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handle inverse and doubtful taxon relations in Berlin Model import
[cdmlib.git] / cdmlib-io / src / main / java / eu / etaxonomy / cdm / io / berlinModel / BerlinModelTransformer.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.io.berlinModel;
11
12 import java.sql.ResultSet;
13 import java.sql.SQLException;
14 import java.util.UUID;
15
16 import org.apache.log4j.Logger;
17
18 import eu.etaxonomy.cdm.common.ResultWrapper;
19 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
20 import eu.etaxonomy.cdm.model.common.Language;
21 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
22 import eu.etaxonomy.cdm.model.common.RelationshipBase;
23 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
24 import eu.etaxonomy.cdm.model.description.AbsenceTerm;
25 import eu.etaxonomy.cdm.model.description.Feature;
26 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
27 import eu.etaxonomy.cdm.model.description.PresenceTerm;
28 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
29 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
30 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
31 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
32 import eu.etaxonomy.cdm.model.name.Rank;
33 import eu.etaxonomy.cdm.model.name.RankClass;
34 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
35 import eu.etaxonomy.cdm.model.reference.ISection;
36 import eu.etaxonomy.cdm.model.reference.Reference;
37 import eu.etaxonomy.cdm.model.reference.ReferenceType;
38 import eu.etaxonomy.cdm.model.taxon.Synonym;
39 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
40 import eu.etaxonomy.cdm.model.taxon.Taxon;
41 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
42 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
43 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
44
45 /**
46 * @author a.mueller
47 * @created 20.03.2008
48 */
49 public class BerlinModelTransformer {
50 private static final Logger logger = Logger.getLogger(BerlinModelTransformer.class);
51
52 //source Refs
53 public static final UUID uuidSourceRefEuroMed = UUID.fromString("0603a84a-f024-4454-ab92-9e2ac0139126");
54
55 //ranks
56 public static UUID uuidRankCollSpecies = UUID.fromString("e14630ee-9446-4bb4-a7b7-4c3881bc5d94");
57 public static UUID uuidRankProles = UUID.fromString("8810d1ba-6a34-4ae3-a355-919ccd1cd1a5");
58 public static UUID uuidRankRace = UUID.fromString("196dee39-cfd8-4460-8bf0-88b83da27f62");
59 public static UUID uuidRankSublusus = UUID.fromString("1fafa596-a8e7-4e62-a378-3cc8cb3627ca");
60
61 //named areas
62 public static UUID euroMedUuid = UUID.fromString("9fe09988-58c0-4c06-8474-f660a0c50014");
63
64 public static UUID uuidEasternEuropeanRussia = UUID.fromString("3f013375-0e0a-40c3-8a14-84c0535fab40");
65 public static UUID uuidSerbiaMontenegro = UUID.fromString("8926dbe6-863e-47a9-98a0-7dc9ed2c57f7");
66 public static UUID uuidSerbia = UUID.fromString("4ffed197-3d7e-4cd9-8984-e64b8dee9512");
67 public static UUID uuidLebanonSyria = UUID.fromString("0c45f250-99da-4b19-aa89-c3e56cfdf103");
68 public static UUID uuidUssr = UUID.fromString("a512e00a-45f3-4be5-82fa-bba8d675696f");
69 public static UUID uuidSicilyMalta = UUID.fromString("424d81ee-d272-4ae8-9600-0a334049cd72");
70
71 public static UUID uuidDesertas = UUID.fromString("36f5e93e-34e8-45b5-a401-f0e0faad21cf");
72 public static UUID uuidMadeira = UUID.fromString("086e27ee-78ff-4236-aca9-9850850cd355");
73 public static UUID uuidPortoSanto = UUID.fromString("1f9ab6a0-a402-4dfe-8c5b-b1844eb4d8e5");
74 //azores
75 public static UUID uuidFlores = UUID.fromString("ef0067c2-8bbb-4e37-8462-97b03f51ba43");
76 public static UUID uuidCorvo = UUID.fromString("b1e6117c-2be1-43a3-9233-227dd90bdee9");
77 public static UUID uuidFaial = UUID.fromString("14f6dcdb-6524-4700-b80c-66424952ef2b");
78 public static UUID uuidGraciosa = UUID.fromString("05f93a7b-d813-4833-864f-eedbba747133");
79 public static UUID uuidSaoJorge = UUID.fromString("578e0ecd-b5e3-4c87-8ecc-0fc4c7e217d9");
80 public static UUID uuidSaoMiguel = UUID.fromString("0e2f6ad8-7afb-4f01-b134-4f71991e877a");
81 public static UUID uuidPico = UUID.fromString("98cc566f-4110-43d5-830f-68436a009f49");
82 public static UUID uuidSantaMaria = UUID.fromString("bd5e5d4a-22b7-41aa-8e58-1d1d73a9954d");
83 public static UUID uuidTerceira = UUID.fromString("6fc257c0-a131-41f0-b6c3-51ef9c4fa962");
84 //Canyry islands
85 public static UUID uuidGranCanaria = UUID.fromString("a0240c35-0e05-4157-8321-67ba8e31fdb9");
86 public static UUID uuidFuerteventura = UUID.fromString("549ce2c1-6d49-4bf3-b75d-cf3f4b5a1398");
87 public static UUID uuidGomera = UUID.fromString("895fab09-7478-4210-b42a-423d23c6f85e");
88 public static UUID uuidHierro = UUID.fromString("d137b6a5-31bc-418c-9403-f042017dc04b");
89 public static UUID uuidLanzaroteWithGraciosa = UUID.fromString("c9b08dc1-f301-4d9d-b447-b8744602c776");
90 public static UUID uuidLaPalma = UUID.fromString("fdb3f2b2-f154-4f04-9f31-240a47a0e780");
91 public static UUID uuidTenerife = UUID.fromString("73658c7e-a568-465e-bd84-4554fc93ca56");
92 //Baleares
93 public static UUID uuidIbizaWithFormentera = UUID.fromString("1cda2a33-3469-49d5-8e77-cb5451110519");
94 public static UUID uuidMallorca = UUID.fromString("a10cba04-b4b5-4a4b-b69a-fcd4b3916fec");
95 public static UUID uuidMenorca = UUID.fromString("9f6ede48-27f8-4270-bf4e-c97eaa86aab7");
