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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.io.caryo;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.RankClass;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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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.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.IdentifierType;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author a.mueller
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* @since 17.02.2020
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*/
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@Component
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public class CaryoAizoaceaeExcelImport extends SimpleExcelTaxonImport<CaryoAizoaceaeExcelImportConfigurator>{
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private static final long serialVersionUID = -729761811965260921L;
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private static final Logger logger = LogManager.getLogger();
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private static final String ACCEPTED_PLANT_NAME_ID = "accepted_plant_name_id";
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private static final String NOMENCLATURAL_REMARKS = "nomenclatural_remarks";
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private static final String TAXON_RANK = "taxon_rank";
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private static final String NAME_CIT = "NameCit";
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private static final String KEW_NAME4CDM_LINK = "KewName4CDMLink";
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private static final String KEW_F_NAME4CDM_LINK = "KewFName4CDMLink";
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private static final String TAXON_STATUS = "taxon_status";
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private static final String PLANT_NAME_ID = "plant_name_id";
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private static final String IPNI_ID = "ipni_id";
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private Map<String, UUID> taxonMapping = new HashMap<>();
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private Reference secRef = null;
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private Set<String> neglectedRecords = new HashSet<>();
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private Set<UUID> createdNames = new HashSet<>();
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private SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state;
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
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int line = state.getCurrentLine();
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if ((line % 500) == 0){
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newTransaction(state);
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System.out.println(line);
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}
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this.state = state;
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Map<String, String> record = state.getOriginalRecord();
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String fullCitation = getValue(record, NAME_CIT);
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String nameCache = getValue(record, KEW_NAME4CDM_LINK);
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String fullName = getValue(record, KEW_F_NAME4CDM_LINK);
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String status = getValue(record, TAXON_STATUS);
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String sourceId = getValue(record, PLANT_NAME_ID);
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String ipniId = getValue(record, IPNI_ID);
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String rankStr = getValue(record, TAXON_RANK);
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String nomenclaturalRemarks = getValue(record, NOMENCLATURAL_REMARKS);
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String accId = getValue(record, ACCEPTED_PLANT_NAME_ID);
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String row = String.valueOf(line) + "("+fullName+"): ";
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if("Misapplied".equals(status)){
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neglectedRecords.add(sourceId);
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return;
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}
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boolean isNewName = false;
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try {
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List<NomenclaturalStatusType> statusTypes = new ArrayList<>();
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Class<? extends CdmBase> clazz = makeStatus(status, sourceId, accId, row, statusTypes);
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TaxonName name;
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Rank rank = state.getTransformer().getRankByKey(rankStr);
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List<TaxonName> existingNames = getNameService().getNamesByNameCache(nameCache);
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Iterator<TaxonName> it = existingNames.iterator();
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while (it.hasNext()){
