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/**
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* Copyright (C) 2020 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.app.pesi.merging;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Optional;
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import java.util.Set;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import org.apache.log4j.Logger;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.service.DeleteResult;
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import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.common.CdmRegEx;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;
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import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Credit;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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/**
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* @author a.mueller
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* @since 20.01.2020
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*/
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public class PesiCommandLineMerge extends PesiMergeBase {
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private static final Logger logger = Logger.getLogger(PesiCommandLineMerge.class);
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static final ICdmDataSource pesiSource = CdmDestinations.cdm_pesi2019_final();
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private CdmIoApplicationController app;
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private void invoke(ICdmDataSource source){
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app = CdmIoApplicationController.NewInstance(source, DbSchemaValidation.VALIDATE, false);
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doInvoke();
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}
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private void doInvoke(){
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List<List<String>> fileData = null;
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String next = nextMerge(fileData);
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while(next.equalsIgnoreCase("m")|| next.equals("f")){
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TransactionStatus tx = app.startTransaction();
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TaxonInformation taxonInformation;
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if (next.equalsIgnoreCase("f")){
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if (fileData == null){
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fileData = getFileData();
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}else if (fileData.isEmpty()){
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fileData = null;
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next = nextMerge(fileData);
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continue;
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}
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taxonInformation = readLineFromFile(fileData);
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if (taxonInformation == null){
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app.rollbackTransaction(tx);
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nextMerge(fileData);
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continue;
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}
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}else{
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TaxonBase<?>[] taxa = null;
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while (taxa == null) {
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taxa = readTaxa();
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}
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taxonInformation = new TaxonInformation();
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taxonInformation.taxon2 = taxa[0];
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taxonInformation.taxon1 = taxa[1];
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}
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try {
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mergeTaxa(tx, taxonInformation);
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} catch (Exception e) {
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e.printStackTrace();
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app.rollbackTransaction(tx);
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continue;
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}
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next = nextMerge(fileData);
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}
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}
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private boolean mergeTaxa(TransactionStatus tx, TaxonInformation taxonInformation) {
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boolean commit = compareTaxa(taxonInformation);
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if (commit){
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moveTaxonInformation(taxonInformation);
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}
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if (commit){
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app.commitTransaction(tx);
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if (taxonInformation.taxonToUse == 1 && taxonInformation.nameToUse == 1){
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removeTaxon(taxonInformation.taxon2);
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}else if (booleanAnswer("Information moved. Delete old taxon")){
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removeTaxon(taxonInformation.taxonToUse == 2 ? taxonInformation.taxon1 : taxonInformation.taxon2);
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}
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}else{
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app.rollbackTransaction(tx);
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}
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return commit;
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}
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private class TaxonInformation{
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TaxonBase<?> taxon1;
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TaxonBase<?> taxon2;
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int taxonToUse = 1; //
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int nameToUse = 1;
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}
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/**
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* Reads a line from the file, returns it's taxon information and removes
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* the line from the input list.