96
97 //russia
98 public static UUID uuidRussiaNorthern = UUID.fromString("c23bc1c9-a775-4426-b883-07d4d7d47eed");
99 public static UUID uuidRussiaBaltic = UUID.fromString("579dad44-9439-4b19-8716-ab90d8f27944");
100 public static UUID uuidRussiaCentral = UUID.fromString("8bbc8c6a-2ef2-4024-ad51-66fe34c70092");
101 public static UUID uuidRussiaSouthWest = UUID.fromString("daa5c207-5567-4690-8742-5e4d153b6a64");
102 public static UUID uuidRussiaSouthEast = UUID.fromString("e8516598-b529-489e-9ee8-63bbbd295c1b");
103 public static UUID uuidEastAegeanIslands = UUID.fromString("1c429593-c493-46e6-971a-0d70be690da8");
104 public static UUID uuidTurkishEastAegeanIslands = UUID.fromString("ba35dba3-ac70-41ae-81c2-2070943f44f2");
105 public static UUID uuidBalticStates = UUID.fromString("bf9d64f6-3183-4fa5-8e90-73090e7a2282");
106 public static final UUID uuidTurkey = UUID.fromString("d344ee2c-14c8-438d-b03d-11538edb1268");
107 public static final UUID uuidCaucasia = UUID.fromString("ebfd3fd1-3859-4e5e-95c7-f66010599d7e");
108
109 //language areas
110 public static final UUID uuidUkraineAndCrimea = UUID.fromString("99d4d1c2-09f6-416e-86a3-bdde5cae52af");
111 public static final UUID uuidAzerbaijanNakhichevan = UUID.fromString("232fbef0-9f4a-4cab-8ac1-e14c717e9de6");
112
113 //Marker Types
114 public static final UUID uuidMisappliedCommonName = UUID.fromString("25f5cfc3-16ab-4aba-a008-0db0f2cf7f9d");
115 public static final UUID uuidEurArea = UUID.fromString("71dd0368-835c-4b53-889a-2bf316e10297");
116 public static final UUID uuidEurMedArea = UUID.fromString("aa6a5b25-3ee3-4771-b4d1-b91918f23fa5");
117
118
119 //Extension Types
120 public static final UUID uuidSpeciesExpertName = UUID.fromString("2e8153d2-7412-49e4-87e1-5c38f4c5153a");
121 public static final UUID uuidExpertName = UUID.fromString("24becb79-a90c-47d3-be35-efc87bb48fd3");
122
123 public static final UUID DETAIL_EXT_UUID = UUID.fromString("c3959b4f-d876-4b7a-a739-9260f4cafd1c");
124 public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");
125 public static final UUID uuidIsoCode = UUID.fromString("048b8153-e3ee-451c-a72c-f1c8bc291c3e");
126 public static final UUID uuidTdwgAreaCode = UUID.fromString("73ad0288-b71b-4a14-9c2e-7f81f1e64a36");
127 public static final UUID uuidMclCode = UUID.fromString("aa27083a-6a96-42aa-a2f8-5541cf057067");
128
129 //Area Level
130 public static final UUID uuidAreaLevelTop = UUID.fromString("190d5758-4b96-4016-9412-6dc9c36ef5fd");
131 public static final UUID uuidAreaLevelFirst = UUID.fromString("d21503e3-875e-4abc-82ec-f812e3cfea84");
132 public static final UUID uuidAreaLevelSecond = UUID.fromString("97ac0bf5-b31c-487a-8ed5-a576f46c902c");
133
134
135 //languages
136 public static final UUID uuidLangMajorcan = UUID.fromString("82d696d7-cb4e-49de-ac89-63a0e12ca766");
137
138 //REFERENCES
139 public static int REF_ARTICLE = 1;
140 public static int REF_PART_OF_OTHER_TITLE = 2;
141 public static int REF_BOOK = 3;
142 public static int REF_DATABASE = 4;
143 public static int REF_INFORMAL = 5;
144 public static int REF_NOT_APPLICABLE = 6;
145 public static int REF_WEBSITE = 7;
146 public static int REF_CD = 8;
147 public static int REF_JOURNAL = 9;
148 public static int REF_UNKNOWN = 10;
149 public static int REF_PRINT_SERIES = 55;
150 public static int REF_CONFERENCE_PROCEEDINGS = 56;
151 public static int REF_JOURNAL_VOLUME = 57;
152
153
154
155 //NameStatus
156 public static int NAME_ST_NOM_INVAL = 1;
157 public static int NAME_ST_NOM_ILLEG = 2;
158 public static int NAME_ST_NOM_NUD = 3;
159 public static int NAME_ST_NOM_REJ = 4;
160 public static int NAME_ST_NOM_REJ_PROP = 5;
161 public static int NAME_ST_NOM_UTIQUE_REJ = 6;
162 public static int NAME_ST_NOM_UTIQUE_REJ_PROP = 7;
163 public static int NAME_ST_NOM_CONS = 8;
164 public static int NAME_ST_NOM_CONS_PROP = 9;
165 public static int NAME_ST_ORTH_CONS = 10;
166 public static int NAME_ST_ORTH_CONS_PROP = 11;
167 public static int NAME_ST_NOM_SUPERFL = 12;
168 public static int NAME_ST_NOM_AMBIG = 13;
169 public static int NAME_ST_NOM_PROVIS = 14;
170 public static int NAME_ST_NOM_DUB = 15;
171 public static int NAME_ST_NOM_NOV = 16;
172 public static int NAME_ST_NOM_CONFUS = 17;
173 public static int NAME_ST_NOM_ALTERN = 18;
174 public static int NAME_ST_COMB_INVAL = 19;
175
176
177 //NameRelationShip
178 public static int NAME_REL_IS_BASIONYM_FOR = 1;
179 public static int NAME_REL_IS_LATER_HOMONYM_OF = 2;
180 public static int NAME_REL_IS_REPLACED_SYNONYM_FOR = 3;
181 public static int NAME_REL_IS_VALIDATION_OF = 4;
182 public static int NAME_REL_IS_LATER_VALIDATION_OF = 5;
183 public static int NAME_REL_IS_TYPE_OF = 6;
184 public static int NAME_REL_IS_CONSERVED_TYPE_OF =7;
185 public static int NAME_REL_IS_REJECTED_TYPE_OF = 8;
186 public static int NAME_REL_IS_FIRST_PARENT_OF = 9;
187 public static int NAME_REL_IS_SECOND_PARENT_OF = 10;
188 public static int NAME_REL_IS_FEMALE_PARENT_OF = 11;
189 public static int NAME_REL_IS_MALE_PARENT_OF = 12;
190 public static int NAME_REL_IS_CONSERVED_AGAINST =13;
191 public static int NAME_REL_IS_REJECTED_IN_FAVOUR_OF = 14;
192 public static int NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF = 15;
193 public static int NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF = 16;
194 public static int NAME_REL_IS_ALTERNATIVE_NAME_FOR = 17;