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TaxonName next = it.next();
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if (createdNames.contains(next.getUuid())){
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it.remove();
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}
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}
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List<TaxonName> fullNameMatches = new ArrayList<>();
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@SuppressWarnings("rawtypes")
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List<TaxonBase> allFullNameTaxa = new ArrayList<>();
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@SuppressWarnings("rawtypes")
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List<TaxonBase> allNameCacheTaxa = new ArrayList<>();
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for (TaxonName existingName : existingNames){
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if (existingName.getTitleCache().equals(fullName)){
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fullNameMatches.add(existingName);
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allFullNameTaxa.addAll(existingName.getTaxonBases());
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}
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allNameCacheTaxa.addAll(existingName.getTaxonBases());
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}
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logMultipleCandidates(row, existingNames, fullNameMatches);
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TaxonBase<?> existingTaxon;
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if(allFullNameTaxa.size()>1){
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existingTaxon = findBestMatchingTaxon(allFullNameTaxa, clazz, row);
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name = existingTaxon.getName();
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}else if (allFullNameTaxa.size()==1){
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existingTaxon = allFullNameTaxa.iterator().next();
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name = existingTaxon.getName();
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}else{
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existingTaxon = null;
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if (!fullNameMatches.isEmpty()){
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logger.warn(row + "None of the existing names exists as taxon/synonym. Existing name taken as base for new taxon/synonym created.");
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if (fullNameMatches.size()>1){
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logger.warn(row + "More than 1 matching full names exist as candidats for new taxon/synonym. Arbitrary one taken.");
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}
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name = fullNameMatches.iterator().next();
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}else if (!existingNames.isEmpty()){
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if (!allNameCacheTaxa.isEmpty()){
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logger.warn(row + "Taxa exist with matching nameCache but not matching fullname cache. New name and new taxon/synonym created. Other authors are " + getOtherAuthors(existingNames));
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name = null;
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}else{
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logger.warn(row + "No matching fullnames exist but namecache matches. None of the matches is used in a taxon/synonym. Other authors are " + getOtherAuthors(existingNames));
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name = null;
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}
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}else{
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name = null;
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}
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}
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if (existingTaxon == null){
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if (rank == null){
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logger.warn(row + "Name has no rank " + nameCache);
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}else if (rank.equals(Rank.GENUS())){
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logger.warn(row + "No name exists for genus " + nameCache + ". This is unexpected.");
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}
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}else{
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if (existingTaxon.isInstanceOf(Taxon.class)){
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if (!CdmBase.deproxy(existingTaxon, Taxon.class).getTaxonNodes().isEmpty()){
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neglectedRecords.add(sourceId);
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}
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}else{
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Taxon taxon = CdmBase.deproxy(existingTaxon, Synonym.class).getAcceptedTaxon();
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if (taxon != null && !taxon.getTaxonNodes().isEmpty()){