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*/
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private TaxonInformation readLineFromFile(List<List<String>> fileData) {
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List<String> line = fileData.get(0);
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TaxonInformation taxonInformation = new TaxonInformation();
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taxonInformation.taxon1 = taxonByString(line.get(0));
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taxonInformation.taxon2 = taxonByString(line.get(1));
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if (taxonInformation.taxon1 == null || taxonInformation.taxon2 == null){
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boolean cancel = booleanAnswer("Taxon1 or Taxon2 could not be read from DB! Cancel record");
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if (cancel){
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fileData.remove(0);
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}
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return null;
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}
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try {
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Integer taxonToUse = Integer.valueOf(line.get(2));
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if (1 != taxonInformation.taxonToUse){
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booleanAnswer("Stay taxon is not '1'");
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}
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Integer nameToUse = "".equals(line.get(3))? taxonToUse: Integer.valueOf(line.get(3));
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if (taxonToUse != 1 && taxonToUse != 2 && taxonToUse != 0){
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boolean cancel = booleanAnswer("taxonToUse is not 0, 1 or 2. Cancel record");
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if (cancel){
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fileData.remove(0);
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}
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return null;
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}else if (taxonToUse == 0){
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logger.warn("Record marked as homonym. No merge: " + taxonInformation.taxon1.getName().getNameCache());
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fileData.remove(0);
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return null;
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}else{
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taxonInformation.taxonToUse = taxonToUse;
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}
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if (nameToUse == null){
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nameToUse = taxonToUse;
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}
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if (nameToUse != 1 && nameToUse != 2){
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logger.warn("Name to use has incorrect value: " + nameToUse);
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}else{
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taxonInformation.nameToUse = nameToUse;
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}
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} catch (NumberFormatException e) {
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e.printStackTrace();
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taxonInformation = null;
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}
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fileData.remove(0);
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return taxonInformation;
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}
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private List<List<String>> getFileData() {
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List<List<String>> result = null;
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while(result == null){
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String input = CdmUtils.readInputLine("Path and filename: ");
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result = readCsvFile(input);
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}
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return result;
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}
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private String nextMerge(List<List<String>> fileData) {
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if (fileData != null){
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return "f";
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}
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do{
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String input = CdmUtils.readInputLine("Next input: manual[m], file[f], quit[q]: ");
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if (input.matches("[mMfFqQ]")){
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return input;
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}
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}while (true);
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}
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private boolean compareTaxa(TaxonInformation taxonInformation) {
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TaxonBase<?> removeTaxon = taxonInformation.taxon2;
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TaxonBase<?> stayTaxon = taxonInformation.taxon1;
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String nc1 = removeTaxon.getName().getNameCache();
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String nc2 = stayTaxon.getName().getNameCache();
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String ft1 = removeTaxon.getName().getFullTitleCache();
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String ft2 = stayTaxon.getName().getFullTitleCache();
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System.out.println("Remove " + getStatusStr(removeTaxon) + ft1);
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System.out.println("Stay " + getStatusStr(stayTaxon) + ft2);
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boolean isStandard = taxonInformation.taxonToUse == 1 && taxonInformation.nameToUse == 1;
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if (!nc1.equals(nc2)){
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return booleanAnswer("Name Cache differs!!! Do you really want to merge???");
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}else if (!ft1.equals(ft2)){
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return isStandard || booleanAnswer("Full title cache differs! Do you really want to merge anyway");
