Revision 9ff7f3d8
Added by Katja Luther over 3 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsFindIdenticalNamesActivator.java | ||
|---|---|---|
| 95 | 95 |
resultOK = resultOK && sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv"); |
| 96 | 96 |
resultOK = resultOK &&sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv"); |
| 97 | 97 |
resultOK = resultOK &&sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv"); |
| 98 |
resultOK = resultOK &&sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv"); |
|
| 98 |
//do not create the phylum file, explanation inside the method writeSameNamesdifferentPhylumToCsv |
|
| 99 |
//resultOK = resultOK &&sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv"); |
|
| 99 | 100 |
resultOK = resultOK &&sc.writeSameNamesDifferentParentToCsv(mergingObjects, sFileName + "parent.csv"); |
| 100 | 101 |
|
| 101 | 102 |
System.err.println("End merging Fauna Europaea and Erms" + resultOK);
|
| ... | ... | |
| 125 | 126 |
private boolean writeSameNamesdifferentPhylumToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
|
| 126 | 127 |
try |
| 127 | 128 |
{
|
| 129 |
//do we really need this?? it is a taxon needed merged like all others? for erms only one taxon has different phylum. (Valencia, but these are not the same taxa -> fish and ribbon worms) |
|
| 128 | 130 |
FileWriter writer = new FileWriter(sfileName); |
| 129 | 131 |
|
| 130 | 132 |
//create Header |
| ... | ... | |
| 133 | 135 |
|
| 134 | 136 |
//write data |
| 135 | 137 |
for (FaunaEuErmsMerging merging : mergingObjects){
|
| 136 |
//TODO |
|
| 138 |
//TODO the phyllum is always different doing it this way, maybe we need to merge the phylum taxa first and then
|
|
| 137 | 139 |
if ((merging.getPhylumInErms()== null )^ (merging.getPhylumInFaunaEu()== null)){
|
| 138 | 140 |
writeCsvLine(writer, merging) ; |
| 139 | 141 |
}else if(!((merging.getPhylumInErms()==null) && (merging.getPhylumInFaunaEu()==null))){
|
| 140 |
if(!merging.getPhylumInErms().equals(merging.getPhylumInFaunaEu())){
|
|
| 142 |
if(!merging.getPhylumInErms().getNameTitleCache().equals(merging.getPhylumInFaunaEu().getNameTitleCache())){
|
|
| 141 | 143 |
writeCsvLine(writer, merging) ; |
| 142 | 144 |
} |
| 143 | 145 |
} |
| ... | ... | |
| 214 | 216 |
writer.append(';');
|
| 215 | 217 |
writer.append("id in Fauna Europaea");
|
| 216 | 218 |
writer.append(';');
|
| 217 |
writer.append("name");
|
|
| 219 |
writer.append("name in FE");
|
|
| 218 | 220 |
writer.append(';');
|
| 219 |
writer.append("author");
|
|
| 221 |
writer.append("author in FE");
|
|
| 220 | 222 |
writer.append(';');
|
| 221 |
writer.append("rank");
|
|
| 223 |
writer.append("rank in FE");
|
|
| 222 | 224 |
writer.append(';');
|
| 223 |
writer.append("state");
|
|
| 225 |
writer.append("state in FE");
|
|
| 224 | 226 |
writer.append(';');
|
| 225 |
writer.append("phylum");
|
|
| 227 |
writer.append("phylum in FE");
|
|
| 226 | 228 |
writer.append(';');
|
| 227 |
writer.append("parent");
|
|
| 229 |
writer.append("parent in FE");
|
|
| 228 | 230 |
writer.append(';');
|
| 229 |
writer.append("parent rank");
|
|
| 231 |
writer.append("parent rank in FE");
|
|
| 230 | 232 |
writer.append(';');
|
| 231 | 233 |
|
| 232 | 234 |
writer.append("uuid in Erms");
|
| 233 | 235 |
writer.append(';');
|
| 234 | 236 |
writer.append("id in Erms");
|
| 235 | 237 |
writer.append(';');
|
| 236 |
writer.append("name");
|
|
| 238 |
writer.append("name in Erms");
|
|
| 237 | 239 |
writer.append(';');
|
| 238 |
writer.append("author");
|
|
| 240 |
writer.append("author in Erms");
|
|
| 239 | 241 |
writer.append(';');
|
| 240 |
writer.append("rank");
|
|
| 242 |
writer.append("rank in Erms");
|
|
| 241 | 243 |
writer.append(';');
|
| 242 |
writer.append("state");
|
|
| 244 |
writer.append("state in Erms");
|
|
| 243 | 245 |
writer.append(';');
|
