Revision 45c2e0b4
Added by Andreas Müller over 3 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiCommandLineMerge.java | ||
|---|---|---|
| 111 | 111 |
} |
| 112 | 112 |
if (commit){
|
| 113 | 113 |
app.commitTransaction(tx); |
| 114 |
if (taxonInformation.taxonToUse == 1 && taxonInformation.nameToUse == 1){
|
|
| 114 |
if (isAutomatedAnswer(taxonInformation)){
|
|
| 115 | 115 |
removeTaxon(taxonInformation.taxon2); |
| 116 | 116 |
}else if (booleanAnswer("Information moved. Delete old taxon")){
|
| 117 | 117 |
removeTaxon(taxonInformation.taxonToUse == 2 ? taxonInformation.taxon1 : taxonInformation.taxon2); |
| ... | ... | |
| 122 | 122 |
return commit; |
| 123 | 123 |
} |
| 124 | 124 |
|
| 125 |
private boolean isAutomatedAnswer(TaxonInformation taxonInformation) {
|
|
| 126 |
return taxonInformation.taxonToUse == 2 && taxonInformation.nameToUse == 2 && false; |
|
| 127 |
} |
|
| 128 |
|
|
| 125 | 129 |
private class TaxonInformation{
|
| 126 | 130 |
TaxonBase<?> taxon1; |
| 127 | 131 |
TaxonBase<?> taxon2; |
| ... | ... | |
| 206 | 210 |
private boolean compareTaxa(TaxonInformation taxonInformation) {
|
| 207 | 211 |
TaxonBase<?> removeTaxon = taxonInformation.taxon2; |
| 208 | 212 |
TaxonBase<?> stayTaxon = taxonInformation.taxon1; |
| 213 |
if(removeTaxon.getId() == stayTaxon.getId()){
|
|
| 214 |
logger.warn("Same taxon: "+ removeTaxon.getTitleCache());
|
|
| 215 |
return false; |
|
| 216 |
} |
|
| 209 | 217 |
String nc1 = removeTaxon.getName().getNameCache(); |
| 210 | 218 |
String nc2 = stayTaxon.getName().getNameCache(); |
| 211 | 219 |
|
| ... | ... | |
| 213 | 221 |
String ft2 = stayTaxon.getName().getFullTitleCache(); |
| 214 | 222 |
System.out.println("Remove " + getStatusStr(removeTaxon) + ft1);
|
| 215 | 223 |
System.out.println("Stay " + getStatusStr(stayTaxon) + ft2);
|
| 216 |
boolean isStandard = taxonInformation.taxonToUse == 1 && taxonInformation.nameToUse == 1;
|
|
| 224 |
boolean isStandard = isAutomatedAnswer(taxonInformation);
|
|
| 217 | 225 |
if (!nc1.equals(nc2)){
|
| 218 | 226 |
return booleanAnswer("Name Cache differs!!! Do you really want to merge???");
|
| 219 | 227 |
}else if (!ft1.equals(ft2)){
|
| ... | ... | |
| 307 | 315 |
mergeHybridRelationships(removeName, stayName); |
| 308 | 316 |
mergeNameDescriptions(removeName, stayName); |
| 309 | 317 |
|
| 310 |
if(taxonInformation.taxonToUse == 1 && taxonInformation.nameToUse == 1){
|
|
| 318 |
if(isAutomatedAnswer(taxonInformation)){
|
|
| 311 | 319 |
return true; |
| 312 | 320 |
}else{
|
| 313 | 321 |
return booleanAnswer("Commit moved information");
|
| ... | ... | |
| 393 | 401 |
} |
| 394 | 402 |
} |
| 395 | 403 |
TaxonNode removeNode = removeTaxon.getTaxonNodes().iterator().next(); |
| 404 |
if(removeNode.getChildNodes().isEmpty()){
|
|
| 405 |
return true; |
|
| 406 |
} |
|
| 407 |
|
|
| 408 |
stayTaxon = reallyAccTaxon(stayTaxon); |
|
| 396 | 409 |
TaxonNode stayNode = stayTaxon.getTaxonNodes().iterator().next(); |
| 397 | 410 |
Set<UUID> removeNodeChildrenUuids = removeNode.getChildNodes() |
| 398 | 411 |
.stream().map(tn->tn.getUuid()).collect(Collectors.toSet()); |