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}else{
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return isStandard || booleanAnswer("Same title. Merge");
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}
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}
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private String getStatusStr(TaxonBase<?> taxon) {
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//TODO MAN and Taxon Synonyms
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if (taxon.isInstanceOf(Synonym.class)){
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return "Syn: ";
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}else{
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return "Acc: ";
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}
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}
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private void removeTaxon(TaxonBase<?> taxonBase) {
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DeleteResult result;
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if (taxonBase.isInstanceOf(Taxon.class)){
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Taxon taxonToRemove = CdmBase.deproxy(taxonBase, Taxon.class);
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TaxonDeletionConfigurator config = new TaxonDeletionConfigurator();
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if (isTaxonSynonym(taxonToRemove)){
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result = app.getTaxonService().deleteTaxon(taxonToRemove.getUuid(), config, null);
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}else{
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TaxonNode nodeToRemove = taxonToRemove.getTaxonNodes().iterator().next();
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result = app.getTaxonNodeService().deleteTaxonNode(nodeToRemove.getUuid(), config);
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}
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}else{
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Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
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SynonymDeletionConfigurator config = new SynonymDeletionConfigurator();
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result = app.getTaxonService().deleteSynonym(syn.getUuid(), config);
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}
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if (!result.isOk()){
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System.out.println("Remove taxon was not successful.");
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}
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254
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}
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255
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256
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private boolean booleanAnswer(String message) {
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String answer = "";
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258
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while (!(answer.equalsIgnoreCase("y") || answer.equalsIgnoreCase("n"))){
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answer = CdmUtils.readInputLine(message + " (y/n)? ");
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}
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return answer.equalsIgnoreCase("y");
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}
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263
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264
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private boolean moveTaxonInformation(TaxonInformation taxonInformation) {
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try {
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TaxonBase<?> removeTaxon = CdmBase.deproxy(taxonInformation.taxonToUse == 2 ? taxonInformation.taxon1: taxonInformation.taxon2);
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TaxonBase<?> stayTaxon = CdmBase.deproxy(taxonInformation.taxonToUse == 2 ? taxonInformation.taxon2 : taxonInformation.taxon1);
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//mergeTaxa;
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mergeSources(removeTaxon, stayTaxon);
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mergeAnnotations(removeTaxon, stayTaxon);
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mergeMarkers(removeTaxon, stayTaxon);
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//TODO for
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mergeExtensions(removeTaxon, stayTaxon);
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mergeCredits(removeTaxon, stayTaxon);
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277
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if (removeTaxon.isInstanceOf(Taxon.class)){
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Taxon removeAccTaxon = CdmBase.deproxy(removeTaxon, Taxon.class);
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279
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280
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Taxon stayAccTaxon = accTaxon(stayTaxon);
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mergeDescriptions(removeAccTaxon, accTaxon(stayTaxon));
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boolean isTaxonSynonym = isTaxonSynonym(removeAccTaxon);
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283
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mergeSynonyms(removeAccTaxon, stayAccTaxon, isTaxonSynonym);
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284
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mergeChildren(removeAccTaxon, stayAccTaxon, isTaxonSynonym);
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285
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//TODO taxon synonym relations
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286
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mergeTaxonRelations(removeAccTaxon, stayAccTaxon, isTaxonSynonym);
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287
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}
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288
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289
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//mergeNames;
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290
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TaxonName removeName;
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291
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TaxonName stayName;
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292
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if (taxonInformation.nameToUse == taxonInformation.taxonToUse){
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removeName = CdmBase.deproxy(removeTaxon.getName());
