Revision 58cd368c
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 46 | 46 |
import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper; |
| 47 | 47 |
import eu.etaxonomy.cdm.io.common.mapping.out.ObjectChangeMapper; |
| 48 | 48 |
import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer; |
| 49 |
import eu.etaxonomy.cdm.model.common.Annotation; |
|
| 50 | 49 |
import eu.etaxonomy.cdm.model.common.AnnotationType; |
| 51 | 50 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 52 | 51 |
import eu.etaxonomy.cdm.model.common.Extension; |
| 53 | 52 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| 54 | 53 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
| 55 | 54 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 56 |
import eu.etaxonomy.cdm.model.common.Language; |
|
| 57 | 55 |
import eu.etaxonomy.cdm.model.common.Marker; |
| 58 | 56 |
import eu.etaxonomy.cdm.model.common.MarkerType; |
| 59 | 57 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
| ... | ... | |
| 309 | 307 |
} |
| 310 | 308 |
|
| 311 | 309 |
//TODO switch on again, leads to some warnings in ERMS for taxa of not correctly handled kingdoms |
| 312 |
// validatePhaseOne(taxon, nvn);
|
|
| 310 |
validatePhaseOne(taxon, nvn); |
|
| 313 | 311 |
} |
| 314 | 312 |
|
| 315 | 313 |
// Commit transaction |
| ... | ... | |
| 336 | 334 |
private void validatePhaseOne(TaxonBase<?> taxon, TaxonName taxonName) {
|
| 337 | 335 |
|
| 338 | 336 |
// Check whether some rules are violated |
| 339 |
NomenclaturalCode nomenclaturalCode = taxonName.getNameType(); |
|
| 340 | 337 |
String genusOrUninomial = taxonName.getGenusOrUninomial(); |
| 341 | 338 |
String specificEpithet = taxonName.getSpecificEpithet(); |
| 342 | 339 |
String infraSpecificEpithet = taxonName.getInfraSpecificEpithet(); |
| 343 | 340 |
String infraGenericEpithet = taxonName.getInfraGenericEpithet(); |
| 344 |
Integer rankFk = getRankFk(taxonName, nomenclaturalCode);
|
|
| 341 |
Rank rank = taxonName.getRank();
|
|
| 345 | 342 |
|
| 346 |
if (rankFk == null) {
|
|
| 347 |
logger.error("Rank was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
| 348 |
} else {
|
|
| 343 |
//as kingdomFk can not be defined in Phase 01 the below code was switched to use the CDM rank. This may be changed if we move validation to Phase03 or later |
|
| 344 |
// Integer rankFk = getRankFk(taxonName, taxonName.getNameType()); |
|
| 345 |
// if (rankFk == null) {
|
|
| 346 |
// logger.error("Rank was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
| 347 |
// } else {
|
|
| 349 | 348 |
|
| 350 | 349 |
// Check whether infraGenericEpithet is set correctly |
| 351 | 350 |
// 1. Childs of an accepted taxon of rank subgenus that are accepted taxa of rank species have to have an infraGenericEpithet |
| ... | ... | |
| 370 | 369 |
} |
| 371 | 370 |
} |
| 372 | 371 |
|
| 373 |
if (infraGenericEpithet == null && rankFk.intValue() == 190) {
|
|
| 374 |
logger.warn("InfraGenericEpithet was not determined although it should exist for rank 190: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
| 372 |
if (infraGenericEpithet == null && rank.isInfraGenericButNotSpeciesGroup()) {
|
|
| 373 |
logger.warn("InfraGenericEpithet was not determined although it should exist for infra generic names: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
| 375 | 374 |
} |
| 376 |
if (specificEpithet != null && rankFk.intValue() < 216) {
|
|
| 377 |
logger.warn("SpecificEpithet was determined for rank " + rankFk + " although it should only exist for ranks higher or equal to 220: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 375 |