195 public static int NAME_REL_HAS_SAME_TYPE_AS = 18;
196 public static int NAME_REL_IS_LECTOTYPE_OF = 61;
197 public static int NAME_REL_TYPE_NOT_DESIGNATED = 62;
198
199 //NameFacts
200 public static String NAME_FACT_PROTOLOGUE = "Protologue";
201 public static String NAME_FACT_ALSO_PUBLISHED_IN = "Also published in";
202 public static String NAME_FACT_BIBLIOGRAPHY = "Bibliography";
203
204 //TaxonRelationShip
205 public static int TAX_REL_IS_INCLUDED_IN = 1;
206 public static int TAX_REL_IS_SYNONYM_OF = 2;
207 public static int TAX_REL_IS_MISAPPLIED_NAME_OF = 3;
208 public static int TAX_REL_IS_PROPARTE_SYN_OF = 4;
209 public static int TAX_REL_IS_PARTIAL_SYN_OF = 5;
210 public static int TAX_REL_IS_HETEROTYPIC_SYNONYM_OF = 6;
211 public static int TAX_REL_IS_HOMOTYPIC_SYNONYM_OF = 7;
212 public static int TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF = 101;
213 public static int TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF = 102;
214 public static int TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF = 103;
215 public static int TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF = 104;
216
217
218
219 //TaxonStatus
220 public static int T_STATUS_ACCEPTED = 1;
221 public static int T_STATUS_SYNONYM = 2;
222 public static int T_STATUS_PARTIAL_SYN = 3;
223 public static int T_STATUS_PRO_PARTE_SYN = 4;
224 public static int T_STATUS_UNRESOLVED = 5;
225 public static int T_STATUS_ORPHANED = 6;
226
227
228 //Facts
229 public static int FACT_DESCRIPTION = 1;
230 public static int FACT_GROWTH_FORM = 2;
231 public static int FACT_HARDINESS = 3;
232 public static int FACT_ECOLOGY = 4;
233 public static int FACT_PHENOLOGY = 5;
234 public static int FACT_KARYOLOGY = 6;
235 public static int FACT_ILLUSTRATION = 7;
236 public static int FACT_IDENTIFICATION = 8;
237 public static int FACT_OBSERVATION = 9;
238 public static int FACT_DISTRIBUTION_EM = 10;
239 public static int FACT_DISTRIBUTION_WORLD = 11;
240 //E+M
241 public static final UUID uuidFeatureMaps = UUID.fromString("8367730e-f3c3-4361-8360-a2057e4295ed");
242 public static final UUID uuidFeatureConservationStatus = UUID.fromString("a32f33cd-1966-4a22-986c-94c5e688bbd1");
243 public static final UUID uuidFeatureUse = UUID.fromString("199bbbd8-2db6-4335-b454-2e92ae02b699");
244 public static final UUID uuidFeatureComments = UUID.fromString("31cc2b92-5cad-44e9-b50f-b8af591a527c");
245 public static final UUID uuidFeatureDistrEM = UUID.fromString("a5ba7e7f-ca7f-4f50-afc7-73e76b3231d4");
246 public static final UUID uuidFeatureDistrWorld = UUID.fromString("e4e24080-7017-47e6-924e-d2560fa68fb8");
247 public static final UUID uuidFeatureEditorBrackets = UUID.fromString("b3b5bc1a-7ba8-4a39-9c0d-63ba599eb5d8");
248 public static final UUID uuidFeatureEditorParenthesis = UUID.fromString("6ee10a2e-ff02-4cf4-a520-89630edc5b44");
249 public static final UUID uuidFeatureInedited = UUID.fromString("c93e2968-bc52-4165-9755-ce37611faf01");
250 public static final UUID uuidFeatureCommentsEditing = UUID.fromString("7a155021-158a-48bb-81d0-9a72b718e2de");
251
252
253
254 public static UUID uuidNomStatusCombIned = UUID.fromString("dde8a2e7-bf9e-42ec-b186-d5bde9c9c128");
255 public static UUID uuidNomStatusSpNovIned = UUID.fromString("1a359ca1-9364-43bc-93e4-834bdcd52b72");
256 public static UUID uuidNomStatusNomOrthCons = UUID.fromString("0f838183-ffa0-4014-928e-0e3a27eb3918");
257
258 static NomenclaturalStatusType nomStatusCombIned;
259 static NomenclaturalStatusType nomStatusSpNovIned;
260 static NomenclaturalStatusType nomStatusNomOrthCons;
261
262 public static NomenclaturalStatusType nomStatusTypeAbbrev2NewNomStatusType(String nomStatus){
263 NomenclaturalStatusType result = null;
264 if (nomStatus == null){
265 return null;
266 }else if (nomStatus.equalsIgnoreCase("comb. ined.")){
267 if (nomStatusCombIned == null){
268 nomStatusCombIned = NomenclaturalStatusType.NewInstance("comb. ined.", "comb. ined.", "comb. ined.", Language.LATIN());
269 nomStatusCombIned.setUuid(uuidNomStatusCombIned);
270 NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusCombIned);
271 }
272 result = nomStatusCombIned;
273 }else if (nomStatus.equalsIgnoreCase("sp. nov. ined.")){
274 if (nomStatusSpNovIned == null){
275 nomStatusSpNovIned = NomenclaturalStatusType.NewInstance("sp. nov. ined.", "sp. nov. ined.", "sp. nov. ined.", Language.LATIN());
276 nomStatusSpNovIned.setUuid(uuidNomStatusSpNovIned);
277 NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusSpNovIned);
278 }
279 result = nomStatusSpNovIned;
280 }else if (nomStatus.equalsIgnoreCase("nom. & orth. cons.")){
281 if (nomStatusNomOrthCons == null){
282 nomStatusNomOrthCons = NomenclaturalStatusType.NewInstance("nom. & orth. cons.", "nom. & orth. cons.", "nom. & orth. cons.", Language.LATIN());
283 nomStatusNomOrthCons.setUuid(uuidNomStatusNomOrthCons);
284 NomenclaturalStatusType.ALTERNATIVE().getVocabulary().addTerm(nomStatusNomOrthCons);
285 }
286 result = nomStatusNomOrthCons;
287 }
288 return result;
289 }
290
291
292 public static NomenclaturalStatus nomStatusFkToNomStatus(int nomStatusFk, String nomStatusLabel) throws UnknownCdmTypeException{
293 if (nomStatusFk == NAME_ST_NOM_INVAL){
294 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.INVALID());
295 }else if (nomStatusFk == NAME_ST_NOM_ILLEG){
296 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE());
297 }else if (nomStatusFk == NAME_ST_NOM_NUD){
