Revision 1a0cbb31
Added by Andreas Müller about 16 years ago
| .gitattributes | ||
|---|---|---|
| 46 | 46 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelReferenceIO.java -text |
| 47 | 47 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonIO.java -text |
| 48 | 48 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonNameIO.java -text |
| 49 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonNameRelationIO.java -text |
|
| 50 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonRelationIO.java -text |
|
| 49 | 51 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTransformer.java -text |
| 50 | 52 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTypesIO.java -text |
| 51 | 53 |
cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/CdmBooleanMapper.java -text |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelImport.java | ||
|---|---|---|
| 7 | 7 |
|
| 8 | 8 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
| 9 | 9 |
import eu.etaxonomy.cdm.api.service.IService; |
| 10 |
import eu.etaxonomy.cdm.database.DataSourceNotFoundException; |
|
| 11 | 10 |
import eu.etaxonomy.cdm.io.common.MapWrapper; |
| 12 | 11 |
import eu.etaxonomy.cdm.io.common.Source; |
| 13 | 12 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 14 |
import eu.etaxonomy.cdm.model.common.init.TermNotFoundException; |
|
| 15 | 13 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 16 | 14 |
import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
| 17 | 15 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 81 | 79 |
|
| 82 | 80 |
//check RelNames |
| 83 | 81 |
if(bmiConfig.isDoRelNames()){
|
| 84 |
result &= BerlinModelTaxonNameIO.checkRelations(bmiConfig);
|
|
| 82 |
result &= BerlinModelTaxonNameRelationIO.check(bmiConfig);
|
|
| 85 | 83 |
} |
| 86 | 84 |
|
| 87 | 85 |
//check nameFacts |
| ... | ... | |
| 106 | 104 |
|
| 107 | 105 |
//check RelPTaxa |
| 108 | 106 |
if(bmiConfig.isDoRelTaxa()){
|
| 109 |
result &= BerlinModelTaxonIO.checkRelations(bmiConfig);
|
|
| 107 |
result &= BerlinModelTaxonRelationIO.check(bmiConfig);
|
|
| 110 | 108 |
} |
| 111 | 109 |
|
| 112 | 110 |
//check Facts |
| ... | ... | |
| 184 | 182 |
|
| 185 | 183 |
//make and save RelNames |
| 186 | 184 |
if(bmiConfig.isDoRelNames()){
|
| 187 |
if (! BerlinModelTaxonNameIO.invokeRelations(bmiConfig, cdmApp, taxonNameStore, referenceStore)){
|
|
| 185 |
if (! BerlinModelTaxonNameRelationIO.invoke(bmiConfig, cdmApp, taxonNameStore, referenceStore)){
|
|
| 188 | 186 |
return false; |
| 189 | 187 |
} |
| 190 | 188 |
}else{
|
| ... | ... | |
| 231 | 229 |
|
| 232 | 230 |
//make and save RelPTaxa |
| 233 | 231 |
if(bmiConfig.isDoRelTaxa()){
|
| 234 |
if (! BerlinModelTaxonIO.invokeRelations(bmiConfig, cdmApp, taxonStore, referenceStore)){
|
|
| 232 |
if (! BerlinModelTaxonRelationIO.invoke(bmiConfig, cdmApp, taxonStore, referenceStore)){
|
|
| 235 | 233 |
return false; |
| 236 | 234 |
} |
| 237 | 235 |
}else{
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonIO.java | ||
|---|---|---|
| 43 | 43 |
return result; |
| 44 | 44 |
} |
| 45 | 45 |
|
| 46 |
public static boolean checkRelations(BerlinModelImportConfigurator bmiConfig){
|
|
| 47 |
boolean result = true; |
|
| 48 |
logger.warn("Checking for TaxonRelations not yet fully implemented");
|
|
| 49 |
result &= checkTaxonStatus(bmiConfig); |
|
| 50 |
//result &= checkArticlesWithoutJournal(bmiConfig); |
|
| 51 |
|
|
| 52 |
return result; |
|
| 53 |
} |
|
| 54 |
|
|
| 55 |
private static boolean checkTaxonStatus(BerlinModelImportConfigurator bmiConfig){
|
|
| 56 |
try {
|
|
| 57 |
boolean result = true; |
|
| 58 |
Source source = bmiConfig.getSource(); |
|
| 59 |
String strQueryPartOfJournal = " SELECT RelPTaxon.RelQualifierFk, RelPTaxon.relPTaxonId, PTaxon.PTNameFk, PTaxon.PTRefFk, PTaxon_1.PTNameFk AS Expr1, PTaxon.RIdentifier, PTaxon_1.RIdentifier AS Expr3, Name.FullNameCache " + |
|
| 60 |
" FROM RelPTaxon " + |
