSubvariety = UUID.fromString("9a83862a-7aee-480c-a98d-4bceaf8712ca");
120 private static final UUID uuidSubsubvariety = UUID.fromString("bff22f84-553a-4429-a4e7-c4b3796c3a18");
121
122 private static final UUID uuidProles = UUID.fromString("8810d1ba-6a34-4ae3-a355-919ccd1cd1a5");
123 private static final UUID uuidRace = UUID.fromString("196dee39-cfd8-4460-8bf0-88b83da27f62");
124 private static final UUID uuidSublusus = UUID.fromString("1fafa596-a8e7-4e62-a378-3cc8cb3627ca");
125
126 private static final UUID uuidConvar = UUID.fromString("2cc740c9-cebb-43c8-9b06-1bef79e6a56a");
127 private static final UUID uuidForm = UUID.fromString("0461281e-458a-47b9-8d41-19a3d39356d5");
128 private static final UUID uuidSpecialForm = UUID.fromString("bed20aee-2f5a-4635-9c02-eff06246d067");
129 private static final UUID uuidSubform = UUID.fromString("47cfc5b0-0fb7-4ceb-b61d-e1dd8de8b569");
130 private static final UUID uuidSubsubform = UUID.fromString("1c8ac389-4349-4ae0-87be-7239f6635068");
131 public static final UUID uuidInfraspecificTaxon = UUID.fromString("eb75c27d-e154-4570-9d96-227b2df60474");
132 private static final UUID uuidCandidate = UUID.fromString("ead9a1f5-dfd4-4de2-9121-70a47accb10b");
133 private static final UUID uuidDenominationClass = UUID.fromString("49bdf74a-2170-40ed-8be2-887a0db517bf");
134 private static final UUID uuidGrex = UUID.fromString("08dcb4ff-ac58-48a3-93af-efb3d836ac84");
135 private static final UUID uuidGraftChimaera = UUID.fromString("6b4063bc-f934-4796-9bf3-0ef3aea5c1cb");
136 private static final UUID uuidCultivarGroup = UUID.fromString("d763e7d3-e7de-4bb1-9d75-225ca6948659");
137 private static final UUID uuidCultivar = UUID.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
138 private static final UUID uuidUnknownRank = UUID.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
139
140 //additional (not yet in csv files, but used in single databases)
141 //https://dev.e-taxonomy.eu/redmine/issues/7285
142 public static final UUID uuidCohort = UUID.fromString("3e4dc2fa-79e8-4ee7-b7d8-4c02a18fe555"); //edaphobase
143 public static final UUID uuidHyporder = UUID.fromString("2a1bdf1f-80fc-4846-b4d7-edcbf664f270"); //edaphobase
144
145
146
147 private static Map<String, UUID> idInVocMap = null;
148 private static Map<String, UUID> labelMap = null;
149
150 protected static Map<UUID, Rank> termMap = null;
151
152 //*********************** Factory methods ********************************************/
153
154 // /**
155 // * Creates a new empty rank.
156 // *
157 // * @see #NewInstance(String, String, String)
158 // */
159 // private static Rank NewInstance(){
160 // return new Rank();
161 // }
162
163 /**
164 * Creates an additional rank with a description (in the {@link Language#DEFAULT() default language}),
165 * a label and a label abbreviation.
166 *
167 * @param term the string (in the default language) describing the
168 * new rank to be created
169 * @param label the string identifying the new rank to be created
170 * @param labelAbbrev the string identifying (in abbreviated form) the
171 * new rank to be created
172 * @see #NewInstance()
173 */
174 public static Rank NewInstance(RankClass rankClass, String term, String label, String labelAbbrev){
175 return new Rank(rankClass, term, label, labelAbbrev);
176 }
177
178 /**
179 * The {@link RankClass rank class} of a rank. It is usually needed for correct formatting of a
180 * rank by using e.g. isSupraGeneric(). Prior to v3.3 this was computed by comparison of ranks.
181 */
182 @XmlAttribute(name ="RankClass")
183 @NotNull
184 @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
185 parameters = {@org.hibernate.annotations.Parameter(name="enumClass", value="eu.etaxonomy.cdm.model.name.RankClass")}
186 )
187 @Audited
188 private RankClass rankClass;
189
190
191 //********************************** Constructor *********************************/
192
193 //for hibernate use only
194 @Deprecated
195 protected Rank() {
196 super(TermType.Rank);
197 }
198
199 /**
200 * Class constructor: creates an additional rank instance with a description
201 * (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and a label abbreviation.