| ... | ... | |
| 405 | 418 |
return true; |
| 406 | 419 |
} |
| 407 | 420 |
|
| 421 |
private Taxon reallyAccTaxon(Taxon stayTaxon) {
|
|
| 422 |
if (isTaxonSynonym(stayTaxon)){
|
|
| 423 |
for (TaxonRelationship rel: stayTaxon.getRelationsFromThisTaxon()){
|
|
| 424 |
boolean isPseudo = TaxonRelationshipType.pseudoTaxonUuids().contains(rel.getType().getUuid()); |
|
| 425 |
if (isPseudo){
|
|
| 426 |
return rel.getToTaxon(); |
|
| 427 |
} |
|
| 428 |
} |
|
| 429 |
} |
|
| 430 |
return stayTaxon; |
|
| 431 |
} |
|
| 408 | 432 |
private boolean mergeSynonyms(Taxon removeTaxon, Taxon stayTaxon, boolean isTaxonSynonym) {
|
| 409 | 433 |
if (isTaxonSynonym){
|
| 410 | 434 |
if (!removeTaxon.getSynonyms().isEmpty()){
|
| ... | ... | |
| 467 | 491 |
} |
| 468 | 492 |
} |
| 469 | 493 |
|
| 470 |
private IdentifiableEntity<?> selectStay(IdentifiableEntity<?> removeEntity, IdentifiableEntity<?> stayEntity, String type) {
|
|
| 494 |
private <T extends IdentifiableEntity<?>> T selectStay(T removeEntity, T stayEntity, String type) {
|
|
| 471 | 495 |
if(removeEntity.isInstanceOf(Taxon.class) && stayEntity.isInstanceOf(Synonym.class)){
|
| 472 | 496 |
String answer = ""; |
| 473 | 497 |
while(!(answer.matches("[sSaAcC]"))){
|
| ... | ... | |
| 476 | 500 |
if (answer.equalsIgnoreCase("c")){
|
| 477 | 501 |
return null; |
| 478 | 502 |
}else if (answer.equalsIgnoreCase("a")){
|
| 479 |
return accTaxon(CdmBase.deproxy(stayEntity, Synonym.class)); |
|
| 503 |
return (T)accTaxon(CdmBase.deproxy(stayEntity, Synonym.class));
|
|
| 480 | 504 |
}else{
|
| 481 | 505 |
return stayEntity; |
| 482 | 506 |
} |
| ... | ... | |
| 525 | 549 |
IdentifiableEntity<?> stayEntity) throws CloneNotSupportedException {
|
| 526 | 550 |
String className = removeEntity.getClass().getSimpleName(); |
| 527 | 551 |
for (IdentifiableSource source: removeEntity.getSources()){
|
| 528 |
System.out.println("Move "+className+" source: " + source.getType().getMessage() + ": " + source.getCitation().getTitleCache() + "; " + source.getIdInSource() + "/" + source.getIdNamespace());
|
|
| 552 |
System.out.println("Move "+className+" source: " + source.getType().getLabel() + ": " + source.getCitation().getTitleCache() + "; " + source.getIdInSource() + "/" + source.getIdNamespace());
|
|
| 529 | 553 |
stayEntity.addSource((IdentifiableSource)source.clone()); |
| 530 | 554 |
} |
| 531 | 555 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiMergeObject.java | ||
|---|---|---|
| 1 | 1 |
package eu.etaxonomy.cdm.app.pesi.merging; |
| 2 | 2 |
|
| 3 |
import java.util.List; |
|
| 4 |
|
|
| 5 |
import eu.etaxonomy.cdm.common.CdmUtils; |
|
| 3 | 6 |
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
| 4 | 7 |
|
| 5 | 8 |
public class PesiMergeObject {
|
| ... | ... | |
| 12 | 15 |
|
| 13 | 16 |
private String idTaxon; |
| 14 | 17 |
|
| 15 |
private String uuidTaxonNode; |
|
| 16 |
|
|
| 17 | 18 |
private String idInSource; |
| 18 | 19 |
|
| 19 | 20 |
private String nameCache; |
| ... | ... | |
| 30 | 31 |
|
| 31 | 32 |
private TaxonNodeDto kingdom; |
| 32 | 33 |
|
| 33 |
private TaxonNodeDto family; |
|
| 34 |
private TaxonNodeDto tclass; |