|
| 61 |
" INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " + |
|
| 62 |
" INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk " + |
|
| 63 |
" INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " + |
|
| 64 |
" WHERE (dbo.PTaxon.StatusFk = 1) AND ((RelPTaxon.RelQualifierFk = 7) OR (RelPTaxon.RelQualifierFk = 6) OR (RelPTaxon.RelQualifierFk = 2)) "; |
|
| 65 |
ResultSet rs = source.getResultSet(strQueryPartOfJournal); |
|
| 66 |
boolean firstRow = true; |
|
| 67 |
int i = 0; |
|
| 68 |
while (rs.next()){
|
|
| 69 |
i++; |
|
| 70 |
if (firstRow){
|
|
| 71 |
System.out.println("========================================================");
|
|
| 72 |
logger.warn("There are taxa that have a 'is synonym of' - relationship but having taxon status 'accepted'!");
|
|
| 73 |
System.out.println("========================================================");
|
|
| 74 |
} |
|
| 75 |
int rIdentifier = rs.getInt("RIdentifier");
|
|
| 76 |
int nameFk = rs.getInt("PTNameFk");
|
|
| 77 |
int refFk = rs.getInt("PTRefFk");
|
|
| 78 |
int relPTaxonId = rs.getInt("relPTaxonId");
|
|
| 79 |
String taxonName = rs.getString("FullNameCache");
|
|
| 80 |
|
|
| 81 |
System.out.println("RIdentifier:" + rIdentifier + "\n name: " + nameFk +
|
|
| 82 |
"\n taxonName: " + taxonName + "\n refId: " + refFk + "\n RelPTaxonId: " + relPTaxonId ); |
|
| 83 |
result = firstRow = false; |
|
| 84 |
} |
|
| 85 |
if (i > 0){
|
|
| 86 |
System.out.println(" ");
|
|
| 87 |
} |
|
| 88 |
|
|
| 89 |
return result; |
|
| 90 |
} catch (SQLException e) {
|
|
| 91 |
e.printStackTrace(); |
|
| 92 |
return false; |
|
| 93 |
} |
|
| 94 |
} |
|
| 95 |
|
|
| 96 |
|
|
| 97 | 46 |
public static boolean invoke(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp, |
| 98 | 47 |
MapWrapper<TaxonBase> taxonMap, MapWrapper<TaxonNameBase> taxonNameMap, MapWrapper<ReferenceBase> referenceMap, MapWrapper<ReferenceBase> nomRefMap){
|
| 99 | 48 |
Source source = bmiConfig.getSource(); |
| ... | ... | |
| 103 | 52 |
logger.info("start makeTaxa ...");
|
| 104 | 53 |
|
| 105 | 54 |
ITaxonService taxonService = cdmApp.getTaxonService(); |
| 106 |
boolean delete = bmiConfig.isDeleteAll(); |
|
| 107 | 55 |
|
| 108 | 56 |
try {
|
| 109 | 57 |
//get data from database |
| ... | ... | |
| 208 | 156 |
|
| 209 | 157 |
} |
| 210 | 158 |
|
| 211 |
|
|
| 212 |
public static boolean invokeRelations(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp, |
|
| 213 |
MapWrapper<TaxonBase> taxonMap, MapWrapper<ReferenceBase> referenceMap){
|
|
| 214 |
|
|
| 215 |
Set<TaxonBase> taxonStore = new HashSet<TaxonBase>(); |
|
| 216 |
Source source = bmiConfig.getSource(); |
|
| 217 |
String dbAttrName; |
|
| 218 |
String cdmAttrName; |
|
| 219 |
|
|
| 220 |
logger.info("start makeTaxonRelationships ...");
|
|
| 221 |
|
|
| 222 |
ITaxonService taxonService = cdmApp.getTaxonService(); |
|
| 223 |
boolean delete = bmiConfig.isDeleteAll(); |
|
| 224 |
|
|
| 225 |
try {
|
|
| 226 |
//get data from database |
|
| 227 |
String strQuery = |
|
| 228 |
" SELECT RelPTaxon.*, FromTaxon.RIdentifier as taxon1Id, ToTaxon.RIdentifier as taxon2Id " + |
|
| 229 |
" FROM PTaxon as FromTaxon INNER JOIN " + |
|
| 230 |
" RelPTaxon ON FromTaxon.PTNameFk = RelPTaxon.PTNameFk1 AND FromTaxon.PTRefFk = RelPTaxon.PTRefFk1 INNER JOIN " + |
|
| 231 |
" PTaxon AS ToTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk "+ |
|
| 232 |
" WHERE (1=1)"; |
|
| 233 |
ResultSet rs = source.getResultSet(strQuery) ; |
|
| 234 |
|
|
| 235 |
int i = 0; |
|
| 236 |
//for each reference |
|
| 237 |
while (rs.next()){
|
|
| 238 |
|
|
| 239 |
if ((i++ % modCount) == 0){ logger.info("RelPTaxa handled: " + (i-1));}
|
|
| 240 |
|
|
| 241 |
int relPTaxonId = rs.getInt("RelPTaxonId");
|
|
| 242 |
int taxon1Id = rs.getInt("taxon1Id");
|
|
| 243 |
int taxon2Id = rs.getInt("taxon2Id");
|
|
| 244 |
int relRefFk = rs.getInt("relRefFk");
|
|
| 245 |