if (specificEpithet != null && (rank.isInfraGenericButNotSpeciesGroup()||rank.isGenus()||rank.isSupraGeneric())) {
|
|
| 376 |
logger.warn("SpecificEpithet was determined for rank " + rank.getTitleCache() + " although it should only exist for species aggregates, species or infraspecific taxa: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 378 | 377 |
} |
| 379 |
if (infraSpecificEpithet != null && rankFk.intValue() < 225) {
|
|
| 380 |
String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rankFk + " although it should only exist for ranks higher or equal to 230: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";
|
|
| 378 |
if (infraSpecificEpithet != null && !rank.isInfraSpecific()) {
|
|
| 379 |
String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rank.getTitleCache() + " although it should only exist for rank species and higher: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";
|
|
| 381 | 380 |
if (StringUtils.isNotBlank(infraSpecificEpithet)){
|
| 382 | 381 |
logger.warn(message); |
| 383 | 382 |
}else{
|
| 384 | 383 |
logger.warn(message); |
| 385 | 384 |
} |
| 386 | 385 |
} |
| 387 |
} |
|
| 386 |
// }
|
|
| 388 | 387 |
if (infraSpecificEpithet != null && specificEpithet == null) {
|
| 389 | 388 |
logger.warn("An infraSpecificEpithet was determined, but a specificEpithet was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
| 390 | 389 |
} |
| ... | ... | |
| 508 | 507 |
doCount(count++, modCount, pluralString); |
| 509 | 508 |
Integer typeNameFk = getTypeNameFk(taxonName, state); |
| 510 | 509 |
Integer kingdomFk = findKingdomIdFromTreeIndex(taxon, state); |
| 511 |
// PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode); |
|
| 512 |
|
|
| 513 |
//TODO why are expertFks needed? (Andreas M.) |
|
| 514 |
// if (expertFk != null || speciesExpertFk != null) {
|
|
| 515 |
NomenclaturalCode nomCode = taxonName.getNameType(); |
|
| 516 |
//is there a reason why we do pass nomCode separately? Before nomCode was class variable, but not clear why and when it was set |
|
| 517 |
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, nomCode, state.getDbId(taxon), |
|
| 518 |
typeNameFk, kingdomFk, state); |
|
| 519 |
// } |
|
| 510 |
|
|
| 511 |
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, state.getDbId(taxon), |
|
| 512 |
typeNameFk, kingdomFk, state); |
|
| 520 | 513 |
} |
| 521 | 514 |
|
| 522 | 515 |
// Commit transaction |
| ... | ... | |
| 712 | 705 |
// Save Rank Data and KingdomFk for inferred synonyms |
| 713 | 706 |
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
| 714 | 707 |
TaxonName taxonName = inferredSynonymsDataToBeSaved.get(taxonFk); |
| 715 |
NomenclaturalCode nomCode = taxonName.getNameType(); //nomCode was class variable before, not sure if this was important |
|
| 716 |
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomCode, taxonFk, kingdomFk, state); |
|
| 708 |
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), taxonFk, kingdomFk, state); |
|
| 717 | 709 |
} |
| 718 | 710 |
|
| 719 | 711 |
// Start transaction |
| ... | ... | |
| 743 | 735 |
// Save Rank Data and KingdomFk for inferred synonyms |
| 744 | 736 |
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
| 745 | 737 |
TaxonName taxonName = inferredSynonymsDataToBeSaved.get(taxonFk); |
| 746 |
NomenclaturalCode nomCode = taxonName.getNameType(); //nomCode was class variable before, not sure if this was important |
|
| 747 |
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomCode, taxonFk, kingdomFk, state); |
|
| 738 |
