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721766b0
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Andreas Müller
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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.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.common.utils.ImportDeduplicationHelper;
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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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fb7aa32c
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Andreas Müller
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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721766b0
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Andreas Müller
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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.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.DefinedTerm;
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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 = Logger.getLogger(CaryoAizoaceaeExcelImport.class);
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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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private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> dedupHelper = null;
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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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26f92af1
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Andreas Müller
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name = dedupliateNameParts(name);
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721766b0
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Andreas Müller
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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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26f92af1
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Andreas Müller
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if (!isBlank(ipniId)){
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DefinedTerm ipniIdIdentifierType = DefinedTerm.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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721766b0
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Andreas Müller
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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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26f92af1
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Andreas Müller
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if (state.getConfig().isDoDeduplicate()){
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getDedupHelper().replaceAuthorNamesAndNomRef(state, name);
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}
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721766b0
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Andreas Müller
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return name;
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}
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private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> getDedupHelper() {
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if (dedupHelper == null){
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dedupHelper
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= ImportDeduplicationHelper.NewInstance(this, state);
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}
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return dedupHelper;
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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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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());
|
318 |
|
|
}else{
|
319 |
|
|
logger.warn(row + "Unhandled status: " + status);
|
320 |
|
|
clazz = Taxon.class; //to do something