int relQualifierFk = rs.getInt("relQualifierFk");
|
|
| 246 |
|
|
| 247 |
TaxonBase taxon1 = taxonMap.get(taxon1Id); |
|
| 248 |
TaxonBase taxon2 = taxonMap.get(taxon2Id); |
|
| 249 |
|
|
| 250 |
//TODO |
|
| 251 |
ReferenceBase citation = null; |
|
| 252 |
String microcitation = null; |
|
| 253 |
|
|
| 254 |
if (taxon2 != null && taxon1 != null){
|
|
| 255 |
if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){
|
|
| 256 |
((Taxon)taxon2).addTaxonomicChild((Taxon)taxon1, citation, microcitation); |
|
| 257 |
}else if (relQualifierFk == TAX_REL_IS_SYNONYM_OF){
|
|
| 258 |
((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.SYNONYM_OF()); |
|
| 259 |
}else if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF){
|
|
| 260 |
if (taxon1 instanceof Synonym){
|
|
| 261 |
((Taxon)taxon2).addHomotypicSynonym((Synonym)taxon1, citation, microcitation); |
|
| 262 |
}else{
|
|
| 263 |
logger.error("Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Synonym");
|
|
| 264 |
} |
|
| 265 |
}else if (relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
|
|
| 266 |
if (Synonym.class.isAssignableFrom(taxon1.getClass())){
|
|
| 267 |
((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
| 268 |
}else{
|
|
| 269 |
logger.error("Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can not be casted to Synonym");
|
|
| 270 |
} |
|
| 271 |
}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
|
|
| 272 |
((Taxon)taxon2).addMisappliedName((Taxon)taxon1, citation, microcitation); |
|
| 273 |
}else {
|
|
| 274 |
//TODO |
|
| 275 |
logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented");
|
|
| 276 |
} |
|
| 277 |
taxonStore.add(taxon2); |
|
| 278 |
|
|
| 279 |
//TODO |
|
| 280 |
//Reference |
|
| 281 |
//ID |
|
| 282 |
//etc. |
|
| 283 |
}else{
|
|
| 284 |
//TODO |
|
| 285 |
logger.warn("Taxa for RelPTaxon " + relPTaxonId + " do not exist in store");
|
|
| 286 |
} |
|
| 287 |
} |
|
| 288 |
logger.info("Taxa to save: " + taxonStore.size());
|
|
| 289 |
taxonService.saveTaxonAll(taxonStore); |
|
| 290 |
|
|
| 291 |
logger.info("end makeRelTaxa ...");
|
|
| 292 |
return true; |
|
| 293 |
} catch (SQLException e) {
|
|
| 294 |
logger.error("SQLException:" + e);
|
|
| 295 |
return false; |
|
| 296 |
} |
|
| 297 |
|
|
| 298 |
} |
|
| 299 |
|
|
| 300 |
|
|
| 301 | 159 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonNameIO.java | ||
|---|---|---|
| 7 | 7 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REJECTED_TYPE_OF; |
| 8 | 8 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REPLACED_SYNONYM_FOR; |
| 9 | 9 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF; |
| 10 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_COMB_INVAL; |
|
| 11 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_ALTERN; |
|
| 12 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_AMBIG; |
|
| 13 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_CONFUS; |
|
| 14 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_CONS; |
|
| 15 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_CONS_PROP; |
|
| 16 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_DUB; |
|
| 17 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_ILLEG; |
|
| 18 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_INVAL; |
|
| 19 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_NOV; |
|
| 20 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_NUD; |
|
| 21 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_PROVIS; |
|
| 22 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_REJ; |
|
| 23 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_REJ_PROP; |
|
| 24 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_SUPERFL; |
|
| 25 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_UTIQUE_REJ; |
|
| 26 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_NOM_UTIQUE_REJ_PROP; |
|
| 27 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_ORTH_CONS; |
|