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stayName = CdmBase.deproxy(stayTaxon.getName());
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295
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}else{
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removeName = CdmBase.deproxy(stayTaxon.getName());
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297
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stayName = CdmBase.deproxy(removeTaxon.getName());
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298
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stayTaxon.setName(stayName);
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299
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}
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300
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//TODO unclear if name information should be merged at all
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301
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mergeSources(removeName, stayName);
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302
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mergeAnnotations(removeName, stayName);
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303
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mergeMarkers(removeName, stayName);
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304
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mergeExtensions(removeName, stayName);
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305
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mergeCredits(removeName, stayName);
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306
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mergeNameRelationships(removeName, stayName);
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307
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mergeHybridRelationships(removeName, stayName);
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308
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mergeNameDescriptions(removeName, stayName);
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309
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310
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if(taxonInformation.taxonToUse == 1 && taxonInformation.nameToUse == 1){
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311
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return true;
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312
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}else{
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313
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return booleanAnswer("Commit moved information");
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314
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}
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315
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} catch (CloneNotSupportedException e) {
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316
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e.printStackTrace();
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317
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return false;
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318
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}
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319
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}
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320
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321
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private boolean isTaxonSynonym(Taxon removeAccTaxon) {
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322
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for (TaxonRelationship rel: removeAccTaxon.getRelationsFromThisTaxon()){
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323
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boolean isPseudo = TaxonRelationshipType.pseudoTaxonUuids().contains(rel.getType().getUuid());
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324
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if (isPseudo){
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325
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return true;
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326
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}
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327
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}
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328
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return false;
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329
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}
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330
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331
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private Taxon accTaxon(TaxonBase<?> stayTaxon) {
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332
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if (stayTaxon.isInstanceOf(Synonym.class)){
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333
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return CdmBase.deproxy(stayTaxon, Synonym.class).getAcceptedTaxon();
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334
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}else{
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335
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return CdmBase.deproxy(stayTaxon, Taxon.class);
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336
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}
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337
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}
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338
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339
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private boolean mergeTaxonRelations(Taxon removeTaxon, Taxon stayTaxon, boolean isTaxonSynonym) {
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340
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if (isTaxonSynonym){
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341
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if (!removeTaxon.getRelationsToThisTaxon().isEmpty()){
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342
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logger.warn("taxon synonym has taxon relations to itself. This should not happen. Handle manually.");
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343
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return false;
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344
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}else{
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345
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return true;