202 *
203 * @param term the string (in the default language) describing the
204 * new rank to be created
205 * @param label the string identifying the new rank to be created
206 * @param labelAbbrev the string identifying (in abbreviated form) the
207 * new rank to be created
208 * @see #Rank()
209 */
210 protected Rank(RankClass rankClass, String term, String label, String labelAbbrev) {
211 super(TermType.Rank, term, label, labelAbbrev);
212 this.rankClass = rankClass;
213 }
214
215
216 //********* METHODS **************************************/
217
218 /* (non-Javadoc)
219 * @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
220 */
221 @Override
222 public void resetTerms(){
223 termMap = null;
224 }
225
226
227
228 protected static Rank getTermByUuid(UUID uuid){
229 if (termMap == null || termMap.isEmpty()){
230 return getTermByClassAndUUID(Rank.class, uuid);
231 } else {
232 return termMap.get(uuid);
233 }
234 }
235
236 public static final Rank EMPIRE(){
237 return getTermByUuid(uuidEmpire);
238 }
239 public static final Rank DOMAIN(){
240 return getTermByUuid(uuidDomain);
241 }
242 public static final Rank SUPERKINGDOM(){
243 return getTermByUuid(uuidSuperkingdom);
244 }
245 public static final Rank KINGDOM(){
246 return getTermByUuid(uuidKingdom);
247 }
248 public static final Rank SUBKINGDOM(){
249 return getTermByUuid(uuidSubkingdom);
250 }
251 public static final Rank INFRAKINGDOM(){
252 return getTermByUuid(uuidInfrakingdom);
253 }
254 public static final Rank SUPERPHYLUM(){
255 return getTermByUuid(uuidSuperphylum);
256 }
257 public static final Rank PHYLUM(){
258 return getTermByUuid(uuidPhylum);
259 }
260 public static final Rank SUBPHYLUM(){
261 return getTermByUuid(uuidSubphylum);
262 }
263 public static final Rank INFRAPHYLUM(){
264 return getTermByUuid(uuidInfraphylum);
265 }
266 public static final Rank SUPERDIVISION(){
267 return getTermByUuid(uuidSuperdivision);
268 }
269 public static final Rank DIVISION(){
270 return getTermByUuid(uuidDivision);
271 }
272 public static final Rank SUBDIVISION(){
273 return getTermByUuid(uuidSubdivision);
274 }
275 public static final Rank INFRADIVISION(){
276 return getTermByUuid(uuidInfradivision);
277 }
278 public static final Rank SUPERCLASS(){
279 return getTermByUuid(uuidSuperclass);
280 }
281 public static final Rank CLASS(){
282 return getTermByUuid(uuidClass);
283 }
284 public static final Rank SUBCLASS(){
285 return getTermByUuid(uuidSubclass);
286 }
287 public static final Rank INFRACLASS(){
288 return getTermByUuid(uuidInfraclass);
289 }
290 public static final Rank SUPERORDER(){
291 return getTermByUuid(uuidSuperorder);
292 }
293 public static final Rank ORDER(){
294 return getTermByUuid(uuidOrder);
295 }
296 public static final Rank SUBORDER(){
297 return getTermByUuid(uuidSuborder);
298 }
299 public static final Rank INFRAORDER(){
300 return getTermByUuid(uuidInfraorder);
301 }
302 public static final Rank SUPERFAMILY(){
303 return getTermByUuid(uuidSuperfamily);
304 }
305 public static final Rank FAMILY(){
306 return getTermByUuid(uuidFamily);
307 }
308 public static final Rank SUBFAMILY(){
309 return getTermByUuid(uuidSubfamily);
310 }
311 public static final Rank INFRAFAMILY(){
312 return getTermByUuid(uuidInfrafamily);
313 }
314 public static final Rank SUPERTRIBE(){
315 return getTermByUuid(uuidSupertribe);
316 }
317 public static final Rank TRIBE(){
318 return getTermByUuid(uuidTribe);
319 }
320 public static final Rank SUBTRIBE(){
321 return getTermByUuid(uuidSubtribe);
322 }
323 public static final Rank INFRATRIBE(){
324 return getTermByUuid(uuidInfratribe);
325 }
326 public static final Rank SUPRAGENERICTAXON(){
327 return getTermByUuid(uuidSupragenericTaxon);
328 }
329 public static final Rank GENUS(){
330 return getTermByUuid(uuidGenus);
331 }
332 public static final Rank SUBGENUS(){
333 return getTermByUuid(uuidSubgenus);
334 }
335 public static final Rank INFRAGENUS(){
336 return getTermByUuid(uuidInfragenus);
337 }
338 public static final Rank SECTION_BOTANY(){
339 return getTermByUuid(uuidSectionBotany);
340 }
341 public static final Rank SUBSECTION_BOTANY(){
342 return getTermByUuid(uuidSubsectionBotany);
343 }
344 public static final Rank SECTION_ZOOLOGY(){
345 return getTermByUuid(uuidSectionZoology);
346 }
347 public static final Rank SUBSECTION_ZOOLOGY(){
348 return getTermByUuid(uuidSubsectionZoology);
349 }
350 public static final Rank SERIES(){
351 return getTermByUuid(uuidSeries);
352 }
353 public static final Rank SUBSERIES(){
354 return getTermByUuid(uuidSubseries);
355 }
356 public static final Rank SPECIESAGGREGATE(){
357 return getTermByUuid(uuidSpeciesAggregate);
358 }
359 public static final Rank SPECIESGROUP(){
360 return getTermByUuid(uuidSpeciesGroup);
361 }
362 /**
363 * 'Unranked infrageneric'. An infrageneric rank which is on purpose not further defined.
