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Revision bd1bdb28

Added by Andreas Müller over 4 years ago

ref #1444 some changes due to upgrade to ERMS v2019

View differences:

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportRankMap.java
61 61
				NomenclaturalCode nc = ErmsTransformer.kingdomId2NomCode(kingdomId);
62 62

  
63 63
				Map<Integer, Rank> kingdomMap = makeKingdomMap(rankMap, rankId);
64
				rankName = rankName.replace("Forma", "Form").replace("Subforma", "Subform");
64
				rankName = rankName.replace("Forma", "Form").replace("Subforma", "Subform")
65
				        .replace("Phylum (Division)", "Phylum").replace("Subphylum (Subdivision)", "Subphylum");
66

  
65 67
				Rank rank = null;
66 68
				@SuppressWarnings("unchecked")
67 69
				OrderedTermVocabulary<Rank> voc = CdmBase.deproxy(Rank.GENUS().getVocabulary(), OrderedTermVocabulary.class);
......
90 92
                        }
91 93
                    }
92 94
					if (rank == null){
93
	                      logger.warn("Rank could not be defined: " + rankName + "; nomcode = " + nc + ", kingdom_id = " + kingdomId);
95
	                      logger.warn("Rank could not be defined: " + rankName + "; nomcode = " + nc + ", kingdom_id = " + kingdomId + ", rank_id = " + rankId);
94 96
					}
95 97
					kingdomMap.put(kingdomId, rank);
96 98
				}
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsReferenceImport.java
118 118
			ref = ReferenceFactory.newGeneric();
119 119
	        MarkerType markerType = getMarkerType(state, ErmsTransformer.uuidMarkerRefInformal, "Informal", "Informal", "e");
120 120
	        ref.addMarker(markerType, true);
121
		}else if (type.equalsIgnoreCase("i")){
122
			ref = ReferenceFactory.newGeneric();
123
	        MarkerType markerType = getMarkerType(state, ErmsTransformer.uuidMarkerRefTypeI, "Ref type i", "Ref type i", "i");
124
	        ref.addMarker(markerType, true);
125 121
		}else{
126 122
			ref = ReferenceFactory.newGeneric();
127 123
			logger.warn("Unknown reference type: " + type + ". Created generic instead.");
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTransformer.java
69 69
    public static final UUID uuidBalticProper = UUID.fromString("12ddfcad-bf8f-43d8-a772-15ae69d37b20");
70 70
    public static final UUID uuidBalearSea = UUID.fromString("478f30f0-01b1-4772-9d01-3a0a571f41c3");
71 71
    public static final UUID uuidBalticSea = UUID.fromString("0031cda2-4b27-49de-afa3-fdec75ee5060");
72
    public static final UUID uuidBarentsSea = UUID.fromString("b6fd9a4d-0ad0-4481-a0b4-5dd71c8fda8b");
72
    public static final UUID uuidBarentszSea = UUID.fromString("b6fd9a4d-0ad0-4481-a0b4-5dd71c8fda8b");
73 73
    public static final UUID uuidBelgianExclusiveEconomicZone = UUID.fromString("02138b0f-cee1-4c56-ae12-72a5b36839af");
74
    public static final UUID uuidBeltSea = UUID.fromString("780f4144-f157-45e8-ae42-cacb3ec369ba");
74
    public static final UUID uuidBaeltSea = UUID.fromString("780f4144-f157-45e8-ae42-cacb3ec369ba");
75 75
    public static final UUID uuidBiscayBay = UUID.fromString("36ffc01e-85a2-4f71-91fd-012d0b1eeff5");
76 76
    public static final UUID uuidBlackSea = UUID.fromString("1f110909-7462-4ee8-a7ff-9f976701dd1d");
77 77
    public static final UUID uuidBothnianSea = UUID.fromString("926f7fa3-b0a4-4763-85eb-4c3804a72333");
......
114 114
	public static final UUID uuidWaddenSea = UUID.fromString("ae0c4555-8e19-479d-8a4f-e1b62939c09b");
115 115
	public static final UUID uuidWhiteSea = UUID.fromString("bf14bfb6-8925-4696-911c-56d3e90d4491");
116 116

