ref #8509 handle new ERMS quality status "Thematic Editor"
[cdmlib-apps.git] / cdm-pesi / src / main / java / eu / etaxonomy / cdm / io / pesi / out / PesiTransformer.java
1 /**
2 * Copyright (C) 2009 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.io.pesi.out;
10
11 import java.sql.ResultSet;
12 import java.sql.SQLException;
13 import java.util.EnumSet;
14 import java.util.HashMap;
15 import java.util.HashSet;
16 import java.util.Map;
17 import java.util.Set;
18 import java.util.UUID;
19
20 import org.apache.commons.lang.StringUtils;
21 import org.apache.log4j.Logger;
22
23 import eu.etaxonomy.cdm.common.CdmUtils;
24 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
25 import eu.etaxonomy.cdm.io.common.Source;
26 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
27 import eu.etaxonomy.cdm.io.common.mapping.out.ExportTransformerBase;
28 import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;
29 import eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer;
30 import eu.etaxonomy.cdm.io.pesi.out.PesiExportBase.PesiSource;
31 import eu.etaxonomy.cdm.model.common.CdmBase;
32 import eu.etaxonomy.cdm.model.common.Language;
33 import eu.etaxonomy.cdm.model.common.RelationshipBase;
34 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
35 import eu.etaxonomy.cdm.model.description.Feature;
36 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
37 import eu.etaxonomy.cdm.model.location.Country;
38 import eu.etaxonomy.cdm.model.location.NamedArea;
39 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
40 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
41 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
42 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
43 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
44 import eu.etaxonomy.cdm.model.name.Rank;
45 import eu.etaxonomy.cdm.model.name.TaxonName;
46 import eu.etaxonomy.cdm.model.reference.Reference;
47 import eu.etaxonomy.cdm.model.reference.ReferenceType;
48 import eu.etaxonomy.cdm.model.taxon.Synonym;
49 import eu.etaxonomy.cdm.model.taxon.SynonymType;
50 import eu.etaxonomy.cdm.model.taxon.Taxon;
51 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
52 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
53 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
54 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
55 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
56
57 /**
58 * @author e.-m.lee
59 * @author a.mueller (update)
60 * @since 16.02.2010
61 */
62 public final class PesiTransformer extends ExportTransformerBase{
63
64 private static final Logger logger = Logger.getLogger(PesiTransformer.class);
65
66 public static final String AUCT_STRING = "auct.";
67
68 //sourceRefUUIDs
69 public static final UUID uuidSourceRefEuroMed = UUID.fromString("51b3900c-91e0-4cc5-94f3-577a352ca9c4");
70 public static final UUID uuidSourceRefFaunaEuropaea = UUID.fromString("f27a5e67-d065-4b79-8d41-eabd3ae0edd0");
71 public static final UUID uuidSourceRefErms = UUID.fromString("7744bc26-f914-42c4-b54a-dd2a030a8bb7");
72 public static final UUID uuidSourceRefIndexFungorum = UUID.fromString("8de25d27-7d40-47f4-af3b-59d64935a843");
73 public static final UUID uuidSourceRefAuct = UUID.fromString("5f79f96c-c100-4cd8-b78e-2b2dacf09a23");
74 public static final UUID uuidSourceRefFaunaEuropaea_fromSql = UUID.fromString("6786d863-75d4-4796-b916-c1c3dff4cb70");
75
76 public static final UUID uuidTaxonValuelessEuroMed = UUID.fromString("f0a9322b-a57e-447b-9a75-a909f2f2a994");
77
78 public static final String SOURCE_STR_EM = "E+M";
79 public static final String SOURCE_STR_FE = "FaEu";
80 public static final String SOURCE_STR_IF = "IF";
81 public static final String SOURCE_STR_ERMS = "ERMS";
82
83 // status keys
84 private static int QUALITY_STATUS_CHECKED_EDITOR_ERMS_1_1 = 0;
85 private static int QUALITY_STATUS_ADD_BY_DBMT= 2;
86 private static int QUALITY_STATUS_CHECKED_EDITOR = 3;
87 private static int QUALITY_STATUS_EDITED_BY_DBMT = 4;
88 private static int QUALITY_STATUS_THEMATIC_EDITOR = 5;
89
90 // marker type
91 public static final UUID uuidMarkerGuidIsMissing = UUID.fromString("24e70843-05e2-44db-954b-84df0d23ea20");
92 public static final UUID uuidMarkerTypeHasNoLastAction = UUID.fromString("99652d5a-bc92-4251-b57d-0fec4d258ab7");
93 // public static final UUID uuidMarkerFossil = UUID.fromString("761ce108-031a-4e07-b444-f8d757070312");
94
95
96 //extension type uuids
97 public static final UUID uuidExtCacheCitation = UUID.fromString("29656168-32d6-4301-9067-d57c63be5c67");
98 //public static final UUID expertUserIdUuid = UUID.fromString("e25813d3-c67c-4585-9aa0-970fafde50b4");
99 //public static final UUID speciesExpertUserIdUuid = UUID.fromString("6d42abd8-8894-4980-ae07-e918affd4172");
100 public static final UUID uuidExtExpertName = BerlinModelTransformer.uuidExpertName;
101 public static final UUID uuidExtSpeciesExpertName = BerlinModelTransformer.uuidSpeciesExpertName;
102 public static final UUID uuidExtLastActionDate = UUID.fromString("8d0a7d81-bb83-4576-84c3-8c906ef039b2");
103 public static final UUID uuidExtLastAction = UUID.fromString("bc20d5bc-6161-4279-9499-89ea26ce5f6a");
104 public static final UUID uuidExtTaxComment = UUID.fromString("8041a752-0479-4626-ab1b-b266b751f816");
105 public static final UUID uuidExtFauComment = UUID.fromString("054f773a-41c8-4ad5-83e3-981320c1c126");
106 public static final UUID uuidExtFauExtraCodes = UUID.fromString("b8c7e77d-9869-4787-bed6-b4b302dbc5f5");
107
108 // References
109 private static int REF_ARTICLE_IN_PERIODICAL = 1;
110 private static int REF_PART_OF_OTHER = 2;
111 public static int REF_BOOK = 3;
112 public static int REF_DATABASE = 4;
113 private static int REF_INFORMAL = 5;
114 private static int REF_NOT_APPLICABLE = 6;
115 private static int REF_WEBSITE = 7;
116 public static int REF_PUBLISHED_CD = 8;
117 public static int REF_JOURNAL = 9;
118 public static int REF_UNRESOLVED = 10;
119 public static int REF_PUBLICATION = 11;
120 public static String REF_STR_UNRESOLVED = "unresolved";
121
122 private static int LANG_UNKNOWN = -99;
123 private static int LANG_DUTCH = 11;
124 private static int LANG_VALENCIAN = 65;
125 private static int LANG_HIGH_ARAGONES = 66;
126 private static int LANG_MAJORCAN = 67;
127
128
129 // NameStatus
130 public static UUID uuidNomStatusTemporaryName = UUID.fromString("aa6ada5a-ca21-4fef-b76f-9ae237e9c4ae");
131
132 private static int NAME_ST_NOM_INVAL = 1;
133 private static int NAME_ST_NOM_ILLEG = 2;
134 private static int NAME_ST_NOM_NUD = 3;
135 private static int NAME_ST_NOM_REJ = 4;
136 private static int NAME_ST_NOM_REJ_PROP = 5;
137 private static int NAME_ST_NOM_UTIQUE_REJ = 6;
138 private static int NAME_ST_NOM_UTIQUE_REJ_PROP = 7;
139 private static int NAME_ST_NOM_CONS = 8;
140 private static int NAME_ST_NOM_CONS_PROP = 9;
141 private static int NAME_ST_ORTH_CONS = 10;
142 private static int NAME_ST_ORTH_CONS_PROP = 11;
143 private static int NAME_ST_NOM_SUPERFL = 12;
144 private static int NAME_ST_NOM_AMBIG = 13;
145 private static int NAME_ST_NOM_PROVIS = 14;
146 private static int NAME_ST_NOM_DUB = 15;
147 private static int NAME_ST_NOM_NOV = 16;
148 private static int NAME_ST_NOM_CONFUS = 17;
149 private static int NAME_ST_NOM_ALTERN = 18;
150 private static int NAME_ST_COMB_INVAL = 19;
151 private static int NAME_ST_LEGITIMATE = 20; // PESI specific from here
152 private static int NAME_ST_COMB_INED = 21;
153 private static int NAME_ST_COMB_AND_STAT_INED = 22;
154 private static int NAME_ST_NOM_AND_ORTH_CONS = 23;
155 private static int NAME_ST_NOM_NOV_INED = 24;
156 private static int NAME_ST_SP_NOV_INED = 25;
157 private static int NAME_ST_ALTERNATE_REPRESENTATION = 26;
158 private static int NAME_ST_TEMPORARY_NAME = 27;
159 private static int NAME_ST_SPECIES_INQUIRENDA = 28;
160
161 // TaxonStatus
162 public static int T_STATUS_ACCEPTED = 1;
163 public static int T_STATUS_SYNONYM = 2;
164 public static int T_STATUS_PARTIAL_SYN = 3;
165 public static int T_STATUS_PRO_PARTE_SYN = 4;
166 private static int T_STATUS_UNRESOLVED = 5;
167 private static int T_STATUS_ORPHANED = 6;
168 public static int T_STATUS_UNACCEPTED = 7;
169 private static int T_STATUS_NOT_ACCEPTED_VALUELESS = 8;
170
171 // TypeDesginationStatus // -> not a table anymore
172 private static int TYPE_BY_ORIGINAL_DESIGNATION = 1;
173 private static int TYPE_BY_SUBSEQUENT_DESIGNATION = 2;
174 private static int TYPE_BY_MONOTYPY = 3;
175 private static String TYPE_STR_BY_ORIGINAL_DESIGNATION = "Type by original designation";
176 private static String TYPE_STR_BY_SUBSEQUENT_DESIGNATION = "Type by subsequent designation";
177 private static String TYPE_STR_BY_MONOTYPY = "Type by monotypy";
178
179 // RelTaxonQualifier
180 private static int IS_BASIONYM_FOR = 1;
181 private static int IS_LATER_HOMONYM_OF = 2;
182 private static int IS_REPLACED_SYNONYM_FOR = 3;
183 private static int IS_VALIDATION_OF = 4;
184 private static int IS_LATER_VALIDATION_OF = 5;
185 private static int IS_TYPE_OF = 6;
186 private static int IS_CONSERVED_TYPE_OF = 7;
187 private static int IS_REJECTED_TYPE_OF = 8;
188 private static int IS_FIRST_PARENT_OF = 9;
189 private static int IS_SECOND_PARENT_OF = 10;
190 private static int IS_FEMALE_PARENT_OF = 11;
191 private static int IS_MALE_PARENT_OF = 12;
192 private static int IS_CONSERVED_AGAINST = 13;
193 private static int IS_REJECTED_IN_FAVOUR_OF = 14;
194 private static int IS_TREATED_AS_LATER_HOMONYM_OF = 15;
195 private static int IS_ORTHOGRAPHIC_VARIANT_OF = 16;
196 private static int IS_ALTERNATIVE_NAME_FOR = 17;
197 private static int HAS_SAME_TYPE_AS = 18;
198 private static int IS_ORIGINAL_SPELLING_FOR = 19;
199 private static int IS_BLOCKING_NAME_FOR = 20;
200 private static int IS_LECTOTYPE_OF = 61;
201 private static int TYPE_NOT_DESIGNATED = 62;
202 public static int IS_TAXONOMICALLY_INCLUDED_IN = 101;
203 public static int IS_SYNONYM_OF = 102;
204 private static int IS_MISAPPLIED_NAME_FOR = 103;
205 private static int IS_PRO_PARTE_SYNONYM_OF = 104;
206 private static int IS_PARTIAL_SYNONYM_OF = 105;
207 private static int IS_HETEROTYPIC_SYNONYM_OF = 106;
208 private static int IS_HOMOTYPIC_SYNONYM_OF = 107;
209 private static int IS_PRO_PARTE_MISAPPLIED_NAME_FOR = 108;
210 private static int IS_PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF = 201;
211 private static int IS_PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF = 202;
212 private static int IS_PARTIAL_AND_HOMOTYPIC_SYNONYM_OF = 203;
213 private static int IS_PARTIAL_AND_HETEROTYPIC_SYNONYM_OF = 204;
214 private static int IS_INFERRED_EPITHET_FOR = 301;
215 private static int IS_INFERRED_GENUS_FOR = 302;
216 private static int IS_POTENTIAL_COMBINATION_FOR = 303;
217
218 //namespaces
219 public static String STR_NAMESPACE_NOMINAL_TAXON = "Nominal taxon from TAX_ID:";
220 public static String STR_NAMESPACE_INFERRED_EPITHET = "Inferred epithet from TAX_ID:";
221 public static String STR_NAMESPACE_INFERRED_GENUS = "Inferred genus from TAX_ID:";
222 public static String STR_NAMESPACE_POTENTIAL_COMBINATION = "Potential combination from TAX_ID:";
223
224 // Kingdoms
225 private static final int KINGDOM_NULL = 0;
226 private static final int KINGDOM_ANIMALIA = 2;
227 private static final int KINGDOM_PLANTAE = 3;
228 private static final int KINGDOM_FUNGI = 4;
229 private static final int KINGDOM_PROTOZOA = 5;
230 private static final int KINGDOM_BACTERIA = 6;
231 private static final int KINGDOM_CHROMISTA = 7;
232
233 // Kingdoms
234 private static Map<String, Integer> pesiKingdomMap = new HashMap<>();
235
236 //Kingdom title
237 private static String KINGDOM_PLANTAE_STRING = "Plantae";
238 private static String KINGDOM_FUNGI_STRING = "Fungi";
239 private static String KINGDOM_PROTOZOA_STRING = "Protozoa";
240 private static String kINGDOM_BACTERIA_STRING = "Bacteria";
241 private static String KINGDOM_CHROMISTA_STRING = "Chromista";
242
243 //ranks of all kingdoms
244 private static int Kingdom = 10;
245 private static int Subkingdom = 20;
246 private static int Phylum = 30; //Phylum and Division is same (#8541) according to ICNAFP
247 private static int Division = 30;
248 private static int Subphylum = 40; //See above comment
249 private static int Subdivision = 40;
250 private static int Class = 60;
251 private static int Subclass = 70;
252 private static int Order = 100;
253 private static int Suborder = 110;
254 private static int Family = 140;
255 private static int Subfamily = 150;
256 private static int Tribe = 160;
257 private static int Subtribe = 170;
258 private static int Genus = 180;
259 private static int Subgenus = 190;
260 private static int Species =220;
261 private static int Subspecies = 230;
262 private static int Variety = 240;
263 private static int Forma = 260;
264
265 //ranks of some kingdoms
266 private static int Infrakingdom = 25; //2,3,5,7
267 private static int Infraphylum = 45; //2,7
268 private static int Superclass = 50; //2,5,6,7
269 private static int Infraclass = 80; //2,5,6,7
270 private static int Superorder = 90; //2,3,5,6,7
271 private static int Infraorder = 120; //2,5,6,7
272 private static int Superfamily = 130; //2,5,6,7
273 private static int Bot_Section = 200; //3,4,7
274 private static int Bot_Subsection = 210; //3,4,7
275 private static int Subvariety = 250; //2,3,4,7
276 private static int Subform = 270; //2,3,4
277 private static int Forma_spec = 275; //3,4,5,7
278
279 // Animalia Ranks
280 private static int Superphylum = 28;
281 private static int Subterclass = 85;
282 private static int Parvorder = 122;
283 private static int Animalia_Section = 125;
284 private static int Animalia_Subsection = 127;
285 private static int Natio = 235;
286
287 // Plantae Ranks
288 private static int Series = 212;
289 private static int Subseries = 214;
290 private static int Aggregate = 216;
291 private static int Coll_Species = 218;
292 private static int Grex = 225;
293 private static int Proles = 232;
294 private static int Race = 234;
295 private static int Convarietas = 236;
296 private static int Taxa_infragen = 280;
297 private static int Taxa_infraspec = 285;
298
299
300 //NoteCategory
301 private static int NoteCategory_description = 1;
302 public static int NoteCategory_ecology = 4;
303 private static int NoteCategory_phenology = 5;
304 private static int NoteCategory_general_distribution_euromed = 10;
305 private static int NoteCategory_general_distribution_world = 11;
306 private static int NoteCategory_Common_names = 12;
307 private static int NoteCategory_Occurrence = 13;
308 private static int NoteCategory_Maps =14;
309 private static int NoteCategory_Link_to_maps = 20;
310 private static int NoteCategory_Link_to_images = 21;