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346
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}
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347
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}
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348
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for (TaxonRelationship rel : removeTaxon.getRelationsToThisTaxon()){
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349
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System.out.println("Move taxon relationship: " + rel.getType().getTitleCache() + ": " + rel.getFromTaxon().getTitleCache());
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350
|
|
|
351
|
rel.setToTaxon(stayTaxon);
|
|
352
|
// if (!synonymExists()){
|
|
353
|
// //TODO homotypical group
|
|
354
|
// stayTaxon.addSynonym(synonym, synonym.getType());
|
|
355
|
// }else{
|
|
356
|
// //TODO merge synonym names
|
|
357
|
// }
|
|
358
|
}
|
|
359
|
if(!removeTaxon.getRelationsFromThisTaxon().isEmpty()){
|
|
360
|
logger.warn("Taxon-from-relations not yet implemented");
|
|
361
|
}
|
|
362
|
return true;
|
|
363
|
}
|
|
364
|
|
|
365
|
private void mergeNameDescriptions(TaxonName removeName, @SuppressWarnings("unused") TaxonName stayName) {
|
|
366
|
if(!removeName.getDescriptions().isEmpty()){
|
|
367
|
logger.warn("Name description exist but merge not yet implemented");
|
|
368
|
}
|
|
369
|
}
|
|
370
|
|
|
371
|
private void mergeHybridRelationships(TaxonName removeName, @SuppressWarnings("unused") TaxonName stayName) {
|
|
372
|
if(!removeName.getHybridChildRelations().isEmpty()){
|
|
373
|
logger.warn("Hybrid child relation exist but merge not yet implemented");
|
|
374
|
}
|
|
375
|
if(!removeName.getHybridParentRelations().isEmpty()){
|
|
376
|
logger.warn("Hybrid parent relation exist but merge not yet implemented");
|
|
377
|
}
|
|
378
|
}
|
|
379
|
|
|
380
|
private void mergeNameRelationships(TaxonName removeName, @SuppressWarnings("unused") TaxonName stayName) {
|
|
381
|
if(!removeName.getNameRelations().isEmpty()){
|
|
382
|
logger.warn("Name relations exist but merge not yet implemented");
|
|
383
|
}
|
|
384
|
}
|
|
385
|
|
|
386
|
private boolean mergeChildren(Taxon removeTaxon, Taxon stayTaxon, boolean isTaxonSynonym) {
|
|
387
|
if (isTaxonSynonym){
|
|
388
|
if (!removeTaxon.getTaxonNodes().isEmpty()){
|
|
389
|
logger.warn("taxon synonym has taxon node itself. This should not happen. Handle manually.");
|
|
390
|
return false;
|
|
391
|
}else{
|
|
392
|
return true;
|
|
393
|
}
|
|
394
|
}
|
|
395
|
TaxonNode removeNode = removeTaxon.getTaxonNodes().iterator().next();
|
|
396
|
TaxonNode stayNode = stayTaxon.getTaxonNodes().iterator().next();
|
|
397
|
Set<UUID> removeNodeChildrenUuids = removeNode.getChildNodes()
|
|
398
|
.stream().map(tn->tn.getUuid()).collect(Collectors.toSet());
|
|
399
|
|
|
400
|
if(!removeNodeChildrenUuids.isEmpty()){
|
|
401
|
app.getTaxonNodeService().moveTaxonNodes(removeNodeChildrenUuids,
|
|
402
|
stayNode.getUuid(), 0, null);
|
|
403
|
System.out.println("Child nodes moved: " + removeNodeChildrenUuids.size());
|
|
404
|
}
|
|
405
|
return true;
|
|
406
|
}
|
|
407
|
|
|
408
|
private boolean mergeSynonyms(Taxon removeTaxon, Taxon stayTaxon, boolean isTaxonSynonym) {
|
|
409
|
if (isTaxonSynonym){
|
|
410
|
if (!removeTaxon.getSynonyms().isEmpty()){
|
|
411
|
logger.warn("taxon synonym has synonyms itself. This should not happen. Handle manually.");
|
|
412
|
return false;
|
|
413
|
}else{
|
|
414
|
return true;
|
|
415
|
}
|
|
416
|
}
|
|
417
|
Set<Synonym> synonymsToAdd = new HashSet<>();
|
|
418
|
for (Synonym synonym : removeTaxon.getSynonyms()){
|
|
419
|
if (!synonymExists()){
|
|
420
|
//TODO homotypical group
|
|
421
|
synonymsToAdd.add(synonym);
|
|
422
|
}else{
|
|
423
|
//TODO merge synonym names
|
|
424
|
}
|
|
425
|
}
|
|
426
|
for (Synonym synonym: synonymsToAdd){
|
|
427
|
stayTaxon.addSynonym(synonym, synonym.getType());
|
|
428
|
}
|
|
429
|
return true;
|
|
430
|
}
|
|
431
|
|
|
432
|
private boolean synonymExists() {
|
|
433
|
logger.warn("Synonym dulicate check - not yet implemented");
|
|
434
|
return false;
|
|
435
|
}
|
|
436
|
|
|
437
|
private void mergeDescriptions(Taxon remove, Taxon stay) {
|
|
438
|
//TODO handle duplicates for taxon descriptions
|
|
439
|
for (TaxonDescription description: remove.getDescriptions()){
|
|
440
|
System.out.println("Move taxon description: " + description.getTitleCache());
|
|
441
|
stay.addDescription((TaxonDescription)description.clone());
|
|
442
|
}
|
|
443
|
}
|
|
444
|
|
|
445
|
private void mergeCredits(IdentifiableEntity<?> removeEntity,
|
|
446
|
IdentifiableEntity<?> stayEntity) throws CloneNotSupportedException {
|
|
447
|
String className = removeEntity.getClass().getSimpleName();
|
|
448
|
for (Credit credit: removeEntity.getCredits()){
|
|
449
|
System.out.println("Move "+className+" credit: " + credit.toString());
|
|
450
|
stayEntity.addCredit((Credit)credit.clone());
|
|
451
|
}
|
|
452
|
}
|
|
453
|
|
|
454
|
private void mergeExtensions(IdentifiableEntity<?> removeEntity,
|
|
455
|
IdentifiableEntity<?> stayEntity) throws CloneNotSupportedException {
|
|
456
|
|
|
457
|
String className = removeEntity.getClass().getSimpleName();
|
|
458
|
for (Extension extension: removeEntity.getExtensions()){
|
|
459
|
if (!filterExtension(extension, removeEntity, stayEntity)){
|
|
460
|
System.out.println("Move "+className+" extension: " + extension.getType().getTitleCache() + ": " + extension.getValue());
|
|
461
|
|
|
462
|
IdentifiableEntity<?> thisStayEntity = selectStay(removeEntity, stayEntity, "Extension");
|
|
463
|
if (thisStayEntity != null){
|
|
464
|
thisStayEntity.addExtension((Extension)extension.clone());
|
|
465
|
}
|
|
466
|
}
|
|
467
|
}
|
|
468
|
}
|
|
469
|
|
|
470
|
private IdentifiableEntity<?> selectStay(IdentifiableEntity<?> removeEntity, IdentifiableEntity<?> stayEntity, String type) {
|
|
471
|
if(removeEntity.isInstanceOf(Taxon.class) && stayEntity.isInstanceOf(Synonym.class)){
|
|
472
|
String answer = "";
|
|
473
|
while(!(answer.matches("[sSaAcC]"))){
|
|
474
|
answer = CdmUtils.readInputLine(type + ": Stay is Synonym. Move information to [s]ynonym, to [a]ccepted or [c]ancel extension merge?: ");
|
|
475
|
}
|
|
476
|
if (answer.equalsIgnoreCase("c")){
|
|
477
|
return null;
|
|
478
|
}else if (answer.equalsIgnoreCase("a")){
|
|
479
|
return accTaxon(CdmBase.deproxy(stayEntity, Synonym.class));
|
|
480
|
}else{
|
|
481
|
return stayEntity;
|
|
482
|
}
|
|
483
|
}
|
|
484
|
return stayEntity;
|
|
485
|
}
|
|
486
|
|
|
487
|
private boolean filterExtension(Extension extension,
|
|
488
|
@SuppressWarnings("unused") IdentifiableEntity<?> removeEntity,
|
|
489
|
@SuppressWarnings("unused") IdentifiableEntity<?> stayEntity) {
|
|
490
|
if (extension.getType().getUuid().equals(ErmsTransformer.uuidExtDisplayName)){
|
|
491
|
//for merged taxa display name information is not relevant because name is formatted according to "stay" taxon.