  
117

  
118
	public static final UUID uuidAfghanistan = UUID.fromString("9ecbc81b-9150-45b5-953d-1051cd519dd0");
117 119
	public static final UUID uuidAlboranSea = UUID.fromString("a4f1ef1e-0bda-4be0-95f9-59ed4f536fb6");
118 120
	public static final UUID uuidAlgeria = UUID.fromString("d254b5bb-e24c-4f79-88dd-80a75cd935db");
119 121
	public static final UUID uuidAngola = UUID.fromString("fdb74fd7-e6a1-48ff-8721-f1db6e0d93ee");
122
	public static final UUID uuidArcticOcean = UUID.fromString("4e68ddce-4472-4ae0-b6c3-406f39bf86ec");
120 123
	public static final UUID uuidAustralianExclusiveEconomicZone = UUID.fromString("de8f70b9-3cac-48d5-b456-5cd489df5c26");
121 124
	public static final UUID uuidAzoresExclusiveEconomicZone = UUID.fromString("e0297e2c-d28a-46aa-8b30-694148b0640d");
122 125
	public static final UUID uuidBahamas = UUID.fromString("3e7eb2e5-975b-433c-9dc0-106ba16fd6e4");
......
142 145
	public static final UUID uuidFrance = UUID.fromString("b7876595-230d-4ac8-bbcf-0a271221aeb0");
143 146
	public static final UUID uuidGhana = UUID.fromString("b550ba30-41b8-485a-a1de-ba79b4b6e152");
144 147
	public static final UUID uuidGreece = UUID.fromString("c004a689-048b-4541-9371-063bca1ab20e");
145
	public static final UUID uuidGreekExclusiveEconomicZone = UUID.fromString("6e587a2b-d681-46d3-bede-30411b0707a9");
148
	public static final UUID uuidGermany = UUID.fromString("55d23f99-c517-49ef-936b-3815c10b6303");
149
    public static final UUID uuidGreekExclusiveEconomicZone = UUID.fromString("6e587a2b-d681-46d3-bede-30411b0707a9");
146 150
	public static final UUID uuidGulfOfBothnia = UUID.fromString("e0126fd6-a163-4483-92e4-abe1a96ed025");
147 151
	public static final UUID uuidGulfOfFinland = UUID.fromString("d312ff30-18d0-4f8a-9c80-3a06772cefbb");
148 152
	public static final UUID uuidGulfOfGuinea = UUID.fromString("ea6f3983-64ad-46c4-832a-51bed6507d95");
......
162 166
	public static final UUID uuidMediterraneanSea_EasternBasin = UUID.fromString("a67dfa4d-4a96-403b-a64c-1e294826c2ed");
163 167
	public static final UUID uuidMediterraneanSea_WesternBasin = UUID.fromString("b3e81fa7-ee7a-45d2-965c-88020f9ee1ea");
164 168
	public static final UUID uuidMexico = UUID.fromString("a9be5a5c-99ec-4627-9892-104a0c175118");
169
	public static final UUID uuidMongolia = UUID.fromString("0385e6b1-4796-4e9f-8656-b6092c97c58f");
165 170
	public static final UUID uuidMorocco = UUID.fromString("4948e1ef-f61e-462f-9920-ab44c71ca2ae");
166 171
	public static final UUID uuidNetherlands = UUID.fromString("8d4152fb-bf29-4a24-a772-62ccb4a8c02f");
167 172
	public static final UUID uuidNewZealand = UUID.fromString("f3ff8497-00e0-4d45-9d14-eb80fea0fee0");
......
278 283
			case 2: return NomenclaturalCode.ICZN;  //Animalia
279 284
			case 3: return NomenclaturalCode.ICNAFP;  //Plantae
280 285
			case 4: return NomenclaturalCode.ICNAFP;  //Fungi
281
			case 5: return NomenclaturalCode.ICNAFP ;  //Protozoa  , not sure if correct, they have "subsp."
286
			case 5: return NomenclaturalCode.ICNAFP ;  //Protozoa, not sure if correct, they have "subsp."
282 287
			case 6: return NomenclaturalCode.ICNB ;  //Bacteria
283 288
			case 7: return NomenclaturalCode.ICNAFP;  //Chromista??, not sure if correct, they have "subsp."
284 289
			case 147415: return NomenclaturalCode.ICNB;  //Monera, it is only an alternative name for Bacteria and should not be handled as separate kingdom
285 290
			//-> formatting of infrageneric taxa and available ranks (rank table) let me assume that ICZN is most suitable
286
			//at the same time time formatting of subsp. (with marker!) behaves like ICNAFP so this is unclear
291
			//at the same time formatting of subsp. (with marker!) behaves like ICNAFP so this is unclear
287 292
			default: return null;
288 293
		}
289 294
	}
......
402 407
		}else if (guName.equalsIgnoreCase("Balear Sea")){ return uuidBalearSea;
403 408
		}else if (guName.equalsIgnoreCase("Baltic Proper")){ return uuidBalticProper;
404 409
		}else if (guName.equalsIgnoreCase("Baltic Sea")){ return uuidBalticSea;
405
		}else if (guName.equalsIgnoreCase("Barents Sea")){ return uuidBarentsSea;
410
		}else if (guName.equalsIgnoreCase("Barentsz Sea")){ return uuidBarentszSea;
406 411
		}else if (guName.equalsIgnoreCase("Belgian Exclusive Economic Zone")){ return uuidBelgianExclusiveEconomicZone;
407
		}else if (guName.equalsIgnoreCase("Belt Sea")
408
		        || guName.equalsIgnoreCase("Baelt Sea")){ return uuidBeltSea;
412
		}else if (guName.equalsIgnoreCase("Baelt Sea")){ return uuidBaeltSea;
409 413
		}else if (guName.equalsIgnoreCase("Biscay Bay")){ return uuidBiscayBay;
410 414
		}else if (guName.equalsIgnoreCase("Black Sea")){ return uuidBlackSea;
411 415
		}else if (guName.equalsIgnoreCase("Bothnian Sea")){ return uuidBothnianSea;
......
456 460
		}else if (guName.equalsIgnoreCase("Polish Exclusive Economic Zone")){ return uuidPolishExclusiveEconomicZone;
457 461
		}else if (guName.equalsIgnoreCase("Tyrrhenian Sea")){ return uuidTyrrhenianSea;
458 462

