Revision 0ccecb37
Added by Andreas Müller over 3 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java | ||
|---|---|---|
| 75 | 75 |
private static Map<UUID,String> sourcesLabels = new HashMap<>(); |
| 76 | 76 |
|
| 77 | 77 |
static {
|
| 78 |
sourceRefUuids.addAll(Arrays.asList(new UUID[]{emSourceUuid, ermsSourceUuid, faunaEuSourceUuid, ifSourceUuid}));
|
|
| 78 |
sourceRefUuids.addAll(Arrays.asList(new UUID[]{
|
|
| 79 |
// emSourceUuid, |
|
| 80 |
ermsSourceUuid |
|
| 81 |
,faunaEuSourceUuid |
|
| 82 |
// , ifSourceUuid |
|
| 83 |
})); |
|
| 79 | 84 |
sourcesLabels.put(emSourceUuid, "E+M"); |
| 80 | 85 |
sourcesLabels.put(ermsSourceUuid, "ERMS"); |
| 81 | 86 |
sourcesLabels.put(faunaEuSourceUuid, "FauEu"); |
| ... | ... | |
| 201 | 206 |
differenceExists |= isDifferent(merge1, merge2, method); |
| 202 | 207 |
} |
| 203 | 208 |
} |
| 209 |
int combinations = mergeList1.size() * mergeList2.size(); |
|
| 204 | 210 |
if (differenceExists){
|
| 205 | 211 |
for (PesiMergeObject merge1 : mergeList1){
|
| 206 | 212 |
for (PesiMergeObject merge2 : mergeList2){
|
| 207 |
writeCsvLine(writer, merge1, merge2, method, isNextNameCache); |
|
| 213 |
writeCsvLine(writer, merge1, merge2, method, isNextNameCache, combinations);
|
|
| 208 | 214 |
isNextNameCache = false; |
| 209 | 215 |
} |
| 210 | 216 |
} |
| ... | ... | |
| 225 | 231 |
|
| 226 | 232 |
try {
|
| 227 | 233 |
if (method == null){
|
| 228 |
return true;
|
|
| 234 |
return !merge1.getIdTaxon().equals(merge2.getIdTaxon());
|
|
| 229 | 235 |
} |
| 230 | 236 |
Object value1 = method.invoke(merge1); |
| 231 | 237 |
Object value2 = method.invoke(merge2); |
| ... | ... | |
| 243 | 249 |
writeHeaderPair(writer, "tid"); |
| 244 | 250 |
writer.append("use;");
|
| 245 | 251 |
writer.append("nameUse;");
|
| 246 |
writer.append("next;");
|
|
| 252 |
writer.append("combinations;");
|
|
| 247 | 253 |
writer.append("diff;");
|
| 248 | 254 |
writeHeaderPair(writer, "src"); |
| 249 | 255 |
// writeHeaderPair(writer, "nuuid"); |
| ... | ... | |
| 252 | 258 |
writeHeaderPair(writer, "author"); |
| 253 | 259 |
writeHeaderPair(writer, "nom.ref."); |
| 254 | 260 |
writeHeaderPair(writer, "rank"); |
| 261 |
writeHeaderPair(writer, "classification"); |
|
| 255 | 262 |
writeHeaderPair(writer, "kingdom"); |
| 256 | 263 |
writeHeaderPair(writer, "phylum"); |
| 264 |
writeHeaderPair(writer, "class"); |
|
| 265 |
writeHeaderPair(writer, "order"); |
|
| 257 | 266 |
writeHeaderPair(writer, "family"); |
| 258 | 267 |
writeHeaderPair(writer, "parentString"); |
| 259 | 268 |
writeHeaderPair(writer, "parentRankString"); |
| 260 | 269 |
writeHeaderPair(writer, "status"); |
| 261 | 270 |
writeHeaderPair(writer, "tuuid"); |
| 271 |
writer.append("firstAuthor;");
|
|
| 272 |
writer.append("firstRank;");
|
|
| 273 |
writer.append("firstClassification;");
|
|
| 274 |
writer.append("firstKingdom;");
|
|
| 275 |
writer.append("firstPhylum;");
|
|
| 276 |
writer.append("firstClass;");
|
|
| 277 |
writer.append("firstOrder;");
|
|
| 278 |
writer.append("firstFamily;");
|
|
| 279 |
writer.append("firstStatus;");
|
|
| 262 | 280 |
|