311 public static int NoteCategory_Link_to_taxonomy = 22;
312 public static int NoteCategory_Link_to_general_information = 23;
313 public static int NoteCategory_undefined_link = 24;
314 private static int NoteCategory_Editor_Braces = 249;
315 private static int NoteCategory_Editor_Brackets = 250;
316 private static int NoteCategory_Editor_Parenthesis = 251;
317 private static int NoteCategory_Inedited = 252;
318 private static int NoteCategory_Comments_on_editing_process = 253;
319 private static int NoteCategory_Publication_date = 254;
320 private static int NoteCategory_Morphology = 255;
321 private static int NoteCategory_Acknowledgments = 257;
322 private static int NoteCategory_Original_publication = 258;
323 private static int NoteCategory_Type_locality = 259;
324 private static int NoteCategory_Environment = 260;
325 private static int NoteCategory_Spelling = 261;
326 private static int NoteCategory_Systematics = 262;
327 private static int NoteCategory_Remark = 263;
328 private static int NoteCategory_Additional_information = 266;
329 private static int NoteCategory_Status = 267;
330 private static int NoteCategory_Nomenclature = 268;
331 private static int NoteCategory_Homonymy = 269;
332 private static int NoteCategory_Taxonomy = 270;
333 private static int NoteCategory_Taxonomic_status = 272;
334 private static int NoteCategory_Authority = 273;
335 private static int NoteCategory_Identification = 274;
336 private static int NoteCategory_Validity = 275;
337 private static int NoteCategory_Classification = 276;
338 private static int NoteCategory_Distribution = 278;
339 private static int NoteCategory_Synonymy = 279;
340 private static int NoteCategory_Habitat = 280;
341 private static int NoteCategory_Biology = 281;
342 private static int NoteCategory_Diagnosis = 282;
343 private static int NoteCategory_Host = 283;
344 private static int NoteCategory_Note = 284;
345 private static int NoteCategory_Rank = 285;
346 private static int NoteCategory_Taxonomic_Remark = 286;
347 private static int NoteCategory_Taxonomic_Remarks = 287;
348 private static int NoteCategory_Etymology = 288;
349 private static int NoteCategory_Type_species = 289;
350 private static int NoteCategory_Depth_Range = 290;
351 private static int NoteCategory_Grammatical_Gender = 291;
352 private static int NoteCategory_Introduced_Species_Remark = 292;
353 private static int NoteCategory_Alien_Species = 293;
354 private static int NoteCategory_Dimensions = 294;
355 private static int NoteCategory_New_Combination = 295;
356 private static int NoteCategory_Original_Combination = 296;
357
358 private static int NoteCategory_Conservation_Status= 301;
359 private static int NoteCategory_Use = 302;
360 private static int NoteCategory_Comments = 303;
361 private static int NoteCategory_Diet = 304;
362 private static int NoteCategory_Fossil_Range = 305;
363 private static int NoteCategory_Original_Description = 306;
364 private static int NoteCategory_Reproduction = 307;
365 private static int NoteCategory_Specimen = 308;
366 private static int NoteCategory_Type_Specimen = 309;
367 private static int NoteCategory_Type_Material = 310;
368 private static int NoteCategory_Editors_Comment = 311;
369 private static int NoteCategory_Syntype = 312;
370
371 // FossilStatus
372 private static int FOSSILSTATUS_RECENT_ONLY = 1;
373 private static int FOSSILSTATUS_FOSSIL_ONLY = 2;
374 private static int FOSSILSTATUS_RECENT_FOSSIL = 3;
375 public static String STR_FOSSIL_ONLY = "fossil only"; //still used for Index Fungorum
376
377 // SourceUse
378 private static int ORIGINAL_DESCRIPTION = 1;
379 private static int BASIS_OF_RECORD = 2;
380 private static int ADDITIONAL_SOURCE = 3;
381 private static int SOURCE_OF_SYNONYMY = 4;
382 private static int REDESCRIPTION = 5;
383 private static int NEW_COMBINATION_REFERENCE = 6;
384 private static int STATUS_SOURCE = 7;
385 public static int NOMENCLATURAL_REFERENCE = 8;
386 public static String STR_NOMENCLATURAL_REFERENCE = "nomenclatural reference";
387
388 // Area
389 private static int AREA_EAST_AEGEAN_ISLANDS = 1;
390 private static int AREA_GREEK_EAST_AEGEAN_ISLANDS = 2;
391 private static int AREA_TURKISH_EAST_AEGEAN_ISLANDS = 3;
392 private static int AREA_ALBANIA = 4;
393 private static int AREA_AUSTRIA_WITH_LIECHTENSTEIN = 5;
394 private static int AREA_AUSTRIA = 6;
395 private static int AREA_LIECHTENSTEIN = 7;
396 private static int AREA_AZORES = 8;
397 private static int AREA_CORVO = 9;
398 private static int AREA_FAIAL = 10;
399 private static int AREA_GRACIOSA = 11;
400 private static int AREA_SAO_JORGE = 12;
401 private static int AREA_FLORES = 13;
402 private static int AREA_SAO_MIGUEL = 14;
403 private static int AREA_PICO = 15;
404 private static int AREA_SANTA_MARIA = 16;
405 private static int AREA_TERCEIRA = 17;
406 private static int AREA_BELGIUM_WITH_LUXEMBOURG = 18;
407 private static int AREA_BELGIUM = 19;
408 private static int AREA_LUXEMBOURG = 20;
409 private static int AREA_BOSNIA_HERZEGOVINA = 21;
410 private static int AREA_BALEARES = 22;
411 private static int AREA_IBIZA_WITH_FORMENTERA = 23;
412 private static int AREA_MALLORCA = 24;
413 private static int AREA_MENORCA = 25;
414 private static int AREA_GREAT_BRITAIN = 26;
415 private static int AREA_BALTIC_STATES_ESTONIA_LATVIA_LITHUANIA_AND_KALININGRAD_REGION = 27;
416 private static int AREA_BULGARIA = 28;
417 private static int AREA_BELARUS = 29;
418 private static int AREA_CANARY_ISLANDS = 30;
419 private static int AREA_GRAN_CANARIA = 31;
420 private static int AREA_FUERTEVENTURA_WITH_LOBOS = 32;
421 private static int AREA_GOMERA = 33;
422 private static int AREA_HIERRO = 34;
423 private static int AREA_LANZAROTE_WITH_GRACIOSA = 35;
424 private static int AREA_LA_PALMA = 36;
425 private static int AREA_TENERIFE = 37;
426 private static int AREA_MONTENEGRO = 38;
427 private static int AREA_CORSE = 39;
428 private static int AREA_CRETE_WITH_KARPATHOS_KASOS_AND_GAVDHOS = 40;
429 private static int AREA_CZECH_REPUBLIC = 41;
430 private static int AREA_CROATIA = 42;
431 private static int AREA_CYPRUS = 43;
432 private static int AREA_FORMER_CZECHOSLOVAKIA = 44;
433 private static int AREA_DENMARK_WITH_BORNHOLM = 45;
434 private static int AREA_ESTONIA = 46;
435 private static int AREA_FAROE_ISLANDS = 47;
436 private static int AREA_FINLAND_WITH_AHVENANMAA = 48;
437 private static int AREA_FRANCE = 49;
438 private static int AREA_CHANNEL_ISLANDS = 50;
439 private static int AREA_FRENCH_MAINLAND = 51;
440 private static int AREA_MONACO = 52;
441 private static int AREA_GERMANY = 53;
442 private static int AREA_GREECE_WITH_CYCLADES_AND_MORE_ISLANDS = 54;
443 private static int AREA_IRELAND = 55;
444 private static int AREA_REPUBLIC_OF_IRELAND = 56;
445 private static int AREA_NORTHERN_IRELAND = 57;
446 private static int AREA_SWITZERLAND = 58;
447 private static int AREA_NETHERLANDS = 59;
448 private static int AREA_SPAIN = 60;
449 private static int AREA_ANDORRA = 61;
450 private static int AREA_GIBRALTAR = 62;
451 private static int AREA_KINGDOM_OF_SPAIN = 63;
452 private static int AREA_HUNGARY = 64;
453 private static int AREA_ICELAND = 65;
454 private static int AREA_ITALY = 66;
455 private static int AREA_ITALIAN_MAINLAND = 67;
456 private static int AREA_SAN_MARINO = 68;
457 private static int AREA_FORMER_JUGOSLAVIA = 69;
458 private static int AREA_LATVIA = 70;
459 private static int AREA_LITHUANIA = 71;
460 private static int AREA_PORTUGUESE_MAINLAND = 72;
461 private static int AREA_MADEIRA_ARCHIPELAGO = 73;
462 private static int AREA_DESERTAS = 74;
463 private static int AREA_MADEIRA = 75;
464 private static int AREA_PORTO_SANTO = 76;
465 private static int AREA_THE_FORMER_JUGOSLAV_REPUBLIC_OF_MAKEDONIJA = 77;
466 private static int AREA_MOLDOVA = 78;
467 private static int AREA_NORWEGIAN_MAINLAND = 79;
468 private static int AREA_POLAND = 80;
469 private static int AREA_THE_RUSSIAN_FEDERATION = 81;
470 private static int AREA_NOVAYA_ZEMLYA_AND_FRANZ_JOSEPH_LAND = 82;
471 private static int AREA_CENTRAL_EUROPEAN_RUSSIA = 83;
472 private static int AREA_EASTERN_EUROPEAN_RUSSIA = 84;
473 private static int AREA_KALININGRAD = 85;
474 private static int AREA_NORTHERN_EUROPEAN_RUSSIA = 86;
475 private static int AREA_NORTHWEST_EUROPEAN_RUSSIA = 87;
476 private static int AREA_SOUTH_EUROPEAN_RUSSIA = 88;
477 private static int AREA_ROMANIA = 89;
478 private static int AREA_FORMER_USSR = 90;
479 private static int AREA_RUSSIA_BALTIC = 91;
480 private static int AREA_RUSSIA_CENTRAL = 92;
481 private static int AREA_RUSSIA_SOUTHEAST = 93;
482 private static int AREA_RUSSIA_NORTHERN = 94;
483 private static int AREA_RUSSIA_SOUTHWEST = 95;
484 private static int AREA_SARDEGNA = 96;
485 private static int AREA_SVALBARD_WITH_BJORNOYA_AND_JAN_MAYEN = 97;
486 private static int AREA_SELVAGENS_ISLANDS = 98;
487 private static int AREA_SICILY_WITH_MALTA = 99;
488 private static int AREA_MALTA = 100;
489 private static int AREA_SICILY = 101;
490 private static int AREA_SLOVAKIA = 102;
491 private static int AREA_SLOVENIA = 103;
492 private static int AREA_SERBIA_WITH_MONTENEGRO = 104;
493 private static int AREA_SERBIA_INCLUDING_VOJVODINA_AND_WITH_KOSOVO = 105;
494 private static int AREA_SWEDEN = 106;
495 private static int AREA_EUROPEAN_TURKEY = 107;
496 private static int AREA_UKRAINE_INCLUDING_CRIMEA = 108;
497 private static int AREA_CRIMEA = 109;
498 private static int AREA_UKRAINE = 110;
499 private static int AREA_GREEK_MAINLAND = 111;
500 private static int AREA_CRETE = 112;
501 private static int AREA_DODECANESE_ISLANDS = 113;
502 private static int AREA_CYCLADES_ISLANDS = 114;
503 private static int AREA_NORTH_AEGEAN_ISLANDS = 115;
504 private static int AREA_VATICAN_CITY = 116;
505 private static int AREA_FRANZ_JOSEF_LAND = 117;
506 private static int AREA_NOVAYA_ZEMLYA = 118;
507 private static int AREA_AZERBAIJAN_INCLUDING_NAKHICHEVAN = 119;
508 private static int AREA_AZERBAIJAN = 120;
509 private static int AREA_NAKHICHEVAN = 121;
510 private static int AREA_ALGERIA = 122;
511 private static int AREA_ARMENIA = 123;
512 private static int AREA_CAUCASUS_REGION = 124;
513 private static int AREA_EGYPT = 125;
514 private static int AREA_GEORGIA = 126;
515 private static int AREA_ISRAEL_JORDAN = 127;
516 private static int AREA_ISRAEL = 128;
517 private static int AREA_JORDAN = 129;
518 private static int AREA_LEBANON = 130;
519 private static int AREA_LIBYA = 131;
520 private static int AREA_LEBANON_SYRIA = 132;
521 private static int AREA_MOROCCO = 133;
522 private static int AREA_NORTH_CAUCASUS = 134;
523 private static int AREA_SINAI = 135;
524 private static int AREA_SYRIA = 136;
525 private static int AREA_TUNISIA = 137;
526 private static int AREA_ASIATIC_TURKEY = 138;
527 private static int AREA_TURKEY = 139;
528 private static int AREA_NORTHERN_AFRICA = 140;
529 private static int AREA_AFRO_TROPICAL_REGION = 141;
530 private static int AREA_AUSTRALIAN_REGION = 142;
531 private static int AREA_EAST_PALAEARCTIC = 143;
532 private static int AREA_NEARCTIC_REGION = 144;
533 private static int AREA_NEOTROPICAL_REGION = 145;
534 private static int AREA_NEAR_EAST = 146;
535 private static int AREA_ORIENTAL_REGION = 147;
536 private static int AREA_EUROPEAN_MARINE_WATERS = 148;
537 private static int AREA_MEDITERRANEAN_SEA = 149;
538 private static int AREA_WHITE_SEA = 150;
539 private static int AREA_NORTH_SEA = 151;
540 private static int AREA_BALTIC_SEA = 152;
541 private static int AREA_BLACK_SEA = 153;
542 private static int AREA_BARENTSZ_SEA = 154;
543 private static int AREA_CASPIAN_SEA = 155;
544 private static int AREA_PORTUGUESE_EXCLUSIVE_ECONOMIC_ZONE = 156;
545 private static int AREA_BELGIAN_EXCLUSIVE_ECONOMIC_ZONE = 157;
546 private static int AREA_FRENCH_EXCLUSIVE_ECONOMIC_ZONE = 158;
547 private static int AREA_ENGLISH_CHANNEL = 159;
548 private static int AREA_ADRIATIC_SEA = 160;
549 private static int AREA_BISCAY_BAY = 161;
550 private static int AREA_DUTCH_EXCLUSIVE_ECONOMIC_ZONE = 162;
551 private static int AREA_UNITED_KINGDOM_EXCLUSIVE_ECONOMIC_ZONE = 163;
552 private static int AREA_SPANISH_EXCLUSIVE_ECONOMIC_ZONE = 164;
553 private static int AREA_EGYPTIAN_EXCLUSIVE_ECONOMIC_ZONE = 165;
554 private static int AREA_GREEK_EXCLUSIVE_ECONOMIC_ZONE = 166;
555 private static int AREA_TIRRENO_SEA = 167;
556 private static int AREA_ICELANDIC_EXCLUSIVE_ECONOMIC_ZONE = 168;
557 private static int AREA_IRISH_EXCLUSIVE_ECONOMIC_ZONE = 169;
558 private static int AREA_IRISH_SEA = 170;
559 private static int AREA_ITALIAN_EXCLUSIVE_ECONOMIC_ZONE = 171;
560 private static int AREA_NORWEGIAN_SEA = 172;
561 private static int AREA_MOROCCAN_EXCLUSIVE_ECONOMIC_ZONE = 173;
562 private static int AREA_NORWEGIAN_EXCLUSIVE_ECONOMIC_ZONE = 174;
563 private static int AREA_SKAGERRAK = 175;
564 private static int AREA_TUNISIAN_EXCLUSIVE_ECONOMIC_ZONE = 176;
565 private static int AREA_WADDEN_SEA = 177;
566 private static int AREA_BELT_SEA = 178;
567 private static int AREA_MARMARA_SEA = 179;
568 private static int AREA_SEA_OF_AZOV = 180;
569 private static int AREA_AEGEAN_SEA = 181;
570 private static int AREA_BULGARIAN_EXCLUSIVE_ECONOMIC_ZONE = 182;
571 private static int AREA_SOUTH_BALTIC_PROPER = 183;
572 private static int AREA_BALTIC_PROPER = 184;
573 private static int AREA_NORTH_BALTIC_PROPER = 185;
574 private static int AREA_ARCHIPELAGO_SEA = 186;
575 private static int AREA_BOTHNIAN_SEA = 187;
576 private static int AREA_GERMAN_EXCLUSIVE_ECONOMIC_ZONE = 188;
577 private static int AREA_SWEDISH_EXCLUSIVE_ECONOMIC_ZONE = 189;
578 private static int AREA_UKRAINIAN_EXCLUSIVE_ECONOMIC_ZONE = 190;
579 private static int AREA_MADEIRAN_EXCLUSIVE_ECONOMIC_ZONE = 191;
580 private static int AREA_LEBANESE_EXCLUSIVE_ECONOMIC_ZONE = 192;
581 private static int AREA_SPANISH_EXCLUSIVE_ECONOMIC_ZONE_MEDITERRANEAN_PART = 193;
582 private static int AREA_ESTONIAN_EXCLUSIVE_ECONOMIC_ZONE = 194;
583 private static int AREA_CROATIAN_EXCLUSIVE_ECONOMIC_ZONE = 195;
584 private static int AREA_BALEAR_SEA = 196;
585 private static int AREA_TURKISH_EXCLUSIVE_ECONOMIC_ZONE = 197;
586 private static int AREA_DANISH_EXCLUSIVE_ECONOMIC_ZONE = 198;
587 private static int AREA_TRANSCAUCASUS = 199;
588
589 private static int AREA_GEORGIA_G = 200;
590 private static int AREA_ABKHAZIA = 201;
591 private static int AREA_ADZARIA = 202;
592
593 private static int AREA_UNITED_KINGDOM = 203;
594 private static int AREA_DENMARK_COUNTRY = 204;
595 private static int AREA_TURKEY_COUNTRY = 205;
596 private static int AREA_SPAIN_COUNTRY = 206;
597 private static int AREA_GREECE_COUNTRY = 207;
598 private static int AREA_PORTUGAL_COUNTRY = 208;
599 //continued ERMS areas without variables
600 //...