  
463
        }else if (guName.equalsIgnoreCase("Afghanistan")){ return uuidAfghanistan;
459 464
		}else if (guName.equalsIgnoreCase("Alboran Sea")){ return uuidAlboranSea;
460 465
		}else if (guName.equalsIgnoreCase("Algeria")){ return uuidAlgeria;
461 466
		}else if (guName.equalsIgnoreCase("Angola")){ return uuidAngola;
462
		}else if (guName.equalsIgnoreCase("Australian Exclusive Economic Zone")){ return uuidAustralianExclusiveEconomicZone;
467
		}else if (guName.equalsIgnoreCase("Arctic Ocean")){ return uuidArcticOcean;
468
        }else if (guName.equalsIgnoreCase("Australian Exclusive Economic Zone")){ return uuidAustralianExclusiveEconomicZone;
463 469
		}else if (guName.equalsIgnoreCase("Bahamas")){ return uuidBahamas;
464 470
		}else if (guName.equalsIgnoreCase("Balearic Sea")){ return uuidBalearicSea;
465 471
		}else if (guName.equalsIgnoreCase("Belgium")){ return uuidBelgium;
......
482 488
		}else if (guName.equalsIgnoreCase("France")){ return uuidFrance;
483 489
		}else if (guName.equalsIgnoreCase("Ghana")){ return uuidGhana;
484 490
		}else if (guName.equalsIgnoreCase("Greece")){ return uuidGreece;
485
		}else if (guName.equalsIgnoreCase("Gulf of Bothnia")){ return uuidGulfOfBothnia;
491
		}else if (guName.equalsIgnoreCase("Germany")){ return uuidGermany;
492
        }else if (guName.equalsIgnoreCase("Gulf of Bothnia")){ return uuidGulfOfBothnia;
486 493
		}else if (guName.equalsIgnoreCase("Gulf of Finland")){ return uuidGulfOfFinland;
487 494
		}else if (guName.equalsIgnoreCase("Gulf of Guinea")){ return uuidGulfOfGuinea;
488 495
		}else if (guName.equalsIgnoreCase("Gulf of Mexico")){ return uuidGulfOfMexico;
......
501 508
		}else if (guName.equalsIgnoreCase("Mediterranean Sea - Eastern Basin")){ return uuidMediterraneanSea_EasternBasin;
502 509
		}else if (guName.equalsIgnoreCase("Mediterranean Sea - Western Basin")){ return uuidMediterraneanSea_WesternBasin;
503 510
		}else if (guName.equalsIgnoreCase("Mexico")){ return uuidMexico;
504
		}else if (guName.equalsIgnoreCase("Morocco")){ return uuidMorocco;
511
		}else if (guName.equalsIgnoreCase("Mongolia")){ return uuidMongolia;
512
        }else if (guName.equalsIgnoreCase("Morocco")){ return uuidMorocco;
505 513
		}else if (guName.equalsIgnoreCase("Netherlands")){ return uuidNetherlands;
506 514
		}else if (guName.equalsIgnoreCase("New Zealand")){ return uuidNewZealand;
507 515
		}else if (guName.equalsIgnoreCase("New Zealand Exclusive Economic Zone")){ return uuidNewZealandExclusiveEconomicZone;