invokeRankDataAndKingdomFk(taxonName, taxonFk, kingdomFk, state); |
|
| 748 | 739 |
} |
| 749 | 740 |
|
| 750 | 741 |
// Start transaction |
| ... | ... | |
| 1057 | 1048 |
* @param kindomFk The KingdomFk. |
| 1058 | 1049 |
* @return Whether save was successful or not. |
| 1059 | 1050 |
*/ |
| 1060 |
private boolean invokeRankDataAndKingdomFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode, Integer taxonFk, Integer kingdomFk, PesiExportState state) {
|
|
| 1061 |
try {
|
|
| 1062 |
Integer rankFk = getRankFk(taxonName, nomenclaturalCode); |
|
| 1051 |
private boolean invokeRankDataAndKingdomFk(TaxonName taxonName, |
|
| 1052 |
Integer taxonFk, Integer kingdomFk, PesiExportState state) {
|
|
| 1053 |
|
|
| 1054 |
try {
|
|
| 1055 |
Integer rankFk = getRankFk(taxonName, kingdomFk); |
|
| 1063 | 1056 |
if (rankFk != null) {
|
| 1064 | 1057 |
rankUpdateStmt.setInt(1, rankFk); |
| 1065 | 1058 |
} else {
|
| 1066 | 1059 |
rankUpdateStmt.setObject(1, null); |
| 1067 | 1060 |
} |
| 1068 | 1061 |
|
| 1069 |
String rankCache = getRankCache(taxonName, nomenclaturalCode, state);
|
|
| 1062 |
String rankCache = getRankCache(taxonName, kingdomFk, state);
|
|
| 1070 | 1063 |
if (rankCache != null) {
|
| 1071 | 1064 |
rankUpdateStmt.setString(2, rankCache); |
| 1072 | 1065 |
} else {
|
| ... | ... | |
| 1107 | 1100 |
* @param speciesExpertFk The SpeciesExpertFk. |
| 1108 | 1101 |
* @return Whether save was successful or not. |
| 1109 | 1102 |
*/ |
| 1110 |
private boolean invokeRankDataAndTypeNameFkAndKingdomFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode,
|
|
| 1103 |
private boolean invokeRankDataAndTypeNameFkAndKingdomFk(TaxonName taxonName, |
|
| 1111 | 1104 |
Integer taxonFk, Integer typeNameFk, Integer kingdomFk, PesiExportState state) {
|
| 1112 | 1105 |
|
| 1106 |
NomenclaturalCode nomenclaturalCodes = taxonName.getNameType(); |
|
| 1107 |
|
|
| 1113 | 1108 |
Integer rankFk = null; |
| 1114 | 1109 |
try {
|
| 1115 | 1110 |
int index = 1; |
| 1116 |
rankFk = getRankFk(taxonName, nomenclaturalCode);
|
|
| 1111 |
rankFk = getRankFk(taxonName, kingdomFk);
|
|
| 1117 | 1112 |
if (rankFk != null) {
|
| 1118 | 1113 |
rankTypeExpertsUpdateStmt.setInt(index++, rankFk); |
| 1119 | 1114 |
} else {
|
| 1120 | 1115 |
rankTypeExpertsUpdateStmt.setObject(index++, null); |
| 1121 | 1116 |
} |
| 1122 | 1117 |
|
| 1123 |
String rankCache = getRankCache(taxonName, nomenclaturalCode, state);
|
|
| 1118 |
String rankCache = getRankCache(taxonName, kingdomFk, state);
|
|
| 1124 | 1119 |
if (rankCache != null) {
|
| 1125 | 1120 |
rankTypeExpertsUpdateStmt.setString(index++, rankCache); |
| 1126 | 1121 |
} else {
|
| ... | ... | |
| 1191 | 1186 |
return true; |
| 1192 | 1187 |
} |
| 1193 | 1188 |
|
| 1194 |
/** |
|
| 1195 |
* Returns the rankFk for the taxon name based on the names nomenclatural code. |
|
| 1196 |
* You may not use this method for kingdoms other then Animalia, Plantae and Bacteria. |
|
| 1197 |
* @param taxonName |
|
| 1198 |
* @return |
|
| 1199 |
*/ |
|
| 1200 |
@SuppressWarnings("unused") //used by mapper
|
|
| 1201 |
private static Integer getRankFk(TaxonName taxonName) {
|
|
| 1202 |
return getRankFk(taxonName, taxonName.getNameType()); |
|
| 1189 |
private static Integer getRankFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode) {
|
|
| 1190 |
Integer kingdomId = PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
|
| 1191 |
return getRankFk(taxonName, kingdomId); |
|
| 1203 | 1192 |
} |
| 1204 | 1193 |
|
| 1205 | 1194 |
/** |
| ... | ... | |
| 1209 | 1198 |
* @return The <code>RankFk</code> attribute. |
| 1210 | 1199 |