601 private static int AREA_WALES = 293;
602
603 //new E+M areas
604 private static int AREA_SERBIA = 294;
605 private static int AREA_KOSOVO = 295;
606
607
608 //FauEu area UUIDs
609 private static UUID uuidAreaAD = UUID.fromString("38dd31d2-8275-4b05-8b85-eb71a390d67f");
610 private static UUID uuidAreaAFR = UUID.fromString("c3123386-51a4-42a4-9ff4-b3905b18a83c");//x
611 private static UUID uuidAreaAL = UUID.fromString("84c54f15-fc90-44bb-a45d-26b7daa26ceb");
612 private static UUID uuidAreaAT = UUID.fromString("d285e4a5-d027-4610-a4ff-f5e6dd16cdc3");
613 private static UUID uuidAreaAUS = UUID.fromString("930e6455-de5e-4002-bfc3-45eecd07e4f3");//x
614 private static UUID uuidAreaBA = UUID.fromString("946a06ea-200f-409e-bb2f-05e64e55ed41");
615 private static UUID uuidAreaBE = UUID.fromString("f914f7fd-d5a3-4165-8409-004f197ae4e9");
616 private static UUID uuidAreaBG = UUID.fromString("9586daca-a739-4d28-836e-6d15861375e1");
617 private static UUID uuidAreaBY = UUID.fromString("b6f94a56-990d-41da-8e92-abf757afeca1");
618 private static UUID uuidAreaCH = UUID.fromString("cccc1da5-6a0e-47c2-900e-e274fd593ff0");
619 private static UUID uuidAreaCY = UUID.fromString("78950366-3f15-48bb-80c9-8b24afedcd3c");
620 private static UUID uuidAreaCZ = UUID.fromString("d1221dbc-a7c5-4805-b7c8-15ae56557825");
621 private static UUID uuidAreaDE = UUID.fromString("6f31223e-9a10-4c97-b482-85d96f195a23");
622 private static UUID uuidAreaDK_DEN = UUID.fromString("4ed51fa9-f89a-47c8-a9ce-43d462f74c53");
623 private static UUID uuidAreaDK_FOR = UUID.fromString("272874cf-b6f7-4805-8a0c-1a0efbbf0a21");
624 private static UUID uuidAreaEE = UUID.fromString("1472705d-c94e-41e8-9482-adb46f201f71");
625 private static UUID uuidAreaEPA = UUID.fromString("2f162235-6c5a-4ad4-8ba0-8dca28826dab");//x
626 private static UUID uuidAreaES_BAL = UUID.fromString("d5466ee2-38fa-47e8-8109-008b71a2f47b");
627 private static UUID uuidAreaES_CNY = UUID.fromString("1f19cdaa-af1e-406c-bb58-25f17ee00228");
628 private static UUID uuidAreaES_SPA = UUID.fromString("d3cc7b05-b506-44b7-a49a-77d36974bd5f");
629 private static UUID uuidAreaFI = UUID.fromString("93d6e2ba-308b-4d57-851c-94583e139806");
630 private static UUID uuidAreaFR_COR = UUID.fromString("f7088b27-805f-46df-916f-eeed47a2e336");
631 private static UUID uuidAreaFR_FRA = UUID.fromString("83d2df98-c0b4-4ad8-9a02-7cdfcfa74371");
632 private static UUID uuidAreaGB_CI = UUID.fromString("a97807d0-e7e2-4ee0-8567-07f3a72d91bb");
633 private static UUID uuidAreaGB_GI = UUID.fromString("4441b42a-7c9f-4a39-89d6-5c9c9dab9c05");
634 private static UUID uuidAreaGB_GRB = UUID.fromString("94561875-19a6-4bf4-ade7-340c245ffd67");
635 private static UUID uuidAreaGB_NI = UUID.fromString("791be300-6e86-4253-b1ba-aef46ea6bfb9");
636 private static UUID uuidAreaGR_AEG = UUID.fromString("efb2f01a-f01e-4da2-ba02-464b0e1687e5");//x
637 private static UUID uuidAreaGR_CYC = UUID.fromString("f9ad21b1-c9ed-4062-9086-cba6e6ef353b");//x
638 private static UUID uuidAreaGR_DOD = UUID.fromString("7a84feae-9d93-4408-8122-e82b9485fc0f");//x
639 private static UUID uuidAreaGR_GRC = UUID.fromString("a392dbac-8671-40e6-95c7-a0d2db8f7d9c");//x
640 private static UUID uuidAreaGR_KRI = UUID.fromString("ed8e7bcd-2267-4953-b422-bc2ff45238f7");//x
641 private static UUID uuidAreaHR = UUID.fromString("83323e5b-8a62-4784-956a-5f21ddc853b9");
642 private static UUID uuidAreaHU = UUID.fromString("ab6985e7-e718-4bcb-bc84-55e563870998");
643 private static UUID uuidAreaIE = UUID.fromString("6a623016-2cd7-4391-8bc9-ae8af50060b4");
644 private static UUID uuidAreaIS = UUID.fromString("b8469350-7c87-4202-9cb1-5f0ad11ec89c");
645 private static UUID uuidAreaIT_ITA = UUID.fromString("43df04d6-90b4-4cf4-8dfc-f60ae921f92c");
646 private static UUID uuidAreaIT_SAR = UUID.fromString("f68d9695-238d-4684-901a-f4bbc24813ee");
647 private static UUID uuidAreaIT_SI = UUID.fromString("1889a571-d12a-48f1-a49f-112e60c699ef");
648 private static UUID uuidAreaLI = UUID.fromString("ebad24b5-559e-46c4-8b0d-87107e05169e");
649 private static UUID uuidAreaLT = UUID.fromString("d00df2a8-8d5d-4c36-b3a2-4afc9006be70");
650 private static UUID uuidAreaLU = UUID.fromString("65bbbb63-3351-4fda-a8f8-50557bc34e0d");
651 private static UUID uuidAreaLV = UUID.fromString("997d97ea-4678-4e01-9a81-518c09da7d7c");
652 private static UUID uuidAreaMC = UUID.fromString("0debabad-e7e2-4aad-b959-876d3d85a4b1");
653 private static UUID uuidAreaMD = UUID.fromString("7a4ffe59-f8d6-4a58-bb4e-449fbe8420b3");
654 private static UUID uuidAreaMK = UUID.fromString("40140714-6214-4338-bc45-f85455f7eaed");
655 private static UUID uuidAreaMT = UUID.fromString("b36c2f47-47d5-497f-9235-2faf0d9a6e6c");
656 private static UUID uuidAreaNAF = UUID.fromString("e3b2193d-e23a-47a7-9bf5-7f7eebe61afb");//x
657 private static UUID uuidAreaNEA = UUID.fromString("d6082e94-7289-45a3-a298-5cb730cfbd7f");//x
658 private static UUID uuidAreaNEO = UUID.fromString("7a530ae7-d070-49aa-8496-7b06c4ed735b");//x
659 private static UUID uuidAreaNL = UUID.fromString("7b74033f-ada3-4956-87b7-ec9bf0cb4c76");
660 private static UUID uuidAreaNO_NOR = UUID.fromString("11b26fc9-3da4-4323-8b03-e960e8b1c914");
661 private static UUID uuidAreaNO_SVA = UUID.fromString("9a3fe056-2011-4b02-a416-59de00eaf533");
662 private static UUID uuidAreaNRE = UUID.fromString("5e005e59-b313-4c5b-8702-c2f88317db25");//x
663 private static UUID uuidAreaORR = UUID.fromString("2047d0dd-12dc-4454-8344-07ad52fa0af0");//x
664 private static UUID uuidAreaPL = UUID.fromString("68edc557-dbed-494e-9549-6746f11fb904");
665 private static UUID uuidAreaPT_AZO = UUID.fromString("6f5e4eb5-83c8-4baf-99f2-cb6e25d8ac9d");
666 private static UUID uuidAreaPT_MDR = UUID.fromString("97bed937-f4ad-4b42-ba0c-8832816fa234");
667 private static UUID uuidAreaPT_POR = UUID.fromString("09107b85-2bdb-4534-a51c-8d02cdd71590");
668 private static UUID uuidAreaPT_SEL = UUID.fromString("e067287c-50c6-4e54-9859-91aa15aa289a");
669 private static UUID uuidAreaRO = UUID.fromString("de3e2ca8-d2ea-4c1f-8a19-a7a0b5daf39d");
670 private static UUID uuidAreaRU_FJL = UUID.fromString("2b79434b-df7d-4dc5-996f-1ca4227f6e0e");//x
671 private static UUID uuidAreaRU_KGD = UUID.fromString("227a661b-91de-489c-88ed-6b72f78481f0");
672 private static UUID uuidAreaRU_NOZ = UUID.fromString("2b26f68a-fdac-41ab-bce0-105b24d7eb26");//x
673 private static UUID uuidAreaRU_RUC = UUID.fromString("235748eb-9eef-48a8-9b9a-c4abd00b6244");
674 private static UUID uuidAreaRU_RUE = UUID.fromString("5ad5b07e-518f-44ee-ac96-c7608d93e757");
675 private static UUID uuidAreaRU_RUN = UUID.fromString("05d35653-9f67-442c-8d99-4a7ae68cf5d1");
676 private static UUID uuidAreaRU_RUS = UUID.fromString("98b00cf8-7bd6-4f44-885c-0927bbc1d456");
677 private static UUID uuidAreaRU_RUW = UUID.fromString("ae84bc08-957a-4c62-a828-1fb3fc2f0c3e");
678 private static UUID uuidAreaSE = UUID.fromString("8ff37027-4832-4ce1-9f25-e21eaf26299c");
679 private static UUID uuidAreaSI = UUID.fromString("0b76b448-5564-415c-bc18-727c37e62bf1");
680 private static UUID uuidAreaSK = UUID.fromString("e966cd7c-3e68-4153-887b-54920eb6eb47");
681 private static UUID uuidAreaSM = UUID.fromString("c40b8a71-c50c-4636-96de-be0bb48ed025");
682 private static UUID uuidAreaTR_TUE = UUID.fromString("807317b3-746b-4916-9441-d8086d0d1cb1");
683 private static UUID uuidAreaUA = UUID.fromString("2f80440d-cb03-499c-a829-c4ac4c6608d3");//x
684 private static UUID uuidAreaVA = UUID.fromString("cd256143-1b74-4a7d-998f-ba0a9c01bb3e");
685 private static UUID uuidAreaYU = UUID.fromString("cd80a852-1993-465a-b0e3-8c73218d4d90");
686
687
688 // OccurrenceStatus
689 private static int STATUS_PRESENT = 1;
690 public static int STATUS_ABSENT = 2;
691 public static int STATUS_NATIVE = 3;
692 public static int STATUS_INTRODUCED = 4;
693 public static int STATUS_NATURALISED = 5;
694 private static int STATUS_INVASIVE = 6;
695 public static int STATUS_MANAGED = 7;
696 public static int STATUS_DOUBTFUL = 8;
697
698 private final Map<String, Integer> tdwgKeyMap = new HashMap<>();
699 private final Map<Integer, String> areaCacheMap = new HashMap<>();
700 private final Map<Integer, String> languageCacheMap = new HashMap<>();
701 private static final Map<String,Integer> languageCodeToKeyMap = new HashMap<>();
702
703 private final Map<Integer, String> featureCacheMap = new HashMap<>();
704 private final Map<Integer, String> nameStatusCacheMap = new HashMap<>();
705 private final Map<Integer, String> qualityStatusCacheMap = new HashMap<>();
706 private final Map<Integer, String> taxonStatusCacheMap = new HashMap<>();
707 private final Map<Integer, String> taxRelQualifierCacheMap = new HashMap<>();
708 private final Map<Integer, String> taxRelZooQualifierCacheMap = new HashMap<>();
709 private final Map<Integer, String> sourceUseCacheMap = new HashMap<>();
710 private final Map<Integer, String> fossilStatusCacheMap = new HashMap<>();
711 private final Map<Integer, String> typeDesigStatusCacheMap = new HashMap<>();
712 private final Map<Integer, String> sourceCategoryCacheMap = new HashMap<>();
713 private final Map<Integer, String> occurrenceStatusCacheMap = new HashMap<>();
714 private final Map<Integer, Map<Integer, String>> rankCacheMap = new HashMap<>();
715 private final Map<Integer, Map<Integer, String>> rankAbbrevCacheMap = new HashMap<>();
716
717
718 private final Source destination;
719
720 public PesiTransformer(Source destination) {
721 super();
722 this.destination = destination;
723 fillMaps();
724 }
725
726 private void fillMaps() {
727 try {
728 //TDWG
729 String sql = " SELECT AreaId, AreaName, AreaTdwgCode, AreaEmCode, AreaFaEuCode FROM Area";
730 ResultSet rs = destination.getResultSet(sql);
731 while (rs.next()){
732 String tdwg = rs.getString("AreaTdwgCode");
733 Integer id = rs.getInt("AreaId");
734 String label = rs.getString("AreaName");
735
736 if (StringUtils.isNotBlank(tdwg)){
737 this.tdwgKeyMap.put(tdwg, id);
738 }
739 this.areaCacheMap.put(id, label);
740 }
741
742 //rankCache
743 sql = " SELECT KingdomId, RankId, Rank, RankAbbrev, Kingdom FROM Rank";
744 rs = destination.getResultSet(sql);
745 while (rs.next()){
746 String rank = rs.getString("Rank");
747 String abbrev = rs.getString("RankAbbrev");
748 Integer rankId = rs.getInt("RankId");
749 Integer kingdomId = rs.getInt("KingdomId");
750 String kingdom = rs.getString("Kingdom");
751
752 //rank str
753 Map<Integer, String> kingdomMap = rankCacheMap.get(kingdomId);
754 if (kingdomMap == null){
755 kingdomMap = new HashMap<>();
756 rankCacheMap.put(kingdomId, kingdomMap);
757 }
758 kingdomMap.put(rankId, rank);
759
760 if (rank.equals("Kingdom")){
761 pesiKingdomMap.put(kingdom, kingdomId);
762 }
763
764 //rank abbrev
765 Map<Integer, String> kingdomAbbrevMap = rankAbbrevCacheMap.get(kingdomId);
766 if (kingdomAbbrevMap == null){
767 kingdomAbbrevMap = new HashMap<>();
768 rankAbbrevCacheMap.put(kingdomId, kingdomAbbrevMap);
769 }
770 if (StringUtils.isNotBlank(abbrev)){
771 kingdomAbbrevMap.put(rankId, abbrev);
772 }
773 }
774
775 //languageCache
776 fillSingleMap(languageCacheMap, "Language");
777
778 //feature / note category
779 fillSingleMap(featureCacheMap, "NoteCategory");
780
781 //nameStatusCache
782 fillSingleMap(nameStatusCacheMap, "NameStatus", "NomStatus");
783
784 //qualityStatusCache
785 fillSingleMap(qualityStatusCacheMap, "QualityStatus");
786
787 //taxonStatusCache
788 fillSingleMap(taxonStatusCacheMap, "TaxonStatus", "Status");
789
790 //sourceUse
791 fillSingleMap(sourceUseCacheMap, "SourceUse");
792
793 //fossil status
794 fillSingleMap(fossilStatusCacheMap, "FossilStatus");
795
796 //fossil status
797 fillSingleMap(typeDesigStatusCacheMap, "FossilStatus");
798
799 //fossil status
800 fillSingleMap(occurrenceStatusCacheMap, "OccurrenceStatus");
801
802 //source category
803 fillSingleMap(sourceCategoryCacheMap, "SourceCategory", "Category", "SourceCategoryId");
804
805 //RelTaxonQualifier
806 sql = " SELECT QualifierId, Qualifier, ZoologQualifier FROM RelTaxonQualifier ";
807 rs = destination.getResultSet(sql);
808 while (rs.next()){
809 Integer key = rs.getInt("QualifierId");
810 String cache = rs.getString("Qualifier");
811 if (StringUtils.isNotBlank(cache)){
812 this.taxRelQualifierCacheMap.put(key, cache);
813 }
814 String zoologCache = rs.getString("ZoologQualifier");
815 if (StringUtils.isNotBlank(zoologCache)){
816 this.taxRelZooQualifierCacheMap.put(key, zoologCache);
817 }
818 }
819
820 //language code map
821 sql = " SELECT LanguageId, Language, ISO639_1, ISO639_2, ISO639_3 FROM Language";
822 rs = destination.getResultSet(sql);
823 while (rs.next()){
824 Integer id = rs.getInt("LanguageId");
825 Integer oldId;
826 String iso639_1 = rs.getString("ISO639_1");
827 if (StringUtils.isNotBlank(iso639_1)){
828 oldId = languageCodeToKeyMap.put(iso639_1, id);
829 checkOldId(id, oldId, iso639_1);
830 }
831 String iso639_2 = rs.getString("ISO639_2");
832 if (StringUtils.isNotBlank(iso639_2)){
833 oldId = languageCodeToKeyMap.put(iso639_2, id);
834 checkOldId(id, oldId, iso639_1);
835 }
836 String iso639_3 = rs.getString("ISO639_3");
837 if (StringUtils.isNotBlank(iso639_3)){
838 oldId = languageCodeToKeyMap.put(iso639_3, id);
839 checkOldId(id, oldId, iso639_1);
840 }
841
842 }
843 rs = null;
844 } catch (Exception e) {
845 logger.error("Exception when trying to read area map", e);
846 e.printStackTrace();
847 }
848 }
849
850 private void checkOldId(Integer id, Integer oldId, String isoCode) {
851 if (oldId != null && !oldId.equals(id)){
852 logger.warn("Language code " + isoCode + " exists for >1 language IDs. This should not happen.");
853 }
854 }
855
856 private void fillSingleMap(Map<Integer, String> map, String tableName) throws SQLException {
857 fillSingleMap(map, tableName, tableName, tableName + "Id");
858 }
859
860 private void fillSingleMap(Map<Integer, String> map, String tableName, String attr) throws SQLException {
861 fillSingleMap(map, tableName, attr, attr + "Id");
862 }
863
864 private void fillSingleMap(Map<Integer, String> map, String tableName, String attr, String idAttr) throws SQLException {
865 String sql;
866 ResultSet rs;
867 sql = " SELECT %s, %s FROM %s ";
868 sql = String.format(sql, idAttr, attr, tableName);
869 rs = destination.getResultSet(sql);
870 while (rs.next()){
871 Integer key = rs.getInt(idAttr);
872 String cache = rs.getString(attr);
873 if (StringUtils.isNotBlank(cache)){
874 map.put(key, cache);
875 }
876 }
877 }
878
879 /**
880 * Converts the databaseString to its abbreviation if its known.
881 * Otherwise the databaseString is returned.
882 * @param databaseString
883 * @return
884 */
885 public static String databaseString2Abbreviation(String databaseString) {
886 String result = databaseString;
887 if (databaseString.equals("Fauna Europaea database")) {
888 result = "FaEu";
889 }
890 return result;
891 }
892
893 /**
894 * Returns the OccurrenceStatusId for a given PresenceAbsenceTerm.