| 244 |
writer.append("phylum");
|
|
| 246 |
writer.append("phylum in Erms");
|
|
| 245 | 247 |
writer.append(';');
|
| 246 |
writer.append("parent");
|
|
| 248 |
writer.append("parent in Erms");
|
|
| 247 | 249 |
writer.append(';');
|
| 248 |
writer.append("parent rank");
|
|
| 250 |
writer.append("parent rank in Erms");
|
|
| 249 | 251 |
writer.append('\n');
|
| 250 | 252 |
} |
| 251 | 253 |
|
| ... | ... | |
| 348 | 350 |
} |
| 349 | 351 |
|
| 350 | 352 |
writer.append(';');
|
| 351 |
writer.append(merging.getPhylumInErms() != null? merging.getPhylumInErms().getTaxonTitleCache():"");
|
|
| 353 |
writer.append(merging.getPhylumInErms() != null? merging.getPhylumInErms().getTitleCache():""); |
|
| 352 | 354 |
writer.append(';');
|
| 353 | 355 |
writer.append(merging.getParentStringInErms()); |
| 354 | 356 |
writer.append(';');
|
| ... | ... | |
| 537 | 539 |
mergeObject.setRankInErms(ermsName.getRank().getLabel()); |
| 538 | 540 |
mergeObject.setRankInFaunaEu(faunaEuName.getRank().getLabel()); |
| 539 | 541 |
|
| 540 |
//set parent informations |
|
| 541 |
|
|
| 542 |
|
|
| 543 |
/* |
|
| 544 |
Set<HybridRelationship> parentRelations = zooName.getParentRelationships(); |
|
| 545 |
Iterator parentIterator = parentRelations.iterator(); |
|
| 546 |
HybridRelationship parentRel; |
|
| 547 |
ZoologicalName parentName; |
|
| 548 |
while (parentIterator.hasNext()){
|
|
| 549 |
parentRel = (HybridRelationship)parentIterator.next(); |
|
| 550 |
parentName = (ZoologicalName)parentRel.getParentName(); |
|
| 551 |
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel()); |
|
| 552 |
mergeObject.setParentStringInErms(parentName.getNameCache()); |
|
| 553 |
} |
|
| 554 |
|
|
| 555 |
parentRelations = zooName2.getParentRelationships(); |
|
| 556 |
parentIterator = parentRelations.iterator(); |
|
| 557 |
|
|
| 558 |
while (parentIterator.hasNext()){
|
|
| 559 |
parentRel = (HybridRelationship)parentIterator.next(); |
|
| 560 |
parentName = (ZoologicalName)parentRel.getParentName(); |
|
| 561 |
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel()); |
|
| 562 |
mergeObject.setParentStringInFaunaEu(parentName.getNameCache()); |
|
| 563 |
}*/ |
|
| 542 |
|
|
| 564 | 543 |
merge.add(mergeObject); |
| 565 | 544 |
} |
| 566 |
// } |
|
| 545 |
|
|
| 567 | 546 |
|
| 568 | 547 |
return merge; |
| 569 | 548 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/FaunaEuErmsMergeActivator.java | ||
|---|---|---|
| 19 | 19 |
import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException; |
| 20 | 20 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
| 21 | 21 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 22 |
|
|
| 23 | 22 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 24 | 23 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 25 | 24 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
| ... | ... | |
| 36 | 35 |
import eu.etaxonomy.cdm.model.name.NameRelationship; |
| 37 | 36 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 38 | 37 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 38 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
|
| 39 | 39 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 41 | 41 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| ... | ... | |
| 50 | 50 |
static final int ermsUuid = 9; |
| 51 | 51 |
static final int rankFaunaEu = 4; |
| 52 | 52 |
static final int rankErms = 13; |
| 53 |
Classification faunaEuClassification; |
|
| 54 |
Classification ermsClassification; |
|
| 53 | 55 |
|
| 54 | 56 |
CdmApplicationController appCtrInit; |
| 55 | 57 |
|
| ... | ... | |
| 71 | 73 |
FaunaEuErmsMergeActivator sc = new FaunaEuErmsMergeActivator(); |
| 72 | 74 |
|
| 73 | 75 |
sc.initDb(faunaEuropaeaSource); |
| 74 |
//we also need to merge names completely identical! |
|
| 76 |
//we also need to merge names completely identical!