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neglectedRecords.add(sourceId);
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}
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}
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}
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if (name == null){
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NonViralNameParserImpl parser = new NonViralNameParserImpl();
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name = parser.parseReferencedName(fullCitation, NomenclaturalCode.ICNAFP, rank);
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if (name.isProtectedFullTitleCache() || name.isProtectedTitleCache() || name.isProtectedNameCache()
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|| name.isProtectedAuthorshipCache()){
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logger.warn(row + "Name not parsable: " + fullCitation);
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name.setTitleCache(fullName, true);
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name.setNameCache(nameCache, true);
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}else{
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testParsedName(state, name, row, null);
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}
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name.addImportSource(sourceId, PLANT_NAME_ID, getSourceReference(state), "line " + state.getCurrentLine());
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name = dedupliateNameParts(name);
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getNameService().saveOrUpdate(name);
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isNewName = true;
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createdNames.add(name.getUuid());
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}else{
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testParsedName(state, name, row, fullCitation);
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}
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handleNomenclRemarkAndNameStatus(nomenclaturalRemarks, row, isNewName, name, statusTypes);
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TaxonBase<?> taxonBase = existingTaxon;
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if (taxonBase == null){
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if (clazz == Taxon.class){
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taxonBase = Taxon.NewInstance(name, getSecRef());
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}else{
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taxonBase = Synonym.NewInstance(name, getSecRef());
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}
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taxonBase.addImportSource(sourceId, PLANT_NAME_ID, getSourceReference(state), "line " + state.getCurrentLine());
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getTaxonService().saveOrUpdate(taxonBase);
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}
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if (!isBlank(ipniId)){
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IdentifierType ipniIdIdentifierType = IdentifierType.IDENTIFIER_NAME_IPNI();
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name.addIdentifier(ipniId, ipniIdIdentifierType);
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}else{
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logger.warn(row + "IPNI id is missing.");
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}
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taxonMapping.put(sourceId, taxonBase.getUuid());
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// if("Accepted".equals(status)){
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if(taxonBase.isInstanceOf(Taxon.class)){
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UUID existingUuid = taxonMapping.put(name.getNameCache(), taxonBase.getUuid());
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if (existingUuid != null){
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logger.warn(row + name.getNameCache() + " has multiple instances in file");
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}
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}
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace();
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}
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}
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private TaxonName dedupliateNameParts(TaxonName name) {
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if (state.getConfig().isDoDeduplicate()){
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state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(name);
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}
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return name;
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}
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private String getOtherAuthors(List<TaxonName> otherNames) {
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String result = "";
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for (TaxonName name : otherNames){
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result = CdmUtils.concat(";", result, name.getAuthorshipCache());
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}
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return result;