* @see MethodMapper |
| 1211 | 1200 |
*/ |
| 1212 |
private static Integer getRankFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode) {
|
|
| 1201 |
private static Integer getRankFk(TaxonName taxonName, Integer kingdomId) {
|
|
| 1213 | 1202 |
Integer result = null; |
| 1214 | 1203 |
try {
|
| 1215 |
if (nomenclaturalCode != null) {
|
|
| 1216 |
if (taxonName != null) {
|
|
| 1217 |
if (taxonName.getRank() == null) {
|
|
| 1218 |
logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1219 |
} else {
|
|
| 1220 |
result = PesiTransformer.rank2RankId(taxonName.getRank(), PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode)); |
|
| 1221 |
} |
|
| 1222 |
if (result == null) {
|
|
| 1223 |
logger.warn("Rank could not be determined for PESI-Kingdom-Id " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode) + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1224 |
} |
|
| 1204 |
if (taxonName != null) {
|
|
| 1205 |
if (taxonName.getRank() == null) {
|
|
| 1206 |
logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1207 |
} else {
|
|
| 1208 |
result = PesiTransformer.rank2RankId(taxonName.getRank(), kingdomId); |
|
| 1209 |
} |
|
| 1210 |
if (result == null) {
|
|
| 1211 |
logger.warn("Rank could not be determined for PESI-Kingdom-Id " + kingdomId + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
| 1225 | 1212 |
} |
| 1226 | 1213 |
} |
| 1227 | 1214 |
} catch (Exception e) {
|
| ... | ... | |
| 1231 | 1218 |
} |
| 1232 | 1219 |
|
| 1233 | 1220 |
private static String getRankCache(TaxonName taxonName, PesiExportState state) {
|
| 1234 |
return getRankCache(taxonName, taxonName.getNameType(), state); |
|
| 1221 |
List<TaxonNode> nodes = getTaxonNodes(taxonName); |
|
| 1222 |
Integer kingdomId = findKingdomIdFromTreeIndex(nodes.iterator().next().getTaxon(), state); |
|
| 1223 |
return getRankCache(taxonName, kingdomId, state); |
|
| 1235 | 1224 |
} |
| 1236 | 1225 |
|
| 1237 | 1226 |
|
| ... | ... | |
| 1243 | 1232 |
* @return The <code>RankCache</code> attribute. |
| 1244 | 1233 |
* @see MethodMapper |
| 1245 | 1234 |
*/ |
| 1246 |
private static String getRankCache(TaxonName taxonName, NomenclaturalCode nomenclaturalCode, PesiExportState state) {
|
|
| 1247 |
List<TaxonNode> nodes = getTaxonNodes(taxonName); |
|
| 1235 |
private static String getRankCache(TaxonName taxonName, Integer kingdomFk, PesiExportState state) {
|
|
| 1248 | 1236 |
if (Rank.DOMAIN().equals(taxonName.getRank())){
|
| 1249 | 1237 |
return state.getTransformer().getCacheByRankAndKingdom(Rank.DOMAIN(), null); |
| 1250 |
}else if (!nodes.isEmpty()) {
|
|
| 1251 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), findKingdomIdFromTreeIndex(nodes.iterator().next().getTaxon(), state)); //PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode));
|
|
| 1252 |
}else if (nomenclaturalCode != null){
|
|
| 1253 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode));
|
|
| 1238 |
}else if (kingdomFk != null) {
|
|
| 1239 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), kingdomFk);
|
|
| 1240 |
}else if (taxonName.getNameType() != null){
|
|
| 1241 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenclaturalCode2Kingdom(taxonName.getNameType()));
|
|
| 1254 | 1242 |
}else{
|
| 1255 |
logger.warn("No nomenclatural code defined for name " + taxonName.getUuid());
|
|
| 1243 |
logger.warn("No kingdom ID could be defined for name " + taxonName.getUuid());
|
|
| 1256 | 1244 |
return null; |
| 1257 | 1245 |
} |
| 1258 | 1246 |
} |
Also available in: Unified diff
ref #8509 use kingdomId to define rank for PESI export