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java
538 538
	private static int AREA_NORTH_SEA = 151;
539 539
	private static int AREA_BALTIC_SEA = 152;
540 540
	private static int AREA_BLACK_SEA = 153;
541
	private static int AREA_BARENTS_SEA = 154;
541
	private static int AREA_BARENTSZ_SEA = 154;
542 542
	private static int AREA_CASPIAN_SEA = 155;
543 543
	private static int AREA_PORTUGUESE_EXCLUSIVE_ECONOMIC_ZONE = 156;
544 544
	private static int AREA_BELGIAN_EXCLUSIVE_ECONOMIC_ZONE = 157;
......
1298 1298
			else if (uuidArea.equals(ErmsTransformer.uuidBalticSea)) { return AREA_BALTIC_SEA; }
1299 1299
			else if (//(namedArea.getRepresentation(Language.DEFAULT()).getAbbreviatedLabel()).equals("BLS") ||   /carefull: NPE!
1300 1300
					(uuidArea.equals(ErmsTransformer.uuidBlackSea))) { return AREA_BLACK_SEA; } // abbreviated label missing
1301
			else if (uuidArea.equals(ErmsTransformer.uuidBarentsSea)) { return AREA_BARENTS_SEA; }
1301
			else if (uuidArea.equals(ErmsTransformer.uuidBarentszSea)) { return AREA_BARENTSZ_SEA; }
1302 1302
			else if (//(namedArea.getRepresentation(Language.DEFAULT()).getAbbreviatedLabel()).equals("CAS") ||   /carefull: NPE!
1303 1303
					(uuidArea.equals(ErmsTransformer.uuidCaspianSea))) { return AREA_CASPIAN_SEA; } // abbreviated label missing
1304 1304
			else if (uuidArea.equals(ErmsTransformer.uuidPortugueseExclusiveEconomicZone)) { return AREA_PORTUGUESE_EXCLUSIVE_ECONOMIC_ZONE; }
......
1323 1323
			else if (uuidArea.equals(ErmsTransformer.uuidSkagerrak)) { return AREA_SKAGERRAK; }
1324 1324
			else if (uuidArea.equals(ErmsTransformer.uuidTunisianExclusiveEconomicZone)) { return AREA_TUNISIAN_EXCLUSIVE_ECONOMIC_ZONE; }
1325 1325
			else if (uuidArea.equals(ErmsTransformer.uuidWaddenSea)) { return AREA_WADDEN_SEA; }
1326
			else if (uuidArea.equals(ErmsTransformer.uuidBeltSea)) { return AREA_BELT_SEA; }
1326
			else if (uuidArea.equals(ErmsTransformer.uuidBaeltSea)) { return AREA_BELT_SEA; }
1327 1327
			else if (uuidArea.equals(ErmsTransformer.uuidMarmaraSea)) { return AREA_MARMARA_SEA; }
1328 1328
			else if (uuidArea.equals(ErmsTransformer.uuidSeaofAzov)) { return AREA_SEA_OF_AZOV; }
1329 1329
			else if (uuidArea.equals(ErmsTransformer.uuidAegeanSea)) { return AREA_AEGEAN_SEA; }
......
1345 1345
			else if (uuidArea.equals(ErmsTransformer.uuidTurkishExclusiveEconomicZone)) { return AREA_TURKISH_EXCLUSIVE_ECONOMIC_ZONE; }
1346 1346
			else if (uuidArea.equals(ErmsTransformer.uuidDanishExclusiveEconomicZone)) { return AREA_DANISH_EXCLUSIVE_ECONOMIC_ZONE; }
1347 1347