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}
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private TaxonBase<?> findBestMatchingTaxon(@SuppressWarnings("rawtypes") List<TaxonBase> allFullNameTaxa,
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Class<? extends CdmBase> clazz, String row) {
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TaxonBase<?> result = null;
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TaxonBase<?> otherStatus = null;
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for (TaxonBase<?> taxonBase : allFullNameTaxa) {
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if (taxonBase.isInstanceOf(clazz)){
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if (result != null){
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logger.warn(row + "More than 1 taxon with matching full name AND matching status exists. This is not further handled. Arbitrary one taken.");
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}
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result = taxonBase;
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}else{
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otherStatus = taxonBase;
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}
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}
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if (result == null && allFullNameTaxa.size()>1){
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logger.warn(row + "More than 1 taxon with matching fullname but NOT matching status exists. This is not further handled. Arbitrary one taken.");
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}
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return result == null? otherStatus :result ;
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}
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private void logMultipleCandidates(String row, List<TaxonName> existingNames, List<TaxonName> fullNameMatches) {
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if(fullNameMatches.size()>1){
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String message = row + "More than one name with matching full name exists in DB. Try to take best matching.";
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if (existingNames.size()>fullNameMatches.size()){
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message += " Additionally names with matching name cache exist.";
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}
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logger.warn(message);
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}else if (existingNames.size()>1){
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String message = row + "More than one name with matching nameCache exists in DB. ";
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if(fullNameMatches.isEmpty()){
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message += "But none matches full name.";
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}else{
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message += "But exactly 1 matches full name.";
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}
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logger.warn(message);
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}
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}
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private Class<? extends CdmBase> makeStatus(String status, String sourceId,
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String accId, String row, List<NomenclaturalStatusType> statusTypes) {
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292
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293
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Class<? extends CdmBase> clazz;
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if ("Accepted".equals(status) || "Unplaced".equals(status) || "Artificial Hybrid".equals(status) ){
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clazz = Taxon.class;
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}else if ("Synonym".equals(status) || "Orthographic".equals(status)){
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clazz = (accId == null)? Taxon.class : Synonym.class;
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if("Orthographic".equals(status)){
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statusTypes.add(NomenclaturalStatusType.SUPERFLUOUS());
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// addStatus(NomenclaturalStatusType.SUPERFLUOUS(), row, isNewName, statusAdded, statusTypes, null);
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}
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}else if("Illegitimate".equals(status)){
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clazz = getIllegInvalidStatus(sourceId, accId);
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statusTypes.add(NomenclaturalStatusType.ILLEGITIMATE());
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// addStatus(NomenclaturalStatusType.ILLEGITIMATE(), row, isNewName, statusAdded, statusTypes, getSecRef());
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}else if ("Invalid".equals(status)){
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clazz = getIllegInvalidStatus(sourceId, accId);
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statusTypes.add(NomenclaturalStatusType.INVALID());
