Revision 3f131c46
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/merging/PesiFindIdenticalNamesActivator.java | ||
|---|---|---|
| 11 | 11 |
import java.util.ArrayList; |
| 12 | 12 |
import java.util.Arrays; |
| 13 | 13 |
import java.util.HashMap; |
| 14 |
import java.util.HashSet; |
|
| 14 | 15 |
import java.util.Iterator; |
| 15 | 16 |
import java.util.List; |
| 16 | 17 |
import java.util.Map; |
| ... | ... | |
| 18 | 19 |
import java.util.UUID; |
| 19 | 20 |
|
| 20 | 21 |
import org.apache.log4j.Logger; |
| 22 |
import org.springframework.transaction.TransactionStatus; |
|
| 21 | 23 |
|
| 22 | 24 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
| 23 | 25 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| ... | ... | |
| 36 | 38 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 37 | 39 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 38 | 40 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 41 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
|
| 42 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
|
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto; |
| 40 | 44 |
|
| 41 | 45 |
public class PesiFindIdenticalNamesActivator {
|
| ... | ... | |
| 85 | 89 |
System.out.println("Start getIdenticalNames...");
|
| 86 | 90 |
|
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Map<String, Map<UUID, Set<TaxonName>>> namesOfIdenticalTaxa; |
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TransactionStatus tx = app.startTransaction(true); |
|
| 88 | 93 |
try {
|
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namesOfIdenticalTaxa = app.getTaxonService().findIdenticalTaxonNames(sourceRefUuids, propertyPaths); |
| 90 | 95 |
} catch (Exception e) {
|
| ... | ... | |
| 93 | 98 |
} |
| 94 | 99 |
System.out.println("Start creating merging objects");
|
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List<Map<UUID, PesiMergeObject>> mergingObjects = createMergeObjects(namesOfIdenticalTaxa, app); |
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app.commitTransaction(tx); |
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|
|
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boolean resultOK = true; |
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System.out.println("Start creating csv files");
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resultOK &= writeSameNamesDifferentAuthorToCsv(mergingObjects, sources, path + "_authors.csv"); |
| ... | ... | |
| 180 | 187 |
} |
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} |
| 182 | 189 |
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private boolean isDifferent(Map<UUID, PesiMergeObject> merging, Method method) throws IllegalAccessException, IllegalArgumentException, InvocationTargetException {
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private boolean isDifferent(Map<UUID, PesiMergeObject> merging, Method method) |
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throws IllegalAccessException, IllegalArgumentException, InvocationTargetException {
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|
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|
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if (method == null){
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return true; |
| ... | ... | |
| 218 | 226 |
writer.append(';');
|
| 219 | 227 |
writer.append("rank"+i);
|
| 220 | 228 |
writer.append(';');
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writer.append("state"+i);
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writer.append("status"+i);
|
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writer.append(';');
|
| 223 | 231 |
writer.append("phylum"+i);
|
| 224 | 232 |
writer.append(';');
|
| ... | ... | |
| 237 | 245 |
if(merging == null){
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continue; |
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} |
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writer.append(sources.get(uuid)).append(";");
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writer.append(merging.getUuidName()).append(";");
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writer.append(merging.getIdInSource()).append(";");
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writer.append(merging.getNameCache()).append(";");
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writer.append(merging.getAuthor()).append(";");
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writer.append(merging.getRank()).append(";");
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writer.append(Nz(sources.get(uuid))).append(";");
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writer.append(Nz(merging.getUuidName())).append(";");
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writer.append(Nz(merging.getIdInSource())).append(";");
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writer.append(Nz(merging.getNameCache())).append(";");
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writer.append(Nz(merging.getAuthor())).append(";");
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writer.append(Nz(merging.getRank())).append(";");
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if (merging.isStatus()){
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writer.append("accepted").append(";");;
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writer.append("accepted").append(";");
|
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| 248 | 256 |
}else{
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writer.append("synonym").append(";");;
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writer.append("synonym").append(";");
|
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} |
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writer.append(merging.getPhylum() != null? merging.getPhylum().getTitleCache(): "").append(";");
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writer.append(merging.getParentString()).append(";");