| 263 | 281 |
writer.append('\n');
|
| 264 | 282 |
} catch (IOException e) {
|
| ... | ... | |
| 271 | 289 |
writer.append(header+"2").append(';');
|
| 272 | 290 |
} |
| 273 | 291 |
|
| 292 |
//needs to be synchronized with writeHeader() |
|
| 274 | 293 |
private void writeCsvLine(Writer writer, |
| 275 | 294 |
PesiMergeObject merge1, PesiMergeObject merge2, |
| 276 |
Method method, boolean isNextNameCache){
|
|
| 295 |
Method method, boolean isNextNameCache, int combinations){ //isNextNameCache probably not needed anymore
|
|
| 277 | 296 |
|
| 278 | 297 |
writePair(writer, merge1, merge2, "IdTaxon", Compare.NO); |
| 279 | 298 |
writeSingleValue(writer, ""); |
| 280 | 299 |
writeSingleValue(writer, ""); |
| 281 |
writeSingleValue(writer, isNextNameCache?"1":"0"); |
|
| 300 |
// writeSingleValue(writer, isNextNameCache?"1":"0"); |
|
| 301 |
writeSingleValue(writer, String.valueOf(combinations)); |
|
| 282 | 302 |
boolean different = isDifferent(merge1, merge2, method); |
| 283 | 303 |
writeSingleValue(writer, different?"1":"0"); |
| 284 | 304 |
writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge1.getUuidSource()))); |
| ... | ... | |
| 290 | 310 |
writePair(writer, merge1, merge2, "Author", Compare.YES); |
| 291 | 311 |
writePair(writer, merge1, merge2, "NomenclaturalReference", Compare.YES); |
| 292 | 312 |
writePair(writer, merge1, merge2, "Rank", Compare.YES); |
| 293 |
writePair(writer, merge1, merge2, "KingdomCache", Compare.KEEP_FIRST); |
|
| 313 |
writePair(writer, merge1, merge2, "ClassificationCache", Compare.YES); |
|
| 314 |
writePair(writer, merge1, merge2, "KingdomCache", Compare.YES); |
|
| 294 | 315 |
writePair(writer, merge1, merge2, "PhylumCache", Compare.YES); |
| 316 |
writePair(writer, merge1, merge2, "ClassCache", Compare.YES); |
|
| 317 |
writePair(writer, merge1, merge2, "OrderCache", Compare.YES); |
|
| 295 | 318 |
writePair(writer, merge1, merge2, "FamilyCache", Compare.YES); |
| 296 | 319 |
writePair(writer, merge1, merge2, "ParentString", Compare.YES); |
| 297 | 320 |
writePair(writer, merge1, merge2, "ParentRankString", Compare.YES); |
| 298 | 321 |
writePair(writer, merge1, merge2, "StatusStr", Compare.YES); |
| 299 | 322 |
writePair(writer, merge1, merge2, "UuidTaxon", Compare.YES); |
| 323 |
writeSingleValue(writer, merge1.getAuthor()); |
|
| 324 |
writeSingleValue(writer, merge1.getRank()); |
|
| 325 |
writeSingleValue(writer, merge1.getClassificationCache()); |
|
| 326 |
writeSingleValue(writer, merge1.getKingdomCache()); |
|
| 327 |
writeSingleValue(writer, merge1.getPhylumCache()); |
|
| 328 |
writeSingleValue(writer, merge1.getClassCache()); |
|
| 329 |
writeSingleValue(writer, merge1.getOrderCache()); |
|
| 330 |
writeSingleValue(writer, merge1.getFamilyCache()); |
|
| 331 |
writeSingleValue(writer, merge1.getStatusStr()); |
|
| 332 |
|
|
| 300 | 333 |
|
| 301 | 334 |
try {
|
| 302 | 335 |
writer.append('\n');
|
| ... | ... | |
| 319 | 352 |
KEEP_FIRST; |
| 320 | 353 |
|
| 321 | 354 |
boolean isAnyCompare(){
|
| 322 |
return this == NO;
|
|
| 355 |
return this != NO;
|
|
| 323 | 356 |
} |
| 324 | 357 |