|
| 35 |
|
|
| 36 |
private TaxonNodeDto order; |
|
| 37 |
|
|
| 38 |
private TaxonNodeDto family; |
|
| 39 |
|
|
| 40 |
private List<TaxonNodeDto> higherClassification; |
|
| 34 | 41 |
|
| 35 | 42 |
private String parentString; |
| 36 | 43 |
|
| ... | ... | |
| 127 | 134 |
this.phylum = phylum; |
| 128 | 135 |
} |
| 129 | 136 |
|
| 137 |
//class and getClass are part of java core therefore use other name |
|
| 138 |
public TaxonNodeDto getTClass() {
|
|
| 139 |
return tclass; |
|
| 140 |
} |
|
| 141 |
public String getClassCache() {
|
|
| 142 |
return tclass == null? null : tclass.getNameCache(); |
|
| 143 |
} |
|
| 144 |
public void setTClass(TaxonNodeDto tclass) {
|
|
| 145 |
this.tclass = tclass; |
|
| 146 |
} |
|
| 147 |
|
|
| 148 |
//order |
|
| 149 |
public TaxonNodeDto getOrder() {
|
|
| 150 |
return order; |
|
| 151 |
} |
|
| 152 |
public String getOrderCache() {
|
|
| 153 |
return order == null? null : order.getNameCache(); |
|
| 154 |
} |
|
| 155 |
public void setOrder(TaxonNodeDto order) {
|
|
| 156 |
this.order = order; |
|
| 157 |
} |
|
| 158 |
|
|
| 159 |
//family |
|
| 130 | 160 |
public TaxonNodeDto getFamily() {
|
| 131 | 161 |
return family; |
| 132 | 162 |
} |
| ... | ... | |
| 137 | 167 |
this.family = family; |
| 138 | 168 |
} |
| 139 | 169 |
|
| 170 |
//classification |
|
| 171 |
public List<TaxonNodeDto> getHigherClassification() {
|
|
| 172 |
return higherClassification; |
|
| 173 |
} |
|
| 174 |
public String getClassificationCache() {
|
|
| 175 |
return higherClassification == null? null : classificationCache(); |
|
| 176 |
} |
|
| 177 |
public void setHigherClassification(List<TaxonNodeDto> higherClassification) {
|
|
| 178 |
this.higherClassification = higherClassification; |
|
| 179 |
} |
|
| 180 |
|
|
| 181 |
private String classificationCache() {
|
|
| 182 |
String result = ""; |
|
| 183 |
for (TaxonNodeDto dto : this.higherClassification){
|
|
| 184 |
result = CdmUtils.concat("-", result, dto.getNameCache());
|
|
| 185 |
} |
|
| 186 |
return result; |
|
| 187 |
} |
|
| 188 |
|
|
| 189 |
//taxon uuid |
|
| 140 | 190 |
public String getUuidTaxon() {
|
| 141 | 191 |
return uuidTaxon; |
| 142 | 192 |
} |
| 143 |
|
|
| 144 | 193 |
public void setUuidTaxon(String uuidTaxon) {
|
| 145 | 194 |
this.uuidTaxon = uuidTaxon; |
| 146 | 195 |
} |
| 147 | 196 |
|
| 197 |
//taxon id |
|
| 148 | 198 |
public String getIdTaxon() {
|
| 149 | 199 |
return idTaxon; |
| 150 | 200 |
} |
| 151 |
|
|
| 152 | 201 |
public void setIdTaxon(String idTaxon) {
|
| 153 | 202 |
this.idTaxon = idTaxon; |
| 154 | 203 |
} |
| 155 | 204 |
|
| 205 |
//source uuid |
|
| 156 | 206 |
public String getUuidSource() {
|
| 157 | 207 |
return uuidSource; |
| 158 | 208 |
} |
| 159 |
|
|
| 160 | 209 |
public void setUuidSource(String uuidSource) {
|
| 161 | 210 |
this.uuidSource = uuidSource; |
| 162 | 211 |
} |
| 163 | 212 |
|
| 213 |
//nom.ref. |
|
| 164 | 214 |
public String getNomenclaturalReference() {
|
| 165 | 215 |
return nomenclaturalReference; |
| 166 | 216 |
} |
Also available in: Unified diff
ref #1447 latest changes to PesiCommandLineMerge and PesiMergeObject