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writer.append(merging.getParentRankString()).append(";");;
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writer.append(Nz(merging.getPhylum() != null? merging.getPhylum().getTitleCache(): "")).append(";");
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writer.append(Nz(merging.getParentString())).append(";");
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writer.append(Nz(merging.getParentRankString())).append(";");
|
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} |
| 255 | 263 |
writer.append('\n');
|
| 256 | 264 |
} |
| 257 | 265 |
|
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private List<Map<UUID,PesiMergeObject>> createMergeObjects(Map<String, Map<UUID, Set<TaxonName>>> names,
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private List<Map<UUID,PesiMergeObject>> createMergeObjects(Map<String, Map<UUID, Set<TaxonName>>> names,
|
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CdmApplicationController appCtr){
|
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|
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List<Map<UUID,PesiMergeObject>> merge = new ArrayList<>(); |
| ... | ... | |
| 298 | 306 |
//TODO: find the two correct names |
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logger.warn("Name has not exact 1 but " + taxonBases.size() + " taxon base attached. This is not yet handled. Take arbitrary one.");
|
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} |
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TaxonBase<?> taxonBase = taxonBases.iterator().next(); |
|
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|
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//uuid |
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mergeObject.setUuidName(name.getUuid().toString()); |
| ... | ... | |
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mergeObject.setRank(name.getRank().getLabel()); |
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|
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//Phylum |
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TaxonNodeDto phylum = null; |
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if (name.getRank().equals(Rank.PHYLUM())) {
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Taxon taxon = getAcceptedTaxon(name); |
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if (taxon != null) {
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if (taxon.getTaxonNodes().size()>1){
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logger.warn("More than 1 node not yet handled for getPhylum. Take arbitrary one.");
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} |
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TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
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phylum = new TaxonNodeDto(node); |
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} |
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|
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} |
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if (phylum == null && !name.getRank().isHigher(Rank.PHYLUM())){
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Taxon taxon = getAcceptedTaxon(name); |
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if (!taxon.getTaxonNodes().isEmpty()){
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if (taxon.getTaxonNodes().size()>1){
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logger.warn("More than 1 node not yet handled for getPhylum. Take arbitrary one.");
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} |
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TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
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phylum = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(node.getClassification(), Rank.PHYLUM(), name); |
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} |
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} |
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TaxonNodeDto phylum = getPhylum(appCtr, name); |
|
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mergeObject.setPhylum(phylum); |
| 339 | 325 |
|
| 340 | 326 |
//idInSource |
| ... | ... | |
| 348 | 334 |
|
| 349 | 335 |
//status and parent |
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Set<Taxon> taxa = name.getTaxa(); |
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taxa = getReallyAcceptedTaxa(taxa); |
|
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if (!taxa.isEmpty()){
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mergeObject.setStatus(true); |
| 353 | 340 |
Iterator<Taxon> taxaIterator = taxa.iterator(); |
| ... | ... | |
| 416 | 403 |
merge.add(mergeMap); |
| 417 | 404 |
} |
| 418 | 405 |
|
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private TaxonNodeDto getPhylum(CdmApplicationController appCtr, TaxonName name) {
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TaxonNodeDto phylum = null; |
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if (name.getRank().equals(Rank.PHYLUM())) {
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Taxon taxon = getAcceptedTaxon(name); |
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if (taxon != null) {
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if (taxon.getTaxonNodes().size()>1){
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logger.warn("More than 1 node not yet handled for getPhylum. Take arbitrary one.");
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} |
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TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
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phylum = new TaxonNodeDto(node); |
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} |
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|