364 * This sometimes holds for names from the 19th century.
365 */
366 public static final Rank INFRAGENERICTAXON(){
367 return getTermByUuid(uuidInfragenericTaxon);
368 }
369 public static final Rank SPECIES(){
370 return getTermByUuid(uuidSpecies);
371 }
372 public static final Rank SUBSPECIFICAGGREGATE(){
373 return getTermByUuid(uuidSubspecificAggregate);
374 }
375 public static final Rank SUBSPECIES(){
376 return getTermByUuid(uuidSubspecies);
377 }
378 public static final Rank INFRASPECIES(){
379 return getTermByUuid(uuidInfraspecies);
380 }
381 public static final Rank VARIETY(){
382 return getTermByUuid(uuidVariety);
383 }
384 public static final Rank BIOVARIETY(){
385 return getTermByUuid(uuidBioVariety);
386 }
387 public static final Rank PATHOVARIETY(){
388 return getTermByUuid(uuidPathoVariety);
389 }
390 public static final Rank SUBVARIETY(){
391 return getTermByUuid(uuidSubvariety);
392 }
393 public static final Rank SUBSUBVARIETY(){
394 return getTermByUuid(uuidSubsubvariety );
395 }
396 public static final Rank PROLES(){
397 return getTermByUuid(uuidProles);
398 }
399 public static final Rank RACE(){
400 return getTermByUuid(uuidRace);
401 }
402 public static final Rank SUBLUSUS(){
403 return getTermByUuid(uuidSublusus);
404 }
405
406 public static final Rank CONVAR(){
407 return getTermByUuid(uuidConvar);
408 }
409 public static final Rank FORM(){
410 return getTermByUuid(uuidForm);
411 }
412 public static final Rank SPECIALFORM(){
413 return getTermByUuid(uuidSpecialForm);
414 }
415 public static final Rank SUBFORM(){
416 return getTermByUuid(uuidSubform);
417 }
418 public static final Rank SUBSUBFORM(){
419 return getTermByUuid(uuidSubsubform);
420 }
421 /**
422 * 'Unranked infraspecific'. An infraspecific rank which is on purpose not further defined.
423 * This sometimes holds for names from the 19th century.
424 */
425 public static final Rank INFRASPECIFICTAXON(){
426 return getTermByUuid(uuidInfraspecificTaxon);
427 }
428 public static final Rank CANDIDATE(){
429 return getTermByUuid(uuidCandidate);
430 }
431 public static final Rank DENOMINATIONCLASS(){
432 return getTermByUuid(uuidDenominationClass);
433 }
434 public static final Rank GREX(){
435 return getTermByUuid(uuidGrex);
436 }
437 public static final Rank GRAFTCHIMAERA(){
438 return getTermByUuid(uuidGraftChimaera);
439 }
440 public static final Rank CULTIVARGROUP(){
441 return getTermByUuid(uuidCultivarGroup);
442 }
443 public static final Rank CULTIVAR(){
444 return getTermByUuid(uuidCultivar);
445 }
446 public static final Rank UNKNOWN_RANK(){
447 return getTermByUuid(uuidUnknownRank);
448 }
449 public static final Rank NATIO(){
450 return getTermByUuid(uuidNatio);
451 }
452 /**
453 * @see #INFRASPECIFICTAXON()
454 */
455 public static final Rank UNRANKED_INFRASPECIFIC(){
456 return getTermByUuid(uuidInfraspecificTaxon);
457 }
458 /**
459 * @see #INFRAGENERICTAXON()
460 */
461 public static final Rank UNRANKED_INFRAGENERIC(){
462 return getTermByUuid(uuidInfragenericTaxon);
463 }
464
465 // ************************ GETTER / SETTER **********************************/
466
467 public RankClass getRankClass() {
468 return rankClass;
469 }
470
471 public void setRankClass(RankClass rankClass) {
472 this.rankClass = rankClass;
473 }
474
475 // ******************************** METHODS ***************************************/
476
477 /**
478 * Returns the boolean value indicating whether <i>this</i> rank is higher than
479 * the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
480 *
481 * @see #isGenus()
482 * @see #isInfraGeneric()
483 * @see #isSpecies()
484 * @see #isInfraSpecific()
485 */
486 @Transient
487 public boolean isSupraGeneric(){
488 return this.rankClass.equals(RankClass.Suprageneric); // (this.isHigher(Rank.GENUS()));
489 }
490
491 /**
492 * Returns the boolean value indicating whether <i>this</i> rank is the genus rank
493 * (true) or not (false). Returns false if <i>this</i> rank is null.