|
321 |
|
|
}
|
322 |
|
|
return clazz;
|
323 |
|
|
}
|
324 |
|
|
|
325 |
|
|
private void handleNomenclRemarkAndNameStatus(String nomenclaturalRemarks, String row, boolean isNewName, TaxonName name,
|
326 |
|
|
List<NomenclaturalStatusType> statusTypes) {
|
327 |
|
|
|
328 |
|
|
NomenclaturalStatusType remarkType = null;
|
329 |
|
|
NomenclaturalStatusType statusType = statusTypes.isEmpty()? null: statusTypes.iterator().next();
|
330 |
|
|
if (nomenclaturalRemarks == null){
|
331 |
|
|
//nothing to do
|
332 |
|
|
}else if (", nom. illeg.".equals(nomenclaturalRemarks)){
|
333 |
|
|
remarkType = NomenclaturalStatusType.ILLEGITIMATE();
|
334 |
|
|
}else if (", nom. cons.".equals(nomenclaturalRemarks)){
|
335 |
|
|
remarkType = NomenclaturalStatusType.CONSERVED();
|
336 |
|
|
}else if (", nom. nud.".equals(nomenclaturalRemarks)){
|
337 |
|
|
remarkType = NomenclaturalStatusType.NUDUM();
|
338 |
|
|
}else if (", nom. provis.".equals(nomenclaturalRemarks)){
|
339 |
|
|
remarkType = NomenclaturalStatusType.PROVISIONAL();
|
340 |
|
|
}else if (", nom. rej.".equals(nomenclaturalRemarks)){
|
341 |
|
|
remarkType = NomenclaturalStatusType.REJECTED();
|
342 |
|
|
}else if (", nom. subnud.".equals(nomenclaturalRemarks)){
|
343 |
|
|
remarkType = NomenclaturalStatusType.SUBNUDUM();
|
344 |
|
|
}else if (", nom. superfl.".equals(nomenclaturalRemarks)){
|
345 |
|
|
remarkType = NomenclaturalStatusType.SUPERFLUOUS();
|
346 |
|
|
}else if (", not validly publ.".equals(nomenclaturalRemarks)){
|
347 |
|
|
statusTypes.add(NomenclaturalStatusType.INVALID());
|
348 |
|
|
}else if (", opus utique oppr.".equals(nomenclaturalRemarks)){
|
349 |
|
|
statusTypes.add(NomenclaturalStatusType.OPUS_UTIQUE_OPPR());
|
350 |
|
|
}else {
|
351 |
|
|
logger.warn(row + "Unhandled nomenclatural remark: " + nomenclaturalRemarks);
|
352 |
|
|
}
|
353 |
|
|
|
354 |
|
|
NomenclaturalStatusType kewType = remarkType != null? remarkType : statusType;
|
355 |
|
|
if (isNewName){
|
356 |
|
|
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
357 |
|
|
logger.warn(row + "Kew suggests 2 different nom. status. types for new name. The status from nomenclatural_remarks was taken.");
|
358 |
|
|
}
|
359 |
|
|
if (kewType != null){
|
360 |
|
|
name.addStatus(kewType, getSecRef(), null);
|
361 |
|
|
}
|
362 |
|
|
}else{
|
363 |
|
|
NomenclaturalStatusType existingType = null;
|
364 |
|
|
if (!name.getStatus().isEmpty()){
|
365 |
|
|
existingType = name.getStatus().iterator().next().getType();
|
366 |
|
|
}
|
367 |
|
|
if (existingType != null && kewType != null){
|
368 |
|
|
if (!existingType.equals(kewType)){
|
369 |
|
|
logger.warn(row + "Existing name status "+existingType.getTitleCache()+" differs from Kew status " + kewType.getTitleCache() + ". Key status ignored");
|
370 |
|
|
}
|
371 |
|
|
}else if (existingType != null && kewType == null){
|
372 |
|
|
logger.warn(row + "Info: Existing name has a name status "+existingType.getTitleCache()+" but Kew name has no status. Existing status kept.");
|
373 |
|
|
}else if (existingType == null && kewType != null){
|
374 |
|
|
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
375 |
|
|
logger.warn(row + "Existing name has no status while Kew name suggests a status (but 2 different status form status and nomenclatural_remarks field).");
|
376 |
|
|
}else{
|
377 |
|
|
logger.warn(row + "Existing name has no status while Kew name suggests a status ("+kewType.getTitleCache()+"). Kew status ignored.");
|
378 |
|
|
}
|
379 |
|
|
}
|
380 |
|
|
}
|
381 |
|
|
}
|
382 |
|
|
|
383 |
|
|
private void newTransaction(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
|
384 |
|
|
commitTransaction(state.getTransactionStatus());
|
385 |
|
|
secRef = null;
|
386 |
|
|
dedupHelper = null;
|
387 |
26f92af1
|
Andreas Müller
|
state.setSourceReference(null);
|
388 |
721766b0
|
Andreas Müller
|
System.gc();
|
389 |
|
|
state.setTransactionStatus(startTransaction());
|
390 |
|
|
}
|
391 |
|
|
|