298 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.NUDUM());
299 }else if (nomStatusFk == NAME_ST_NOM_REJ){
300 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.REJECTED());
301 }else if (nomStatusFk == NAME_ST_NOM_REJ_PROP){
302 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.REJECTED_PROP());
303 }else if (nomStatusFk == NAME_ST_NOM_UTIQUE_REJ){
304 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.UTIQUE_REJECTED());
305 }else if (nomStatusFk == NAME_ST_NOM_UTIQUE_REJ_PROP){
306 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.UTIQUE_REJECTED_PROP());
307 }else if (nomStatusFk == NAME_ST_NOM_CONS){
308 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED());
309 }else if (nomStatusFk == NAME_ST_NOM_CONS_PROP){
310 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED_PROP());
311 }else if (nomStatusFk == NAME_ST_ORTH_CONS){
312 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED());
313 }else if (nomStatusFk == NAME_ST_ORTH_CONS_PROP){
314 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP());
315 }else if (nomStatusFk == NAME_ST_NOM_SUPERFL){
316 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.SUPERFLUOUS());
317 }else if (nomStatusFk == NAME_ST_NOM_AMBIG){
318 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.AMBIGUOUS());
319 }else if (nomStatusFk == NAME_ST_NOM_PROVIS){
320 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.PROVISIONAL());
321 }else if (nomStatusFk == NAME_ST_NOM_DUB){
322 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.DOUBTFUL());
323 }else if (nomStatusFk == NAME_ST_NOM_NOV){
324 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.NOVUM());
325 }else if (nomStatusFk == NAME_ST_NOM_CONFUS){
326 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONFUSUM());
327 }else if (nomStatusFk == NAME_ST_NOM_ALTERN){
328 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ALTERNATIVE());
329 }else if (nomStatusFk == NAME_ST_COMB_INVAL){
330 return NomenclaturalStatus.NewInstance(NomenclaturalStatusType.COMBINATION_INVALID());
331 }else {
332 NomenclaturalStatusType statusType = nomStatusTypeAbbrev2NewNomStatusType(nomStatusLabel);
333 NomenclaturalStatus result = NomenclaturalStatus.NewInstance(statusType);
334 if (result != null){
335 return result;
336 }
337 throw new UnknownCdmTypeException("Unknown NomenclaturalStatus (id=" + Integer.valueOf(nomStatusFk).toString() + ")");
338 }
339 }
340
341
342 //TypeDesignation
343 public static SpecimenTypeDesignationStatus typeStatusId2TypeStatus (int typeStatusId) throws UnknownCdmTypeException{
344 switch (typeStatusId){
345 case 0: return null;
346 case 1: return SpecimenTypeDesignationStatus.HOLOTYPE();
347 case 2: return SpecimenTypeDesignationStatus.LECTOTYPE();
348 case 3: return SpecimenTypeDesignationStatus.NEOTYPE();
349 case 4: return SpecimenTypeDesignationStatus.EPITYPE();
350 case 5: return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
351 case 6: return SpecimenTypeDesignationStatus.ISONEOTYPE();
352 case 7: return SpecimenTypeDesignationStatus.ISOTYPE();
353 case 8: return SpecimenTypeDesignationStatus.PARANEOTYPE();
354 case 9: return SpecimenTypeDesignationStatus.PARATYPE();
355 case 10: return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
356 case 11: return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
357 case 12: return SpecimenTypeDesignationStatus.SYNTYPE();
358 case 21: return SpecimenTypeDesignationStatus.ICONOTYPE();
359 case 22: return SpecimenTypeDesignationStatus.PHOTOTYPE();
360 default: {
361 throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(typeStatusId).toString() + ")");
362 }
363 }
364 }
365
366 //TypeDesignation
367 public static TaxonRelationshipType taxonRelId2TaxonRelType (int relTaxonTypeId, ResultWrapper<Boolean> isInverse, ResultWrapper<Boolean> isDoubtful) throws UnknownCdmTypeException{
368 isInverse.setValue(false);
369 switch (relTaxonTypeId){
370 case 0: return null;
371 case 11: return TaxonRelationshipType.CONGRUENT_TO();
372 case 12: isInverse.setValue(true); return TaxonRelationshipType.INCLUDES();
373 case 13: isInverse.setValue(true); return TaxonRelationshipType.CONGRUENT_OR_INCLUDES();
374 case 14: return TaxonRelationshipType.INCLUDES();
375 case 15: return TaxonRelationshipType.CONGRUENT_OR_INCLUDES();
376 case 16: return TaxonRelationshipType.INCLUDED_OR_INCLUDES();
377 case 17: return TaxonRelationshipType.CONGRUENT_OR_INCLUDED_OR_INCLUDES();
378 case 18: return TaxonRelationshipType.OVERLAPS();
379 case 19: return TaxonRelationshipType.CONGRUENT_OR_OVERLAPS();
380 case 20: isInverse.setValue(true); return TaxonRelationshipType.INCLUDES_OR_OVERLAPS();
381 case 21: isInverse.setValue(true); return TaxonRelationshipType.CONGRUENT_OR_INCLUDES_OR_OVERLAPS();
382 case 22: return TaxonRelationshipType.INCLUDES_OR_OVERLAPS();
383 case 23: return TaxonRelationshipType.CONGRUENT_OR_INCLUDES_OR_OVERLAPS();
384 case 24: return TaxonRelationshipType.INCLUDED_OR_INCLUDES_OR_OVERLAPS();
385
386 case 26: return TaxonRelationshipType.EXCLUDES();
387
388 //TODO other relationshipTypes
389
390 case 40: return TaxonRelationshipType.NOT_CONGRUENT_TO();
391
392 //FIXME doubtful
393 case 43: logger.warn("Doubful not yet implemented for Taxon Relationship congruent_to"); return TaxonRelationshipType.CONGRUENT_TO();
394 default: {