895 * @param term
896 * @return
897 * @throws UnknownCdmTypeException
898 */
899 public static Integer presenceAbsenceTerm2OccurrenceStatusId(PresenceAbsenceTerm term) {
900 Integer result = null;
901 if (term == null){
902 return null;
903 //present
904 }else if (term.isInstanceOf(PresenceAbsenceTerm.class)) {
905 PresenceAbsenceTerm presenceTerm = CdmBase.deproxy(term, PresenceAbsenceTerm.class);
906 if (presenceTerm.equals(PresenceAbsenceTerm.PRESENT()) ||
907 presenceTerm.equals(PresenceAbsenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED()) ||
908 presenceTerm.equals(PresenceAbsenceTerm.NATIVE_DOUBTFULLY_NATIVE())) {
909 result = STATUS_PRESENT;
910 } else if (presenceTerm.equals(PresenceAbsenceTerm.NATIVE())) {
911 result = STATUS_NATIVE;
912 } else if (presenceTerm.equals(PresenceAbsenceTerm.INTRODUCED()) ||
913 presenceTerm.equals(PresenceAbsenceTerm.CASUAL()) ||
914 presenceTerm.equals(PresenceAbsenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION())) {
915 result = STATUS_INTRODUCED;
916 } else if (presenceTerm.equals(PresenceAbsenceTerm.NATURALISED())
917 || presenceTerm.equals(PresenceAbsenceTerm.NATURALISED())) {
918 result = STATUS_NATURALISED;
919 } else if (presenceTerm.equals(PresenceAbsenceTerm.INVASIVE())) {
920 result = STATUS_INVASIVE;
921 } else if (presenceTerm.equals(PresenceAbsenceTerm.CULTIVATED())) {
922 result = STATUS_MANAGED;
923 } else if (presenceTerm.equals(PresenceAbsenceTerm.PRESENT_DOUBTFULLY())||
924 presenceTerm.equals(PresenceAbsenceTerm.INTRODUCED_PRESENCE_QUESTIONABLE()) ||
925 presenceTerm.equals(PresenceAbsenceTerm.NATIVE_PRESENCE_QUESTIONABLE() )) {
926 result = STATUS_DOUBTFUL;
927 //absent
928 }else if (presenceTerm.equals(PresenceAbsenceTerm.ABSENT()) || presenceTerm.equals(PresenceAbsenceTerm.NATIVE_FORMERLY_NATIVE()) ||
929 presenceTerm.equals(PresenceAbsenceTerm.CULTIVATED_REPORTED_IN_ERROR()) || presenceTerm.equals(PresenceAbsenceTerm.INTRODUCED_REPORTED_IN_ERROR()) ||
930 presenceTerm.equals(PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED()) || presenceTerm.equals(PresenceAbsenceTerm.NATIVE_REPORTED_IN_ERROR() ) ) {
931 result = STATUS_ABSENT;
932 } else {
933 logger.error("PresenceAbsenceTerm could not be translated to datawarehouse occurrence status id: " + presenceTerm.getLabel());
934 }
935 }
936 return result;
937 }
938
939 @Override
940 public String getCacheByPresenceAbsenceTerm(PresenceAbsenceTerm status) throws UndefinedTransformerMethodException {
941 if (status == null){
942 return null;
943 }else{
944 return this.occurrenceStatusCacheMap.get(getKeyByPresenceAbsenceTerm(status));
945 }
946 }
947
948 @Override
949 public Object getKeyByPresenceAbsenceTerm(PresenceAbsenceTerm status) throws UndefinedTransformerMethodException {
950 return presenceAbsenceTerm2OccurrenceStatusId(status);
951 }
952
953 @Override
954 public String getCacheByNamedArea(NamedArea namedArea) throws UndefinedTransformerMethodException {
955 NamedArea area = CdmBase.deproxy(namedArea);
956 if (area == null){
957 return null;
958 }else{
959 return this.areaCacheMap.get(getKeyByNamedArea(area));
960 }
961 }
962
963 @Override
964 public Object getKeyByNamedArea(NamedArea area) throws UndefinedTransformerMethodException {
965 NamedArea namedArea = CdmBase.deproxy(area);
966
967 if (area == null) {
968 return null;
969 //TDWG areas
970 } else if (area.getVocabulary().getUuid().equals(NamedArea.uuidTdwgAreaVocabulary)) {
971 String abbrevLabel = namedArea.getRepresentation(Language.DEFAULT()).getAbbreviatedLabel();
972 Integer result = this.tdwgKeyMap.get(abbrevLabel);
973 if (result == null){
974 logger.warn("Unknown TDWGArea: " + area.getTitleCache());
975 }
976 return result;
977 //countries
978 }else if (namedArea.isInstanceOf(Country.class)){
979 if (namedArea.equals(Country.UKRAINE())) { return AREA_UKRAINE_INCLUDING_CRIMEA; }
980 else if (namedArea.equals(Country.AZERBAIJANREPUBLICOF())) { return AREA_AZERBAIJAN_INCLUDING_NAKHICHEVAN; }
981 else if (namedArea.equals(Country.GEORGIA())) { return AREA_GEORGIA; }
982 else if (namedArea.equals(Country.RUSSIANFEDERATION())) { return AREA_THE_RUSSIAN_FEDERATION; }
983 else if (namedArea.equals(Country.UNITEDKINGDOMOFGREATBRITAINANDNORTHERNIRELAND())) { return AREA_UNITED_KINGDOM; }
984 else if (namedArea.equals(Country.DENMARKKINGDOMOF())) { return AREA_DENMARK_COUNTRY; }
985 else if (namedArea.equals(Country.TURKEYREPUBLICOF())) { return AREA_TURKEY_COUNTRY; }
986 else {
987 logger.warn("Unknown Country: " + area.getTitleCache());
988 }
989
990 }else if (area.getVocabulary().getUuid().equals(BerlinModelTransformer.uuidVocEuroMedAreas)){
991 if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEM)) {
992 // logger.warn("E+M area not available in PESI");
993 return null;
994 }
995 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEUR)) { logger.warn("EUR area not available in PESI"); return null; }
996 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAb)) { return AREA_AZERBAIJAN_INCLUDING_NAKHICHEVAN; }
997 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAb_A)) { return AREA_AZERBAIJAN; }
998 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAb_N)) { return AREA_NAKHICHEVAN; }
999 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAE)) { return AREA_EAST_AEGEAN_ISLANDS; }
1000 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAE_G)) { return AREA_GREEK_EAST_AEGEAN_ISLANDS; }
1001 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAE_T)) { return AREA_TURKISH_EAST_AEGEAN_ISLANDS; }
1002 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAg)) { return AREA_ALGERIA; }
1003 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAl)) { return AREA_ALBANIA; }
1004 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAr)) { return AREA_ARMENIA; }
1005 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAu)) { return AREA_AUSTRIA_WITH_LIECHTENSTEIN; }
1006 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAu_A)) { return AREA_AUSTRIA; }
1007 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAu_L)) { return AREA_LIECHTENSTEIN; }
1008 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz)) { return AREA_AZORES; }
1009 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_C)) { return AREA_CORVO; }
1010 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_F)) { return AREA_FAIAL; }
1011 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_G)) { return AREA_GRACIOSA; }
1012 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_J)) { return AREA_SAO_JORGE; }
1013 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_L)) { return AREA_FLORES; }
1014 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_M)) { return AREA_SAO_MIGUEL; }
1015 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_P)) { return AREA_PICO; }
1016 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_S)) { return AREA_SANTA_MARIA; }
1017 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAz_T)) { return AREA_TERCEIRA; }
1018 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBe)) { return AREA_BELGIUM_WITH_LUXEMBOURG; }
1019 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBe_B)) { return AREA_BELGIUM; }
1020 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBe_L)) { return AREA_LUXEMBOURG; }
1021 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBH)) { return AREA_BOSNIA_HERZEGOVINA; }
1022 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBl)) { return AREA_BALEARES; }
1023 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBl_I)) { return AREA_IBIZA_WITH_FORMENTERA; }
1024 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBl_M)) { return AREA_MALLORCA; }
1025 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBl_N)) { return AREA_MENORCA; }
1026 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBr)) { return AREA_GREAT_BRITAIN; }
1027 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBt)) { return AREA_BALTIC_STATES_ESTONIA_LATVIA_LITHUANIA_AND_KALININGRAD_REGION; }
1028 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBu)) { return AREA_BULGARIA; }
1029 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidBy)) { return AREA_BELARUS; }
1030 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa)) { return AREA_CANARY_ISLANDS; }
1031 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_C)) { return AREA_GRAN_CANARIA; }
1032 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_F)) { return AREA_FUERTEVENTURA_WITH_LOBOS; }
1033 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_G)) { return AREA_GOMERA; }
1034 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_H)) { return AREA_HIERRO; }
1035 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_L)) { return AREA_LANZAROTE_WITH_GRACIOSA; }
1036 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_P)) { return AREA_LA_PALMA; }
1037 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCa_T)) { return AREA_TENERIFE; }
1038 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCc)) { return AREA_CAUCASUS_REGION; }
1039 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCg)) { return AREA_MONTENEGRO; }
1040 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCo)) { return AREA_CORSE; }
1041 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCr)) { return AREA_CRETE_WITH_KARPATHOS_KASOS_AND_GAVDHOS; }
1042 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCs)) { return AREA_CZECH_REPUBLIC; }
1043 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCt)) { return AREA_CROATIA; }
1044 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCy)) { return AREA_CYPRUS; }
1045 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCz)) { return AREA_FORMER_CZECHOSLOVAKIA; }
1046 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidDa)) { return AREA_DENMARK_WITH_BORNHOLM; }
1047 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEg)) { return AREA_EGYPT; }
1048 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEs)) { return AREA_ESTONIA; }
1049 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidFa)) { return AREA_FAROE_ISLANDS; }
1050 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidFe)) { return AREA_FINLAND_WITH_AHVENANMAA; }
1051 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa)) { return AREA_FRANCE; }
1052 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa_C)) { return AREA_CHANNEL_ISLANDS; }
1053 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa_F)) { return AREA_FRENCH_MAINLAND; }
1054 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa_M)) { return AREA_MONACO; }
1055
1056 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGe)) { return AREA_GERMANY; }
1057 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg)) { return AREA_GEORGIA; }
1058
1059 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg_G)) { return AREA_GEORGIA_G; }
1060 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg_A)) { return AREA_ABKHAZIA; }
1061 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg_D)) { return AREA_ADZARIA; }
1062
1063 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGr)) { return AREA_GREECE_WITH_CYCLADES_AND_MORE_ISLANDS; }
1064 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHb)) { return AREA_IRELAND; }
1065 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHb_E)) { return AREA_REPUBLIC_OF_IRELAND; }
1066 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHb_N)) { return AREA_NORTHERN_IRELAND; }
1067 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHe)) { return AREA_SWITZERLAND; }
1068 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHo)) { return AREA_NETHERLANDS; }
1069 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHs)) { return AREA_SPAIN; }
1070 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHs_A)) { return AREA_ANDORRA; }
1071 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHs_G)) { return AREA_GIBRALTAR; }
1072 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHs_S)) { return AREA_KINGDOM_OF_SPAIN; }
1073 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHu)) { return AREA_HUNGARY; }
1074 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIJ)) { return AREA_ISRAEL_JORDAN; }
1075 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIr)) { return AREA_ISRAEL; }
1076 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIs)) { return AREA_ICELAND; }
1077 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIt)) { return AREA_ITALY; }
1078 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIt_I)) { return AREA_ITALIAN_MAINLAND; }
1079 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIt_S)) { return AREA_SAN_MARINO; }
1080 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidJo)) { return AREA_JORDAN; }
1081 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidJu)) { return AREA_FORMER_JUGOSLAVIA; }
1082 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidKo)) { return AREA_KOSOVO; }
1083 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLa)) { return AREA_LATVIA; }
1084 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLe)) { return AREA_LEBANON; }
1085 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLi)) { return AREA_LIBYA; }
1086 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLS)) { return AREA_LEBANON_SYRIA; }
1087 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLt)) { return AREA_LITHUANIA; }
1088 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidLu)) { return AREA_PORTUGUESE_MAINLAND; }
1089 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMa)) { return AREA_MOROCCO; }
1090 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd)) { return AREA_MADEIRA_ARCHIPELAGO; }
1091 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd_D)) { return AREA_DESERTAS; }
1092 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd_M)) { return AREA_MADEIRA; }
1093 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMd_P)) { return AREA_PORTO_SANTO; }
1094 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMk)) { return AREA_THE_FORMER_JUGOSLAV_REPUBLIC_OF_MAKEDONIJA; }
1095 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMo)) { return AREA_MOLDOVA; }
1096 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidNo)) { return AREA_NORWEGIAN_MAINLAND; }
1097 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidPo)) { return AREA_POLAND; }
1098 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf)) { return AREA_THE_RUSSIAN_FEDERATION; }
1099 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_A)) { return AREA_NOVAYA_ZEMLYA_AND_FRANZ_JOSEPH_LAND; }
1100 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_C)) { return AREA_CENTRAL_EUROPEAN_RUSSIA; }
1101 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_CS)) { return AREA_NORTH_CAUCASUS; }
1102 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_E)) { return AREA_EASTERN_EUROPEAN_RUSSIA; }
1103 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_K)) { return AREA_KALININGRAD; }
1104 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_N)) { return AREA_NORTHERN_EUROPEAN_RUSSIA; }
1105 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_NW)) { return AREA_NORTHWEST_EUROPEAN_RUSSIA; }
1106 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRf_S)) { return AREA_SOUTH_EUROPEAN_RUSSIA; }
1107 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRm)) { return AREA_ROMANIA; }
1108 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs)) { return AREA_FORMER_USSR; }
1109 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs_B)) { return AREA_RUSSIA_BALTIC; }
1110 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs_C)) { return AREA_RUSSIA_CENTRAL; }
1111 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs_E)) { return AREA_RUSSIA_SOUTHEAST; }
1112 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs_K)) { return AREA_CRIMEA; }
1113 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs_N)) { return AREA_RUSSIA_NORTHERN; }
1114 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRs_W)) { return AREA_RUSSIA_SOUTHWEST; }
1115 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSa)) { return AREA_SARDEGNA; }
1116 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSb)) { return AREA_SVALBARD_WITH_BJORNOYA_AND_JAN_MAYEN; }
1117 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSe)) { return AREA_SERBIA; }
1118 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSg)) { return AREA_SELVAGENS_ISLANDS; }
1119 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSi)) { return AREA_SICILY_WITH_MALTA; }
1120 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSi_M)) { return AREA_MALTA; }
1121 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSi_S)) { return AREA_SICILY; }
1122 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSk)) { return AREA_SLOVAKIA; }
1123 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSl)) { return AREA_SLOVENIA; }
1124 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSM)) { return AREA_SERBIA_WITH_MONTENEGRO; }
1125 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSn)) { return AREA_SINAI; }
1126 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSr)) { return AREA_SERBIA_INCLUDING_VOJVODINA_AND_WITH_KOSOVO; }
1127 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSu)) { return AREA_SWEDEN; }
1128 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidSy)) { return AREA_SYRIA; }
1129 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTcs)) { return AREA_TRANSCAUCASUS; }
1130 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTn)) { return AREA_TUNISIA; }
1131 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTu)) { return AREA_TURKEY; }
1132 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTu_A)) { return AREA_ASIATIC_TURKEY; }
1133 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTu_E)) { return AREA_EUROPEAN_TURKEY; }
1134 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUk)) { return AREA_UKRAINE_INCLUDING_CRIMEA; }
1135 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUk_K)) { return AREA_CRIMEA; }
1136 else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUk_U)) { return AREA_UKRAINE; }
1137 else {
1138 logger.warn("Unknown EuroMed distribution area: " + area.getTitleCache());
1139 }
1140 }else if (area.getVocabulary().getUuid().equals(BerlinModelTransformer.uuidVocEuroMedCommonNameAreas)){
1141 UUID uuidArea = namedArea.getUuid();
1142 if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameAlbania)) { return AREA_ALBANIA; }
1143 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameAndorra)) { return AREA_ANDORRA; }
1144 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameArmenia)) { return AREA_ARMENIA; }
1145 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameAustria)) { return AREA_AUSTRIA; }
1146 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameAzerbaijan)) { return AREA_AZERBAIJAN; }
1147 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameAzores)) { return AREA_AZORES; }
1148 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameBaleares)) { return AREA_BALEARES; }
1149 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameBelarus)) { return AREA_BELARUS; }
1150 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameBelgium)) { return AREA_BELGIUM; }
1151 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameBulgaria)) { return AREA_BULGARIA; }
1152 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameCanaryIs)) { return AREA_CANARY_ISLANDS; }
1153 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameCorse)) { return AREA_CORSE; }
1154 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameCrete)) { return AREA_CRETE; }
1155 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameCrimea)) { return AREA_CRIMEA; }
1156 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameCroatia)) { return AREA_CROATIA; }
1157 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameCzechRepublic)) { return AREA_CZECH_REPUBLIC; }
1158 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameDenmark)) { return AREA_DENMARK_COUNTRY; } //??
1159 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameEastAegeanIslands)) { return AREA_EAST_AEGEAN_ISLANDS; }
1160 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameEstonia)) { return AREA_ESTONIA; }
1161 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameEstonia)) { return AREA_ESTONIA; }
1162 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameFaroer)) { return AREA_FAROE_ISLANDS; }
1163 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameFinland)) { return AREA_FINLAND_WITH_AHVENANMAA; } //??
1164 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameFinlandWithAhvenanmaa)) { return AREA_FINLAND_WITH_AHVENANMAA; }
1165 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameFrance)) { return AREA_FRANCE; }
1166 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameGeorgia)) { return AREA_GEORGIA; }
1167 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameGermany)) { return AREA_GERMANY; }
1168 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameGreatBritain)) { return AREA_GREAT_BRITAIN; }
1169 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameGreece)) { return AREA_GREECE_COUNTRY; } //??
1170 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameHungary)) { return AREA_HUNGARY; }
1171 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameIbizaWithFormentera)) { return AREA_IBIZA_WITH_FORMENTERA; }
1172 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameIceland)) { return AREA_ICELAND; }
1173 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameIreland)) { return AREA_IRELAND; }
1174 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameIsrael)) { return AREA_ISRAEL; }
1175 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameItaly)) { return AREA_ITALY; }
1176 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameLaPalma)) { return AREA_LA_PALMA; }
1177 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameLativa)) { return AREA_LATVIA; }
1178 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameLebanon)) { return AREA_LEBANON; }
1179 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameLibya)) { return AREA_LIBYA; }
1180 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameLithuania)) { return AREA_LITHUANIA; }
1181 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameMadeira)) { return AREA_MADEIRA; }
1182 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameMallorca)) { return AREA_MALLORCA; }
1183 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameMalta)) { return AREA_MALTA; }
1184 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameMenorca)) { return AREA_MENORCA; }
1185 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameMoldova)) { return AREA_MOLDOVA; }
1186 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameMorocco)) { return AREA_MOROCCO; }
1187 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameNetherlands)) { return AREA_NETHERLANDS; }
1188 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameNorway)) { return AREA_NORWEGIAN_MAINLAND; }
1189 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNamePoland)) { return AREA_POLAND; }
1190 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNamePortugal)) { return AREA_PORTUGAL_COUNTRY; } //??
1191 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameRomania)) { return AREA_ROMANIA; }
1192 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameRussiaCentral)) { return AREA_RUSSIA_CENTRAL; }
1193 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameRussianFederation)) { return AREA_THE_RUSSIAN_FEDERATION; }
1194 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSardegna)) { return AREA_SARDEGNA; }
1195 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSerbiaMontenegro)) { return AREA_SERBIA_WITH_MONTENEGRO; }
1196 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSlovakia)) { return AREA_SLOVAKIA; }
1197 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSlovenia)) { return AREA_SLOVENIA; }
1198 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSouthEuropeanRussia)) { return AREA_SOUTH_EUROPEAN_RUSSIA; }
1199 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSpain)) { return AREA_SPAIN; }
1200 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSweden)) { return AREA_SWEDEN; }
1201 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSwitzerland)) { return AREA_SWITZERLAND; }
1202 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameSyria)) { return AREA_SYRIA; }
1203 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameTenerife)) { return AREA_TENERIFE; }
1204 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameTurkey)) { return AREA_TURKEY; } //??
1205 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameUkraine)) { return AREA_UKRAINE; } //??