494 *
495 * @see #isSupraGeneric()
496 * @see #isInfraGeneric()
497 * @see #isSpecies()
498 * @see #isInfraSpecific()
499 */
500 @Transient
501 public boolean isGenus(){
502 return this.rankClass.equals(RankClass.Genus); // (this.equals(Rank.GENUS()));
503 }
504
505 /**
506 * Returns the boolean value indicating whether <i>this</i> rank is higher than the
507 * species rank and lower than the genus rank (true) or not (false). Species groups or
508 * aggregates are also handled as infrageneric ranks.
509 * Returns false if <i>this</i> rank is null.
510 *
511 * @see #isSupraGeneric()
512 * @see #isGenus()
513 * @see #isInfraGenericButNotSpeciesGroup()
514 * @see #isSpeciesAggregate()
515 * @see #isSpecies()
516 * @see #isInfraSpecific()
517 */
518 @Transient
519 public boolean isInfraGeneric(){
520 return this.rankClass.equals(RankClass.Infrageneric) || this.rankClass.equals(RankClass.SpeciesGroup) ; //(this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
521 }
522
523 /**
524 * Returns the boolean value indicating whether <i>this</i> rank is higher than the
525 * species aggregate/group rank and lower than the genus rank (true) or not (false).
526 * Returns false if <i>this</i> rank is null.
527 *
528 * @see #isSupraGeneric()
529 * @see #isGenus()
530 * @see #isInfraGeneric()
531 * @see #isSpeciesAggregate()
532 * @see #isSpecies()
533 * @see #isInfraSpecific()
534 */
535 @Transient
536 public boolean isInfraGenericButNotSpeciesGroup(){
537 return this.rankClass.equals(RankClass.Infrageneric) ;
538 }
539
540 /**
541 * Returns true if this rank indicates a rank that aggregates species
542 * like species aggregates or species groups, false otherwise.
543 * @return
544 */
545 @Transient
546 public boolean isSpeciesAggregate(){
547 return this.rankClass.equals(RankClass.SpeciesGroup); //(this.equals(Rank.SPECIESAGGREGATE()) || (this.isLower(Rank.SPECIESAGGREGATE()) && this.isHigher(Rank.SPECIES())));
548 }
549
550 /**
551 * Returns the boolean value indicating whether <i>this</i> rank is the species
552 * rank (true) or not (false). Returns false if <i>this</i> rank is null.
553 *
554 * @see #isSupraGeneric()
555 * @see #isGenus()
556 * @see #isInfraGeneric()
557 * @see #isInfraSpecific()
558 */
559 @Transient
560 public boolean isSpecies(){
561 return this.rankClass.equals(RankClass.Species); //(this.equals(Rank.SPECIES()));
562 }
563
564 /**
565 * Returns the boolean value indicating whether <i>this</i> rank is lower than the
566 * species rank (true) or not (false). Returns false if <i>this</i> rank is null.
567 *
568 * @see #isSupraGeneric()
569 * @see #isGenus()
570 * @see #isInfraGeneric()
571 * @see #isSpecies()
572 */
573 @Transient
574 public boolean isInfraSpecific(){
575 return this.rankClass.equals(RankClass.Infraspecific); // (this.isLower(Rank.SPECIES()));
576 }
577
578
579 /**
580 * Returns the rank identified through a label or the identifier within the vocabulary
581 * Preliminary implementation for BotanicalNameParser.
582 *
583 * @param strRank the string identifying the rank
584 * @return the rank
585 */
586 public static Rank getRankByNameOrIdInVoc(String strRank) throws UnknownCdmTypeException{
587 return getRankByNameOrIdInVoc(strRank, false);
588 }
589
590 /**
591 * Returns the rank identified through a label or the identifier within the vocabulary
592 * for a given nomenclatural code.
593 * Preliminary implementation for BotanicalNameParser.
594 *
595 * @param strRank the string identifying the rank
596 * @param nc the nomenclatural code
597 * @return the rank
598 */
599 public static Rank getRankByNameOrIdInVoc(String strRank, NomenclaturalCode nc) throws UnknownCdmTypeException{
600 return getRankByNameOrIdInVoc(strRank, nc, false);
601 }
602
603 // TODO
604 // Preliminary implementation for BotanicalNameParser.
605 // not yet complete
606 /**
607 * Returns the rank identified through a label or the identifier within the vocabulary.
608 * Preliminary implementation for BotanicalNameParser.