395 throw new UnknownCdmTypeException("Unknown TypeDesignationStatus (id=" + Integer.valueOf(relTaxonTypeId).toString() + ")");
396 }
397 }
398 }
399
400 //TypeDesignation
401 public static HybridRelationshipType relNameId2HybridRel (int relNameId) throws UnknownCdmTypeException{
402 switch (relNameId){
403 case 0: return null;
404 case 9: return HybridRelationshipType.FIRST_PARENT();
405 case 10: return HybridRelationshipType.SECOND_PARENT();
406 case 11: return HybridRelationshipType.FEMALE_PARENT();
407 case 12: return HybridRelationshipType.MALE_PARENT();
408 default: {
409 throw new UnknownCdmTypeException("Unknown HybridRelationshipType (id=" + Integer.valueOf(relNameId).toString() + ")");
410 }
411 }
412 }
413
414 //OccStatus
415 public static PresenceAbsenceTermBase<?> occStatus2PresenceAbsence (int occStatusId) throws UnknownCdmTypeException{
416 switch (occStatusId){
417 case 0: return null;
418 case 110: return AbsenceTerm.CULTIVATED_REPORTED_IN_ERROR();
419 case 120: return PresenceTerm.CULTIVATED();
420 case 210: return AbsenceTerm.INTRODUCED_REPORTED_IN_ERROR();
421 case 220: return PresenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE();
422 case 230: return AbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED();
423 case 240: return PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED();
424 case 250: return PresenceTerm.INTRODUCED();
425 case 260: return PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION();
426 case 270: return PresenceTerm.INTRODUCED_ADVENTITIOUS();
427 case 280: return PresenceTerm.INTRODUCED_NATURALIZED();
428 case 310: return AbsenceTerm.NATIVE_REPORTED_IN_ERROR();
429 case 320: return PresenceTerm.NATIVE_PRESENCE_QUESTIONABLE();
430 case 330: return AbsenceTerm.NATIVE_FORMERLY_NATIVE();
431 case 340: return PresenceTerm.NATIVE_DOUBTFULLY_NATIVE();
432 case 350: return PresenceTerm.NATIVE();
433 case 999: {
434 logger.info("endemic for EM can not be transformed in legal status. Used 'PRESENT' instead");
435 //TODO preliminary
436 return PresenceTerm.PRESENT();
437 }
438 default: {
439 throw new UnknownCdmTypeException("Unknown occurrence status (id=" + Integer.valueOf(occStatusId).toString() + ")");
440 }
441 }
442 }
443
444
445 //FactCategory
446 public static Feature factCategory2Feature (int factCategoryId) throws UnknownCdmTypeException{
447 switch (factCategoryId){
448 case 0: return null;
449 case 1: return Feature.DESCRIPTION();
450 case 4: return Feature.ECOLOGY();
451 case 5: return Feature.PHENOLOGY();
452 case 12: return Feature.COMMON_NAME();
453 case 13: return Feature.OCCURRENCE();
454 case 99: return Feature.CITATION();
455 default: {
456 throw new UnknownCdmTypeException("Unknown FactCategory (id=" + Integer.valueOf(factCategoryId).toString() + ")");
457 }
458 }
459 }
460
461 public static UUID getFeatureUuid(String key) throws UndefinedTransformerMethodException {
462 if (key == null){
463 return null;
464 }else if (key.equalsIgnoreCase("14-Maps")){ return uuidFeatureMaps;
465 }else if (key.equalsIgnoreCase("301-Conservation Status")){ return uuidFeatureConservationStatus;
466 }else if (key.equalsIgnoreCase("302-Use")){ return uuidFeatureUse;
467 }else if (key.equalsIgnoreCase("303-Comments")){ return uuidFeatureComments;
468
469 }else if (key.equalsIgnoreCase("10-general distribution (Euro+Med)")){ return uuidFeatureDistrEM;
470 }else if (key.equalsIgnoreCase("11-general distribution (world)")){ return uuidFeatureDistrWorld;
471 }else if (key.equalsIgnoreCase("250-Editor_Brackets")){ return uuidFeatureEditorBrackets;
472 }else if (key.equalsIgnoreCase("251-Editor_Parenthesis")){ return uuidFeatureEditorParenthesis;
473 }else if (key.equalsIgnoreCase("252-Inedited")){ return uuidFeatureInedited;
474 }else if (key.equalsIgnoreCase("253-Comments on editing process")){ return uuidFeatureCommentsEditing;
475
476 }else{
477 return null;
478 }
479 }
480
481
482 static Rank collSpeciesRank;
483 /**
484 * @param i
485 * @return
486 */
487 private static Rank rankId2NewRank(Integer rankId, boolean switchRank) {
488 Rank result = null;
489 if (rankId == null){
490 return null;
491 }else if (rankId == 57){
492
493 if (collSpeciesRank == null){
494 collSpeciesRank = Rank.NewInstance(RankClass.SpeciesGroup, "Collective species", "Coll. species", "coll.");
495 collSpeciesRank.setUuid(uuidRankCollSpecies);
496 OrderedTermVocabulary<Rank> voc = (OrderedTermVocabulary<Rank>)Rank.SPECIES().getVocabulary();
497 voc.addTermBelow(collSpeciesRank, Rank.SPECIESGROUP());
498 }
499 result = collSpeciesRank;
500 }
501 return result;
502 }
503
504
505 public static Rank rankId2Rank (ResultSet rs, boolean useUnknown, boolean switchSpeciesGroup) throws UnknownCdmTypeException{
506 Rank result;
507 try {
508 int rankId = rs.getInt("rankFk");
509
510 String abbrev = rs.getString("rankAbbrev");
511 String rankName = rs.getString("rank");
512 if (logger.isDebugEnabled()){logger.debug(rankId);}
513 if (logger.isDebugEnabled()){logger.debug(abbrev);}
514 if (logger.isDebugEnabled()){logger.debug(rankName);}
515
516 if (switchSpeciesGroup){
517 if (rankId == 59){
518 rankId = 57;
519 }else if (rankId == 57){
520 rankId = 59;
521 }
522 }
523 try {
524 result = Rank.getRankByNameOrIdInVoc(abbrev);
525 } catch (UnknownCdmTypeException e) {
526 try {
527 result = Rank.getRankByNameOrIdInVoc(rankName);
528 } catch (UnknownCdmTypeException e1) {
529 switch (rankId){
530 case 0: return null;
531 case 1: return Rank.KINGDOM();