| 28 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_ST_ORTH_CONS_PROP; |
|
| 29 | 10 |
|
| 30 | 11 |
import java.sql.ResultSet; |
| 31 | 12 |
import java.sql.SQLException; |
| ... | ... | |
| 45 | 26 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 46 | 27 |
import eu.etaxonomy.cdm.model.name.CultivarPlantName; |
| 47 | 28 |
import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
| 48 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
|
| 49 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
|
| 50 | 29 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 51 | 30 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 52 | 31 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| ... | ... | |
| 70 | 49 |
return result; |
| 71 | 50 |
} |
| 72 | 51 |
|
| 73 |
public static boolean checkRelations(BerlinModelImportConfigurator bmiConfig){
|
|
| 74 |
boolean result = true; |
|
| 75 |
logger.warn("Checking for TaxonNameRelations not yet implemented");
|
|
| 76 |
//result &= checkArticlesWithoutJournal(bmiConfig); |
|
| 77 |
//result &= checkPartOfJournal(bmiConfig); |
|
| 78 |
|
|
| 79 |
return result; |
|
| 80 |
} |
|
| 81 |
|
|
| 82 | 52 |
public static boolean invoke(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp, |
| 83 | 53 |
MapWrapper<TaxonNameBase> taxonNameMap, MapWrapper<ReferenceBase> nomRefMap, MapWrapper<ReferenceBase> referenceMap, MapWrapper<TeamOrPersonBase> authorMap){
|
| 84 | 54 |
|
| ... | ... | |
| 304 | 274 |
} |
| 305 | 275 |
} |
| 306 | 276 |
|
| 307 |
|
|
| 308 |
public static boolean invokeRelations(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp, |
|
| 309 |
MapWrapper<TaxonNameBase> nameMap, MapWrapper<ReferenceBase> referenceMap){
|
|
| 310 |
|
|
| 311 |
Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>(); |
|
| 312 |
Source source = bmiConfig.getSource(); |
|
| 313 |
String dbAttrName; |
|
| 314 |
String cdmAttrName; |
|
| 315 |
|
|
| 316 |
logger.info("start makeNameRelationships ...");
|
|
| 317 |
|
|
| 318 |
INameService nameService = cdmApp.getNameService(); |
|
| 319 |
boolean delete = bmiConfig.isDeleteAll(); |
|
| 320 |
|
|
| 321 |
try {
|
|
| 322 |
//get data from database |
|
| 323 |
String strQuery = |
|
| 324 |
" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " + |
|
| 325 |
" FROM Name as FromName INNER JOIN " + |
|
| 326 |
" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " + |
|
| 327 |
" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+ |
|
| 328 |
" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " + |
|
| 329 |
" WHERE (1=1)"; |
|
| 330 |
ResultSet rs = source.getResultSet(strQuery) ; |
|
| 331 |
|
|
| 332 |
int i = 0; |
|
| 333 |
//for each reference |
|
| 334 |
while (rs.next()){
|
|
| 335 |
|
|
| 336 |
if ((i++ % modCount) == 0){ logger.info("RelName handled: " + (i-1));}
|
|
| 337 |
|
|
| 338 |
int relNameId = rs.getInt("RelNameId");
|
|
| 339 |
int name1Id = rs.getInt("name1Id");
|
|
| 340 |
int name2Id = rs.getInt("name2Id");
|
|
| 341 |
int relRefFk = rs.getInt("refFk");
|
|
| 342 |
String details = rs.getString("details");
|
|
| 343 |
int relQualifierFk = rs.getInt("relNameQualifierFk");
|
|
| 344 |
|
|
| 345 |
TaxonNameBase nameFrom = nameMap.get(name1Id); |
|
| 346 |
TaxonNameBase nameTo = nameMap.get(name2Id); |
|
| 347 |
|
|
| 348 |
ReferenceBase citation = referenceMap.get(relRefFk); |
|
| 349 |
//TODO (preliminaryFlag = true testen |
|
| 350 |
String microcitation = details; |
|
| 351 |
|
|
| 352 |
if (nameFrom != null && nameTo != null){
|
|
| 353 |
if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
|
|
| 354 |
//TODO references, mikroref, etc |
|
| 355 |
nameTo.addBasionym(nameFrom); |
|
| 356 |
}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
|
|
| 357 |
String rule = null; //TODO |
|
| 358 |
nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), rule) ; |
|
| 359 |
//TODO reference |
|
| 360 |
}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