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// addStatus(NomenclaturalStatusType.INVALID(), row, isNewName, statusAdded, statusTypes, getSecRef());
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}else{
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logger.warn(row + "Unhandled status: " + status);
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clazz = Taxon.class; //to do something
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}
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return clazz;
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315
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}
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private void handleNomenclRemarkAndNameStatus(String nomenclaturalRemarks, String row, boolean isNewName, TaxonName name,
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List<NomenclaturalStatusType> statusTypes) {
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319
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NomenclaturalStatusType remarkType = null;
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NomenclaturalStatusType statusType = statusTypes.isEmpty()? null: statusTypes.iterator().next();
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if (nomenclaturalRemarks == null){
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//nothing to do
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}else if (", nom. illeg.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.ILLEGITIMATE();
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}else if (", nom. cons.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.CONSERVED();
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328
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}else if (", nom. nud.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.NUDUM();
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}else if (", nom. provis.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.PROVISIONAL();
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332
|
}else if (", nom. rej.".equals(nomenclaturalRemarks)){
|
|
333
|
remarkType = NomenclaturalStatusType.REJECTED();
|
|
334
|
}else if (", nom. subnud.".equals(nomenclaturalRemarks)){
|
|
335
|
remarkType = NomenclaturalStatusType.SUBNUDUM();
|
|
336
|
}else if (", nom. superfl.".equals(nomenclaturalRemarks)){
|
|
337
|
remarkType = NomenclaturalStatusType.SUPERFLUOUS();
|
|
338
|
}else if (", not validly publ.".equals(nomenclaturalRemarks)){
|
|
339
|
statusTypes.add(NomenclaturalStatusType.INVALID());
|
|
340
|
}else if (", opus utique oppr.".equals(nomenclaturalRemarks)){
|
|
341
|
statusTypes.add(NomenclaturalStatusType.OPUS_UTIQUE_OPPR());
|
|
342
|
}else {
|
|
343
|
logger.warn(row + "Unhandled nomenclatural remark: " + nomenclaturalRemarks);
|
|
344
|
}
|
|
345
|
|
|
346
|
NomenclaturalStatusType kewType = remarkType != null? remarkType : statusType;
|
|
347
|
if (isNewName){
|
|
348
|
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
|
349
|
logger.warn(row + "Kew suggests 2 different nom. status. types for new name. The status from nomenclatural_remarks was taken.");
|
|
350
|
}
|
|
351
|
if (kewType != null){
|
|
352
|
name.addStatus(kewType, getSecRef(), null);
|
|
353
|
}
|
|
354
|
}else{
|
|
355
|
NomenclaturalStatusType existingType = null;
|
|
356
|
if (!name.getStatus().isEmpty()){
|
|
357
|
existingType = name.getStatus().iterator().next().getType();
|
|
358
|
}
|
|
359
|
if (existingType != null && kewType != null){
|
|
360
|
if (!existingType.equals(kewType)){
|
|
361
|
logger.warn(row + "Existing name status "+existingType.getTitleCache()+" differs from Kew status " + kewType.getTitleCache() + ". Key status ignored");
|
|
362
|
}
|
|
363
|
}else if (existingType != null && kewType == null){
|
|
364
|
logger.warn(row + "Info: Existing name has a name status "+existingType.getTitleCache()+" but Kew name has no status. Existing status kept.");
|
|
365
|
}else if (existingType == null && kewType != null){
|
|
366
|
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
|
367
|
logger.warn(row + "Existing name has no status while Kew name suggests a status (but 2 different status form status and nomenclatural_remarks field).");
|
|
368
|
}else{
|
|
369
|
logger.warn(row + "Existing name has no status while Kew name suggests a status ("+kewType.getTitleCache()+"). Kew status ignored.");
|
|
370
|
}
|
|
371
|
}
|
|
372
|
}
|
|
373
|
}
|
|
374
|
|
|
375
|
private void newTransaction(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
|
|
376
|
commitTransaction(state.getTransactionStatus());
|
|
377
|
secRef = null;
|
|
378
|
state.getDeduplicationHelper().reset();
|
|
379
|
state.setSourceReference(null);
|
|
380
|
System.gc();
|
|
381
|
state.setTransactionStatus(startTransaction());
|
|
382
|
}
|
|
383
|
|
|
384
|
private Reference getSecRef() {
|
|
385
|
if (secRef == null){
|
|
386
|
secRef = getReferenceService().find(state.getConfig().getSecUuid());
|
|
387
|
}
|
|
388
|
return secRef;
|
|
389
|
}
|
|
390
|
|
|
391
|
private Class<? extends CdmBase> getIllegInvalidStatus(String sourceId, String accId) {
|
|
392
|
if (sourceId.equals(accId)){
|
|
393
|
return Taxon.class;
|
|
394
|
}else if(accId != null){
|
|
395
|
return Synonym.class;
|
|
396
|
}
|
|
397
|
return null;
|
|
398
|
}
|
|
399
|
|
|
400
|
|
|
401
|
private void testParsedName(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state, TaxonName name,
|
|
402
|
