@Override
public void run() throws TaxomaticException {
List<Taxon> taxaToSave = new ArrayList<Taxon>();
for (Taxon mergedTaxon : taxaToMerge) {
mergedTaxon.setStatus(TaxonStatus.STATUS_SYNONYM);
{
Synonym synonym = Taxon.synonymizeTaxon(mergedTaxon);
synonym.setStatus(Synonym.MERGE);
synonym.setTaxon(mergeTarget);
mergeTarget.getSynonyms().add(synonym);
}
{
Synonym synonym = Taxon.synonymizeTaxon(mergeTarget);
synonym.setStatus(Synonym.MERGE);
synonym.setTaxon(mergedTaxon);
mergedTaxon.getSynonyms().add(synonym);
}
for (Taxon child : mergedTaxon.getChildren()) {
child.setParent(mergeTarget);
mergeTarget.getChildren().add(child);
taxaToSave.add(child);
}
taxaToSave.add(mergedTaxon);
}
taxaToSave.add(mergeTarget);
taxomaticIO.updateAndSave(taxaToSave, operation.getUser(), true);
recordOperationHistory(taxaToSave, operation);
}
public MergeNodesOperation(
Session session, User user, Taxon mergeTarget, List<Taxon> taxaToMerge) {
super(session, TaxomaticIO.MERGE);
TaxomaticOperation operation = new TaxomaticOperation();
operation.setDate(new Date());
operation.setInstructions(generateInstructions(mergeTarget, taxaToMerge));
operation.setDetails(generateDetails(mergeTarget, taxaToMerge));
operation.setOperation(TaxomaticIO.MERGE);
operation.setUser(user);
this.operation = operation;
this.mergeTarget = mergeTarget;
this.taxaToMerge = taxaToMerge;
}
public MergeNodesOperation(Session session, TaxomaticOperation operation) {
super(session, TaxomaticIO.MERGE);
this.operation = operation;
this.mergeTarget = loadMergeTarget(operation.getInstructions());
this.taxaToMerge = loadTaxaToMerge(operation.getInstructions());
}