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} |
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if (phylum == null && !name.getRank().isHigher(Rank.PHYLUM())){
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Taxon taxon = getAcceptedTaxon(name); |
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if (!taxon.getTaxonNodes().isEmpty()){
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if (taxon.getTaxonNodes().size()>1){
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logger.warn("More than 1 node not yet handled for getPhylum. Take arbitrary one.");
|
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} |
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TaxonNode node = taxon.getTaxonNodes().iterator().next(); |
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phylum = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(node.getClassification(), Rank.PHYLUM(), name); |
|
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} |
|
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} |
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return phylum; |
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} |
|
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|
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| 419 | 432 |
private TaxonNode getAcceptedNode(TaxonName ermsName) {
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TaxonNode parentNode = null; |
|
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Set<TaxonBase> taxonBases = ermsName.getTaxonBases(); |
| 421 |
Taxon taxon = null;
|
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if (taxonBases != null && !taxonBases.isEmpty()) {
|
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if (!taxonBases.isEmpty()) {
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Taxon taxon = null;
|
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TaxonBase<?> taxonBase = taxonBases.iterator().next(); |
| 424 | 438 |
if (taxonBase instanceof Synonym) {
|
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taxon = ((Synonym)taxonBase).getAcceptedTaxon(); |
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}else{
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taxon = getAccTaxonForTaxonSynonym((Taxon)taxonBase); |
|
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} |
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Set<TaxonNode> nodes = taxon.getTaxonNodes(); |
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if (!nodes.isEmpty()) {
|
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parentNode = nodes.iterator().next(); |
|
| 426 | 446 |
} |
| 427 | 447 |
} |
| 428 | 448 |
|
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Set<TaxonNode> nodes = taxon.getTaxonNodes(); |
|
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|
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TaxonNode parentNode = null; |
|
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if (nodes != null && !nodes.isEmpty()) {
|
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parentNode = nodes.iterator().next(); |
|
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} |
|
| 435 | 449 |
return parentNode; |
| 436 | 450 |
} |
| 437 | 451 |
|
| ... | ... | |
| 440 | 454 |
//prefer accepted taxon |
| 441 | 455 |
if (name.getTaxa() != null && !name.getTaxa().isEmpty()){
|
| 442 | 456 |
taxon = name.getTaxa().iterator().next(); |
| 457 |
taxon = getAccTaxonForTaxonSynonym(taxon); |
|
| 443 | 458 |
//else take synonym |
| 444 | 459 |
}else if (name.getTaxonBases() != null && !name.getTaxonBases().isEmpty()){
|
| 445 | 460 |
TaxonBase<?> taxonBase = name.getTaxonBases().iterator().next(); |
| ... | ... | |
| 451 | 466 |
return taxon; |
| 452 | 467 |
} |
| 453 | 468 |
|
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private Taxon getAccTaxonForTaxonSynonym(Taxon taxon) {
|
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if (!taxon.getRelationsFromThisTaxon().isEmpty()){
|
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for (TaxonRelationship rel: taxon.getRelationsFromThisTaxon()){
|
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UUID uuidType = rel.getType().getUuid(); |
|
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if (uuidType.equals(TaxonRelationshipType.uuidSynonymOfTaxonRelationship) |
|
| 474 |
|| uuidType.equals(TaxonRelationshipType.uuidHeterotypicSynonymTaxonRelationship) |
|
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|| uuidType.equals(TaxonRelationshipType.uuidHomotypicSynonymTaxonRelationship)){
|
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taxon = rel.getToTaxon(); |
|
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} |
|
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} |
|
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} |
|
| 480 |
return taxon; |
|
| 481 |
} |
|
| 482 |
|
|
| 483 |
/** |
|
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* Filters out the ERMS taxon synonyms |
|
| 485 |
*/ |
|
| 486 |
private Set<Taxon> getReallyAcceptedTaxa(Set<Taxon> taxa) {
|
|
| 487 |
Set<Taxon> result = new HashSet<>(); |
|
| 488 |
for (Taxon taxon : taxa){
|
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| 489 |
Taxon accTaxon = getAccTaxonForTaxonSynonym(taxon); |
|
| 490 |
if(taxon.equals(accTaxon)) {
|
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result.add(taxon); |
|
| 492 |
} |
|
| 493 |
} |
|
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return result; |
|
| 495 |
} |
|
| 496 |
|
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| 497 |
private CharSequence Nz(String str) {
|
|
| 498 |
return CdmUtils.Nz(str); |
|
| 499 |
} |
|
| 500 |
|
|
| 454 | 501 |
public static void main(String[] args) {
|
| 455 | 502 |
PesiFindIdenticalNamesActivator activator = new PesiFindIdenticalNamesActivator(); |
| 456 | 503 |
activator.invoke(pesiSource); |
Also available in: Unified diff
ref #1447 handle null and ERMS pseudo taxa and some minor changes