String row, String fullCitation) throws UndefinedTransformerMethodException {
|
|
403
|
Map<String, String> record = state.getOriginalRecord();
|
|
404
|
|
|
405
|
String nameCache = getValue(record, KEW_NAME4CDM_LINK);
|
|
406
|
String fullName = getValue(record, KEW_F_NAME4CDM_LINK);
|
|
407
|
String rankStr = getValue(record, TAXON_RANK);
|
|
408
|
String genusHybrid = getValue(record, "genus_hybrid");
|
|
409
|
String genus = getValue(record, "genus");
|
|
410
|
String speciesHybrid = getValue(record, "species_hybrid");
|
|
411
|
String species = getValue(record, "species");
|
|
412
|
String infraSpecRank = getValue(record, "infraspecific_rank");
|
|
413
|
String infraspecies = getValue(record, "infraspecies");
|
|
414
|
String basionymAuthor = getValue(record, "parenthetical_author");
|
|
415
|
String combinationAuthor = getValue(record, "primary_author");
|
|
416
|
String authors = getValue(record, "taxon_authors");
|
|
417
|
String year = getValue(record, "KewYear4CDM");
|
|
418
|
String pubType = getValue(record, "PubType");
|
|
419
|
String place_of_publication = getValue(record, "place_of_publication");
|
|
420
|
String volume_and_page = getValue(record, "volume_and_page");
|
|
421
|
|
|
422
|
if (!CdmUtils.nullSafeEqual(name.getNameCache(), nameCache)){
|
|
423
|
logger.warn(row + "Unexpected nameCache: " + nameCache);
|
|
424
|
}
|
|
425
|
if (!CdmUtils.nullSafeEqual(name.getTitleCache(), fullName)){
|
|
426
|
logger.warn(row + "Unexpected titleCache: <->" + name.getTitleCache());
|
|
427
|
}
|
|
428
|
if (isBlank(genusHybrid) == name.isMonomHybrid()){
|
|
429
|
logger.warn(row + "Unexpected genus hybrid: " + genusHybrid);
|
|
430
|
}
|
|
431
|
if (!CdmUtils.nullSafeEqual(name.getGenusOrUninomial(),genus)){
|
|
432
|
logger.warn(row + "Unexpected genus: " + genus);
|
|
433
|
}if (isBlank(speciesHybrid) == name.isBinomHybrid()){
|
|
434
|
logger.warn(row + "Unexpected species hybrid: " + speciesHybrid);
|
|
435
|
}
|
|
436
|
if (!CdmUtils.nullSafeEqual(name.getSpecificEpithet(),species)){
|
|
437
|
logger.warn(row + "Unexpected species epithet: " + name.getSpecificEpithet() +"<->"+ species);
|
|
438
|
}
|
|
439
|
if (!CdmUtils.nullSafeEqual(name.getInfraSpecificEpithet(), infraspecies)){
|
|
440
|
logger.warn(row + "Unexpected infraspecific epithet: " + name.getInfraSpecificEpithet() +"<->"+ infraspecies);
|
|
441
|
}
|
|
442
|
if (!CdmUtils.nullSafeEqual(name.getAuthorshipCache(),authors)){
|
|
443
|
logger.warn(row + "Unexpected authors: " + name.getAuthorshipCache() +"<->"+ authors);
|
|
444
|
}
|
|
445
|
String combinationAndExAuthor = authorTitle(name.getCombinationAuthorship(), name.getExCombinationAuthorship());
|
|
446
|
if (!CdmUtils.nullSafeEqual(combinationAndExAuthor, combinationAuthor)){
|
|
447
|
logger.warn(row + "Unexpected combination author: " + combinationAndExAuthor +"<->"+ combinationAuthor);
|
|
448
|
}
|
|
449
|
String basionymAndExAuthor = authorTitle(name.getBasionymAuthorship(), name.getExBasionymAuthorship());
|
|
450
|
if (!CdmUtils.nullSafeEqual(basionymAndExAuthor, basionymAuthor)){
|
|
451
|
logger.warn(row + "Unexpected basionym author: " + basionymAndExAuthor +"<->"+ basionymAuthor);
|
|
452
|
}
|
|
453
|
Rank rank = state.getTransformer().getRankByKey(rankStr);
|
|
454
|
if (!rank.equals(name.getRank())){
|
|
455
|
logger.warn(row + "Unexpected rank: " + rankStr);
|
|
456
|
}
|
|
457
|
|
|
458
|
Reference nomRef = name.getNomenclaturalReference();
|
|
459
|
if (nomRef == null){
|
|
460
|
if (fullCitation != null){
|
|
461
|
NonViralNameParserImpl parser = new NonViralNameParserImpl();
|
|
462
|
TaxonName parsedName = parser.parseReferencedName(fullCitation, NomenclaturalCode.ICNAFP, rank);
|
|
463
|
if (parsedName.getNomenclaturalReference() != null){
|
|
464
|
name.setNomenclaturalReference(parsedName.getNomenclaturalReference());
|
|
465
|
logger.warn(row + "Nom.ref. was missing. Taken from Kew");
|
|
466
|
}else{
|
|
467
|
logger.warn(row + "Nom. ref. is missing or can not be parsed");
|
|
468
|
}
|
|
469
|
}else{
|
|
470
|
logger.warn(row + "NomRef is missing.");
|
|
471
|
}
|
|
472
|
}else{
|
|
473
|
if ("A".equals(pubType) && nomRef.getType() != ReferenceType.Article){
|
|
474
|
logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString());
|
|
475
|
}
|
|
476
|
if ("B".equals(pubType) && nomRef.getType() != ReferenceType.Book){
|
|
477
|
logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString());
|
|
478
|
}
|
|
479
|
year = normalizeYear(year);
|
|
480
|
if (!CdmUtils.nullSafeEqual(year, nomRef.getDatePublishedString())){
|
|
481
|
logger.warn(row + "Unexpected year: " + year + "<->" + nomRef.getDatePublishedString());
|
|
482
|
}
|
|
483
|
if (volume_and_page != null && !name.getFullTitleCache().contains(volume_and_page)){
|
|
484
|
logger.warn(row + "volume_and_page not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ volume_and_page);
|
|
485
|
}
|
|
486
|
if (place_of_publication != null && !name.getFullTitleCache().contains(place_of_publication)){
|
|
487
|
logger.warn(row + "place_of_publication not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ place_of_publication);
|
|
488
|
}
|
|
489
|
}
|
|
490
|
if ("subsp.".equals(infraSpecRank) && !rank.equals(Rank.SUBSPECIES())){
|
|
491
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
492
|
}else if ("var.".equals(infraSpecRank) && !rank.equals(Rank.VARIETY())){
|
|
493
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
494
|
}else if ("f.".equals(infraSpecRank) && !rank.equals(Rank.FORM())){