|
|
492
|
return true;
|
|
493
|
}
|
|
494
|
return false;
|
|
495
|
}
|
|
496
|
|
|
497
|
private void mergeMarkers(IdentifiableEntity<?> removeEntity,
|
|
498
|
IdentifiableEntity<?> stayEntity) throws CloneNotSupportedException {
|
|
499
|
String className = removeEntity.getClass().getSimpleName();
|
|
500
|
for (Marker marker: removeEntity.getMarkers()){
|
|
501
|
if (!filterMarker(marker, removeEntity, stayEntity)){
|
|
502
|
System.out.println("Move "+className+" marker: " + marker.getMarkerType().getTitleCache() + ": " + marker.getValue());
|
|
503
|
IdentifiableEntity<?> thisStayEntity = selectStay(removeEntity, stayEntity, "Marker");
|
|
504
|
if (thisStayEntity != null){
|
|
505
|
thisStayEntity.addMarker((Marker)marker.clone());
|
|
506
|
}
|
|
507
|
}
|
|
508
|
}
|
|
509
|
}
|
|
510
|
|
|
511
|
private void mergeAnnotations(IdentifiableEntity<?> removeEntity,
|
|
512
|
IdentifiableEntity<?> stayEntity) throws CloneNotSupportedException {
|
|
513
|
String className = removeEntity.getClass().getSimpleName();
|
|
514
|
for (Annotation annotation: removeEntity.getAnnotations()){
|
|
515
|
if (!filterAnnotation(annotation, removeEntity, stayEntity)){
|
|
516
|
String type = annotation.getAnnotationType() == null? "no type" : annotation.getAnnotationType().getTitleCache();
|
|
517
|
System.out.println("Move "+className+" note: " + type + ": " + annotation.getText());
|
|
518
|
handleRemoveAnnotation(annotation, removeEntity, stayEntity);
|
|
519
|
stayEntity.addAnnotation((Annotation)annotation.clone());
|
|
520
|
}
|
|
521
|
}
|
|
522
|
}
|
|
523
|
|
|
524
|
private void mergeSources(IdentifiableEntity<?> removeEntity,
|
|
525
|
IdentifiableEntity<?> stayEntity) throws CloneNotSupportedException {
|
|
526
|
String className = removeEntity.getClass().getSimpleName();
|
|
527
|
for (IdentifiableSource source: removeEntity.getSources()){
|
|
528
|
System.out.println("Move "+className+" source: " + source.getType().getMessage() + ": " + source.getCitation().getTitleCache() + "; " + source.getIdInSource() + "/" + source.getIdNamespace());
|
|
529
|
stayEntity.addSource((IdentifiableSource)source.clone());
|
|
530
|
}
|
|
531
|
}
|
|
532
|
|
|
533
|
private boolean filterMarker(Marker marker, @SuppressWarnings("unused") IdentifiableEntity<?> removeEntity,
|
|
534
|
IdentifiableEntity<?> stayEntity) {
|
|
535
|
if (isNoLastActionMarker(marker)){
|
|
536
|
for (Annotation annotation : stayEntity.getAnnotations()){
|
|
537
|
if (isLastActionDateAnnotation(annotation)){
|
|
538
|
return true;
|
|
539
|
}
|
|
540
|
}
|
|
541
|
}
|
|
542
|
return false;
|
|
543
|
}
|
|
544
|
|
|
545
|
private boolean isLastActionDateAnnotation(Annotation annotation) {
|
|
546
|
return annotation.getAnnotationType()!= null
|
|
547
|
&& annotation.getAnnotationType().getUuid().equals(DbLastActionMapper.uuidAnnotationTypeLastActionDate)
|
|
548
|
&& !isBlank(annotation.getText());