1206 else if (uuidArea.equals(BerlinModelTransformer.uuidEMAreaCommonNameWales)) { return AREA_WALES; }
1207 else {
1208 logger.warn("Unknown EuroMed common name area: " + area.getTitleCache());
1209 }
1210
1211 }else if (area.getVocabulary().getUuid().equals(FaunaEuropaeaTransformer.uuidFauEuArea)){
1212 UUID uuidArea = namedArea.getUuid();
1213 if (uuidArea.equals(uuidAreaAD)) { return AREA_ANDORRA; }
1214 else if (uuidArea.equals(uuidAreaAFR)) { return AREA_AFRO_TROPICAL_REGION; }
1215 else if (uuidArea.equals(uuidAreaAL)) { return AREA_ALBANIA; }
1216 else if (uuidArea.equals(uuidAreaAT)) { return AREA_AUSTRIA; }
1217 else if (uuidArea.equals(uuidAreaAUS)) { return AREA_AUSTRALIAN_REGION; }
1218 else if (uuidArea.equals(uuidAreaBA)) { return AREA_BOSNIA_HERZEGOVINA; }
1219 else if (uuidArea.equals(uuidAreaBE)) { return AREA_BELGIUM; }
1220 else if (uuidArea.equals(uuidAreaBG)) { return AREA_BULGARIA; }
1221 else if (uuidArea.equals(uuidAreaBY)) { return AREA_BELARUS; }
1222 else if (uuidArea.equals(uuidAreaCH)) { return AREA_SWITZERLAND; }
1223 else if (uuidArea.equals(uuidAreaCY)) { return AREA_CYPRUS; }
1224 else if (uuidArea.equals(uuidAreaCZ)) { return AREA_CZECH_REPUBLIC; }
1225 else if (uuidArea.equals(uuidAreaDE)) { return AREA_GERMANY; }
1226 else if (uuidArea.equals(uuidAreaDK_DEN)) { return AREA_DENMARK_WITH_BORNHOLM; }
1227 else if (uuidArea.equals(uuidAreaDK_FOR)) { return AREA_FAROE_ISLANDS; }
1228 else if (uuidArea.equals(uuidAreaEE)) { return AREA_ESTONIA; }
1229 else if (uuidArea.equals(uuidAreaEPA)) { return AREA_EAST_PALAEARCTIC; }
1230 else if (uuidArea.equals(uuidAreaES_BAL)) { return AREA_BALEARES; }
1231 else if (uuidArea.equals(uuidAreaES_CNY)) { return AREA_CANARY_ISLANDS; }
1232 else if (uuidArea.equals(uuidAreaES_SPA)) { return AREA_KINGDOM_OF_SPAIN; }
1233 else if (uuidArea.equals(uuidAreaFI)) { return AREA_FINLAND_WITH_AHVENANMAA; }
1234 else if (uuidArea.equals(uuidAreaFR_COR)) { return AREA_CORSE; }
1235 else if (uuidArea.equals(uuidAreaFR_FRA)) { return AREA_FRENCH_MAINLAND; }
1236 else if (uuidArea.equals(uuidAreaGB_CI)) { return AREA_CHANNEL_ISLANDS; }
1237 else if (uuidArea.equals(uuidAreaGB_GI)) { return AREA_GIBRALTAR; }
1238 else if (uuidArea.equals(uuidAreaGB_GRB)) { return AREA_GREAT_BRITAIN; }
1239 else if (uuidArea.equals(uuidAreaGB_NI)) { return AREA_NORTHERN_IRELAND; }
1240 else if (uuidArea.equals(uuidAreaGR_AEG)) { return AREA_NORTH_AEGEAN_ISLANDS; }
1241 else if (uuidArea.equals(uuidAreaGR_CYC)) { return AREA_CYCLADES_ISLANDS; }
1242 else if (uuidArea.equals(uuidAreaGR_DOD)) { return AREA_DODECANESE_ISLANDS; }
1243 else if (uuidArea.equals(uuidAreaGR_KRI)) { return AREA_CRETE; }
1244 else if (uuidArea.equals(uuidAreaGR_GRC)) { return AREA_GREEK_MAINLAND; }
1245 else if (uuidArea.equals(uuidAreaHR)) { return AREA_CROATIA; }
1246 else if (uuidArea.equals(uuidAreaHU)) { return AREA_HUNGARY; }
1247 else if (uuidArea.equals(uuidAreaIE)) { return AREA_REPUBLIC_OF_IRELAND; }
1248 else if (uuidArea.equals(uuidAreaIS)) { return AREA_ICELAND; }
1249 else if (uuidArea.equals(uuidAreaIT_ITA)) { return AREA_ITALIAN_MAINLAND; }
1250 else if (uuidArea.equals(uuidAreaIT_SAR)) { return AREA_SARDEGNA; }
1251 else if (uuidArea.equals(uuidAreaIT_SI)) { return AREA_SICILY; }
1252 else if (uuidArea.equals(uuidAreaLI)) { return AREA_LIECHTENSTEIN; }
1253 else if (uuidArea.equals(uuidAreaLT)) { return AREA_LITHUANIA; }
1254 else if (uuidArea.equals(uuidAreaLU)) { return AREA_LUXEMBOURG; }
1255 else if (uuidArea.equals(uuidAreaLV)) { return AREA_LATVIA; }
1256 else if (uuidArea.equals(uuidAreaMC)) { return AREA_MONACO; }
1257 else if (uuidArea.equals(uuidAreaMD)) { return AREA_MOLDOVA; }
1258 else if (uuidArea.equals(uuidAreaMK)) { return AREA_THE_FORMER_JUGOSLAV_REPUBLIC_OF_MAKEDONIJA; }
1259 else if (uuidArea.equals(uuidAreaMT)) { return AREA_MALTA; }
1260 else if (uuidArea.equals(uuidAreaNAF)) { return AREA_NORTHERN_AFRICA; }
1261 else if (uuidArea.equals(uuidAreaNEA)) { return AREA_NEARCTIC_REGION; }
1262 else if (uuidArea.equals(uuidAreaNEO)) { return AREA_NEOTROPICAL_REGION; }
1263 else if (uuidArea.equals(uuidAreaNL)) { return AREA_NETHERLANDS; }
1264 else if (uuidArea.equals(uuidAreaNO_NOR)) { return AREA_NORWEGIAN_MAINLAND; }
1265 else if (uuidArea.equals(uuidAreaNO_SVA)) { return AREA_SVALBARD_WITH_BJORNOYA_AND_JAN_MAYEN; }
1266 else if (uuidArea.equals(uuidAreaNRE)) { return AREA_NEAR_EAST; }
1267 else if (uuidArea.equals(uuidAreaORR)) { return AREA_ORIENTAL_REGION; }
1268 else if (uuidArea.equals(uuidAreaPL)) { return AREA_POLAND; }
1269 else if (uuidArea.equals(uuidAreaPT_AZO)) { return AREA_AZORES; }
1270 else if (uuidArea.equals(uuidAreaPT_MDR)) { return AREA_MADEIRA; }
1271 else if (uuidArea.equals(uuidAreaPT_POR)) { return AREA_PORTUGUESE_MAINLAND; }
1272 else if (uuidArea.equals(uuidAreaPT_SEL)) { return AREA_SELVAGENS_ISLANDS; }
1273 else if (uuidArea.equals(uuidAreaRO)) { return AREA_ROMANIA; }
1274 else if (uuidArea.equals(uuidAreaRU_FJL)) { return AREA_FRANZ_JOSEF_LAND; }
1275 else if (uuidArea.equals(uuidAreaRU_KGD)) { return AREA_KALININGRAD; }
1276 else if (uuidArea.equals(uuidAreaRU_NOZ)) { return AREA_NOVAYA_ZEMLYA; }
1277 else if (uuidArea.equals(uuidAreaRU_RUC)) { return AREA_CENTRAL_EUROPEAN_RUSSIA; }
1278 else if (uuidArea.equals(uuidAreaRU_RUE)) { return AREA_EASTERN_EUROPEAN_RUSSIA; }
1279 else if (uuidArea.equals(uuidAreaRU_RUN)) { return AREA_NORTHERN_EUROPEAN_RUSSIA; }
1280 else if (uuidArea.equals(uuidAreaRU_RUS)) { return AREA_SOUTH_EUROPEAN_RUSSIA; }
1281 else if (uuidArea.equals(uuidAreaRU_RUW)) { return AREA_NORTHWEST_EUROPEAN_RUSSIA; }
1282 else if (uuidArea.equals(uuidAreaSE)) { return AREA_SWEDEN; }
1283 else if (uuidArea.equals(uuidAreaSI)) { return AREA_SLOVENIA; }
1284 else if (uuidArea.equals(uuidAreaSK)) { return AREA_SLOVAKIA; }
1285 else if (uuidArea.equals(uuidAreaSM)) { return AREA_SAN_MARINO; }
1286 else if (uuidArea.equals(uuidAreaTR_TUE)) { return AREA_EUROPEAN_TURKEY; }
1287 else if (uuidArea.equals(uuidAreaUA)) { return AREA_UKRAINE_INCLUDING_CRIMEA; }
1288 else if (uuidArea.equals(uuidAreaVA)) { return AREA_VATICAN_CITY; }
1289 else if (uuidArea.equals(uuidAreaYU)) { return AREA_FORMER_JUGOSLAVIA; }
1290
1291 }else if (area.getVocabulary().getUuid().equals(ErmsTransformer.uuidVocErmsAreas)){
1292 //ERMS
1293 UUID uuidArea = namedArea.getUuid();
1294 if (uuidArea.equals(ErmsTransformer.uuidEuropeanMarineWaters)) { return AREA_EUROPEAN_MARINE_WATERS; }
1295 else if (//(namedArea.getRepresentation(Language.DEFAULT()).getAbbreviatedLabel()).equals("MES") || /carefull: NPE!
1296 (uuidArea.equals(ErmsTransformer.uuidMediterraneanSea))) { return AREA_MEDITERRANEAN_SEA; } // abbreviated label missing
1297 else if (uuidArea.equals(ErmsTransformer.uuidWhiteSea)) { return AREA_WHITE_SEA; }
1298 else if (uuidArea.equals(ErmsTransformer.uuidNorthSea)) { return AREA_NORTH_SEA; }
1299 else if (uuidArea.equals(ErmsTransformer.uuidBalticSea)) { return AREA_BALTIC_SEA; }
1300 else if (//(namedArea.getRepresentation(Language.DEFAULT()).getAbbreviatedLabel()).equals("BLS") || /carefull: NPE!
1301 (uuidArea.equals(ErmsTransformer.uuidBlackSea))) { return AREA_BLACK_SEA; } // abbreviated label missing
1302 else if (uuidArea.equals(ErmsTransformer.uuidBarentszSea)) { return AREA_BARENTSZ_SEA; }
1303 else if (//(namedArea.getRepresentation(Language.DEFAULT()).getAbbreviatedLabel()).equals("CAS") || /carefull: NPE!
1304 (uuidArea.equals(ErmsTransformer.uuidCaspianSea))) { return AREA_CASPIAN_SEA; } // abbreviated label missing
1305 else if (uuidArea.equals(ErmsTransformer.uuidPortugueseExclusiveEconomicZone)) { return AREA_PORTUGUESE_EXCLUSIVE_ECONOMIC_ZONE; }
1306 else if (uuidArea.equals(ErmsTransformer.uuidBelgianExclusiveEconomicZone)) { return AREA_BELGIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1307 else if (uuidArea.equals(ErmsTransformer.uuidFrenchExclusiveEconomicZone)) { return AREA_FRENCH_EXCLUSIVE_ECONOMIC_ZONE; }
1308 else if (uuidArea.equals(ErmsTransformer.uuidEnglishChannel)) { return AREA_ENGLISH_CHANNEL; }
1309 else if (uuidArea.equals(ErmsTransformer.uuidAdriaticSea)) { return AREA_ADRIATIC_SEA; }
1310 else if (uuidArea.equals(ErmsTransformer.uuidBiscayBay)) { return AREA_BISCAY_BAY; }
1311 else if (uuidArea.equals(ErmsTransformer.uuidDutchExclusiveEconomicZone)) { return AREA_DUTCH_EXCLUSIVE_ECONOMIC_ZONE; }
1312 else if (uuidArea.equals(ErmsTransformer.uuidUnitedKingdomExclusiveEconomicZone)) { return AREA_UNITED_KINGDOM_EXCLUSIVE_ECONOMIC_ZONE; }
1313 else if (uuidArea.equals(ErmsTransformer.uuidSpanishExclusiveEconomicZone)) { return AREA_SPANISH_EXCLUSIVE_ECONOMIC_ZONE; }
1314 else if (uuidArea.equals(ErmsTransformer.uuidEgyptianExclusiveEconomicZone)) { return AREA_EGYPTIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1315 else if (uuidArea.equals(ErmsTransformer.uuidTirrenoSea)) { return AREA_TIRRENO_SEA; }
1316 else if (uuidArea.equals(ErmsTransformer.uuidIcelandicExclusiveEconomicZone)) { return AREA_ICELANDIC_EXCLUSIVE_ECONOMIC_ZONE; }
1317 else if (uuidArea.equals(ErmsTransformer.uuidIrishExclusiveeconomicZone)) { return AREA_IRISH_EXCLUSIVE_ECONOMIC_ZONE; }
1318 else if (uuidArea.equals(ErmsTransformer.uuidIrishSea)) { return AREA_IRISH_SEA; }
1319 else if (uuidArea.equals(ErmsTransformer.uuidIsraeliExclusiveEconomicZone)){ return 218;}
1320 else if (uuidArea.equals(ErmsTransformer.uuidItalianExclusiveEconomicZone)) { return AREA_ITALIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1321 else if (uuidArea.equals(ErmsTransformer.uuidNorwegianSea)) { return AREA_NORWEGIAN_SEA; }
1322 else if (uuidArea.equals(ErmsTransformer.uuidMoroccanExclusiveEconomicZone)) { return AREA_MOROCCAN_EXCLUSIVE_ECONOMIC_ZONE; }
1323 else if (uuidArea.equals(ErmsTransformer.uuidNorwegianExclusiveEconomicZone)) { return AREA_NORWEGIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1324 else if (uuidArea.equals(ErmsTransformer.uuidSkagerrak)) { return AREA_SKAGERRAK; }
1325 else if (uuidArea.equals(ErmsTransformer.uuidTunisianExclusiveEconomicZone)) { return AREA_TUNISIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1326 else if (uuidArea.equals(ErmsTransformer.uuidWaddenSea)) { return AREA_WADDEN_SEA; }
1327 else if (uuidArea.equals(ErmsTransformer.uuidBaeltSea)) { return AREA_BELT_SEA; }
1328 else if (uuidArea.equals(ErmsTransformer.uuidMarmaraSea)) { return AREA_MARMARA_SEA; }
1329 else if (uuidArea.equals(ErmsTransformer.uuidSeaofAzov)) { return AREA_SEA_OF_AZOV; }
1330 else if (uuidArea.equals(ErmsTransformer.uuidAegeanSea)) { return AREA_AEGEAN_SEA; }
1331 else if (uuidArea.equals(ErmsTransformer.uuidBulgarianExclusiveEconomicZone)) { return AREA_BULGARIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1332 else if (uuidArea.equals(ErmsTransformer.uuidSouthBalticproper)) { return AREA_SOUTH_BALTIC_PROPER; }
1333 else if (uuidArea.equals(ErmsTransformer.uuidBalticProper)) { return AREA_BALTIC_PROPER; }
1334 else if (uuidArea.equals(ErmsTransformer.uuidNorthBalticproper)) { return AREA_NORTH_BALTIC_PROPER; }
1335 else if (uuidArea.equals(ErmsTransformer.uuidArchipelagoSea)) { return AREA_ARCHIPELAGO_SEA; }
1336 else if (uuidArea.equals(ErmsTransformer.uuidBothnianSea)) { return AREA_BOTHNIAN_SEA; }
1337 else if (uuidArea.equals(ErmsTransformer.uuidGermanExclusiveEconomicZone)) { return AREA_GERMAN_EXCLUSIVE_ECONOMIC_ZONE; }
1338 else if (uuidArea.equals(ErmsTransformer.uuidSwedishExclusiveEconomicZone)) { return AREA_SWEDISH_EXCLUSIVE_ECONOMIC_ZONE; }
1339 else if (uuidArea.equals(ErmsTransformer.uuidUkrainianExclusiveEconomicZone)) { return AREA_UKRAINIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1340 else if (uuidArea.equals(ErmsTransformer.uuidMadeiranExclusiveEconomicZone)) { return AREA_MADEIRAN_EXCLUSIVE_ECONOMIC_ZONE; }
1341 else if (uuidArea.equals(ErmsTransformer.uuidLebaneseExclusiveEconomicZone)) { return AREA_LEBANESE_EXCLUSIVE_ECONOMIC_ZONE; }
1342 else if (uuidArea.equals(ErmsTransformer.uuidSpanishExclusiveEconomicZoneMediterraneanpart)) { return AREA_SPANISH_EXCLUSIVE_ECONOMIC_ZONE_MEDITERRANEAN_PART; }
1343 else if (uuidArea.equals(ErmsTransformer.uuidEstonianExclusiveEconomicZone)) { return AREA_ESTONIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1344 else if (uuidArea.equals(ErmsTransformer.uuidCroatianExclusiveEconomicZone)) { return AREA_CROATIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1345 else if (uuidArea.equals(ErmsTransformer.uuidBalearSea)) { return AREA_BALEAR_SEA; }
1346 else if (uuidArea.equals(ErmsTransformer.uuidTurkishExclusiveEconomicZone)) { return AREA_TURKISH_EXCLUSIVE_ECONOMIC_ZONE; }
1347 else if (uuidArea.equals(ErmsTransformer.uuidDanishExclusiveEconomicZone)) { return AREA_DANISH_EXCLUSIVE_ECONOMIC_ZONE; }
1348
1349 else if (uuidArea.equals(ErmsTransformer.uuidAfghanistan)) { return 297; }
1350 else if (uuidArea.equals(ErmsTransformer.uuidAlboranSea)) { return 219; }
1351 else if (uuidArea.equals(ErmsTransformer.uuidAlgeria)) { return 220; }
1352 else if (uuidArea.equals(ErmsTransformer.uuidAngola)) { return 221; }
1353 else if (uuidArea.equals(ErmsTransformer.uuidArcticOcean)) { return 296; }
1354 else if (uuidArea.equals(ErmsTransformer.uuidAustralianExclusiveEconomicZone)) { return 222; }
1355 else if (uuidArea.equals(ErmsTransformer.uuidBahamas)) { return 223; }
1356 else if (uuidArea.equals(ErmsTransformer.uuidBalearicSea)) { return 224; }
1357 else if (uuidArea.equals(ErmsTransformer.uuidBelgium)) { return 225; }
1358 else if (uuidArea.equals(ErmsTransformer.uuidBelize)) { return 226; }
1359 else if (uuidArea.equals(ErmsTransformer.uuidBrazil)) { return 227; }
1360 else if (uuidArea.equals(ErmsTransformer.uuidBulgaria)) { return 228; }
1361 else if (uuidArea.equals(ErmsTransformer.uuidCanada)) { return 229; }
1362 else if (uuidArea.equals(ErmsTransformer.uuidCapeVerde)) { return 230; }
1363 else if (uuidArea.equals(ErmsTransformer.uuidCapeVerdeanExclusiveEconomicZone)) { return 231; }
1364 else if (uuidArea.equals(ErmsTransformer.uuidCaribbeanSea)) { return 210; }
1365 else if (uuidArea.equals(ErmsTransformer.uuidChile)) { return 232; }
1366 else if (uuidArea.equals(ErmsTransformer.uuidColombia)) { return 233; }
1367 else if (uuidArea.equals(ErmsTransformer.uuidCostaRica)) { return 234; }
1368 else if (uuidArea.equals(ErmsTransformer.uuidCroatia)) { return 235; }
1369 else if (uuidArea.equals(ErmsTransformer.uuidCuba)) { return 236; }
1370 else if (uuidArea.equals(ErmsTransformer.uuidDenmark)) { return 292; }
1371 else if (uuidArea.equals(ErmsTransformer.uuidEgypt)) { return 237; }
1372 else if (uuidArea.equals(ErmsTransformer.uuidEstonia)) { return 238; }
1373 else if (uuidArea.equals(ErmsTransformer.uuidFaeroeExclusiveEconomicZone)) { return 239; }
1374 else if (uuidArea.equals(ErmsTransformer.uuidFrance)) { return 240; }
1375 else if (uuidArea.equals(ErmsTransformer.uuidGhana)) { return 241; }
1376 else if (uuidArea.equals(ErmsTransformer.uuidGreece)) { return 242; }
1377 else if (uuidArea.equals(ErmsTransformer.uuidGermany)) { return 298; }
1378 else if (uuidArea.equals(ErmsTransformer.uuidGreekExclusiveEconomicZone)) { return AREA_GREEK_EXCLUSIVE_ECONOMIC_ZONE; }
1379 else if (uuidArea.equals(ErmsTransformer.uuidGulfOfBothnia)) { return 243; }
1380 else if (uuidArea.equals(ErmsTransformer.uuidGulfOfFinland)) { return 244; }
1381 else if (uuidArea.equals(ErmsTransformer.uuidGulfOfGuinea)) { return 245; }
1382 else if (uuidArea.equals(ErmsTransformer.uuidGulfOfMexico)) { return 246; }
1383 else if (uuidArea.equals(ErmsTransformer.uuidGulfOfRiga)) { return 247; }
1384 else if (uuidArea.equals(ErmsTransformer.uuidIceland)) { return 248; }
1385 else if (uuidArea.equals(ErmsTransformer.uuidIonianSea)) { return 249; }
1386 else if (uuidArea.equals(ErmsTransformer.uuidIreland)) { return 250; }
1387 else if (uuidArea.equals(ErmsTransformer.uuidItaly)) { return 251; }
1388 else if (uuidArea.equals(ErmsTransformer.uuidJamaica)) { return 252; }
1389 else if (uuidArea.equals(ErmsTransformer.uuidKattegat)) { return 253; }
1390 else if (uuidArea.equals(ErmsTransformer.uuidLevantineSea)) { return 254; }
1391 else if (uuidArea.equals(ErmsTransformer.uuidLigurianSea)) { return 255; }
1392 else if (uuidArea.equals(ErmsTransformer.uuidMalteseExclusiveEconomicZone)) { return 256; }
1393 else if (uuidArea.equals(ErmsTransformer.uuidMauritanianExclusiveEconomicZone)) { return 257; }
1394 else if (uuidArea.equals(ErmsTransformer.uuidMediterraneanSea_EasternBasin)) { return 258; }
1395 else if (uuidArea.equals(ErmsTransformer.uuidMediterraneanSea_WesternBasin)) { return 259; }
1396 else if (uuidArea.equals(ErmsTransformer.uuidMexico)) { return 260; }
1397 else if (uuidArea.equals(ErmsTransformer.uuidMongolia)) { return 299; }
1398 else if (uuidArea.equals(ErmsTransformer.uuidMorocco)) { return 261; }
1399 else if (uuidArea.equals(ErmsTransformer.uuidNetherlands)) { return 262; }
1400 else if (uuidArea.equals(ErmsTransformer.uuidNewZealand)) { return 263; }
1401 else if (uuidArea.equals(ErmsTransformer.uuidNewZealandExclusiveEconomicZone)) { return 264; }
1402 else if (uuidArea.equals(ErmsTransformer.uuidNorthAtlanticOcean)) { return 265; }
1403 else if (uuidArea.equals(ErmsTransformer.uuidNorway)) { return 266; }
1404 else if (uuidArea.equals(ErmsTransformer.uuidPanama)) { return 267; }
1405 else if (uuidArea.equals(ErmsTransformer.uuidPanamanianExclusiveEconomicZone)) { return 268; }
1406 else if (uuidArea.equals(ErmsTransformer.uuidPolishExclusiveEconomicZone)) { return 216; }
1407 else if (uuidArea.equals(ErmsTransformer.uuidPortugal)) { return 269; }
1408 else if (uuidArea.equals(ErmsTransformer.uuidPortugueseExclusiveEconomicZone_Azores)) { return 270; }
1409 else if (uuidArea.equals(ErmsTransformer.uuidPortugueseExclusiveEconomicZone_Madeira)) { return 271; }
1410 else if (uuidArea.equals(ErmsTransformer.uuidRedSea)) { return 272; }
1411 else if (uuidArea.equals(ErmsTransformer.uuidRussianExclusiveEconomicZone)) { return 217; }
1412 else if (uuidArea.equals(ErmsTransformer.uuidSeaOfMarmara)) { return 273; }
1413 else if (uuidArea.equals(ErmsTransformer.uuidSenegaleseExclusiveEconomicZone)) { return 274; }
1414 else if (uuidArea.equals(ErmsTransformer.uuidSingapore)) { return 275; }
1415 else if (uuidArea.equals(ErmsTransformer.uuidSlovenianExclusiveEconomicZone)) { return 276; }
1416 else if (uuidArea.equals(ErmsTransformer.uuidSouthAfrica)) { return 277; }
1417 else if (uuidArea.equals(ErmsTransformer.uuidSouthAfricanExclusiveEconomicZone)) { return 278; }
1418 else if (uuidArea.equals(ErmsTransformer.uuidSouthChinaSea)) { return 279; }
1419 else if (uuidArea.equals(ErmsTransformer.uuidSpain)) { return 280; }
1420 else if (uuidArea.equals(ErmsTransformer.uuidSpanishExclusiveEconomicZone_CanaryIslands)) { return 281; }
1421 else if (uuidArea.equals(ErmsTransformer.uuidSriLankanExclusiveEconomicZone)) { return 282; }
1422 else if (uuidArea.equals(ErmsTransformer.uuidStraitOfGibraltar)) { return 283; }
1423 else if (uuidArea.equals(ErmsTransformer.uuidSweden)) { return 284; }
1424 else if (uuidArea.equals(ErmsTransformer.uuidTunisia)) { return 285; }
1425 else if (uuidArea.equals(ErmsTransformer.uuidTurkey)) { return 286; }
1426 else if (uuidArea.equals(ErmsTransformer.uuidTyrrhenianSea)) { return 287; }
1427 else if (uuidArea.equals(ErmsTransformer.uuidUnitedKingdom)) { return 288; }
1428 else if (uuidArea.equals(ErmsTransformer.uuidUnitedStates)) { return 291; }
1429 else if (uuidArea.equals(ErmsTransformer.uuidUnitedStatesExclusiveEconomicZone_Alaska)) { return 289; }
1430 else if (uuidArea.equals(ErmsTransformer.uuidVenezuela)) { return 290; }
1431
1432 else {
1433 logger.warn("Unknown ERMS Area: " + area.getTitleCache());
1434 }
1435
1436 } else {
1437 logger.warn("Unknown NamedArea Area not in a known vocabulary: " + area.getTitleCache());
1438 }
1439 return null;
1440 }
1441
1442
1443 /**
1444 * Returns the PESI SourceUseId for a given CDM sourceUseId.