|
|
495
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
496
|
}
|
|
497
|
}
|
|
498
|
|
|
499
|
private String authorTitle(TeamOrPersonBase<?> author, TeamOrPersonBase<?> exAuthor) {
|
|
500
|
String authorStr = author == null? null: author.getNomenclaturalTitleCache();
|
|
501
|
String exAuthorStr = exAuthor == null? null: exAuthor.getNomenclaturalTitleCache();
|
|
502
|
return CdmUtils.concat(" ex ", exAuthorStr, authorStr);
|
|
503
|
}
|
|
504
|
|
|
505
|
private String normalizeYear(String year) {
|
|
506
|
if (year == null){
|
|
507
|
return null;
|
|
508
|
}else if (year.contains("\" [")){
|
|
509
|
String[] split = year.split("\" \\[");
|
|
510
|
year = split[1].replace("]","") + " [" + split[0]+"\"]";
|
|
511
|
}else if ("?".equals(year)){
|
|
512
|
return null;
|
|
513
|
}
|
|
514
|
return year;
|
|
515
|
}
|
|
516
|
|
|
517
|
@Override
|
|
518
|
protected void secondPass(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
|
|
519
|
Map<String, String> record = state.getOriginalRecord();
|
|
520
|
int line = state.getCurrentLine();
|
|
521
|
String fullName = getValue(record, KEW_F_NAME4CDM_LINK);
|
|
522
|
String status = getValue(record, TAXON_STATUS);
|
|
523
|
String sourceId = getValue(record, PLANT_NAME_ID);
|
|
524
|
String accId = getValue(record, ACCEPTED_PLANT_NAME_ID);
|
|
525
|
String accName = getValue(record, "AcceptedName");
|
|
526
|
String basionymId = getValue(record, "basionym_plant_name_id");
|
|
527
|
String homotypicSynonym = getValue(record, "homotypic_synonym");
|
|
528
|
|
|
529
|
String row = String.valueOf(line) + "("+fullName+"): ";
|
|
530
|
try {
|
|
531
|
if ((line % 500) == 0){
|
|
532
|
newTransaction(state);
|
|
533
|
System.out.println(line);
|
|
534
|
}
|
|
535
|
|
|
536
|
if("Misapplied".equals(status)){
|
|
537
|
return;
|
|
538
|
}else if (neglectedRecords.contains(sourceId)){
|
|
539
|
logger.info(row + "Record ignored.");
|
|
540
|
return;
|
|
541
|
}
|
|
542
|
|
|
543
|
UUID uuid = taxonMapping.get(sourceId);
|
|
544
|
TaxonBase<?> taxonBase = getTaxonService().find(uuid);
|
|
545
|
if (taxonBase == null){
|
|
546
|
logger.warn(row + "taxonBase not found: " + sourceId);
|
|
547
|
return;
|
|
548
|
}
|
|
549
|
|
|
550
|
UUID accUuid = taxonMapping.get(accId);
|
|
551
|
boolean hasAccepted = !sourceId.equals(accId);
|
|
552
|
|
|
553
|
Taxon accTaxon = null;
|
|
554
|
TaxonNode parent = null;
|
|
555
|
Taxon child = null;
|
|
556
|
Synonym syn = null;
|
|
557
|
boolean isSynonymAccepted = false;
|
|
558
|
|
|
559
|
if(accId == null){
|
|
560
|
logger.info(row + "accID is null");
|
|
561
|
child = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
562
|
}else if(hasAccepted){
|
|
563
|
TaxonBase<?> accTaxonBase = getTaxonService().find(accUuid);
|
|
564
|
if (accTaxonBase == null){
|
|
565
|
logger.warn(row + "acctaxon not found: " + accId + "; " + accName);
|
|
566
|
}else if(!accTaxonBase.isInstanceOf(Taxon.class)){
|
|
567
|
logger.warn(row + "acctaxon is synonym: " + accId + "; " + accName);
|
|
568
|
isSynonymAccepted = true;
|
|
569
|
}else{
|
|
570
|
accTaxon = CdmBase.deproxy(accTaxonBase, Taxon.class);
|
|
571
|
if (!accTaxon.getName().getTitleCache().equals(accName)){
|
|
572
|
logger.warn(row + "Accepted name differs: " + accName +" <-> "+ accTaxon.getName().getTitleCache());
|
|
573
|
}
|
|
574
|
}
|
|
575
|
}else if (sourceId.equals(accId)){
|
|
576
|
if (!taxonBase.isInstanceOf(Taxon.class)){
|
|
577
|
logger.warn(row + "child not of class Taxon: " + sourceId);
|
|
578
|
}else{
|
|
579
|
Rank rank = taxonBase.getName().getRank();
|
|
580
|
child = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
581
|
if(rank.equals(Rank.GENUS())){
|
|
582
|
parent = getFamily();
|
|
583
|
}else if (rank.equals(Rank.SPECIES())){
|
|
584
|
String genus = child.getName().getGenusOrUninomial();
|
|
585
|
UUID parentUuid = taxonMapping.get(genus);
|
|
586
|
parent = getParent(parentUuid, row);
|
|
587
|
}else if (rank.isLowerThan(RankClass.Species)){
|
|
588
|
String speciesName = child.getName().getGenusOrUninomial() + " " + child.getName().getSpecificEpithet();
|
|
589
|
UUID parentUuid = taxonMapping.get(speciesName);
|
|
590
|
parent = getParent(parentUuid, row);
|
|
591
|
}
|
|
592
|
}
|
|
593
|
}
|
|
594
|
|
|
595
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
596
|
syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
597
|
}
|
|
598
|
|
|
599
|
if ("Accepted".equals(status)){
|
|
600
|
if (parent == null){
|
|
601
|
logger.warn(row + "Parent is missing. Taxon is moved to 'unresolved' instead'");
|
|
602
|
parent = unresolvedParent();
|
|
603
|
}
|
|
604
|
if (child == null){
|
|
605
|
logger.warn(row + "Child is missing. Taxon not imported.");
|
|
606
|
}else{
|
|
607
|
if (!child.getTaxonNodes().isEmpty()){
|
|
608
|
if(!child.getName().getRank().equals(Rank.GENUS())){
|
|
609
|
logger.warn(row + "Taxon already has a parent. Taxon not attached to any further parent taxon.");
|
|
610
|
}
|
|
611
|
}else{
|
|
612
|
addChild(parent, child, row);
|
|
613
|
}
|
|
614
|
}
|
|
615
|
}else if ("Synonym".equals(status)){
|
|
616
|
if(accTaxon == null){
|
|
617
|
if(isSynonymAccepted){
|
|
618
|
logger.warn(row + "Synonym added to 'unresolved' as accepted taxon is synonym itself.");
|
|
619
|
}else if (accId != null){
|
|
620
|
logger.warn(row + "Accepted taxon for synonym unexpectedly does not exist (it seems not to be a synonym itself). Synonym moved to 'unresolved'");
|
|
621
|
}else{
|