|
|
| 75 | 77 |
sc.mergeAuthors(); |
| 76 | 78 |
|
| 77 | 79 |
//set the ranks of Agnatha and Gnathostomata to 50 instead of 45 |
| ... | ... | |
| 203 | 205 |
|
| 204 | 206 |
TaxonBase<?> taxonFaunaEu; |
| 205 | 207 |
TaxonBase<?> taxonErms; |
| 206 |
|
|
| 208 |
List<String> propertyPaths = new ArrayList<>(); |
|
| 209 |
propertyPaths.add("taxonBases.nodes.*");
|
|
| 207 | 210 |
for (List<String> row: sameStatus){
|
| 208 |
taxonFaunaEu = appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));
|
|
| 209 |
taxonErms = appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));
|
|
| 211 |
taxonFaunaEu = appCtrInit.getTaxonService().load(UUID.fromString(row.get(faunaEuUuid)), propertyPaths);
|
|
| 212 |
taxonErms = appCtrInit.getTaxonService().load(UUID.fromString(row.get(ermsUuid)), propertyPaths);
|
|
| 210 | 213 |
moveAllInformationsFromFaunaEuToErms(taxonFaunaEu, taxonErms); |
| 211 | 214 |
if (taxonErms instanceof Taxon){
|
| 212 | 215 |
moveFaunaEuSynonymsToErmsTaxon((Taxon)taxonFaunaEu, (Taxon)taxonErms); |
| ... | ... | |
| 450 | 453 |
for (Credit credit: credits){
|
| 451 | 454 |
erms.addCredit(credit); |
| 452 | 455 |
} |
| 456 |
//move children to erms taxon |
|
| 457 |
if (faunaEu instanceof Taxon && ((Taxon)faunaEu).getTaxonNode(faunaEuClassification).hasChildNodes()) {
|
|
| 458 |
Taxon acceptedErmsTaxon; |
|
| 459 |
if (erms instanceof Synonym) {
|
|
| 460 |
acceptedErmsTaxon = ((Synonym)erms).getAcceptedTaxon(); |
|
| 461 |
}else {
|
|
| 462 |
acceptedErmsTaxon = (Taxon)erms; |
|
| 463 |
} |
|
| 464 |
TaxonNode node = ((Taxon)acceptedErmsTaxon).getTaxonNode(ermsClassification); |
|
| 465 |
for (TaxonNode child:((Taxon)faunaEu).getTaxonNode(faunaEuClassification).getChildNodes()) {
|
|
| 466 |
//add pesi reference as reference?? |
|
| 467 |
node.addChildNode(child, null, null); |
|
| 468 |
} |
|
| 469 |
} |
|
| 453 | 470 |
} |
| 454 | 471 |
|
| 455 | 472 |
//if name, rank, and status (accepted) are the same, then move the synonyms of faunaEu taxon to the erms taxon |
| ... | ... | |
| 474 | 491 |
//merged taxon should have a new sec reference |
| 475 | 492 |
private void addNewSecForMergedTaxon(Taxon taxon, Reference sec){
|
| 476 | 493 |
taxon.setSec(sec); |
| 477 |
taxon.setUuid(UUID.randomUUID()); |
|
| 494 |
//this does not work!! |
|
| 495 |
//taxon.setUuid(UUID.randomUUID()); |
|
| 478 | 496 |
} |
| 479 | 497 |
|
| 480 | 498 |
// ----------- methods for merging Erms synonyms and Fauna Europaea Taxon |
Also available in: Unified diff
merging fauna Eu - Erms -continue