609 *
610 * @param strRank the string identifying the rank
611 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
612 * unknown or not yet implemented
613 * @return the rank
614 */
615 public static Rank getRankByNameOrIdInVoc(String strRank, boolean useUnknown) throws UnknownCdmTypeException{
616 try {
617 return getRankByIdInVoc(strRank);
618 } catch (UnknownCdmTypeException e) {
619 return getRankByName(strRank, useUnknown);
620 }
621 }
622
623 // TODO
624 // Preliminary implementation for BotanicalNameParser.
625 // not yet complete
626 /**
627 * Returns the rank identified through a label or the identifier within the vocabulary.
628 * Preliminary implementation for BotanicalNameParser.
629 *
630 * @param strRank the string identifying the rank
631 * @param nc the nomenclatural code
632 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
633 * unknown or not yet implemented
634 * @return the rank
635 */
636 public static Rank getRankByNameOrIdInVoc(String strRank, NomenclaturalCode nc, boolean useUnknown)
637 throws UnknownCdmTypeException{
638 try {
639 return getRankByIdInVoc(strRank, nc);
640 } catch (UnknownCdmTypeException e) {
641 return getRankByName(strRank, nc, useUnknown);
642 }
643 }
644
645 /**
646 * Returns the rank identified through the vocabulary identifier.
647 * Preliminary implementation for BotanicalNameParser.<BR>
648 * Note: For abbrev = "[unranked]" the result is undefined.
649 * It maybe the infrageneric unranked or the infraspecific unranked.
650 * You need to define by context which one is correct.
651 *
652 * @param abbrev the string for the name abbreviation
653 * @return the rank
654 */
655 public static Rank getRankByIdInVoc(String abbrev) throws UnknownCdmTypeException{
656 return getRankByIdInVoc(abbrev, false);
657 }
658
659 /**
660 * Returns the rank identified through an abbreviated name for a given nomenclatural code.
661 * See also {@link #getRankByIdInVoc(String, boolean)}
662 *
663 * @param abbrev the string for the name abbreviation
664 * @param nc the nomenclatural code
665 * @return the rank
666 */
667 public static Rank getRankByIdInVoc(String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException{
668 return getRankByIdInVoc(abbrev, nc, false);
669 }
670
671 // TODO
672 // Preliminary implementation for BotanicalNameParser.
673 // not yet complete
674 /**
675 * Returns the rank identified through an abbreviated representation.
676 * At the moment it uses the English abbreviations (being Latin because
677 * we do not have Latin representations yet.
678 * TODO
679 * If no according abbreviation is available it throws either an UnknownCdmTypeException
680 * or an #Rank.UNKNOWN() object depending on the useUnknown flag.
681 *
682 * @param idInVoc the string for the name abbreviation
683 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
684 * unknown or not yet existent
685 * @return the rank
686 */
687 public static Rank getRankByIdInVoc(String idInVoc, boolean useUnknown) throws UnknownCdmTypeException{
688 Rank result = null;
689 if (idInVoc == null){
690 throw new NullPointerException("idInVoc is NULL in getRankByIdInVoc");
691 }
692 if (StringUtils.isBlank(idInVoc)){
693 //handle empty idInVoc as unknown
694 idInVoc = "oijas34\u0155";
695 }
696 if (idInVocMap == null){
697 return null;
698 }
699 idInVoc = normalizeSectionAndSubsection(idInVoc);
700 idInVoc = normalizeSubgen(idInVoc);
701 idInVoc = normalizeSpecialForm(idInVoc);
702 idInVoc = normalizeSsp(idInVoc);
703 idInVoc = normalizeForma(idInVoc);
704 UUID uuid = idInVocMap.get(idInVoc);
705 if (uuid != null ){
706 result = getTermByUuid(uuid);
707 }
708 if (result != null){
709 return result;
710 }else {
711 if (idInVoc == null){
712 idInVoc = "(null)";
713 }
714 if (useUnknown){
715 logger.info("Unknown rank name: " + idInVoc + ". Rank 'UNKNOWN_RANK' created instead");
716 return Rank.UNKNOWN_RANK();
717 }else{
718 throw new UnknownCdmTypeException("Unknown rank abbreviation: " + idInVoc);
719 }
720 }
721 }
722
723 private static String normalizeSectionAndSubsection(String idInVoc) {
724 if (idInVoc.equals("sect.")){
725 return "sect.(bot.)";
726 }else if (idInVoc.equals("subsect.")){
727 return "subsect.(bot.)";
728 }
729 return idInVoc;
730 }
731
732 private static String normalizeSubgen(String idInVoc) {
733 if (idInVoc.equals("subgen.")){
734 return "subg.";
735 }
736 return idInVoc;
737 }
738
739 private static String normalizeSpecialForm(String idInVoc) {
740 if (idInVoc.equals("f.sp.") || idInVoc.equals("f. sp.")){
741 return "f.spec.";
742 }
743 return idInVoc;
744 }
745
746 private static String normalizeForma(String idInVoc) {
747 if (idInVoc.equals("forma")){
748 return "f.";
749 }
750 return idInVoc;
751 }
752
753 private static String normalizeSsp(String idInVoc) {
754 if (idInVoc.equals("ssp.") && !idInVocMap.containsKey("ssp.") && idInVocMap.containsKey("subsp.")){
755 return "subsp.";
756 }
757 return idInVoc;
758 }
759
760 // TODO
761 // Preliminary implementation to cover Botany and Zoology.