1445 * @param sourceUseId
1446 * @return
1447 */
1448 public static Integer sourceUseIdSourceUseId(Integer sourceUseId) {
1449 // TODO: CDM sourceUseId and PESI sourceUseId are equal for now.
1450 Integer result = null;
1451 switch (sourceUseId) {
1452 case 3: return ADDITIONAL_SOURCE;
1453 case 4: return SOURCE_OF_SYNONYMY;
1454 case 8: return NOMENCLATURAL_REFERENCE;
1455 }
1456 return result;
1457 }
1458
1459 @Override
1460 public Object getKeyByLanguage(Language language) throws UndefinedTransformerMethodException {
1461 return language2LanguageId(language);
1462 }
1463
1464 @Override
1465 public String getCacheByLanguage(Language language) throws UndefinedTransformerMethodException {
1466 if (language == null){
1467 return null;
1468 }else{
1469 return this.languageCacheMap.get(getKeyByLanguage(language));
1470 }
1471 }
1472
1473 /**
1474 * Returns the identifier of the given Language.
1475 */
1476 public static Integer language2LanguageId(Language language) {
1477 if (language == null ) {
1478 return null;
1479 }
1480 Integer result;
1481 if ((result = languageCodeToKeyMap.get(language.getIso639_1())) != null){
1482 return result;
1483 }else if ((result = languageCodeToKeyMap.get(language.getIdInVocabulary())) != null){
1484 return result;
1485 //Languages without ISO identifier
1486 }else if (language.getUuid().equals(BerlinModelTransformer.uuidLangValencian)){return LANG_VALENCIAN;
1487 }else if (language.getUuid().equals(BerlinModelTransformer.uuidLangHighAragonese)){return LANG_HIGH_ARAGONES;
1488 }else if (language.getUuid().equals(BerlinModelTransformer.uuidLangMajorcan)){return LANG_MAJORCAN;
1489 //FE wrong mapping in FE, Dutch_Middle should probably be Dutch
1490 }else if (language.equals(Language.DUTCH_MIDDLE())){return LANG_DUTCH;
1491 //some common names from ILDIS have no defined language
1492 }else if (language.equals(Language.UNKNOWN_LANGUAGE())){return LANG_UNKNOWN;
1493 } else {
1494 logger.warn("Unknown Language: " + language.getTitleCache());
1495 return null;
1496 }
1497 }
1498
1499 /**
1500 * Returns the NodeCategoryCache for a given TextData.
1501 */
1502 @Override
1503 public String getCacheByFeature(Feature feature) {
1504 if (feature == null){
1505 return null;
1506 }else{
1507 return this.featureCacheMap.get(feature2NoteCategoryFk(feature));
1508 }
1509 }
1510
1511 /**
1512 * Returns the NodeCategoryFk for a given TextData.
1513 */
1514 public static Integer feature2NoteCategoryFk(Feature feature) {
1515 if (feature == null) {
1516 return null;
1517 }
1518
1519 if (feature.equals(Feature.DESCRIPTION())) {
1520 return NoteCategory_description;
1521 } else if (feature.equals(Feature.ECOLOGY())) {
1522 return NoteCategory_ecology;
1523 } else if (feature.equals(Feature.PHENOLOGY())) {
1524 return NoteCategory_phenology;
1525 } else if (feature.equals(Feature.DIAGNOSIS())) {
1526 return NoteCategory_Diagnosis;
1527 } else if (feature.equals(Feature.COMMON_NAME())) {
1528 return NoteCategory_Common_names;
1529 } else if (feature.equals(Feature.OCCURRENCE())) {
1530 return NoteCategory_Occurrence;
1531 } else if (feature.equals(Feature.DISTRIBUTION())) {
1532 return NoteCategory_Distribution;
1533 } else if (feature.equals(Feature.ETYMOLOGY())) {
1534 return NoteCategory_Etymology;
1535 } else if (feature.getUuid().equals(ErmsTransformer.uuidAcknowledgments)){
1536 return NoteCategory_Acknowledgments;
1537 } else if (feature.getUuid().equals(ErmsTransformer.uuidAdditionalinformation)) {
1538 return NoteCategory_Additional_information;
1539 } else if (feature.getUuid().equals(ErmsTransformer.uuidAlienSpecies)) {
1540 return NoteCategory_Alien_Species;
1541 } else if (feature.getUuid().equals(ErmsTransformer.uuidAuthority)) {
1542 return NoteCategory_Authority;
1543 } else if (feature.getUuid().equals(ErmsTransformer.uuidDepthRange)) {
1544 return NoteCategory_Depth_Range;
1545 } else if (feature.getUuid().equals(ErmsTransformer.uuidBiology)) {
1546 return NoteCategory_Biology;
1547 } else if (feature.getUuid().equals(ErmsTransformer.uuidClassification)) {
1548 return NoteCategory_Classification;
1549 } else if (feature.getUuid().equals(ErmsTransformer.uuidDiet)) {
1550 return NoteCategory_Diet;
1551 } else if (feature.getUuid().equals(ErmsTransformer.uuidDimensions)) {
1552 return NoteCategory_Dimensions;
1553 } else if (feature.getUuid().equals(ErmsTransformer.uuidEditorsComment)) {
1554 return NoteCategory_Editors_Comment;
1555 } else if (feature.getUuid().equals(ErmsTransformer.uuidEnvironment)) {
1556 return NoteCategory_Environment;
1557 } else if (feature.getUuid().equals(ErmsTransformer.uuidFossilRange)) {
1558 return NoteCategory_Fossil_Range;
1559 } else if (feature.getUuid().equals(ErmsTransformer.uuidGrammaticalGender)) {
1560 return NoteCategory_Grammatical_Gender;
1561 } else if (feature.getUuid().equals(ErmsTransformer.uuidHabitat)) {
1562 return NoteCategory_Habitat;
1563 } else if (feature.getUuid().equals(ErmsTransformer.uuidHomonymy)) {
1564 return NoteCategory_Homonymy;
1565 } else if (feature.getUuid().equals(ErmsTransformer.uuidIdentification)) {
1566 return NoteCategory_Identification;
1567 } else if (feature.getUuid().equals(ErmsTransformer.uuidIntroducedSpeciesRemark)) {
1568 return NoteCategory_Introduced_Species_Remark;
1569 } else if (feature.getUuid().equals(ErmsTransformer.uuidMorphology)) {
1570 return NoteCategory_Morphology;
1571 } else if (feature.getUuid().equals(ErmsTransformer.uuidNewCombination)) {
1572 return NoteCategory_New_Combination;
1573 } else if (feature.getUuid().equals(ErmsTransformer.uuidNomenclature)) {
1574 return NoteCategory_Nomenclature;
1575 } else if (feature.getUuid().equals(ErmsTransformer.uuidNote)){
1576 return NoteCategory_Note;
1577 } else if (feature.getUuid().equals(ErmsTransformer.uuidOriginalCombination)) {
1578 return NoteCategory_Original_Combination;
1579 } else if (feature.getUuid().equals(ErmsTransformer.uuidOriginalDescription)) {
1580 return NoteCategory_Original_Description;
1581 } else if (feature.getUuid().equals(ErmsTransformer.uuidOriginalpublication)) {
1582 return NoteCategory_Original_publication;
1583 } else if (feature.getUuid().equals(ErmsTransformer.uuidPublicationdate)) {
1584 return NoteCategory_Publication_date;
1585 } else if (feature.getUuid().equals(ErmsTransformer.uuidRank)) {
1586 return NoteCategory_Rank;
1587 } else if (feature.getUuid().equals(ErmsTransformer.uuidRemark)) {
1588 return NoteCategory_Remark;
1589 } else if (feature.getUuid().equals(ErmsTransformer.uuidReproduction)) {
1590 return NoteCategory_Reproduction;
1591 } else if (feature.getUuid().equals(ErmsTransformer.uuidSpelling)) {
1592 return NoteCategory_Spelling;
1593 } else if (feature.getUuid().equals(ErmsTransformer.uuidSpecimen)) {
1594 return NoteCategory_Specimen;
1595 } else if (feature.getUuid().equals(ErmsTransformer.uuidStatus)){
1596 return NoteCategory_Status;
1597 } else if (feature.getUuid().equals(ErmsTransformer.uuidSynonymy)) {
1598 return NoteCategory_Synonymy;
1599 } else if (feature.getUuid().equals(ErmsTransformer.uuidSyntype)) {
1600 return NoteCategory_Syntype;
1601 } else if (feature.getUuid().equals(ErmsTransformer.uuidSystematics)) {
1602 return NoteCategory_Systematics;
1603 } else if (feature.getUuid().equals(ErmsTransformer.uuidTaxonomicRemarks)) {
1604 return NoteCategory_Taxonomic_Remarks;
1605 } else if (feature.getUuid().equals(ErmsTransformer.uuidTaxonomy)) {
1606 return NoteCategory_Taxonomy;
1607 } else if (feature.getUuid().equals(ErmsTransformer.uuidTaxonomicstatus)) {
1608 return NoteCategory_Taxonomic_status;
1609 } else if (feature.getUuid().equals(ErmsTransformer.uuidTypelocality)) {
1610 return NoteCategory_Type_locality;
1611 } else if (feature.getUuid().equals(ErmsTransformer.uuidTypeMaterial)) {
1612 return NoteCategory_Type_Material;
1613 } else if (feature.getUuid().equals(ErmsTransformer.uuidTypeSpecimen)) {
1614 return NoteCategory_Type_Specimen;
1615 } else if (feature.getUuid().equals(ErmsTransformer.uuidTypespecies)) {
1616 return NoteCategory_Type_species;
1617 } else if (feature.getUuid().equals(ErmsTransformer.uuidTaxonomicRemark)) {
1618 return NoteCategory_Taxonomic_Remark;
1619 } else if (feature.getUuid().equals(ErmsTransformer.uuidValidity)) {
1620 return NoteCategory_Validity;
1621
1622 // } else if (feature.getUuid().equals(ErmsTransformer.uuidSourceOfSynonymy)) {
1623 // logger.debug("Source of synonymy not yet handled");
1624 // return null;
1625 } else if (feature.equals(Feature.CITATION())) {
1626 return null; //citations are handled differently
1627 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureMaps)){
1628 return NoteCategory_Link_to_maps;
1629 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureUse)){
1630 return NoteCategory_Use;
1631 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureComments)){
1632 return NoteCategory_Comments;
1633 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureConservationStatus)){
1634 return NoteCategory_Conservation_Status;
1635
1636 //E+M
1637 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureDistrEM)){
1638 return NoteCategory_general_distribution_euromed;
1639 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureDistrWorld)){
1640 return NoteCategory_general_distribution_world;
1641 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureEditorBrackets)){
1642 return NoteCategory_Editor_Brackets;
1643 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureEditorParenthesis)){
1644 return NoteCategory_Editor_Parenthesis;
1645 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureInedited)){
1646 return NoteCategory_Inedited;
1647 } else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureCommentsEditing)){
1648 return NoteCategory_Comments_on_editing_process;
1649
1650 }else{
1651 logger.warn("Unhandled Feature: " + feature.getTitleCache());
1652 return null;
1653 }
1654 }
1655
1656 /**
1657 * Returns the string representation for a given rank.
1658 */
1659 public String getCacheByRankAndKingdom(Rank rank, Integer pesiKingdomId) {
1660 if (rank == null){
1661 return null;
1662 }else if (pesiKingdomId == null && rank.equals(Rank.DOMAIN())){ //might be Superdomain in future
1663 return this.rankCacheMap.get(0).get(0);
1664 }else{
1665 Map<Integer, String> rankMap = this.rankCacheMap.get(pesiKingdomId);
1666 if (rankMap != null){
1667 return rankMap.get(rank2RankId(rank, pesiKingdomId));
1668 }else{
1669 logger.warn("RankCacheMap is null for " + pesiKingdomId);
1670 return null;
1671 }
1672 }
1673 }
1674
1675 /**
1676 * Returns the identifier of a PESI specific kingdom for a given CDM nomenclatural code.
1677 * @param nomenclaturalCode
1678 * @return KINGDOM_ANIMALIA for NomenclaturalCode.ICZN, KINGDOM_PLANTAE for NomenclaturalCode.ICNAFP
1679 */
1680 public static Integer nomenclaturalCode2Kingdom(NomenclaturalCode nomenclaturalCode) {
1681 Integer result = null;
1682 // TODO: This needs to be refined. For now we differentiate between animalia, plantae and bacteria only.
1683 if (nomenclaturalCode.equals(NomenclaturalCode.ICZN)) {
1684 result = KINGDOM_ANIMALIA;
1685 } else if (nomenclaturalCode.equals(NomenclaturalCode.ICNAFP)) {
1686 result = KINGDOM_PLANTAE;
1687 } else if (nomenclaturalCode.equals(NomenclaturalCode.ICNB)) {
1688 result = KINGDOM_BACTERIA;
1689 // } else if (nomenclaturalCode.equals(NomenclaturalCode.)) { // Biota
1690 // result =
1691 } else {
1692 logger.error("NomenclaturalCode not yet considered: " + nomenclaturalCode.getUuid() + " (" + nomenclaturalCode.getTitleCache() + ")");
1693 }
1694 return result;
1695 }
1696
1697 /**
1698 * Returns the RankId for a Rank.