|
622
|
logger.warn(row + "No accepted taxon given for synonym. Therefore taxon moved to 'unresolved'");
|
|
623
|
}
|
|
624
|
if(accId != null){
|
|
625
|
child = Taxon.NewInstance(syn.getName(), syn.getSec());
|
|
626
|
child.addImportSource(sourceId, PLANT_NAME_ID, getSourceReference(state), "line " + state.getCurrentLine());
|
|
627
|
}
|
|
628
|
addChild(unresolvedParent(), child, row);
|
|
629
|
getTaxonService().deleteSynonym(syn, new SynonymDeletionConfigurator());
|
|
630
|
}else{
|
|
631
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF);
|
|
632
|
}
|
|
633
|
}else if ("Unplaced".equals(status)){
|
|
634
|
parent = unresolvedParent();
|
|
635
|
addChild(parent, child, row);
|
|
636
|
}else if ("Artificial Hybrid".equals(status)){
|
|
637
|
parent = hybridParent();
|
|
638
|
addChild(parent, child, row);
|
|
639
|
}else if ("Orthographic".equals(status)){
|
|
640
|
if(accTaxon == null){
|
|
641
|
logger.warn(row + "'Orthographic' taxon has no acc taxon");
|
|
642
|
}else{
|
|
643
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF);
|
|
644
|
}
|
|
645
|
}else if("Illegitimate".equals(status) || "Invalid".equals(status)){
|
|
646
|
if (hasAccepted){
|
|
647
|
if(accTaxon == null){
|
|
648
|
logger.warn(row + "accepted taxon for illegitimate or invalid taxon not found");
|
|
649
|
}else{
|
|
650
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF);
|
|
651
|
}
|
|
652
|
}else{
|
|
653
|
addChild(unresolvedParent(), child, row);
|
|
654
|
}
|
|
655
|
}else{
|
|
656
|
logger.warn(row + "Unhandled status: " + status);
|
|
657
|
}
|
|
658
|
|
|
659
|
if (basionymId != null && false){
|
|
660
|
UUID basionymUuid = taxonMapping.get(basionymId);
|
|
661
|
TaxonBase<?> basionymTaxon = getTaxonService().find(basionymUuid);
|
|
662
|
if (basionymTaxon != null){
|
|
663
|
if (hasSameAcceptedTaxon(taxonBase, basionymTaxon)){
|
|
664
|
if (taxonBase.getName().getBasionym() == null){
|
|
665
|
taxonBase.getName().addBasionym(basionymTaxon.getName());
|
|
666
|
}
|
|
667
|
}else{
|
|
668
|
logger.warn(row + "Basionym has not same accepted taxon and therefore was ignored.");
|
|
669
|
}
|
|
670
|
}else{
|
|
671
|
logger.warn(row + "Basionym "+basionymId+" not found.");
|
|
672
|
}
|
|
673
|
}
|
|
674
|
} catch (Exception e) {
|
|
675
|
logger.error(row + "Error.");
|
|
676
|
e.printStackTrace();
|
|
677
|
}
|
|
678
|
}
|
|
679
|
|
|
680
|
private boolean hasSameAcceptedTaxon(TaxonBase<?> taxonBase, TaxonBase<?> basionymTaxon) {
|
|
681
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
682
|
taxonBase = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
|
|
683
|
}
|
|
684
|
if (basionymTaxon.isInstanceOf(Synonym.class)){
|
|
685
|
basionymTaxon = CdmBase.deproxy(basionymTaxon, Synonym.class).getAcceptedTaxon();
|
|
686
|
}
|
|
687
|
return taxonBase != null && basionymTaxon != null && taxonBase.equals(basionymTaxon);
|
|
688
|
}
|
|
689
|
|
|
690
|
private TaxonNode getParent(UUID parentUuid, String row) {
|
|
691
|
if(parentUuid == null){
|
|
692
|
logger.warn(row + "Parent uuid is null. No parent found.");
|
|
693
|
return null;
|
|
694
|
}
|
|
695
|
TaxonBase<?> pTaxon = getTaxonService().find(parentUuid);
|
|
696
|
if (pTaxon == null){
|
|
697
|
logger.warn(row + "No parent found for parent UUID. This should not happen.");
|
|
698
|
return null;
|
|
699
|
}
|
|
700
|
if (pTaxon.isInstanceOf(Synonym.class)){
|
|
701
|
logger.warn(row + "Parent is synonym");
|
|
702
|
return null;
|
|
703
|
}else{
|
|
704
|
Taxon ptax = CdmBase.deproxy(pTaxon, Taxon.class);
|
|
705
|
if(ptax.getTaxonNodes().isEmpty()){
|
|
706
|
logger.warn(row + "Parent has no node yet");
|
|
707
|
return null;
|
|
708
|
}else {
|
|
709
|
if(ptax.getTaxonNodes().size()>1){
|
|
710
|
logger.warn("Parent has >1 nodes. Take arbitrary one");
|
|
711
|
}
|
|
712
|
return ptax.getTaxonNodes().iterator().next();
|
|
713
|
}
|
|
714
|
}
|
|
715
|
}
|
|
716
|
|
|
717
|
private void addChild(TaxonNode parent, Taxon child, String row) {
|
|
718
|
if (parent == null){
|
|
719
|
logger.warn(row + "Parent is null");
|
|
720
|
}else if (child == null){
|
|
721
|
logger.warn(row + "Child is null");
|
|
722
|
}else{
|
|
723
|
if (!child.getTaxonNodes().isEmpty()){
|
|
724
|
TaxonNode childNode = child.getTaxonNodes().iterator().next();
|
|
725
|
if (childNode.getParent() != null && childNode.getParent().equals(parent)){
|
|
726
|
logger.info(row + "Parent-child relation exists already.");
|
|
727
|
}else{
|
|
728
|
logger.warn(row + "Child already has different parent. Parent-child relation not added.");
|
|
729
|
}
|
|
730
|
}else{
|
|
731
|
TaxonNode node = parent.addChildTaxon(child, null, null);
|
|
732
|
getTaxonNodeService().saveOrUpdate(node);
|
|
733
|
}
|
|
734
|
}
|
|
735
|
}
|
|
736
|
|
|
737
|
private TaxonNode getFamily(){
|
|
738
|
UUID uuid = UUID.fromString("0334809a-aa20-447d-add9-138194f80f56");
|
|
739
|
TaxonNode aizoaceae = getTaxonNodeService().find(uuid);
|
|
740
|
return aizoaceae;
|
|
741
|
}
|
|
742
|
|
|
743
|
private TaxonNode hybridParent(){
|
|
744
|
UUID uuid = UUID.fromString("2fae0fa1-758a-4fcb-bb6c-a2bd11f40641");
|
|
745
|
TaxonNode hybridParent = getTaxonNodeService().find(uuid);
|
|
746
|
return hybridParent;
|
|
747
|
}
|
|
748
|
private TaxonNode unresolvedParent(){
|
|
749
|
UUID uuid = UUID.fromString("accb1ff6-5748-4b18-b529-9368c331a38d");
|
|
750
|
TaxonNode unresolvedParent = getTaxonNodeService().find(uuid);
|
|
751
|
return unresolvedParent;
|
|
752
|
}
|
|
753
|
}
|