392 |
|
|
private Reference getSecRef() {
|
393 |
|
|
if (secRef == null){
|
394 |
|
|
secRef = getReferenceService().find(state.getConfig().getSecUuid());
|
395 |
|
|
}
|
396 |
|
|
return secRef;
|
397 |
|
|
}
|
398 |
|
|
|
399 |
|
|
private Class<? extends CdmBase> getIllegInvalidStatus(String sourceId, String accId) {
|
400 |
|
|
if (sourceId.equals(accId)){
|
401 |
|
|
return Taxon.class;
|
402 |
|
|
}else if(accId != null){
|
403 |
|
|
return Synonym.class;
|
404 |
|
|
}
|
405 |
|
|
return null;
|
406 |
|
|
}
|
407 |
|
|
|
408 |
|
|
|
409 |
|
|
private void testParsedName(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state, TaxonName name,
|
410 |
|
|
String row, String fullCitation) throws UndefinedTransformerMethodException {
|
411 |
|
|
Map<String, String> record = state.getOriginalRecord();
|
412 |
|
|
|
413 |
|
|
String nameCache = getValue(record, KEW_NAME4CDM_LINK);
|
414 |
|
|
String fullName = getValue(record, KEW_F_NAME4CDM_LINK);
|
415 |
|
|
String rankStr = getValue(record, TAXON_RANK);
|
416 |
|
|
String genusHybrid = getValue(record, "genus_hybrid");
|
417 |
|
|
String genus = getValue(record, "genus");
|
418 |
|
|
String speciesHybrid = getValue(record, "species_hybrid");
|
419 |
|
|
String species = getValue(record, "species");
|
420 |
|
|
String infraSpecRank = getValue(record, "infraspecific_rank");
|
421 |
|
|
String infraspecies = getValue(record, "infraspecies");
|
422 |
|
|
String basionymAuthor = getValue(record, "parenthetical_author");
|
423 |
|
|
String combinationAuthor = getValue(record, "primary_author");
|
424 |
|
|
String authors = getValue(record, "taxon_authors");
|
425 |
|
|
String year = getValue(record, "KewYear4CDM");
|
426 |
|
|
String pubType = getValue(record, "PubType");
|
427 |
|
|
String place_of_publication = getValue(record, "place_of_publication");
|
428 |
|
|
String volume_and_page = getValue(record, "volume_and_page");
|
429 |
|
|
|
430 |
|
|
if (!CdmUtils.nullSafeEqual(name.getNameCache(), nameCache)){
|
431 |
|
|
logger.warn(row + "Unexpected nameCache: " + nameCache);
|
432 |
|
|
}
|
433 |
|
|
if (!CdmUtils.nullSafeEqual(name.getTitleCache(), fullName)){
|
434 |
|
|
logger.warn(row + "Unexpected titleCache: <->" + name.getTitleCache());
|
435 |
|
|
}
|
436 |
|
|
if (isBlank(genusHybrid) == name.isMonomHybrid()){
|
437 |
|
|
logger.warn(row + "Unexpected genus hybrid: " + genusHybrid);
|
438 |
|
|
}
|
439 |
|
|
if (!CdmUtils.nullSafeEqual(name.getGenusOrUninomial(),genus)){
|
440 |
|
|
logger.warn(row + "Unexpected genus: " + genus);
|
441 |
|
|
}if (isBlank(speciesHybrid) == name.isBinomHybrid()){
|
442 |
|
|
logger.warn(row + "Unexpected species hybrid: " + speciesHybrid);
|
443 |
|
|
}
|
444 |
|
|
if (!CdmUtils.nullSafeEqual(name.getSpecificEpithet(),species)){
|
445 |
|
|
logger.warn(row + "Unexpected species epithet: " + name.getSpecificEpithet() +"<->"+ species);
|
446 |
|
|
}
|
447 |
|
|
if (!CdmUtils.nullSafeEqual(name.getInfraSpecificEpithet(), infraspecies)){
|
448 |
|
|
logger.warn(row + "Unexpected infraspecific epithet: " + name.getInfraSpecificEpithet() +"<->"+ infraspecies);
|
449 |
|
|
}
|
450 |
|
|
if (!CdmUtils.nullSafeEqual(name.getAuthorshipCache(),authors)){
|
451 |
|
|
logger.warn(row + "Unexpected authors: " + name.getAuthorshipCache() +"<->"+ authors);
|
452 |
|
|
}
|
453 |
fb7aa32c
|
Andreas Müller
|
String combinationAndExAuthor = authorTitle(name.getCombinationAuthorship(), name.getExCombinationAuthorship());
|
454 |
|
|
if (!CdmUtils.nullSafeEqual(combinationAndExAuthor, combinationAuthor)){
|
455 |
|
|
logger.warn(row + "Unexpected combination author: " + combinationAndExAuthor +"<->"+ combinationAuthor);
|
456 |
|
|
}
|
457 |
|
|
String basionymAndExAuthor = authorTitle(name.getBasionymAuthorship(), name.getExBasionymAuthorship());
|
458 |
|
|
if (!CdmUtils.nullSafeEqual(basionymAndExAuthor, basionymAuthor)){
|
459 |
|
|
logger.warn(row + "Unexpected basionym author: " + basionymAndExAuthor +"<->"+ basionymAuthor);