762 /**
763 * Returns the rank identified through an abbreviated name for a given nomenclatural code.
764 * Preliminary implementation for ICBN and ICZN.
765 * See also {@link #getRankByIdInVoc(String, boolean)}
766
767 *
768 * @param abbrev the string for the name abbreviation
769 * @param nc the nomenclatural code
770 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
771 * unknown or not yet implemented
772 * @return the rank
773 */
774 public static Rank getRankByIdInVoc(String abbrev, NomenclaturalCode nc, boolean useUnknown)
775 throws UnknownCdmTypeException{
776
777 if (nc != null && nc.equals(NomenclaturalCode.ICZN)) {
778 if (abbrev != null){
779 if (abbrev.equalsIgnoreCase("sect.")) {
780 return Rank.SECTION_ZOOLOGY();
781 } else if (abbrev.equalsIgnoreCase("subsect.")) {
782 return Rank.SUBSECTION_ZOOLOGY();
783 }
784 }
785 }else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)) {
786 if (abbrev != null){
787 if (abbrev.equalsIgnoreCase("sect.")) {
788 return Rank.SECTION_BOTANY();
789 } else if (abbrev.equalsIgnoreCase("subsect.")) {
790 return Rank.SUBSECTION_BOTANY();
791 }
792 }
793 }
794 return getRankByIdInVoc(abbrev, useUnknown);
795 }
796
797 // TODO
798 // Preliminary implementation for BotanicalNameParser.
799 // not yet complete
800 /**
801 * Returns the rank identified through a name.
802 * Preliminary implementation for BotanicalNameParser.
803 *
804 * @param rankName the string for the name of the rank
805 * @return the rank
806 */
807 public static Rank getRankByName(String rankName) throws UnknownCdmTypeException{
808 return getRankByName(rankName, false);
809 }
810
811
812 // TODO
813 // Preliminary implementation for ICBN and ICZN.
814 // not yet complete
815 /**
816 * Returns the rank identified through a name for a given nomenclatural code.
817 * Preliminary implementation for ICBN and ICZN.
818 *
819 * @param rankName the string for the name of the rank
820 * @param nc the nomenclatural code
821 * @return the rank
822 */
823 public static Rank getRankByName(String rankName, NomenclaturalCode nc) throws UnknownCdmTypeException{
824 return getRankByName(rankName, nc, false);
825 }
826
827 /**
828 * Returns the rank identified through a name.
829 * Preliminary implementation for BotanicalNameParser.
830 * TODO At the moment we do not have Latin representations yet.
831 *
832 * @param rankName the string for the name of the rank
833 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the rank name is
834 * unknown or not yet implemented
835 * @return the rank
836 */
837 public static Rank getRankByName(String rankName, boolean useUnknown)
838 throws UnknownCdmTypeException{
839 if (rankName.equalsIgnoreCase("Regnum")){ return Rank.KINGDOM();
840 }else if (rankName.equalsIgnoreCase("Subregnum")){ return Rank.SUBKINGDOM();
841 }else if (rankName.equalsIgnoreCase("Phylum")){ return Rank.PHYLUM();
842 }else if (rankName.equalsIgnoreCase("Subphylum")){ return Rank.SUBPHYLUM();
843 }else if (rankName.equalsIgnoreCase("Divisio")){ return Rank.DIVISION();
844 }else if (rankName.equalsIgnoreCase("Subdivisio")){ return Rank.SUBDIVISION();
845 }else if (rankName.equalsIgnoreCase("Classis")){ return Rank.CLASS();
846 }else if (rankName.equalsIgnoreCase("Subclassis")){ return Rank.SUBCLASS();
847 }else if (rankName.equalsIgnoreCase("Superordo")){ return Rank.SUPERORDER();
848 }else if (rankName.equalsIgnoreCase("Ordo")){ return Rank.ORDER();
849 }else if (rankName.equalsIgnoreCase("Subordo")){ return Rank.SUBORDER();
850 }else if (rankName.equalsIgnoreCase("Familia")){ return Rank.FAMILY();
851 }else if (rankName.equalsIgnoreCase("Subfamilia")){ return Rank.SUBFAMILY();
852 }else if (rankName.equalsIgnoreCase("Tribus")){ return Rank.TRIBE();
853 }else if (rankName.equalsIgnoreCase("Subtribus")){ return Rank.SUBTRIBE();
854 }else if (rankName.equalsIgnoreCase("Genus")){ return Rank.GENUS();
855 }else if (rankName.equalsIgnoreCase("Subgenus")){ return Rank.SUBGENUS();
856 }else if (rankName.equalsIgnoreCase("Sectio")){ return Rank.SECTION_BOTANY();
857 }else if (rankName.equalsIgnoreCase("Subsectio")){ return Rank.SUBSECTION_BOTANY();
858 }else if (rankName.equalsIgnoreCase("Series")){ return Rank.SERIES();
859 }else if (rankName.equalsIgnoreCase("Subseries")){ return Rank.SUBSERIES();
860 }else if (rankName.equalsIgnoreCase("Aggregate")){ return Rank.SPECIESAGGREGATE();