|
|
| 361 |
String rule = null; //TODO |
|
| 362 |
nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), rule) ; |
|
| 363 |
//TODO reference |
|
| 364 |
}else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF || relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF ){
|
|
| 365 |
//TODO |
|
| 366 |
String originalNameString = null; |
|
| 367 |
boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF); |
|
| 368 |
boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF); |
|
| 369 |
nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, isRejectedType, isConservedType); |
|
| 370 |
}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
|
|
| 371 |
String rule = null; //TODO |
|
| 372 |
nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), rule) ; |
|
| 373 |
//TODO reference |
|
| 374 |
}else {
|
|
| 375 |
//TODO |
|
| 376 |
logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
|
|
| 377 |
} |
|
| 378 |
nameStore.add(nameFrom); |
|
| 379 |
|
|
| 380 |
//TODO |
|
| 381 |
//ID |
|
| 382 |
//etc. |
|
| 383 |
}else{
|
|
| 384 |
//TODO |
|
| 385 |
if (nameFrom == null){
|
|
| 386 |
logger.warn("from TaxonName for RelName (" + relNameId + ") does not exist in store");
|
|
| 387 |
} |
|
| 388 |
if (nameTo == null){
|
|
| 389 |
logger.warn("to TaxonNames for RelName (" + relNameId + ") does not exist in store");
|
|
| 390 |
} |
|
| 391 |
} |
|
| 392 |
} |
|
| 393 |
logger.info("TaxonName to save: " + nameStore.size());
|
|
| 394 |
nameService.saveTaxonNameAll(nameStore); |
|
| 395 |
|
|
| 396 |
logger.info("end makeRelName ...");
|
|
| 397 |
return true; |
|
| 398 |
} catch (SQLException e) {
|
|
| 399 |
logger.error("SQLException:" + e);
|
|
| 400 |
return false; |
|
| 401 |
} |
|
| 402 |
|
|
| 403 |
} |
|
| 404 |
|
|
| 405 | 277 |
} |
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonNameRelationIO.java | ||
|---|---|---|
| 1 |
package eu.etaxonomy.cdm.io.berlinModel; |
|
| 2 |
|
|
| 3 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_BASIONYM_FOR; |
|
| 4 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_CONSERVED_TYPE_OF; |
|
| 5 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_HOMONYM_OF; |
|
| 6 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF; |
|
| 7 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REJECTED_TYPE_OF; |
|
| 8 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REPLACED_SYNONYM_FOR; |
|
| 9 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF; |
|
| 10 |
|
|
| 11 |
import java.sql.ResultSet; |
|
| 12 |
import java.sql.SQLException; |
|
| 13 |
import java.util.HashSet; |
|
| 14 |
import java.util.Set; |
|
| 15 |
|
|
| 16 |
import org.apache.log4j.Logger; |
|
| 17 |
|
|
| 18 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 19 |
import eu.etaxonomy.cdm.api.service.INameService; |
|
| 20 |
import eu.etaxonomy.cdm.io.common.MapWrapper; |
|
| 21 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 22 |
import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
|
| 23 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 24 |
import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
|
| 25 |
|
|
| 26 |
|
|
| 27 |
public class BerlinModelTaxonNameRelationIO extends BerlinModelIOBase {
|
|
| 28 |
private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameRelationIO.class); |
|
| 29 |
|
|
| 30 |
private static int modCount = 5000; |
|
| 31 |
|
|
| 32 |
public static boolean check(BerlinModelImportConfigurator config){
|
|
| 33 |
boolean result = true; |
|
| 34 |
logger.warn("Checking for TaxonNameRelations not yet implemented");
|
|
| 35 |
//result &= checkArticlesWithoutJournal(bmiConfig); |
|
| 36 |
//result &= checkPartOfJournal(bmiConfig); |
|
| 37 |
|
|
| 38 |
return result; |
|
| 39 |
} |
|
| 40 |
|
|
| 41 |
public static boolean invoke(BerlinModelImportConfigurator config, CdmApplicationController cdmApp, |
|
| 42 |