532 case 3: return Rank.SUBKINGDOM();
533 case 5: return Rank.PHYLUM();
534 case 7: return Rank.SUBPHYLUM();
535 case 8: return Rank.DIVISION();
536 case 9: return Rank.SUBDIVISION();
537 case 10: return Rank.CLASS();
538 case 13: return Rank.SUBCLASS();
539 case 16: return Rank.SUPERORDER();
540 case 18: return Rank.ORDER();
541 case 19: return Rank.SUBORDER();
542 case 20: return Rank.FAMILY();
543 case 25: return Rank.SUBFAMILY();
544 case 30: return Rank.TRIBE();
545 case 35: return Rank.SUBTRIBE();
546 case 40: return Rank.GENUS();
547 case 42: return Rank.SUBGENUS();
548 case 45: return Rank.SECTION_BOTANY();
549 case 47: return Rank.SUBSECTION_BOTANY();
550 case 50: return Rank.SERIES();
551 case 52: return Rank.SUBSERIES();
552 case 58: return Rank.SPECIESAGGREGATE();
553 case 59: return Rank.SPECIESGROUP();
554 case 60: return Rank.SPECIES();
555 case 61: return Rank.GREX();
556 case 65: return Rank.SUBSPECIES();
557 case 66: {System.out.println("Rank 66 not yet implemented"); throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());}
558 case 67: {System.out.println("Rank 67 not yet implemented"); throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());}
559 case 68: return Rank.CONVAR();
560 case 70: return Rank.VARIETY();
561 case 73: return Rank.SUBVARIETY();
562 case 80: return Rank.FORM();
563 case 82: return Rank.SUBFORM();
564 case 84: return Rank.SPECIALFORM();
565 case 98: return Rank.INFRAGENERICTAXON();
566 case 99: return Rank.INFRASPECIFICTAXON();
567
568 case 750: return Rank.SUPERCLASS();
569 case 780: return Rank.INFRACLASS();
570 case 820: return Rank.INFRAORDER();
571
572 case 830: return Rank.SUPERFAMILY();
573
574 default: {
575 Rank rank = rankId2NewRank(57, switchSpeciesGroup);
576 if (rank != null){
577 return rank;
578 }
579 if (useUnknown){
580 logger.error("Rank unknown: " + rankId + ". Created UNKNOWN_RANK");
581 return Rank.UNKNOWN_RANK();
582 }
583 throw new UnknownCdmTypeException("Unknown Rank id" + Integer.valueOf(rankId).toString());
584 }
585 }
586 }
587 }
588 return result;
589 } catch (SQLException e) {
590 e.printStackTrace();
591 logger.warn("Exception occurred. Created UNKNOWN_RANK instead");
592 return Rank.UNKNOWN_RANK();
593 }
594 }
595
596
597 public static Integer rank2RankId (Rank rank){
598 if (rank == null){
599 return null;
600 }
601 else if (rank.equals(Rank.KINGDOM())){ return 1;}
602 else if (rank.equals(Rank.SUBKINGDOM())){ return 3;}
603 else if (rank.equals(Rank.PHYLUM())){ return 5;}
604 else if (rank.equals(Rank.SUBPHYLUM())){ return 7;}
605 else if (rank.equals(Rank.DIVISION())){ return 8;}
606 else if (rank.equals(Rank.SUBDIVISION())){ return 9;}
607
608 else if (rank.equals(Rank.CLASS())){ return 10;}
609 else if (rank.equals(Rank.SUBCLASS())){ return 13;}
610 else if (rank.equals(Rank.SUPERORDER())){ return 16;}
611 else if (rank.equals(Rank.ORDER())){ return 18;}
612 else if (rank.equals(Rank.SUBORDER())){ return 19;}
613 else if (rank.equals(Rank.FAMILY())){ return 20;}
614 else if (rank.equals(Rank.SUBFAMILY())){ return 25;}
615 else if (rank.equals(Rank.TRIBE())){ return 30;}
616 else if (rank.equals(Rank.SUBTRIBE())){ return 35;}
617 else if (rank.equals(Rank.GENUS())){ return 40;}
618 else if (rank.equals(Rank.SUBGENUS())){ return 42;}
619 else if (rank.equals(Rank.SECTION_BOTANY())){ return 45;}
620 else if (rank.equals(Rank.SUBSECTION_BOTANY())){ return 47;}
621 else if (rank.equals(Rank.SERIES())){ return 50;}
622 else if (rank.equals(Rank.SUBSERIES())){ return 52;}
623 else if (rank.equals(Rank.SPECIESAGGREGATE())){ return 58;}
624 //TODO
625 // else if (rank.equals(Rank.XXX())){ return 59;}
626 else if (rank.equals(Rank.SPECIES())){ return 60;}
627 else if (rank.equals(Rank.SUBSPECIES())){ return 65;}
628 else if (rank.equals(Rank.CONVAR())){ return 68;}
629 else if (rank.equals(Rank.VARIETY())){ return 70;}
630 else if (rank.equals(Rank.SUBVARIETY())){ return 73;}
631 else if (rank.equals(Rank.FORM())){ return 80;}
632 else if (rank.equals(Rank.SUBFORM())){ return 82;}
633 else if (rank.equals(Rank.SPECIALFORM())){ return 84;}
634 else if (rank.equals(Rank.INFRAGENERICTAXON())){ return 98;}
635 else if (rank.equals(Rank.INFRASPECIFICTAXON())){ return 99;}
636
637 else if (rank.equals(Rank.SUPERCLASS())){ return 750;}
638 else if (rank.equals(Rank.INFRACLASS())){ return 780;}
639 else if (rank.equals(Rank.INFRAORDER())){ return 820;}
640 else if (rank.equals(Rank.SUPERFAMILY())){ return 830;}
641
642 else {
643 //TODO Exception
644 logger.warn("Rank not yet supported in Berlin Model: "+ rank.getLabel());
645 return null;
646 }
647 }
648
649 public static Integer textData2FactCategoryFk (Feature feature){
650 if (feature == null){return null;}
651 if (feature.equals(Feature.DESCRIPTION())){
652 return 1;
653 }else if (feature.equals(Feature.ECOLOGY())){
654 return 4;
655 }else if (feature.equals(Feature.PHENOLOGY())){
656 return 5;
657 }else if (feature.equals(Feature.COMMON_NAME())){
658 return 12;
659 }else if (feature.equals(Feature.OCCURRENCE())){
660 return 13;
661 }else if (feature.equals(Feature.CITATION())){
662 return 99;
663 }else{
664 logger.debug("Unknown Feature.");
665 return null;
666 }
667 }
668
669
670 public static Integer taxonBase2statusFk (TaxonBase<?> taxonBase){
671 if (taxonBase == null){return null;}
672 if (taxonBase.isInstanceOf(Taxon.class)){
673 return T_STATUS_ACCEPTED;