861 }else if (rankName.equalsIgnoreCase("Speciesgroup")){ return Rank.SPECIESGROUP();
862 }else if (rankName.equalsIgnoreCase("Species")){ return Rank.SPECIES();
863 }else if (rankName.equalsIgnoreCase("Subspecies")){ return Rank.SUBSPECIES();
864 }else if (rankName.equalsIgnoreCase("Convarietas")){ return Rank.CONVAR();
865 }else if (rankName.equalsIgnoreCase("Varietas")){ return Rank.VARIETY();
866 }else if (rankName.equalsIgnoreCase("Subvarietas")){ return Rank.SUBVARIETY();
867 }else if (rankName.equalsIgnoreCase("Forma")){ return Rank.FORM();
868 }else if (rankName.equalsIgnoreCase("Subforma")){ return Rank.SUBFORM();
869 }else if (rankName.equalsIgnoreCase("Forma spec.")){ return Rank.SPECIALFORM();
870 }else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
871 }else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
872 // old ranks
873 }else if (rankName.equalsIgnoreCase("proles")){ return Rank.PROLES();
874 }else if (rankName.equalsIgnoreCase("race")){ return Rank.RACE();
875 }else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.SUBLUSUS();
876
877 }else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put 'taxon' and the infraspeciesepi to the field unnamed namephrase
878
879 }else{
880 if (rankName == null){
881 rankName = "(null)"; //see NPE above
882 }
883 if (useUnknown){
884 if (logger.isInfoEnabled()){logger.info("Unknown rank name: " + rankName+". Rank 'UNKNOWN_RANK' created instead");}
885 return Rank.UNKNOWN_RANK();
886 }else{
887 throw new UnknownCdmTypeException("Unknown rank name: " + rankName);
888 }
889 }
890 }
891
892 /**
893 * Defines the rank according to the English name.
894 * @param rankName English rank name.
895 * @param nc Defines the handling of the section and subsection ranks. These are in different orders depending on the
896 * nomenclatural code.
897 * @param useUnknown if true, the "Unknown" rank is returned as a placeholder.
898 * @return
899 * @throws UnknownCdmTypeException never thrown if useUnknown is true
900 */
901 public static Rank getRankByEnglishName(String rankName, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException{
902 Rank result = null;
903 if (rankName == null){
904 throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
905 }
906 if (labelMap == null){
907 return null;
908 }
909 //handle section and subsection (not unique representations)
910 if (rankName.equalsIgnoreCase("Section")){
911 if (nc != null && nc.equals(NomenclaturalCode.ICZN)){ return Rank.SECTION_ZOOLOGY();
912 }else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)){return Rank.SECTION_BOTANY();
913 }else{
914 String errorWarning = "Section is only defined for ICZN and ICNAFP at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
915 logger.warn(errorWarning);
916 throw new UnknownCdmTypeException (errorWarning);
917 }
918 }else if (rankName.equalsIgnoreCase("Subsection")){
919 if (nc != null && nc.equals(NomenclaturalCode.ICZN)){ return Rank.SUBSECTION_ZOOLOGY();
920 }else if (nc != null && nc.equals(NomenclaturalCode.ICNAFP)){ return Rank.SUBSECTION_BOTANY();
921 }else{
922 String errorWarning = "Subsection is only defined for ICZN and ICBN at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
923 logger.warn(errorWarning);
924 throw new UnknownCdmTypeException (errorWarning);
925 }
926 }
927
928 rankName = rankName.toLowerCase();
929
930 UUID uuid = labelMap.get(rankName);
931 if (uuid != null ){
932 result = getTermByUuid(uuid);
933 }
934 if (result != null){
935 return result;
936 }else {
937 if (rankName == null){
938 rankName = "(null)";
939 }
940 if (useUnknown){
941 if (logger.isInfoEnabled()){logger.info("Unknown rank name: " + rankName + ". Rank 'UNKNOWN_RANK' created instead");}
942 return Rank.UNKNOWN_RANK();
943 }else{
944 throw new UnknownCdmTypeException("Unknown rank: " + rankName);
945 }
946 }
947 }
948
949
950 public static Rank getRankByName(String rankName, NomenclaturalCode nc, boolean useUnknown)
951 throws UnknownCdmTypeException {
952
953 if (nc.equals(NomenclaturalCode.ICZN)) {
954 if (rankName.equalsIgnoreCase("Sectio")) { return Rank.SECTION_ZOOLOGY();
955 }else if (rankName.equalsIgnoreCase("Subsectio")) { return Rank.SUBSECTION_ZOOLOGY();
956 }
957 }
958 return getRankByName(rankName, useUnknown);
959 }
960
961 /**
962 * Returns the abbreviated rank name for <i>this</i> rank according to the English representation
963 * abbreviated label.