MapWrapper<TaxonNameBase> nameMap, MapWrapper<ReferenceBase> referenceMap){
|
|
| 43 |
|
|
| 44 |
Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>(); |
|
| 45 |
Source source = config.getSource(); |
|
| 46 |
String dbAttrName; |
|
| 47 |
String cdmAttrName; |
|
| 48 |
|
|
| 49 |
logger.info("start makeNameRelationships ...");
|
|
| 50 |
|
|
| 51 |
INameService nameService = cdmApp.getNameService(); |
|
| 52 |
try {
|
|
| 53 |
//get data from database |
|
| 54 |
String strQuery = |
|
| 55 |
" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " + |
|
| 56 |
" FROM Name as FromName INNER JOIN " + |
|
| 57 |
" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " + |
|
| 58 |
" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+ |
|
| 59 |
" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " + |
|
| 60 |
" WHERE (1=1)"; |
|
| 61 |
ResultSet rs = source.getResultSet(strQuery) ; |
|
| 62 |
|
|
| 63 |
int i = 0; |
|
| 64 |
//for each reference |
|
| 65 |
while (rs.next()){
|
|
| 66 |
|
|
| 67 |
if ((i++ % modCount) == 0){ logger.info("RelName handled: " + (i-1));}
|
|
| 68 |
|
|
| 69 |
int relNameId = rs.getInt("RelNameId");
|
|
| 70 |
int name1Id = rs.getInt("name1Id");
|
|
| 71 |
int name2Id = rs.getInt("name2Id");
|
|
| 72 |
int relRefFk = rs.getInt("refFk");
|
|
| 73 |
String details = rs.getString("details");
|
|
| 74 |
int relQualifierFk = rs.getInt("relNameQualifierFk");
|
|
| 75 |
|
|
| 76 |
TaxonNameBase nameFrom = nameMap.get(name1Id); |
|
| 77 |
TaxonNameBase nameTo = nameMap.get(name2Id); |
|
| 78 |
|
|
| 79 |
ReferenceBase citation = referenceMap.get(relRefFk); |
|
| 80 |
//TODO (preliminaryFlag = true testen |
|
| 81 |
String microcitation = details; |
|
| 82 |
|
|
| 83 |
if (nameFrom != null && nameTo != null){
|
|
| 84 |
if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
|
|
| 85 |
//TODO references, mikroref, etc |
|
| 86 |
nameTo.addBasionym(nameFrom); |
|
| 87 |
}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
|
|
| 88 |
String rule = null; //TODO |
|
| 89 |
nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), rule) ; |
|
| 90 |
//TODO reference |
|
| 91 |
}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
|
|
| 92 |
String rule = null; //TODO |
|
| 93 |
nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), rule) ; |
|
| 94 |
//TODO reference |
|
| 95 |
}else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF || relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF ){
|
|
| 96 |
//TODO |
|
| 97 |
String originalNameString = null; |
|
| 98 |
boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF); |
|
| 99 |
boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF); |
|
| 100 |
nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, isRejectedType, isConservedType); |
|
| 101 |
}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
|
|
| 102 |
String rule = null; //TODO |
|
| 103 |
nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), rule) ; |
|
| 104 |
//TODO reference |
|
| 105 |
}else {
|
|
| 106 |
//TODO |
|
| 107 |
logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
|
|
| 108 |
} |
|
| 109 |
nameStore.add(nameFrom); |
|
| 110 |
|
|
| 111 |
//TODO |
|
| 112 |
//ID |
|
| 113 |
//etc. |
|
| 114 |
}else{
|
|
| 115 |
//TODO |
|
| 116 |
if (nameFrom == null){
|
|
| 117 |
logger.warn("from TaxonName for RelName (" + relNameId + ") does not exist in store");
|
|
| 118 |
} |
|
| 119 |
if (nameTo == null){
|
|
| 120 |
logger.warn("to TaxonNames for RelName (" + relNameId + ") does not exist in store");
|
|
| 121 |
} |
|
| 122 |
} |
|
| 123 |
} |
|
| 124 |
logger.info("TaxonName to save: " + nameStore.size());
|
|
| 125 |
nameService.saveTaxonNameAll(nameStore); |
|
| 126 |
|
|
| 127 |
logger.info("end makeRelName ...");
|
|
| 128 |
return true; |
|
| 129 |
} catch (SQLException e) {
|
|
| 130 |
logger.error("SQLException:" + e);
|
|
| 131 |
return false; |
|
| 132 |
} |
|
| 133 |
|
|
| 134 |
} |
|
| 135 |
|
|