  
1348
			else if (uuidArea.equals(ErmsTransformer.uuidAlboranSea)) { return 219; }
1348
			else if (uuidArea.equals(ErmsTransformer.uuidAfghanistan)) { return 297; }
1349
            else if (uuidArea.equals(ErmsTransformer.uuidAlboranSea)) { return 219; }
1349 1350
			else if (uuidArea.equals(ErmsTransformer.uuidAlgeria)) { return 220; }
1350 1351
			else if (uuidArea.equals(ErmsTransformer.uuidAngola)) { return 221; }
1351
			else if (uuidArea.equals(ErmsTransformer.uuidAustralianExclusiveEconomicZone)) { return 222; }
1352
			else if (uuidArea.equals(ErmsTransformer.uuidArcticOcean)) { return 296; }
1353
            else if (uuidArea.equals(ErmsTransformer.uuidAustralianExclusiveEconomicZone)) { return 222; }
1352 1354
			else if (uuidArea.equals(ErmsTransformer.uuidBahamas)) { return 223; }
1353 1355
			else if (uuidArea.equals(ErmsTransformer.uuidBalearicSea)) { return 224; }
1354 1356
			else if (uuidArea.equals(ErmsTransformer.uuidBelgium)) { return 225; }
......
1371 1373
			else if (uuidArea.equals(ErmsTransformer.uuidFrance)) { return 240; }
1372 1374
			else if (uuidArea.equals(ErmsTransformer.uuidGhana)) { return 241; }
1373 1375
			else if (uuidArea.equals(ErmsTransformer.uuidGreece)) { return 242; }
1374
			else if (uuidArea.equals(ErmsTransformer.uuidGreekExclusiveEconomicZone)) { return AREA_GREEK_EXCLUSIVE_ECONOMIC_ZONE; }
1376
			else if (uuidArea.equals(ErmsTransformer.uuidGermany)) { return 298; }
1377
            else if (uuidArea.equals(ErmsTransformer.uuidGreekExclusiveEconomicZone)) { return AREA_GREEK_EXCLUSIVE_ECONOMIC_ZONE; }
1375 1378
            else if (uuidArea.equals(ErmsTransformer.uuidGulfOfBothnia)) { return 243; }
1376 1379
			else if (uuidArea.equals(ErmsTransformer.uuidGulfOfFinland)) { return 244; }
1377 1380
			else if (uuidArea.equals(ErmsTransformer.uuidGulfOfGuinea)) { return 245; }
......
1390 1393
			else if (uuidArea.equals(ErmsTransformer.uuidMediterraneanSea_EasternBasin)) { return 258; }
1391 1394
			else if (uuidArea.equals(ErmsTransformer.uuidMediterraneanSea_WesternBasin)) { return 259; }
1392 1395
			else if (uuidArea.equals(ErmsTransformer.uuidMexico)) { return 260; }
1393
			else if (uuidArea.equals(ErmsTransformer.uuidMorocco)) { return 261; }
1396
			else if (uuidArea.equals(ErmsTransformer.uuidMongolia)) { return 299; }
1397
            else if (uuidArea.equals(ErmsTransformer.uuidMorocco)) { return 261; }
1394 1398
			else if (uuidArea.equals(ErmsTransformer.uuidNetherlands)) { return 262; }
1395 1399
			else if (uuidArea.equals(ErmsTransformer.uuidNewZealand)) { return 263; }
1396 1400
			else if (uuidArea.equals(ErmsTransformer.uuidNewZealandExclusiveEconomicZone)) { return 264; }

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