964 * TODO Needs to be changed to Latin as soon as Latin representations are available.
965 *
966 * @return the abbreviation string for <i>this</i> rank
967 */
968 public String getAbbreviation(){
969 Language language = Language.getLanguageFromUuid(Language.uuidEnglish);
970 String result = this.getRepresentation(language).getAbbreviatedLabel();
971 if (result== null) {
972 logger.warn("Abbreviation for rank " + this.toString() + " not yet implemented");
973 return "no abbreviation available.";
974 }else{
975 return result;
976 }
977 }
978
979 @Transient
980 public String getInfraGenericMarker() throws UnknownCdmTypeException{
981 String result = null;
982 if (! this.isInfraGeneric()){
983 throw new IllegalStateException("An infrageneric marker is only available for an infrageneric rank but was asked for rank: " + this.toString());
984 }else{
985 result = this.getAbbreviation();
986 }
987 if (result == null){
988 throw new UnknownCdmTypeException("Abbreviation for rank unknown: " + this.toString());
989 }
990 return result;
991 }
992
993
994
995 @Override
996 public Rank readCsvLine(Class<Rank> termClass, List<String> csvLine, Map<UUID, DefinedTermBase> terms, boolean abbrevAsId) {
997 Rank rank = super.readCsvLine(termClass, csvLine, terms, abbrevAsId);
998 RankClass rankClass = RankClass.getByKey(csvLine.get(5));
999 assert rankClass != null: "XXXXXXXXXXXXXXXXXXXXX Rank class must not be null: " + csvLine ;
1000 rank.setRankClass(rankClass);
1001 return rank;
1002 }
1003
1004 @Override
1005 protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary) {
1006 termMap = new HashMap<UUID, Rank>();
1007 for (Rank term : termVocabulary.getTerms()){
1008 termMap.put(term.getUuid(), term);
1009 addRank(term);
1010 }
1011 }
1012
1013 // FIXME:Remoting This is a ugly hack and need to be removed
1014 // once the static initialisation is refactored
1015 public static void initDefaultTerms() {
1016 TermVocabulary<Rank> vocabulary = getTermByUuid(uuidKingdom).getVocabulary();
1017 if(idInVocMap != null) {
1018 idInVocMap.clear();
1019 }
1020 (new Rank()).setDefaultTerms(vocabulary);
1021 }
1022
1023 /**
1024 * @param term
1025 */
1026 private void addRank(Rank rank) {
1027 if (rank == null){
1028 logger.warn("rank is NULL");
1029 return;
1030 }
1031 if (rank.getUuid().equals(uuidSectionZoology) || rank.getUuid().equals(uuidSubsectionZoology )){
1032 //sect./subsect. is used for botanical sections, see also #getRankByAbbreviation(String, NomenclaturalCode, boolean)
1033 return;
1034 }
1035 Language lang = Language.DEFAULT(); //TODO should be Latin but at the moment we have only English representations
1036 Representation representation = rank.getRepresentation(lang);
1037 String abbrevLabel = representation.getAbbreviatedLabel();
1038 String label = representation.getLabel();
1039
1040 //initialize maps
1041 if (idInVocMap == null){
1042 idInVocMap = new HashMap<String, UUID>();
1043 }
1044 if (labelMap == null){
1045 labelMap = new HashMap<String, UUID>();
1046 }
1047 labelMap.put(label.toLowerCase(), rank.getUuid());
1048 //add to map
1049 if (StringUtils.isBlank(abbrevLabel)){
1050 if (logger.isDebugEnabled()){logger.info("Abbreviated label for rank is NULL or empty.Can't add rank to abbrevLabel map: " + CdmUtils.Nz(rank.getLabel()));}
1051 }else{
1052 idInVocMap.put(abbrevLabel, rank.getUuid());
1053 }
1054 }
1055
1056
1057 /**
1058 * It is necessary to skip the vocabulary check, otherwise we would have
1059 * problems in some CacheStrategies, due to uninitialized Vocabularies.
1060 *
1061 * @see eu.etaxonomy.cdm.model.common.OrderedTermBase#compareTo(eu.etaxonomy.cdm.model.common.OrderedTermBase)
1062 */
1063 @Override
1064 public int compareTo(Rank orderedTerm) {
1065 return performCompareTo(orderedTerm, true);
1066 }
1067
1068 }