| 136 |
} |
|
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/BerlinModelTaxonRelationIO.java | ||
|---|---|---|
| 1 |
/** |
|
| 2 |
* |
|
| 3 |
*/ |
|
| 4 |
package eu.etaxonomy.cdm.io.berlinModel; |
|
| 5 |
|
|
| 6 |
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.*; |
|
| 7 |
|
|
| 8 |
import java.sql.ResultSet; |
|
| 9 |
import java.sql.SQLException; |
|
| 10 |
import java.util.HashSet; |
|
| 11 |
import java.util.Set; |
|
| 12 |
|
|
| 13 |
import org.apache.log4j.Logger; |
|
| 14 |
|
|
| 15 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
|
| 16 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
|
| 17 |
import eu.etaxonomy.cdm.io.common.ImportHelper; |
|
| 18 |
import eu.etaxonomy.cdm.io.common.MapWrapper; |
|
| 19 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 20 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 21 |
import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
|
| 22 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 23 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
|
| 24 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
| 25 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 26 |
|
|
| 27 |
|
|
| 28 |
/** |
|
| 29 |
* @author a.mueller |
|
| 30 |
* |
|
| 31 |
*/ |
|
| 32 |
public class BerlinModelTaxonRelationIO extends BerlinModelIOBase {
|
|
| 33 |
private static final Logger logger = Logger.getLogger(BerlinModelTaxonRelationIO.class); |
|
| 34 |
|
|
| 35 |
private static int modCount = 30000; |
|
| 36 |
|
|
| 37 |
public static boolean check(BerlinModelImportConfigurator bmiConfig){
|
|
| 38 |
boolean result = true; |
|
| 39 |
logger.warn("Checking for TaxonRelations not yet fully implemented");
|
|
| 40 |
result &= checkTaxonStatus(bmiConfig); |
|
| 41 |
//result &= checkArticlesWithoutJournal(bmiConfig); |
|
| 42 |
|
|
| 43 |
return result; |
|
| 44 |
} |
|
| 45 |
|
|
| 46 |
private static boolean checkTaxonStatus(BerlinModelImportConfigurator bmiConfig){
|
|
| 47 |
try {
|
|
| 48 |
boolean result = true; |
|
| 49 |
Source source = bmiConfig.getSource(); |
|
| 50 |
String strQueryPartOfJournal = " SELECT RelPTaxon.RelQualifierFk, RelPTaxon.relPTaxonId, PTaxon.PTNameFk, PTaxon.PTRefFk, PTaxon_1.PTNameFk AS Expr1, PTaxon.RIdentifier, PTaxon_1.RIdentifier AS Expr3, Name.FullNameCache " + |
|
| 51 |
" FROM RelPTaxon " + |
|
| 52 |
" INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " + |
|
| 53 |
" INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk " + |
|
| 54 |
" INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " + |
|
| 55 |
" WHERE (dbo.PTaxon.StatusFk = 1) AND ((RelPTaxon.RelQualifierFk = 7) OR (RelPTaxon.RelQualifierFk = 6) OR (RelPTaxon.RelQualifierFk = 2)) "; |
|
| 56 |
ResultSet rs = source.getResultSet(strQueryPartOfJournal); |
|
| 57 |
boolean firstRow = true; |
|
| 58 |
int i = 0; |
|
| 59 |
while (rs.next()){
|
|
| 60 |
i++; |
|
| 61 |
if (firstRow){
|
|
| 62 |
System.out.println("========================================================");
|
|
| 63 |
logger.warn("There are taxa that have a 'is synonym of' - relationship but having taxon status 'accepted'!");
|
|
| 64 |
System.out.println("========================================================");
|
|
| 65 |
} |
|
| 66 |
int rIdentifier = rs.getInt("RIdentifier");
|
|
| 67 |
int nameFk = rs.getInt("PTNameFk");
|
|
| 68 |
int refFk = rs.getInt("PTRefFk");
|
|
| 69 |
int relPTaxonId = rs.getInt("relPTaxonId");
|
|
| 70 |
String taxonName = rs.getString("FullNameCache");
|
|
| 71 |
|
|
| 72 |
System.out.println("RIdentifier:" + rIdentifier + "\n name: " + nameFk +
|
|
| 73 |
"\n taxonName: " + taxonName + "\n refId: " + refFk + "\n RelPTaxonId: " + relPTaxonId ); |
|
| 74 |
result = firstRow = false; |
|
| 75 |
} |
|
| 76 |
if (i > 0){
|
|
| 77 |
System.out.println(" ");
|
|
| 78 |
} |
|
| 79 |
|
|
| 80 |
return result; |
|
| 81 |
} catch (SQLException e) {
|
|
| 82 |
e.printStackTrace(); |