1699 * @param rank
1700 * @return
1701 */
1702 public static Integer rank2RankId (Rank rank, Integer pesiKingdomId) {
1703 Integer result = null;
1704 if (rank == null) {
1705 return null;
1706 }else if (rank.equals(Rank.DOMAIN())){
1707 return KINGDOM_NULL;
1708 }else if (rank.equals(Rank.KINGDOM())) {
1709 result = Kingdom;
1710 }else if (rank.equals(Rank.SUBKINGDOM())) {
1711 result = Subkingdom;
1712 } else if (rank.equals(Rank.PHYLUM())) {
1713 result = Phylum;
1714 }else if (rank.equals(Rank.DIVISION())) { //same as Phylum
1715 result = Division;
1716 }else if (rank.equals(Rank.SUBPHYLUM())) {
1717 result = Subphylum;
1718 }else if (rank.equals(Rank.SUBDIVISION())) { //same as Subphylum
1719 result = Subdivision;
1720 }else if (rank.equals(Rank.CLASS())) {
1721 result = Class;
1722 } else if (rank.equals(Rank.SUBCLASS())) {
1723 result = Subclass;
1724 } else if (rank.equals(Rank.ORDER())) {
1725 result = Order;
1726 } else if (rank.equals(Rank.SUBORDER())) {
1727 result = Suborder;
1728 } else if (rank.equals(Rank.FAMILY())) {
1729 result = Family;
1730 } else if (rank.equals(Rank.SUBFAMILY())) {
1731 result = Subfamily;
1732 } else if (rank.equals(Rank.TRIBE())) {
1733 result = Tribe;
1734 } else if (rank.equals(Rank.SUBTRIBE())) {
1735 result = Subtribe;
1736 } else if (rank.equals(Rank.GENUS())) {
1737 result = Genus;
1738 } else if (rank.equals(Rank.SUBGENUS())) {
1739 result = Subgenus;
1740 } else if (rank.equals(Rank.SPECIES())) {
1741 result = Species;
1742 } else if (rank.equals(Rank.SUBSPECIES())) {
1743 result = Subspecies;
1744 } else if (rank.equals(Rank.VARIETY())) {
1745 result = Variety;
1746 } else if (rank.equals(Rank.FORM())) {
1747 result = Forma;
1748 } else
1749
1750 // We differentiate between Animalia and Plantae only for now.
1751 if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_ANIMALIA) {
1752 if (rank.equals(Rank.INFRAKINGDOM())) {result = Infrakingdom;
1753 } else if (rank.equals(Rank.SUPERPHYLUM())) {result = Superphylum;
1754 } else if (rank.equals(Rank.INFRAPHYLUM())) {result = Infraphylum;
1755 } else if (rank.equals(Rank.SUPERCLASS())) {result = Superclass;
1756 } else if (rank.equals(Rank.INFRACLASS())) {result = Infraclass;
1757 } else if (rank.getUuid().equals(ErmsTransformer.uuidRankSubterclass)) {result = Subterclass;
1758 } else if (rank.equals(Rank.SUPERORDER())) {result = Superorder;
1759 } else if (rank.equals(Rank.INFRAORDER())) {result = Infraorder;
1760 } else if (rank.getUuid().equals(ErmsTransformer.uuidRankParvorder)) {result = Parvorder;
1761 } else if (rank.equals(Rank.SECTION_ZOOLOGY())) {result = Animalia_Section;
1762 } else if (rank.equals(Rank.SUBSECTION_ZOOLOGY())) {result = Animalia_Subsection;
1763 } else if (rank.equals(Rank.SUPERFAMILY())) {result = Superfamily;
1764 } else if (rank.equals(Rank.NATIO())) {result = Natio;
1765 } else if (rank.equals(Rank.SUBVARIETY())) {result = Subvariety;
1766 } else if (rank.equals(Rank.SUBFORM())) {result = Subform;
1767 } else {
1768 //TODO Exception
1769 logger.warn("Rank for Kingdom Animalia not yet supported in CDM: "+ rank.getLabel());
1770 return null;
1771 }
1772 } else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_PLANTAE) {
1773 if (rank.equals(Rank.INFRAKINGDOM())) {result = Infrakingdom;
1774 } else if (rank.equals(Rank.SUPERORDER())) {result = Superorder;
1775 } else if (rank.equals(Rank.SECTION_BOTANY())) {result = Bot_Section;
1776 } else if (rank.equals(Rank.SUBSECTION_BOTANY())) {result = Bot_Subsection;
1777 } else if (rank.equals(Rank.SERIES())) {result = Series;
1778 } else if (rank.equals(Rank.SUBSERIES())) {result = Subseries;
1779 } else if (rank.equals(Rank.SPECIESAGGREGATE() )) {result = Aggregate;
1780 } else if (rank.equals(Rank.SPECIESGROUP())) {
1781 logger.warn("Rank Species Group not yet implemented");
1782 result = null;
1783 } else if (rank.getUuid().equals(Rank.uuidCollSpecies)) {result = Coll_Species;
1784 } else if (rank.equals(Rank.GREX())) {result = Grex;
1785 } else if (rank.getUuid().equals(Rank.uuidProles) ) {result = Proles;
1786 } else if (rank.getUuid().equals(Rank.uuidRace)) {result = Race;
1787 } else if (rank.equals(Rank.CONVAR())) {result = Convarietas;
1788 } else if (rank.equals(Rank.SUBVARIETY())) {result = Subvariety;
1789 } else if (rank.equals(Rank.SUBFORM())) {result = Subform;
1790 } else if (rank.equals(Rank.SPECIALFORM())) {result = Forma_spec;
1791 } else if (rank.equals(Rank.INFRAGENERICTAXON())) {result = Taxa_infragen;
1792 } else if (rank.equals(Rank.INFRASPECIFICTAXON())) {result = Taxa_infraspec;
1793 } else {
1794 //TODO Exception
1795 logger.warn("Rank for Kingdom Plantae not yet supported in CDM: "+ rank.getLabel());
1796 return null;
1797 }
1798 } else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_FUNGI) {
1799 if (rank.equals(Rank.SECTION_BOTANY())) { result = Bot_Section;
1800 } else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Bot_Subsection;
1801 } else if (rank.equals(Rank.SUBVARIETY())) { result = Subvariety;
1802 } else if (rank.equals(Rank.SUBFORM())) { result = Subform;
1803 } else if (rank.equals(Rank.SPECIALFORM())) {result = Forma_spec;
1804 } else {
1805 //TODO Exception
1806 logger.warn("Rank for Kingdom Fungi not yet supported in CDM: "+ rank.getLabel());
1807 return null;
1808 }
1809 }else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_PROTOZOA) {
1810 if (rank.equals(Rank.INFRAKINGDOM())) { result = Infrakingdom;
1811 } else if (rank.equals(Rank.SUPERCLASS())) { result = Superclass;
1812 } else if (rank.equals(Rank.INFRACLASS())) { result = Infraclass;
1813 } else if (rank.equals(Rank.SUPERORDER())) { result = Superorder;
1814 } else if (rank.equals(Rank.INFRAORDER())) { result = Infraorder;
1815 } else if (rank.equals(Rank.SUPERFAMILY())) { result = Superfamily;
1816 } else if (rank.equals(Rank.SPECIALFORM())) {result = Forma_spec;
1817 } else {
1818 //TODO Exception
1819 logger.warn("Rank for Kingdom Protozoa not yet supported in CDM: "+ rank.getLabel());
1820 return null;
1821 }
1822 } else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_BACTERIA) {
1823 if (rank.equals(Rank.SUPERCLASS())) { result = Superclass;
1824 } else if (rank.equals(Rank.INFRACLASS())) { result = Infraclass;
1825 } else if (rank.equals(Rank.SUPERORDER())) { result = Superorder;
1826 } else if (rank.equals(Rank.INFRAORDER())) { result = Infraorder;
1827 } else if (rank.equals(Rank.SUPERFAMILY())) { result = Superfamily;
1828 } else {
1829 //TODO Exception
1830 logger.warn("Rank for Kingdom Bacteria not yet supported in CDM: "+ rank.getLabel());
1831 return null;
1832 }
1833 }else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_CHROMISTA) {
1834 if (rank.equals(Rank.INFRAKINGDOM())) { result = Infrakingdom;
1835 } else if (rank.equals(Rank.INFRAPHYLUM())) { result = Infraphylum;
1836 } else if (rank.equals(Rank.SUPERCLASS())) { result = Superclass;
1837 } else if (rank.equals(Rank.INFRACLASS())) { result = Infraclass;
1838 } else if (rank.equals(Rank.SUPERORDER())) { result = Superorder;
1839 } else if (rank.equals(Rank.INFRAORDER())) { result = Infraorder;
1840 } else if (rank.equals(Rank.SUPERFAMILY())) { result = Superfamily;
1841 } else if (rank.equals(Rank.SECTION_BOTANY())) { result = Bot_Section;
1842 } else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Bot_Subsection;
1843 } else if (rank.equals(Rank.SUBVARIETY())) { result = Subvariety;
1844 } else if (rank.equals(Rank.SPECIALFORM())) {result = Forma_spec;
1845 } else {
1846 //TODO Exception
1847 logger.warn("Rank for Kingdom Chromista not yet supported in CDM: "+ rank.getLabel());
1848 return null;
1849 }
1850 }else{
1851 //TODO Exception
1852 logger.warn("Kingdom not yet supported in CDM: "+ pesiKingdomId);
1853 return null;
1854 }
1855 return result;
1856 }
1857
1858 public static Integer nameTypeDesignationStatus2TypeDesignationStatusId(NameTypeDesignationStatus nameTypeDesignationStatus) {
1859 if (nameTypeDesignationStatus == null) {
1860 return null;
1861 }
1862 if (nameTypeDesignationStatus.equals(NameTypeDesignationStatus.ORIGINAL_DESIGNATION())) {
1863 return TYPE_BY_ORIGINAL_DESIGNATION;
1864 } else if (nameTypeDesignationStatus.equals(NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION())) {
1865 return TYPE_BY_SUBSEQUENT_DESIGNATION;
1866 } else if (nameTypeDesignationStatus.equals(NameTypeDesignationStatus.MONOTYPY())) {
1867 return TYPE_BY_MONOTYPY;
1868 } else {
1869 //TODO Figure out a way to handle this gracefully.
1870 logger.warn("Name Type Designation Status not yet supported in PESI: "+ nameTypeDesignationStatus.getLabel());
1871 return null;
1872 }
1873
1874 }
1875
1876 public static String nameTypeDesignationStatus2TypeDesignationStatusCache(NameTypeDesignationStatus nameTypeDesignationStatus) {
1877 if (nameTypeDesignationStatus == null) {
1878 return null;
1879 }
1880 if (nameTypeDesignationStatus.equals(NameTypeDesignationStatus.ORIGINAL_DESIGNATION())) {
1881 return TYPE_STR_BY_ORIGINAL_DESIGNATION;
1882 } else if (nameTypeDesignationStatus.equals(NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION())) {
1883 return TYPE_STR_BY_SUBSEQUENT_DESIGNATION;
1884 } else if (nameTypeDesignationStatus.equals(NameTypeDesignationStatus.MONOTYPY())) {
1885 return TYPE_STR_BY_MONOTYPY;
1886 } else {
1887 //TODO Figure out a way to handle this gracefully.
1888 logger.warn("Name Type Designation Status not yet supported in PESI: "+ nameTypeDesignationStatus.getLabel());
1889 return null;
1890 }
1891 }
1892
1893 /**
1894 * @see PesiTaxonExport#doPhaseUpdates(PesiExportState) for further transformation
1895 * @param taxonBase
1896 * @return
1897 */
1898 public static Integer taxonBase2statusFk (TaxonBase<?> taxonBase){
1899 if (taxonBase == null){
1900 return null;
1901 }
1902 if (taxonBase.isInstanceOf(Taxon.class)){
1903 Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
1904 Set<TaxonRelationship> rels = taxon.getRelationsFromThisTaxon();
1905 Set<TaxonNode> nodes = taxon.getTaxonNodes();
1906 if (!rels.isEmpty() && !nodes.isEmpty()){
1907 logger.warn("Taxon has relations and parent. This is not expected in E+M, but maybe possible in ERMS. Check if taxon status is correct.");
1908 }else if (rels.isEmpty() && nodes.isEmpty()){
1909 logger.warn("Taxon has neither relations nor parent. This is not expected. Check if taxon status is correct.");
1910 }
1911 if (!rels.isEmpty()){
1912 //we expect all rels to have same type, maybe not true
1913 UUID relTypeUuid = rels.iterator().next().getType().getUuid();
1914 //E+M
1915 if (TaxonRelationshipType.proParteUuids().contains(relTypeUuid)){
1916 return T_STATUS_PRO_PARTE_SYN;
1917 }else if (TaxonRelationshipType.partialUuids().contains(relTypeUuid)){
1918 return T_STATUS_PARTIAL_SYN;
1919 }else if (TaxonRelationshipType.misappliedNameUuids().contains(relTypeUuid)){
1920 return T_STATUS_SYNONYM; //no explicit MAN status exists in PESI
1921 }
1922 //ERMS
1923 else if (TaxonRelationshipType.pseudoTaxonUuids().contains(relTypeUuid)){
1924 return T_STATUS_SYNONYM;
1925 }
1926 }
1927 if (!nodes.isEmpty()){
1928 TaxonNode parentNode = nodes.iterator().next().getParent();
1929 if (parentNode.getTaxon() != null && !parentNode.getTaxon().isPublish()){
1930 if (parentNode.getTaxon().getUuid().equals(uuidTaxonValuelessEuroMed) ){
1931 return T_STATUS_NOT_ACCEPTED_VALUELESS;
1932 }
1933 }else{
1934 return T_STATUS_ACCEPTED;
1935 }
1936 }
1937 logger.error("Taxon status could not be defined. This should not happen: " + taxonBase.getTitleCache() );
1938 return T_STATUS_UNRESOLVED;
1939 }else if (taxonBase.isInstanceOf(Synonym.class)){
1940 Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
1941 if (taxonBase2statusFk(synonym.getAcceptedTaxon())== T_STATUS_NOT_ACCEPTED_VALUELESS ){
1942 return T_STATUS_NOT_ACCEPTED_VALUELESS;
1943 }else{
1944 return T_STATUS_SYNONYM;
1945 }
1946 }else{
1947 logger.warn("Unresolved taxon status.");
1948 return T_STATUS_UNRESOLVED;
1949 }
1950 //TODO
1951 // public static int T_STATUS_UNRESOLVED = 5;
1952 // public static int T_STATUS_ORPHANED = 6;
1953 }
1954
1955 // /**
1956 // *
1957 // * @param taxonBase
1958 // * @return
1959 // */
1960 // public static String taxonBase2statusCache (TaxonBase<?> taxonBase){
1961 // if (taxonBase == null){return null;}
1962 // if (taxonBase.isInstanceOf(Taxon.class)){
1963 // Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
1964 // if (taxon.getTaxonNodes().size() == 0){
1965 // return T_STATUS_STR_NOT_ACCEPTED;
1966 // }else{
1967 // return T_STATUS_STR_ACCEPTED;
1968 // }
1969 // }else if (taxonBase.isInstanceOf(Synonym.class)){
1970 // return T_STATUS_STR_SYNONYM;
1971 // }else{
1972 // logger.warn("Unknown ");
1973 // return T_STATUS_STR_UNRESOLVED;
1974 // }
1975 // //TODO
1976 // public static int T_STATUS_STR_PARTIAL_SYN = 3;
1977 // public static int T_STATUS_STR_PRO_PARTE_SYN = 4;
1978 // public static int T_STATUS_STR_UNRESOLVED = 5;
1979 // public static int T_STATUS_STR_ORPHANED = 6;
1980 // }
1981
1982 /**
1983 * Returns the {@link SourceCategory SourceCategory} representation of the given {@link ReferenceType ReferenceType} in PESI.
1984 * @param reference The {@link Reference Reference}.
1985 * @return The {@link SourceCategory SourceCategory} representation in PESI.
1986 */
1987 public static Integer reference2SourceCategoryFK(Reference reference) {
1988 if (reference == null){
1989 return null;
1990 } else if (reference.getType().equals(ReferenceType.Article)) {
1991 return REF_ARTICLE_IN_PERIODICAL;
1992 } else if (reference.getType().equals(ReferenceType.Book)) {
1993 return REF_BOOK;
1994 } else if (reference.getType().equals(ReferenceType.BookSection)) {
1995 return REF_PART_OF_OTHER;
1996 } else if (reference.getType().equals(ReferenceType.Section)) {
1997 return REF_PART_OF_OTHER;
1998 } else if (reference.getType().equals(ReferenceType.Database)) {
1999 return REF_DATABASE;
2000 } else if (reference.getType().equals(ReferenceType.WebPage)) {
2001 return REF_WEBSITE;
2002 } else if (reference.getType().equals(ReferenceType.CdDvd)) {
2003 return REF_NOT_APPLICABLE;
2004 } else if (reference.getType().equals(ReferenceType.Journal)) {
2005 return REF_JOURNAL;
2006 } else if (reference.getType().equals(ReferenceType.PrintSeries)) {
2007 return REF_PUBLICATION; //?
2008 } else if (reference.getType().equals(ReferenceType.Proceedings)) {
2009 return REF_PUBLICATION; //?
2010 } else if (reference.getType().equals(ReferenceType.Patent)) {
2011 return REF_NOT_APPLICABLE;
2012 } else if (reference.getType().equals(ReferenceType.PersonalCommunication)) {
2013 return REF_INFORMAL;
2014 } else if (reference.getType().equals(ReferenceType.Report)) {
2015 return REF_NOT_APPLICABLE;
2016 } else if (reference.getType().equals(ReferenceType.Thesis)) {
2017 return REF_NOT_APPLICABLE;
2018 } else if (reference.getType().equals(ReferenceType.Generic)) {
2019 if(reference.hasMarker(ErmsTransformer.uuidMarkerRefPublication, true)){
2020 return REF_PUBLICATION;
2021 }else if(reference.hasMarker(ErmsTransformer.uuidMarkerRefInformal, true)){
2022 return REF_INFORMAL;
2023 }else if(reference.hasMarker(ErmsTransformer.uuidMarkerRefTypeI, true)){
2024 logger.warn("ERMS ref type 'i' is not yet correctly matched to PESI");
2025 return REF_INFORMAL;
2026 }else{
2027 return REF_UNRESOLVED;
2028 }
2029 } else {
2030 logger.warn("Reference type not yet supported in PESI: "+ reference.getType());
2031 return null;
2032 }
2033 }
2034
2035 /**
2036 * Returns the {@link SourceCategoryCache SourceCategoryCache}.
2037 * @param reference The {@link Reference Reference}.
2038 * @return The {@link SourceCategoryCache SourceCategoryCache}.
