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// $Id$
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/**
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* Copyright (C) 2017 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.strategy.homotypicgroup;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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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.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.strategy.StrategyBase;
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/**
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* This class tries to guess all basionym relationships for the synonyms of a given taxon
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* by evaluating the name parts including authors.
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* It adds all {@link TaxonName taxon names} that seem to belong to the same
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* basionym to the homotypic group of this basionym and creates the basionym relationship
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* if not yet added/created.<BR>
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* Also it changes the {@link SynonymType synonym type} of the synonyms
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* that are homotypic to the accepted taxon to
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* {@link SynonymType#HOMOTYPIC_SYNONYM_OF() homotypic synonym of}.
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*
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* NOTE: It is still unclear where to put this kind of operations.
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* The base class, package and even the module may change in future.
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*
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* @author a.mueller
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* @date 22.04.2017
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*
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*/
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public class BasionymRelationCreator extends StrategyBase {
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private static final long serialVersionUID = -4711438819176248413L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(BasionymRelationCreator.class);
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private UUID uuid = UUID.fromString("e9e1d1f5-e398-4ba7-81a6-92875573d7cb");
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/**
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* {@inheritDoc}
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*/
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@Override
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protected UUID getUuid() {
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return uuid;
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}
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public void invoke (Taxon taxon){
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Set<Synonym> synonyms = taxon.getSynonyms();
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//compare accepted against synonyms
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for (Synonym synonym: synonyms){
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TaxonName<?, ?> basionym = compareHomotypic(taxon.getName(), synonym.getName());
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if (basionym != null){
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synonym.setType(SynonymType.HOMOTYPIC_SYNONYM_OF());
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adaptHomotypicGroup(basionym, taxon.getName(), synonym.getName());
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}
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}
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List<Synonym> synonymList = new ArrayList<>(synonyms);
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//compareEachSynonymAgainstEachOther;
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for (int i = 0; i < synonymList.size()-1; i++){
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for (int j = i + 1; j < synonymList.size(); j++){
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Synonym syn1 = synonymList.get(i);
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Synonym syn2 = synonymList.get(j);
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TaxonName<?, ?> basionym = compareHomotypic(syn1.getName(), syn2.getName());
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if (basionym != null){
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adaptHomotypicGroup(basionym, syn1.getName(), syn2.getName());
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if (taxon.getName().getBasionyms().contains(basionym)){
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syn1.setType(SynonymType.HOMOTYPIC_SYNONYM_OF());
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syn2.setType(SynonymType.HOMOTYPIC_SYNONYM_OF());
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}
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}
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}
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}
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}
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/**
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* @param basionym
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* @param name
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* @param name2
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*/
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private void adaptHomotypicGroup(TaxonName<?, ?> basionym,
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TaxonName<?,?> name1, TaxonName<?,?> name2) {
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if (basionym.equals(name1)){
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if (!name2.getBasionyms().contains(name1)){
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name2.addBasionym(name1);
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}
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}else if (basionym.equals(name2)){
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if (!name1.getBasionyms().contains(name2)){
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name1.addBasionym(name2);
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}
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}
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}
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/**
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* @param name
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* @param name2
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*/
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private TaxonName<?,?> compareHomotypic(TaxonName<?,?> name1, TaxonName<?,?> name2) {
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if (name1 == null || name2 == null){
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return null;
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}
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TaxonName<?,?> basionymCandidate = checkAuthors(name1, name2);
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if (basionymCandidate == null){
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return null;
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}else{
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TaxonName<?,?> newCombinationCandidate
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= basionymCandidate == name1? name2: name1;
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boolean isBasionym = compareNameParts(basionymCandidate, newCombinationCandidate);
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if (isBasionym){
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return basionymCandidate;
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}else{
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return null;
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}
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}
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}
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/**
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* @param basionymCandiate
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* @param newCombinationCandidate
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*/
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private boolean compareNameParts(TaxonName<?, ?> basionymCandidate,
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TaxonName<?, ?> newCombinationCandidate) {
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if (basionymCandidate.isGenusOrSupraGeneric() || newCombinationCandidate.isGenusOrSupraGeneric()){
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return false;
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}else if (matchLastNamePart(basionymCandidate, newCombinationCandidate)){
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return true;
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}
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return false;
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}
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/**
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* @param name1
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* @param name2
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* @return
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*/
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private TaxonName<?,?> checkAuthors(TaxonName<?, ?> name1, TaxonName<?, ?> name2) {
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if (hasBasionymAuthorOf(name1, name2)){
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return name1;
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}else if (hasBasionymAuthorOf(name2, name1)){
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return name2;
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}else{
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return null;
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}
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}
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/**
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* @param name1
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* @param name2
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* @return
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*/
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private boolean hasBasionymAuthorOf(TaxonName<?,?> name1, TaxonName<?,?> name2) {
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TeamOrPersonBase<?> basAuthor2 = name2.getBasionymAuthorship();
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TeamOrPersonBase<?> combinationAuthor = name1.getCombinationAuthorship();
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TeamOrPersonBase<?> basAuthor1 = name1.getBasionymAuthorship();
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if (basAuthor2 != null && basAuthor1 == null){
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if (matches(basAuthor2, combinationAuthor)){
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return true;
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}
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}
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return false;
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}
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/**
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* @param basAuthor
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* @param combinationAuthor
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* @return
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*/
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private boolean matches(TeamOrPersonBase<?> basAuthor, TeamOrPersonBase<?> combinationAuthor) {
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//TODO better do with a CDM matcher that also compares other fields and
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//returns false if other fields are contradictory
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if (basAuthor == null || combinationAuthor == null){
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return false;
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}else if (basAuthor == combinationAuthor || basAuthor.equals(combinationAuthor)){
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return true;
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}else if (CdmUtils.nonEmptyEquals(basAuthor.getNomenclaturalTitle(), combinationAuthor.getNomenclaturalTitle())){
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return true;
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}else{
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return false;
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}
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}
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/**
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* @param basionymName
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* @param newCombination
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* @return
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*/
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public static boolean matchLastNamePart(TaxonName<?,?> name1, TaxonName<?,?> name2) {
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String lastNamePart1 = name1.getLastNamePart();
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String lastNamePart2 = name2.getLastNamePart();
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if (lastNamePart1 != null && lastNamePart2 != null){
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lastNamePart1 = normalizeBasionymNamePart(lastNamePart1);
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lastNamePart2 = normalizeBasionymNamePart(lastNamePart2);
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return (lastNamePart1.equals(lastNamePart2));
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}else{
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return false;
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}
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}
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/**
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* @param lastNamePart1
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* @return
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*/
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private static String normalizeBasionymNamePart(String lastNamePart) {
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String namePart = lastNamePart.toLowerCase()
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.replaceAll("(um|us|a|is|e|os|on|or)$", "")
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.replaceAll("er$", "r") //e.g. ruber <-> rubra
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.replaceAll("ese$", "s"); //e.g. cayanensis <-> cayanenese
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//TODO tampensis / tampense
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return namePart;
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}
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}
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