|
460 |
|
|
}
|
461 |
721766b0
|
Andreas Müller
|
Rank rank = state.getTransformer().getRankByKey(rankStr);
|
462 |
|
|
if (!rank.equals(name.getRank())){
|
463 |
|
|
logger.warn(row + "Unexpected rank: " + rankStr);
|
464 |
|
|
}
|
465 |
|
|
|
466 |
|
|
Reference nomRef = name.getNomenclaturalReference();
|
467 |
|
|
if (nomRef == null){
|
468 |
|
|
if (fullCitation != null){
|
469 |
|
|
NonViralNameParserImpl parser = new NonViralNameParserImpl();
|
470 |
|
|
TaxonName parsedName = parser.parseReferencedName(fullCitation, NomenclaturalCode.ICNAFP, rank);
|
471 |
|
|
if (parsedName.getNomenclaturalReference() != null){
|
472 |
|
|
name.setNomenclaturalReference(parsedName.getNomenclaturalReference());
|
473 |
|
|
logger.warn(row + "Nom.ref. was missing. Taken from Kew");
|
474 |
|
|
}else{
|
475 |
|
|
logger.warn(row + "Nom. ref. is missing or can not be parsed");
|
476 |
|
|
}
|
477 |
|
|
}else{
|
478 |
|
|
logger.warn(row + "NomRef is missing.");
|
479 |
|
|
}
|
480 |
|
|
}else{
|
481 |
|
|
if ("A".equals(pubType) && nomRef.getType() != ReferenceType.Article){
|
482 |
|
|
logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString());
|
483 |
|
|
}
|
484 |
|
|
if ("B".equals(pubType) && nomRef.getType() != ReferenceType.Book){
|
485 |
|
|
logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString());
|
486 |
|
|
}
|
487 |
|
|
year = normalizeYear(year);
|
488 |
|
|
if (!CdmUtils.nullSafeEqual(year, nomRef.getDatePublishedString())){
|
489 |
|
|
logger.warn(row + "Unexpected year: " + year + "<->" + nomRef.getDatePublishedString());
|
490 |
|
|
}
|
491 |
26f92af1
|
Andreas Müller
|
if (volume_and_page != null && !name.getFullTitleCache().contains(volume_and_page)){
|
492 |
721766b0
|
Andreas Müller
|
logger.warn(row + "volume_and_page not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ volume_and_page);
|
493 |
|
|
}
|
494 |
26f92af1
|
Andreas Müller
|
if (place_of_publication != null && !name.getFullTitleCache().contains(place_of_publication)){
|
495 |
721766b0
|
Andreas Müller
|
logger.warn(row + "place_of_publication not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ place_of_publication);
|
496 |
|
|
}
|
497 |
|
|
}
|
498 |
|
|
if ("subsp.".equals(infraSpecRank) && !rank.equals(Rank.SUBSPECIES())){
|
499 |
|
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
500 |
|
|
}else if ("var.".equals(infraSpecRank) && !rank.equals(Rank.VARIETY())){
|
501 |
|
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
502 |
|
|
}else if ("f.".equals(infraSpecRank) && !rank.equals(Rank.FORM())){
|
503 |
|
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
504 |
|
|
}
|
505 |
fb7aa32c
|
Andreas Müller
|
}
|
506 |
721766b0
|
Andreas Müller
|
|
507 |
fb7aa32c
|
Andreas Müller
|
private String authorTitle(TeamOrPersonBase<?> author, TeamOrPersonBase<?> exAuthor) {
|
508 |
|
|
String authorStr = author == null? null: author.getNomenclaturalTitle();
|
509 |
|
|
String exAuthorStr = exAuthor == null? null: exAuthor.getNomenclaturalTitle();
|
510 |
|
|
return CdmUtils.concat(" ex ", exAuthorStr, authorStr);
|
511 |
721766b0
|
Andreas Müller
|
}
|
512 |
|
|
|
513 |
|
|
private String normalizeYear(String year) {
|
514 |
|
|
if (year == null){
|
515 |
|
|
return null;
|
516 |
|
|
}else if (year.contains("\" [")){
|
517 |
|
|
String[] split = year.split("\" \\[");
|
518 |
|
|
year = split[1].replace("]","") + " [" + split[0]+"\"]";
|
519 |
|
|
}else if ("?".equals(year)){
|
520 |
|
|
return null;
|
521 |
|
|
}
|
522 |
|
|
return year;
|
523 |
|
|
}
|
524 |
|
|
|
525 |
|
|
@Override
|
526 |
|
|
protected void secondPass(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state) {
|
527 |
|
|
Map<String, String> record = state.getOriginalRecord();
|
528 |
|
|
int line = state.getCurrentLine();
|
529 |
|
|
String fullName = getValue(record, KEW_F_NAME4CDM_LINK);
|
530 |
|
|
String status = getValue(record, TAXON_STATUS);
|
531 |
|
|
String sourceId = getValue(record, PLANT_NAME_ID);
|