2039 */
2040 public String getCacheByReference(Reference reference) {
2041 if (reference == null){
2042 return null;
2043 }else{
2044 return this.sourceCategoryCacheMap.get(reference2SourceCategoryFK(reference));
2045 }
2046 }
2047
2048 @Override
2049 public String getCacheByNomStatus(NomenclaturalStatusType status) {
2050 if (status == null){
2051 return null;
2052 }else{
2053 return this.nameStatusCacheMap.get(nomStatus2nomStatusFk(status));
2054 }
2055 }
2056
2057 public static Integer nomStatus2nomStatusFk (NomenclaturalStatusType status){
2058 if (status == null){
2059 return null;
2060 }
2061 if (status.equals(NomenclaturalStatusType.INVALID())) {return NAME_ST_NOM_INVAL;
2062 }else if (status.equals(NomenclaturalStatusType.ILLEGITIMATE())) {return NAME_ST_NOM_ILLEG;
2063 }else if (status.equals(NomenclaturalStatusType.NUDUM())) {return NAME_ST_NOM_NUD;
2064 }else if (status.equals(NomenclaturalStatusType.REJECTED())) {return NAME_ST_NOM_REJ;
2065 }else if (status.equals(NomenclaturalStatusType.REJECTED_PROP())) {return NAME_ST_NOM_REJ_PROP;
2066 }else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED())) {return NAME_ST_NOM_UTIQUE_REJ;
2067 }else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED_PROP())) {return NAME_ST_NOM_UTIQUE_REJ_PROP;
2068 }else if (status.equals(NomenclaturalStatusType.CONSERVED())) {return NAME_ST_NOM_CONS;
2069
2070 }else if (status.equals(NomenclaturalStatusType.CONSERVED_PROP())) {return NAME_ST_NOM_CONS_PROP;
2071 }else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED())) {return NAME_ST_ORTH_CONS;
2072 }else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP())) {return NAME_ST_ORTH_CONS_PROP;
2073 }else if (status.equals(NomenclaturalStatusType.SUPERFLUOUS())) {return NAME_ST_NOM_SUPERFL;
2074 }else if (status.equals(NomenclaturalStatusType.AMBIGUOUS())) {return NAME_ST_NOM_AMBIG;
2075 }else if (status.equals(NomenclaturalStatusType.PROVISIONAL())) {return NAME_ST_NOM_PROVIS;
2076 }else if (status.equals(NomenclaturalStatusType.DOUBTFUL())) {return NAME_ST_NOM_DUB;
2077 }else if (status.equals(NomenclaturalStatusType.NOVUM())) {return NAME_ST_NOM_NOV;
2078
2079 }else if (status.equals(NomenclaturalStatusType.CONFUSUM())) {return NAME_ST_NOM_CONFUS;
2080 }else if (status.equals(NomenclaturalStatusType.ALTERNATIVE())) {return NAME_ST_NOM_ALTERN;
2081 }else if (status.equals(NomenclaturalStatusType.COMBINATION_INVALID())) {return NAME_ST_COMB_INVAL;
2082 }else if (status.equals(NomenclaturalStatusType.LEGITIMATE())) {return NAME_ST_LEGITIMATE;
2083
2084 }else if (status.getUuid().equals(BerlinModelTransformer.uuidNomStatusCombIned)||
2085 //FIXME deduplicate COMB_NOV
2086 status.equals(NomenclaturalStatusType.COMB_NOV())) {return NAME_ST_COMB_INED;
2087 }else if (status.getUuid().equals(BerlinModelTransformer.uuidNomStatusNomOrthCons)) {return NAME_ST_NOM_AND_ORTH_CONS;
2088 }else if (status.getUuid().equals(BerlinModelTransformer.uuidNomStatusSpNovIned)) {return NAME_ST_SP_NOV_INED;
2089
2090
2091 // The following are non-existent in CDM
2092 // }else if (status.equals(NomenclaturalStatusType.)) {return NAME_ST_COMB_AND_STAT_INED;
2093 // }else if (status.equals(NomenclaturalStatusType.)) {return NAME_ST_NOM_NOV_INED;
2094 }else if (status.getUuid().equals(ErmsTransformer.uuidNomStatusAlternateRepresentation)) {return NAME_ST_ALTERNATE_REPRESENTATION;
2095 }else if (status.getUuid().equals(uuidNomStatusTemporaryName)) {return NAME_ST_TEMPORARY_NAME;
2096 }else if (status.getUuid().equals(ErmsTransformer.uuidNomStatusSpeciesInquirenda)) {return NAME_ST_SPECIES_INQUIRENDA;
2097
2098 //TODO
2099 }else {
2100 //TODO Exception
2101 logger.warn("NomStatus type not yet supported by PESI export: "+ status);
2102 return null;
2103 }
2104 }
2105
2106 /**
2107 * Returns the RelTaxonQualifierCache for a given taxonRelation.
2108 * @param relation
2109 * @return
2110 */
2111 public String getCacheByRelationshipType(RelationshipBase relation, NomenclaturalCode code){
2112 if (relation == null){
2113 return null;
2114 }else{
2115 String result;
2116 Integer key = taxonRelation2RelTaxonQualifierFk(relation);
2117 if (code.equals(NomenclaturalCode.ICZN)){
2118 result = this.taxRelZooQualifierCacheMap.get(key);
2119 if (result == null){
2120 result = this.taxRelQualifierCacheMap.get(key);
2121 }
2122 }else{
2123 result = this.taxRelQualifierCacheMap.get(key);
2124 }
2125 return result;
2126 }
2127 }
2128
2129 public String getCacheBySynonymType(Synonym synonym, NomenclaturalCode code){
2130 if (synonym == null){
2131 return null;
2132 }else{
2133 String result;
2134 Integer key = synonym2RelTaxonQualifierFk(synonym);
2135 if (code.equals(NomenclaturalCode.ICZN)){
2136 result = this.taxRelZooQualifierCacheMap.get(key);
2137 if (result == null){
2138 result = this.taxRelQualifierCacheMap.get(key);
2139 }
2140 }else{
2141 result = this.taxRelQualifierCacheMap.get(key);
2142 }
2143 return result;
2144 }
2145 }
2146
2147 public static Integer synonym2RelTaxonQualifierFk(Synonym synonym) {
2148 if (synonym == null || synonym.getType() == null){
2149 return null;
2150 }
2151 SynonymType type = synonym.getType();
2152 if (type.equals(SynonymType.SYNONYM_OF())) {return IS_SYNONYM_OF;
2153 }else if (type.equals(SynonymType.HOMOTYPIC_SYNONYM_OF())) {return IS_HOMOTYPIC_SYNONYM_OF;
2154 }else if (type.equals(SynonymType.HETEROTYPIC_SYNONYM_OF())) {return IS_HETEROTYPIC_SYNONYM_OF;
2155 }else if (type.equals(SynonymType.INFERRED_EPITHET_OF())) {return IS_INFERRED_EPITHET_FOR;
2156 }else if (type.equals(SynonymType.INFERRED_GENUS_OF())) {return IS_INFERRED_GENUS_FOR;
2157 }else if (type.equals(SynonymType.POTENTIAL_COMBINATION_OF())) {return IS_POTENTIAL_COMBINATION_FOR;
2158 }else if (type.equals(SynonymType.INFERRED_SYNONYM_OF())) {
2159 logger.warn("Inferred synonynm type not yet implemented. Should it realy exist?");
2160 return null;
2161 }else{
2162 logger.warn("Unhandled synonym type: " + type.getTitleCache());
2163 return null;
2164 }
2165 // return IS_PRO_PARTE_SYNONYM_OF;
2166 // return IS_PARTIAL_SYNONYM_OF;
2167 // return IS_PRO_PARTE_AND_HOMOTYPIC_SYNONYM_OF;
2168 // return IS_PARTIAL_AND_HOMOTYPIC_SYNONYM_OF;
2169 // return IS_PRO_PARTE_AND_HETEROTYPIC_SYNONYM_OF;
2170 // return IS_PARTIAL_AND_HETEROTYPIC_SYNONYM_OF;
2171 }
2172
2173
2174 /**
2175 * Returns the RelTaxonQualifierFk for a TaxonRelation.
2176 * @param relation
2177 * @return
2178 */
2179 public static Integer taxonRelation2RelTaxonQualifierFk(RelationshipBase<?,?,?> relation) {
2180 if (relation == null || relation.getType() == null) {
2181 return null;
2182 }
2183 RelationshipTermBase<?> type = relation.getType();
2184 if (type.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {
2185 return IS_MISAPPLIED_NAME_FOR;
2186 } else if (type.equals(TaxonRelationshipType.PRO_PARTE_MISAPPLIED_NAME_FOR())) {
2187 return IS_PRO_PARTE_MISAPPLIED_NAME_FOR;
2188 } else if (type.equals(TaxonRelationshipType.PRO_PARTE_SYNONYM_FOR())) {
2189 return IS_PRO_PARTE_SYNONYM_OF;
2190 } else if (type.equals(TaxonRelationshipType.PARTIAL_SYNONYM_FOR())) {
2191 return IS_PARTIAL_SYNONYM_OF;
2192 } else if (type.equals(NameRelationshipType.BASIONYM())) {
2193 return IS_BASIONYM_FOR;
2194 } else if (type.equals(NameRelationshipType.LATER_HOMONYM())) {
2195 return IS_LATER_HOMONYM_OF;
2196 } else if (type.equals(NameRelationshipType.REPLACED_SYNONYM())) {
2197 return IS_REPLACED_SYNONYM_FOR;
2198 } else if (type.equals(NameRelationshipType.VALIDATED_BY_NAME())) {
2199 return IS_VALIDATION_OF;
2200 } else if (type.equals(NameRelationshipType.LATER_VALIDATED_BY_NAME())) {
2201 return IS_LATER_VALIDATION_OF;
2202 } else if (type.equals(NameRelationshipType.CONSERVED_AGAINST())) {
2203 return IS_CONSERVED_AGAINST;
2204 } else if (type.equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())) {
2205 return IS_TREATED_AS_LATER_HOMONYM_OF;
2206 } else if (type.equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())) {
2207 return IS_ORTHOGRAPHIC_VARIANT_OF;
2208 } else if (type.equals(NameRelationshipType.ORIGINAL_SPELLING())) {
2209 return IS_ORIGINAL_SPELLING_FOR;
2210 } else if (type.equals(NameRelationshipType.BLOCKING_NAME_FOR())) {
2211 return IS_BLOCKING_NAME_FOR;
2212 } else if (type.equals(NameRelationshipType.ALTERNATIVE_NAME())) {
2213 return IS_ALTERNATIVE_NAME_FOR;
2214 } else if (type.equals(HybridRelationshipType.FEMALE_PARENT())) {
2215 return IS_FEMALE_PARENT_OF;
2216 } else if (type.equals(HybridRelationshipType.MALE_PARENT())) {
2217 return IS_MALE_PARENT_OF;
2218 } else if (type.equals(HybridRelationshipType.FIRST_PARENT())) {
2219 return IS_FIRST_PARENT_OF;
2220 } else if (type.equals(HybridRelationshipType.SECOND_PARENT())) {
2221 return IS_SECOND_PARENT_OF;
2222 } else if (type.getUuid().equals(TaxonRelationshipType.uuidSynonymOfTaxonRelationship)) {
2223 return IS_SYNONYM_OF;
2224 } else if (type.getUuid().equals(TaxonRelationshipType.uuidHeterotypicSynonymTaxonRelationship)) {
2225 return IS_HETEROTYPIC_SYNONYM_OF;
2226 } else if (type.getUuid().equals(TaxonRelationshipType.uuidHomotypicSynonymTaxonRelationship)) {
2227 return IS_HOMOTYPIC_SYNONYM_OF;
2228 } else {
2229 logger.warn("No equivalent RelationshipType found in datawarehouse for: " + type.getTitleCache());
2230 }
2231
2232 // The following have no equivalent attribute in CDM
2233 // IS_TYPE_OF
2234 // IS_CONSERVED_TYPE_OF
2235 // IS_REJECTED_TYPE_OF
2236 // IS_REJECTED_IN_FAVOUR_OF
2237 // HAS_SAME_TYPE_AS
2238 // IS_LECTOTYPE_OF
2239 // TYPE_NOT_DESIGNATED
2240
2241
2242 return null;
2243 }
2244 /**
2245 * FIXME still needed?
2246 * Returns the RelTaxonQualifierFk for a TaxonRelation.
2247 * @param relation
2248 * @return
2249 */
2250 public static Integer synonymrelation2RelTaxonQualifierFk(Synonym syn) {
2251 if (syn.getAcceptedTaxon() == null) {
2252 return null;
2253 }
2254 if (syn.getType().equals(SynonymType.HETEROTYPIC_SYNONYM_OF())){
2255 return IS_HETEROTYPIC_SYNONYM_OF;
2256 } else if (syn.getType().equals(SynonymType.HOMOTYPIC_SYNONYM_OF())){
2257 return IS_HOMOTYPIC_SYNONYM_OF;
2258 }else if (syn.getType().equals(SynonymType.INFERRED_EPITHET_OF())) {
2259 return IS_INFERRED_EPITHET_FOR;
2260 } else if (syn.getType().equals(SynonymType.INFERRED_GENUS_OF())) {
2261 return IS_INFERRED_GENUS_FOR;
2262 } else if (syn.getType().equals(SynonymType.POTENTIAL_COMBINATION_OF())) {
2263 return IS_POTENTIAL_COMBINATION_FOR;
2264 }
2265 return IS_SYNONYM_OF;
2266
2267 }
2268
2269 /**
2270 * Returns the StatusFk for a given StatusCache.
2271 * @param StatusCache
2272 * @return
2273 */
2274 public Integer statusCache2StatusFk(String StatusCache) {
2275 Integer result = null;
2276 if (StatusCache.equalsIgnoreCase("Checked by Taxonomic Editor: included in ERMS 1.1")) {
2277 return 0;
2278 } else if (StatusCache.equalsIgnoreCase("Added by Database Management Team")) {
2279 return 2;
2280 } else if (StatusCache.equalsIgnoreCase("Checked by Taxonomic Editor")) {
2281 return 3;
2282 } else if (StatusCache.equalsIgnoreCase("Edited by Database Management Team")) {
2283 return 4;
2284 } else {
2285 logger.error("StatusFk could not be determined. StatusCache unknown: " + StatusCache);
2286 }
2287
2288 return result;
2289 }
2290
2291 /**
2292 * Returns the FossilStatusFk for a given FossilStatusCache.
2293 * @param fossilStatusCache
2294 * @return
2295 */
2296 public Integer fossilStatusCache2FossilStatusFk(String fossilStatusCache) {
2297 Integer result = null;
2298 if (fossilStatusCache.equalsIgnoreCase("recent only")) {
2299 return 1;
2300 } else if (fossilStatusCache.equalsIgnoreCase("fossil only")) {
2301 return 2;
2302 } else if (fossilStatusCache.equalsIgnoreCase("recent + fossil")) {
2303 return 3;
2304 } else {
2305 logger.error("FossilStatusFk could not be determined. FossilStatusCache unknown: " + fossilStatusCache);
2306 }
2307
2308 return result;
2309 }
2310
2311 /**
2312 * Returns the NoteCategoryFk for a given UUID representing an ExtensionType.
2313 * @param uuid
2314 * @return
2315 */
2316 public static Integer getNoteCategoryFk(UUID uuid) {
2317 Integer result = null;
2318 if (uuid.equals(uuidExtTaxComment)) {
2319 result = 270;
2320 } else if (uuid.equals(uuidExtFauComment)) {
2321 result = 281;
2322 } else if (uuid.equals(uuidExtFauExtraCodes)) {
2323 result = 278;
2324 }
2325 return result;
2326 }
2327
2328 /**
2329 * Returns the NoteCategoryCache for a given UUID representing an ExtensionType.
2330 * @param uuid
2331 * @return
2332 */
2333 public static String getNoteCategoryCache(UUID uuid) {
2334 String result = null;
2335 if (uuid.equals(uuidExtTaxComment)) {
2336 result = "Taxonomy";
2337 } else if (uuid.equals(uuidExtFauComment)) {
2338 result = "Biology";
2339 } else if (uuid.equals(uuidExtFauExtraCodes)) {
2340 result = "Distribution";
2341 }
2342 return result;
2343 }
2344
2345 public static Integer getQualityStatusKeyBySource(EnumSet<PesiSource> sources, TaxonName taxonName) {
2346 if (sources.contains(PesiSource.EM)){
2347 return QUALITY_STATUS_ADD_BY_DBMT;
2348 }else if (sources.contains(PesiSource.ERMS)){
2349 Set<String> statusSet = getAllQualityStatus(taxonName);
2350 if (statusSet.size() > 1){
2351 logger.warn("ERMS TaxonName has more than 1 quality status: " + taxonName.getTitleCache() + "; lisd=" + taxonName.getLsid());
2352 }
2353 if (statusSet.contains("Checked by Taxonomic Editor: included in ERMS 1.1")){
2354 return QUALITY_STATUS_CHECKED_EDITOR_ERMS_1_1;
2355 }else if (statusSet.contains("Added by Database Management Team")){
2356 return QUALITY_STATUS_ADD_BY_DBMT;
2357 }else if (statusSet.contains("Checked by Taxonomic Editor")){
2358 return QUALITY_STATUS_CHECKED_EDITOR;
2359 }else if (statusSet.contains("Edited by Database Management Team")){
2360 return QUALITY_STATUS_EDITED_BY_DBMT;
2361 }else if (statusSet.contains("Added/edited by Thematic Editor")){
2362 return QUALITY_STATUS_THEMATIC_EDITOR;
2363 }else{
2364 logger.warn("Unknown ERMS quality status: " + statusSet.iterator().next() + " for taxon name " + taxonName.getTitleCache());
2365 return null;
2366 }
2367 }else{
2368 return null; // TODO needs to be implemented for others
2369 }
2370 }
2371
2372
2373 private static Set<String> getAllQualityStatus(TaxonName taxonName) {
2374 Set<String> result = new HashSet<>();
2375 for (TaxonBase<?> taxonBase : taxonName.getTaxonBases()){
2376 result.addAll(taxonBase.getExtensions(ErmsTransformer.uuidExtQualityStatus));
2377 }
2378 return result;
2379 }
2380
2381 @Override
2382 public String getQualityStatusCacheByKey(Integer qualityStatusId) throws UndefinedTransformerMethodException {
2383 if (qualityStatusId == null){
2384 return null;
2385 }else{
2386 return this.qualityStatusCacheMap.get(qualityStatusId);
2387 }
2388 }
2389
2390
2391 public Object getSourceUseCacheByKey(Integer sourceUseFk) {
2392 if (sourceUseFk == null){
2393 return null;
2394 }else{
2395 return this.sourceUseCacheMap.get(sourceUseFk);
2396 }
2397 }
2398
2399 //TODO create a reverse map
2400 public Integer getSourceUseKeyCacheByCache(String sourceUseCache) {
2401 if (sourceUseCache == null){
2402 return null;
2403 }else{
2404 for (Integer key: sourceUseCacheMap.keySet()){
2405 if (sourceUseCacheMap.get(key).equalsIgnoreCase(sourceUseCache)){
2406 return key;
2407 }
2408 }
2409 }
2410 return null;
2411 }
2412
2413 @Override
2414 public String getTaxonStatusCacheByKey(Integer taxonStatusId) throws UndefinedTransformerMethodException {
2415 if (taxonStatusId == null){
2416 return null;
2417 }else{
2418 return this.taxonStatusCacheMap.get(taxonStatusId);
2419 }
2420 }
2421
2422 public static String getOriginalDbBySources(EnumSet<PesiSource> sources) {
2423 String result = "";
2424 if (sources.contains(PesiSource.EM)){
2425 result = CdmUtils.concat(",", result, SOURCE_STR_EM);
2426 }
2427 if (sources.contains(PesiSource.FE)){
2428 result = CdmUtils.concat(",", result, SOURCE_STR_FE);
2429 }
2430 if (sources.contains(PesiSource.IF)){
2431 result = CdmUtils.concat(",", result, SOURCE_STR_IF);
2432 }
2433 if (sources.contains(PesiSource.ERMS)){
2434 result = CdmUtils.concat(",", result, SOURCE_STR_ERMS);
2435 }
2436
2437 return result;
2438 }
2439
2440 public static Integer pesiKingdomId(String str) {
2441 return pesiKingdomMap.get(str);
2442 }
2443 }