|
|
549
|
}
|
|
550
|
|
|
551
|
private void handleRemoveAnnotation(Annotation annotation,
|
|
552
|
@SuppressWarnings("unused") IdentifiableEntity<?> removeEntity,
|
|
553
|
IdentifiableEntity<?> stayEntity) {
|
|
554
|
if (isLastActionDateAnnotation(annotation)){
|
|
555
|
Optional<Marker> noLastActionMarker = stayEntity.getMarkers().stream().filter(m->isNoLastActionMarker(m)).findFirst();
|
|
556
|
if (noLastActionMarker.isPresent()){
|
|
557
|
stayEntity.removeMarker(noLastActionMarker.get());
|
|
558
|
System.out.println(" NoLastActionDate annotation removed from 'stay' " + stayEntity.getClass().getSimpleName());
|
|
559
|
}
|
|
560
|
}
|
|
561
|
}
|
|
562
|
|
|
563
|
private boolean isNoLastActionMarker(Marker marker) {
|
|
564
|
return marker.getMarkerType().getUuid().equals(PesiTransformer.uuidMarkerTypeHasNoLastAction)
|
|
565
|
&& marker.getValue() == true;
|
|
566
|
}
|
|
567
|
|
|
568
|
@SuppressWarnings("unused")
|
|
569
|
private boolean filterAnnotation(Annotation annotation, IdentifiableEntity<?> removeEntity, IdentifiableEntity<?> stayEntity) {
|
|
570
|
return false;
|
|
571
|
}
|
|
572
|
|
|
573
|
private TaxonBase<?>[] readTaxa() {
|
|
574
|
TaxonBase<?> taxon1 = readTaxon("Taxon to be removed");
|
|
575
|
TaxonBase<?> taxon2 = readTaxon("Taxon to stay");
|
|
576
|
if (taxon1 == null || taxon2 == null){
|
|
577
|
return null;
|
|
578
|
}else{
|
|
579
|
return new TaxonBase<?>[]{taxon1, taxon2};
|
|
580
|
}
|
|
581
|
}
|
|
582
|
|
|
583
|
private TaxonBase<?> readTaxon(String message) {
|
|
584
|
TaxonBase<?> taxon = null;
|
|
585
|
boolean quit = false;
|
|
586
|
while (taxon == null && quit == false){
|
|
587
|
String strTaxon = CdmUtils.readInputLine(message + ": ");
|
|
588
|
if (strTaxon.equalsIgnoreCase("q")){
|
|
589
|
quit = true;
|
|
590
|
}else{
|
|
591
|
taxon = taxonByString(strTaxon);
|
|
592
|
}
|
|
593
|
}
|
|
594
|
if (taxon == null){
|
|
595
|
return null;
|
|
596
|
}else if (taxon.isInstanceOf(Synonym.class)){
|
|
597
|
return CdmBase.deproxy(taxon, Synonym.class);
|
|
598
|
}else{
|
|
599
|
return CdmBase.deproxy(taxon, Taxon.class);
|
|
600
|
}
|
|
601
|
}
|
|
602
|
|
|
603
|
/**
|
|
604
|
* Reads a taxon from database using it's id or uuid as String
|
|
605
|
*/
|
|
606
|
private TaxonBase<?> taxonByString(String strTaxon) {
|
|
607
|
TaxonBase<?> taxon = null;
|
|
608
|
if (strTaxon.matches("\\d{1,10}")){
|
|
609
|
taxon = app.getTaxonService().find(Integer.valueOf(strTaxon));
|
|
610
|
}else if (strTaxon.matches(CdmRegEx.UUID_RE)){
|
|
611
|
taxon = app.getTaxonService().find(UUID.fromString(strTaxon));
|
|
612
|
}
|
|
613
|
return taxon;
|
|
614
|
}
|
|
615
|
|
|
616
|
|
|
617
|
|
|
618
|
public static void main(String[] args) {
|
|
619
|
PesiCommandLineMerge merger = new PesiCommandLineMerge();
|
|
620
|
merger.invoke(pesiSource);
|
|
621
|
System.exit(0);
|
|
622
|
}
|
|
623
|
}
|