674 }else if (taxonBase.isInstanceOf(Synonym.class)){
675 return T_STATUS_SYNONYM;
676 }else{
677 logger.warn("Unknown ");
678 return T_STATUS_UNRESOLVED;
679 }
680 //TODO
681 // public static int T_STATUS_PARTIAL_SYN = 3;
682 // public static int T_STATUS_PRO_PARTE_SYN = 4;
683 // public static int T_STATUS_UNRESOLVED = 5;
684 // public static int T_STATUS_ORPHANED = 6;
685 }
686
687 public static Integer ref2refCategoryId (Reference<?> ref){
688 if (ref == null){
689 return null;
690 }
691 else if (ref.getType().equals(ReferenceType.Article)){ return REF_ARTICLE;}
692 else if (ref instanceof ISection){ return REF_PART_OF_OTHER_TITLE;}
693 else if (ref.getType().equals(ReferenceType.Book)){ return REF_BOOK;}
694 else if (ref.getType().equals(ReferenceType.Database)){ return REF_DATABASE;}
695 // else if (ref instanceof SectionBas){ return REF_INFORMAL;}
696 // else if (ref instanceof SectionBas){ return REF_NOT_APPLICABLE;}
697 else if (ref.getType().equals(ReferenceType.WebPage)){ return REF_WEBSITE;}
698 else if (ref.getType().equals(ReferenceType.CdDvd)){ return REF_CD;}
699 else if (ref.getType().equals(ReferenceType.Journal)){ return REF_JOURNAL;}
700 else if (ref.getType().equals(ReferenceType.Generic)){ return REF_UNKNOWN;}
701 else if (ref.getType().equals(ReferenceType.PrintSeries)){
702 logger.warn("Print Series is not a standard Berlin Model category");
703 return REF_PRINT_SERIES;
704 }
705 else if (ref.getType().equals(ReferenceType.Proceedings)){
706 logger.warn("Proceedings is not a standard Berlin Model category");
707 return REF_CONFERENCE_PROCEEDINGS;
708 }
709 // else if (ref instanceof ){ return REF_JOURNAL_VOLUME;}
710 else if (ref.getType().equals(ReferenceType.Patent)){ return REF_NOT_APPLICABLE;}
711 else if (ref.getType().equals(ReferenceType.PersonalCommunication)){ return REF_INFORMAL;}
712 else if (ref.getType().equals(ReferenceType.Report)){ return REF_NOT_APPLICABLE;}
713 else if (ref.getType().equals(ReferenceType.Thesis)){ return REF_NOT_APPLICABLE;}
714 else if (ref.getType().equals(ReferenceType.Report)){ return REF_NOT_APPLICABLE;}
715
716 else {
717 //TODO Exception
718 logger.warn("Reference type not yet supported in Berlin Model: "+ ref.getClass().getSimpleName());
719 return null;
720 }
721 }
722
723
724 public static Integer taxRelation2relPtQualifierFk (RelationshipBase<?,?,?> rel){
725 if (rel == null){
726 return null;
727 }
728 // else if (rel instanceof SynonymRelationship){
729 // return ;
730 // }else if (rel instanceof TaxonRelationship){
731 RelationshipTermBase<?> type = rel.getType();
732 if (type.equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {return TAX_REL_IS_INCLUDED_IN;
733 }else if (type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {return TAX_REL_IS_MISAPPLIED_NAME_OF;
734 }else if (type.equals(SynonymRelationshipType.SYNONYM_OF())) {return TAX_REL_IS_SYNONYM_OF;
735 }else if (type.equals(SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF())) {return TAX_REL_IS_HOMOTYPIC_SYNONYM_OF;
736 }else if (type.equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())) {return TAX_REL_IS_HETEROTYPIC_SYNONYM_OF;
737 }else if (type.equals(TaxonRelationshipType.CONGRUENT_TO())) {return 11;
738 // public static int TAX_REL_IS_PROPARTE_SYN_OF = 4;
739 // public static int TAX_REL_IS_PARTIAL_SYN_OF = 5;
740 // public static int TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF = 101;
741 // public static int TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF = 102;
742 // public static int TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF = 103;
743 // public static int TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF = 104;
744
745 }else {
746 //TODO Exception
747 logger.warn("Relationship type not yet supported by Berlin Model export: "+ rel.getType());
748 return null;
749 }
750 }
751
752 public static Integer nomStatus2nomStatusFk (NomenclaturalStatusType status){
753 if (status == null){
754 return null;
755 }
756 if (status.equals(NomenclaturalStatusType.INVALID())) {return NAME_ST_NOM_INVAL;
757 }else if (status.equals(NomenclaturalStatusType.ILLEGITIMATE())) {return NAME_ST_NOM_ILLEG;
758 }else if (status.equals(NomenclaturalStatusType.NUDUM())) {return NAME_ST_NOM_NUD;
759 }else if (status.equals(NomenclaturalStatusType.REJECTED())) {return NAME_ST_NOM_REJ;
760 }else if (status.equals(NomenclaturalStatusType.REJECTED_PROP())) {return NAME_ST_NOM_REJ_PROP;
761 }else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED())) {return NAME_ST_NOM_UTIQUE_REJ;
762 }else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED_PROP())) {return NAME_ST_NOM_UTIQUE_REJ_PROP;
763 }else if (status.equals(NomenclaturalStatusType.CONSERVED())) {return NAME_ST_NOM_CONS;
764
765 }else if (status.equals(NomenclaturalStatusType.CONSERVED_PROP())) {return NAME_ST_NOM_CONS_PROP;
766 }else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED())) {return NAME_ST_ORTH_CONS;
767 }else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP())) {return NAME_ST_ORTH_CONS_PROP;
768 }else if (status.equals(NomenclaturalStatusType.SUPERFLUOUS())) {return NAME_ST_NOM_SUPERFL;
769 }else if (status.equals(NomenclaturalStatusType.AMBIGUOUS())) {return NAME_ST_NOM_AMBIG;
770 }else if (status.equals(NomenclaturalStatusType.PROVISIONAL())) {return NAME_ST_NOM_PROVIS;
771 }else if (status.equals(NomenclaturalStatusType.DOUBTFUL())) {return NAME_ST_NOM_DUB;