|
| 83 |
return false; |
|
| 84 |
} |
|
| 85 |
} |
|
| 86 |
|
|
| 87 |
public static boolean invoke(BerlinModelImportConfigurator config, CdmApplicationController cdmApp, |
|
| 88 |
MapWrapper<TaxonBase> taxonMap, MapWrapper<ReferenceBase> referenceMap){
|
|
| 89 |
|
|
| 90 |
Set<TaxonBase> taxonStore = new HashSet<TaxonBase>(); |
|
| 91 |
Source source = config.getSource(); |
|
| 92 |
String dbAttrName; |
|
| 93 |
String cdmAttrName; |
|
| 94 |
|
|
| 95 |
logger.info("start makeTaxonRelationships ...");
|
|
| 96 |
|
|
| 97 |
ITaxonService taxonService = cdmApp.getTaxonService(); |
|
| 98 |
|
|
| 99 |
try {
|
|
| 100 |
//get data from database |
|
| 101 |
String strQuery = |
|
| 102 |
" SELECT RelPTaxon.*, FromTaxon.RIdentifier as taxon1Id, ToTaxon.RIdentifier as taxon2Id " + |
|
| 103 |
" FROM PTaxon as FromTaxon INNER JOIN " + |
|
| 104 |
" RelPTaxon ON FromTaxon.PTNameFk = RelPTaxon.PTNameFk1 AND FromTaxon.PTRefFk = RelPTaxon.PTRefFk1 INNER JOIN " + |
|
| 105 |
" PTaxon AS ToTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk "+ |
|
| 106 |
" WHERE (1=1)"; |
|
| 107 |
ResultSet rs = source.getResultSet(strQuery) ; |
|
| 108 |
|
|
| 109 |
int i = 0; |
|
| 110 |
//for each reference |
|
| 111 |
while (rs.next()){
|
|
| 112 |
|
|
| 113 |
if ((i++ % modCount) == 0){ logger.info("RelPTaxa handled: " + (i-1));}
|
|
| 114 |
|
|
| 115 |
int relPTaxonId = rs.getInt("RelPTaxonId");
|
|
| 116 |
int taxon1Id = rs.getInt("taxon1Id");
|
|
| 117 |
int taxon2Id = rs.getInt("taxon2Id");
|
|
| 118 |
int relRefFk = rs.getInt("relRefFk");
|
|
| 119 |
int relQualifierFk = rs.getInt("relQualifierFk");
|
|
| 120 |
|
|
| 121 |
TaxonBase taxon1 = taxonMap.get(taxon1Id); |
|
| 122 |
TaxonBase taxon2 = taxonMap.get(taxon2Id); |
|
| 123 |
|
|
| 124 |
//TODO |
|
| 125 |
ReferenceBase citation = null; |
|
| 126 |
String microcitation = null; |
|
| 127 |
|
|
| 128 |
if (taxon2 != null && taxon1 != null){
|
|
| 129 |
if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){
|
|
| 130 |
((Taxon)taxon2).addTaxonomicChild((Taxon)taxon1, citation, microcitation); |
|
| 131 |
}else if (relQualifierFk == TAX_REL_IS_SYNONYM_OF){
|
|
| 132 |
((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.SYNONYM_OF()); |
|
| 133 |
}else if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF){
|
|
| 134 |
if (taxon1 instanceof Synonym){
|
|
| 135 |
((Taxon)taxon2).addHomotypicSynonym((Synonym)taxon1, citation, microcitation); |
|
| 136 |
}else{
|
|
| 137 |
logger.error("Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Synonym");
|
|
| 138 |
} |
|
| 139 |
}else if (relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){
|
|
| 140 |
if (Synonym.class.isAssignableFrom(taxon1.getClass())){
|
|
| 141 |
((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF()); |
|
| 142 |
}else{
|
|
| 143 |
logger.error("Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can not be casted to Synonym");
|
|
| 144 |
} |
|
| 145 |
}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){
|
|
| 146 |
((Taxon)taxon2).addMisappliedName((Taxon)taxon1, citation, microcitation); |
|
| 147 |
}else {
|
|
| 148 |
//TODO |
|
| 149 |
logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented");
|
|
| 150 |
} |
|
| 151 |
taxonStore.add(taxon2); |
|
| 152 |
|
|
| 153 |
//TODO |
|
| 154 |
//Reference |
|
| 155 |
//ID |
|
| 156 |
//etc. |
|
| 157 |
}else{
|
|
| 158 |
//TODO |
|
| 159 |
logger.warn("Taxa for RelPTaxon " + relPTaxonId + " do not exist in store");
|
|
| 160 |
} |
|
| 161 |
} |
|
| 162 |
logger.info("Taxa to save: " + taxonStore.size());
|
|
| 163 |
taxonService.saveTaxonAll(taxonStore); |
|
| 164 |
|
|
| 165 |
logger.info("end makeRelTaxa ...");
|
|
| 166 |
return true; |
|
| 167 |
} catch (SQLException e) {
|
|
| 168 |
logger.error("SQLException:" + e);
|
|
| 169 |
return false; |
|
| 170 |
} |
|
| 171 |
|
|
| 172 |
} |
|
| 173 |
|
|
| 174 |
|
|
| 175 |
} |
|
Also available in: Unified diff