} |
| 325 | 358 |
|
| ... | ... | |
| 342 | 375 |
} |
| 343 | 376 |
|
| 344 | 377 |
private String normalize(String val) {
|
| 345 |
return CdmUtils.Nz(val).replace(";", "@");
|
|
| 378 |
return Nz(val).replace(";", "@");
|
|
| 346 | 379 |
} |
| 347 | 380 |
|
| 348 | 381 |
private List<Map<UUID,List<PesiMergeObject>>> createMergeObjects( |
| ... | ... | |
| 403 | 436 |
//rank |
| 404 | 437 |
mergeObject.setRank(name.getRank().getLabel()); |
| 405 | 438 |
|
| 439 |
//higherTaxa |
|
| 440 |
List<TaxonNodeDto> higherTaxa = getHigherTaxa(appCtr, name); |
|
| 441 |
mergeObject.setHigherClassification(higherTaxa); |
|
| 442 |
|
|
| 406 | 443 |
//Kingdom |
| 407 | 444 |
TaxonNodeDto kingdom = getHigherTaxon(appCtr, name, Rank.KINGDOM()); |
| 408 | 445 |
mergeObject.setKingdom(kingdom); |
| ... | ... | |
| 414 | 451 |
} |
| 415 | 452 |
mergeObject.setPhylum(phylum); |
| 416 | 453 |
|
| 454 |
//Class |
|
| 455 |
TaxonNodeDto tclass = getHigherTaxon(appCtr, name, Rank.CLASS()); |
|
| 456 |
mergeObject.setTClass(tclass); |
|
| 457 |
|
|
| 458 |
//Class |
|
| 459 |
TaxonNodeDto order = getHigherTaxon(appCtr, name, Rank.ORDER()); |
|
| 460 |
mergeObject.setOrder(order); |
|
| 461 |
|
|
| 417 | 462 |
//Family |
| 418 | 463 |
TaxonNodeDto family = getHigherTaxon(appCtr, name, Rank.FAMILY()); |
| 419 | 464 |
mergeObject.setFamily(family); |
| ... | ... | |
| 504 | 549 |
} |
| 505 | 550 |
} |
| 506 | 551 |
|
| 552 |
private List<TaxonNodeDto> getHigherTaxa(CdmApplicationController appCtr, TaxonName name) {
|
|
| 553 |
List<TaxonNodeDto> result = new ArrayList<>(); |
|
| 554 |
Taxon taxon = getAcceptedTaxon(name); |
|
| 555 |
if (taxon.getTaxonNodes().isEmpty()){
|
|
| 556 |
return null; //probably MAN |
|
| 557 |
} |
|
| 558 |
if (taxon.getTaxonNodes().size()>1){
|
|
| 559 |
logger.warn("More than 1 node not yet handled for getHigherTaxon. Take arbitrary one.");
|
|
| 560 |
} |
|
| 561 |
TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
|
| 562 |
TaxonNodeDto nodeDto = new TaxonNodeDto(node); |
|
| 563 |
if (!taxon.getName().equals(name)){
|
|
| 564 |
result.add(nodeDto); //for synonyms add accepted taxon as first node |
|
| 565 |
} |
|
| 566 |
while (nodeDto.getTaxonUuid()!= null){
|
|
| 567 |
nodeDto = appCtr.getTaxonNodeService().parentDto(nodeDto.getUuid()); |
|
| 568 |
if (nodeDto.getTaxonUuid()!= null){
|
|
| 569 |
result.add(0, nodeDto); //for synonyms add accepted taxon as first node |
|
| 570 |
} |
|
| 571 |
} |
|
| 572 |
return result; |
|
| 573 |
} |
|
| 574 |
|
|
| 507 | 575 |
private TaxonNodeDto getHigherTaxon(CdmApplicationController appCtr, TaxonName name, Rank rank) {
|
| 508 | 576 |
if (name.getRank().equals(rank)) {
|
| 509 | 577 |
Taxon taxon = getAcceptedTaxon(name); |
| ... | ... | |
| 607 | 675 |
return result; |
| 608 | 676 |
} |
| 609 | 677 |
|
| 610 |
private CharSequence Nz(String str) {
|
|
| 678 |
private String Nz(String str) {
|
|
| 611 | 679 |
return CdmUtils.Nz(str); |
| 612 | 680 |
} |
| 613 | 681 |
|
Also available in: Unified diff
ref #1447 latest changes to PesiFindIdenticalNamesActivator and PesiEuroMedValidator