772 }else if (status.equals(NomenclaturalStatusType.NOVUM())) {return NAME_ST_NOM_NOV;
773
774 }else if (status.equals(NomenclaturalStatusType.CONFUSUM())) {return NAME_ST_NOM_CONFUS;
775 }else if (status.equals(NomenclaturalStatusType.ALTERNATIVE())) {return NAME_ST_NOM_ALTERN;
776 }else if (status.equals(NomenclaturalStatusType.COMBINATION_INVALID())) {return NAME_ST_COMB_INVAL;
777 //TODO
778 }else {
779 //TODO Exception
780 logger.warn("NomStatus type not yet supported by Berlin Model export: "+ status);
781 return null;
782 }
783 }
784
785
786
787 public static Integer nameRel2RelNameQualifierFk (RelationshipBase<?,?,?> rel){
788 if (rel == null){
789 return null;
790 }
791 RelationshipTermBase<?> type = rel.getType();
792 if (type.equals(NameRelationshipType.BASIONYM())) {return NAME_REL_IS_BASIONYM_FOR;
793 }else if (type.equals(NameRelationshipType.LATER_HOMONYM())) {return NAME_REL_IS_LATER_HOMONYM_OF;
794 }else if (type.equals(NameRelationshipType.REPLACED_SYNONYM())) {return NAME_REL_IS_REPLACED_SYNONYM_FOR;
795 //TODO
796 }else if (type.equals(NameRelationshipType.VALIDATED_BY_NAME())) {return NAME_REL_IS_VALIDATION_OF;
797 }else if (type.equals(NameRelationshipType.LATER_VALIDATED_BY_NAME())) {return NAME_REL_IS_LATER_VALIDATION_OF;
798 }else if (type.equals(NameRelationshipType.CONSERVED_AGAINST())) {return NAME_REL_IS_CONSERVED_AGAINST;
799
800
801 }else if (type.equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())) {return NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF;
802 }else if (type.equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())) {return NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
803 }else {
804 //TODO Exception
805 logger.warn("Relationship type not yet supported by Berlin Model export: "+ rel.getType());
806 return null;
807 }
808
809 //NameRelationShip
810
811 // }else if (type.equals(NameRelationshipType.())) {return NAME_REL_IS_REJECTED_IN_FAVOUR_OF;
812
813 // public static int NAME_REL_IS_FIRST_PARENT_OF = 9;
814 // public static int NAME_REL_IS_SECOND_PARENT_OF = 10;
815 // public static int NAME_REL_IS_FEMALE_PARENT_OF = 11;
816 // public static int NAME_REL_IS_MALE_PARENT_OF = 12;
817 //
818 // public static int NAME_REL_IS_REJECTED_IN_FAVOUR_OF = 14;
819 // }else if (type.equals(NameRelationshipType.)) {return NAME_REL_IS_REJECTED_TYPE_OF;
820 //
821 // public static int NAME_REL_HAS_SAME_TYPE_AS = 18;
822 // public static int NAME_REL_IS_LECTOTYPE_OF = 61;
823 // public static int NAME_REL_TYPE_NOT_DESIGNATED = 62;
824
825 // }else if (type.equals(NameRelationshipType.LATER_VALIDATED_BY_NAME())) {return NAME_REL_IS_TYPE_OF;
826
827
828 }
829
830 public static UUID getWebMarkerUuid (int markerCategoryId){
831 if (markerCategoryId == 1){
832 return UUID.fromString("d8554418-d1ae-471d-a1bd-a0cbc7ab860c"); //any as not to find in cichorieae
833 }else if (markerCategoryId == 2){
834 return UUID.fromString("7f189c48-8632-4870-9ec8-e4d2489f324e");
835 }else if (markerCategoryId == 3){
836 return UUID.fromString("9a115e6b-8210-4dd3-825a-6fed11016c63");
837 }else if (markerCategoryId == 4){
838 return UUID.fromString("1d287011-2054-41c5-a919-17ac1d0a9270");
839 }else if (markerCategoryId == 9){
840 return UUID.fromString("cc5eca5c-1ae5-4feb-9a95-507fc167b0c9");
841 //Salvador
842 }else if (markerCategoryId == 5){
843 return UUID.fromString("7d8875b3-107c-4189-97e5-cadb470e543a");
844 }else if (markerCategoryId == 20){
845 return UUID.fromString("3574e2b0-6431-4d71-b456-bc967c80f622");
846 }else if (markerCategoryId == 30){
847 return UUID.fromString("9924b27e-0dbe-4d95-ae9b-096fbbc3edcb");
848 }else if (markerCategoryId == 40){
849 return UUID.fromString("69241b97-f4d2-4f60-9aed-1c4ccb5bced5");
850 }else if (markerCategoryId == 50){
851 return UUID.fromString("f3b62ce3-0212-4542-a74c-0c68d08859b1");
852 }else if (markerCategoryId == 55){
853 return UUID.fromString("bec822f2-8242-425f-ad46-f11f0b82f69b");
854 }else if (markerCategoryId == 60){
855 return UUID.fromString("722fca60-0416-4bf0-aa4b-a07400f9710d");
856 }else if (markerCategoryId == 70){
857 return UUID.fromString("ed57857b-1001-4b09-b48e-d88ab146bb2b");
858 }else if (markerCategoryId == 80){
859 return UUID.fromString("637e8b77-1202-462b-9d77-1023f3c192d9");
860 }else if (markerCategoryId == 90){
861 return UUID.fromString("c769c231-6e76-46df-88f7-2c459342a3c2");
862 }else if (markerCategoryId == 93){
863 return UUID.fromString("075ee97e-246f-4f3d-aa96-16930df6268c");
864 }else if (markerCategoryId == 100){
865 return UUID.fromString("e17065bf-3e44-417a-b05c-f82929f680c3");
866 }else if (markerCategoryId == 110){
867 return UUID.fromString("e2b8de07-770e-4fda-b445-c4735f4e95c8");
868 }else if (markerCategoryId == 900){
869 return UUID.fromString("d029c3c9-944a-4bb9-bba6-12c95da94a04");
870 }else if (markerCategoryId == 920){
871 return UUID.fromString("98af97b1-e5e3-4ee4-902e-15032316bfc3");
872 }else if (markerCategoryId == 930){
873 return UUID.fromString("4b6c3130-4e50-4f45-8461-d2698cf5f80b");
874 }else if (markerCategoryId == 950){
875 return UUID.fromString("1e53f58c-6528-42c6-99ae-0f75a3c3c264");
876 }else if (markerCategoryId == 960){
877 return UUID.fromString("1903d460-94cc-4fc4-b2a8-a3fb0cfd69a0");
878 }else{
879 logger.warn("Unknown webMarker category: " + markerCategoryId);
880 return null;
881 }
882
883 }
884
885 }