532 |
|
|
String accId = getValue(record, ACCEPTED_PLANT_NAME_ID);
|
533 |
|
|
String accName = getValue(record, "AcceptedName");
|
534 |
|
|
String basionymId = getValue(record, "basionym_plant_name_id");
|
535 |
|
|
String homotypicSynonym = getValue(record, "homotypic_synonym");
|
536 |
|
|
|
537 |
|
|
String row = String.valueOf(line) + "("+fullName+"): ";
|
538 |
|
|
try {
|
539 |
26f92af1
|
Andreas Müller
|
if ((line % 500) == 0){
|
540 |
721766b0
|
Andreas Müller
|
newTransaction(state);
|
541 |
|
|
System.out.println(line);
|
542 |
|
|
}
|
543 |
|
|
|
544 |
|
|
if("Misapplied".equals(status)){
|
545 |
|
|
return;
|
546 |
|
|
}else if (neglectedRecords.contains(sourceId)){
|
547 |
|
|
logger.info(row + "Record ignored.");
|
548 |
|
|
return;
|
549 |
|
|
}
|
550 |
|
|
|
551 |
|
|
UUID uuid = taxonMapping.get(sourceId);
|
552 |
|
|
TaxonBase<?> taxonBase = getTaxonService().find(uuid);
|
553 |
|
|
if (taxonBase == null){
|
554 |
|
|
logger.warn(row + "taxonBase not found: " + sourceId);
|
555 |
|
|
return;
|
556 |
|
|
}
|
557 |
|
|
|
558 |
|
|
UUID accUuid = taxonMapping.get(accId);
|
559 |
|
|
boolean hasAccepted = !sourceId.equals(accId);
|
560 |
|
|
|
561 |
|
|
Taxon accTaxon = null;
|
562 |
|
|
TaxonNode parent = null;
|
563 |
|
|
Taxon child = null;
|
564 |
|
|
Synonym syn = null;
|
565 |
|
|
boolean isSynonymAccepted = false;
|
566 |
|
|
|
567 |
|
|
if(accId == null){
|
568 |
|
|
logger.info(row + "accID is null");
|
569 |
|
|
child = CdmBase.deproxy(taxonBase, Taxon.class);
|
570 |
|
|
}else if(hasAccepted){
|
571 |
|
|
TaxonBase<?> accTaxonBase = getTaxonService().find(accUuid);
|
572 |
|
|
if (accTaxonBase == null){
|
573 |
|
|
logger.warn(row + "acctaxon not found: " + accId + "; " + accName);
|
574 |
|
|
}else if(!accTaxonBase.isInstanceOf(Taxon.class)){
|
575 |
|
|
logger.warn(row + "acctaxon is synonym: " + accId + "; " + accName);
|
576 |
|
|
isSynonymAccepted = true;
|
577 |
|
|
}else{
|
578 |
|
|
accTaxon = CdmBase.deproxy(accTaxonBase, Taxon.class);
|
579 |
|
|
if (!accTaxon.getName().getTitleCache().equals(accName)){
|
580 |
|
|
logger.warn(row + "Accepted name differs: " + accName +" <-> "+ accTaxon.getName().getTitleCache());
|
581 |
|
|
}
|
582 |
|
|
}
|
583 |
|
|
}else if (sourceId.equals(accId)){
|
584 |
|
|
if (!taxonBase.isInstanceOf(Taxon.class)){
|
585 |
|
|
logger.warn(row + "child not of class Taxon: " + sourceId);
|
586 |
|
|
}else{
|
587 |
|
|
Rank rank = taxonBase.getName().getRank();
|
588 |
|
|
child = CdmBase.deproxy(taxonBase, Taxon.class);
|
589 |
|
|
if(rank.equals(Rank.GENUS())){
|
590 |
|
|
parent = getFamily();
|
591 |
|
|
}else if (rank.equals(Rank.SPECIES())){
|
592 |
|
|
String genus = child.getName().getGenusOrUninomial();
|
593 |
|
|
UUID parentUuid = taxonMapping.get(genus);
|
594 |
|
|
parent = getParent(parentUuid, row);
|
595 |
|
|
}else if (rank.isLower(Rank.SPECIES())){
|
596 |
|
|
String speciesName = child.getName().getGenusOrUninomial() + " " + child.getName().getSpecificEpithet();
|
597 |
|
|
UUID parentUuid = taxonMapping.get(speciesName);
|
598 |
|
|
parent = getParent(parentUuid, row);
|
599 |
|
|
}
|
600 |
|
|
}
|
601 |
|
|
}
|
602 |
|
|
|
603 |
|
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
604 |
|
|
syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
605 |
|
|
}
|
606 |
|
|
|
607 |
|
|
if ("Accepted".equals(status)){
|
608 |
|
|
if (parent == null){
|
609 |
|
|
logger.warn(row + "Parent is missing. Taxon is moved to 'unresolved' instead'");
|
610 |
|
|
parent = unresolvedParent();
|
611 |
|
|
}
|
612 |
|
|
if (child == null){
|
613 |
|
|
logger.warn(row + "Child is missing. Taxon not imported.");
|
614 |
|
|
}else{
|
615 |
|
|
if (!child.getTaxonNodes().isEmpty()){
|
616 |
|
|
if(!child.getName().getRank().equals(Rank.GENUS())){
|
617 |
|
|
logger.warn(row + "Taxon already has a parent. Taxon not attached to any further parent taxon.");
|
618 |
|
|
}
|
619 |
|
|
}else{
|
620 |
|
|
addChild(parent, child, row);
|
621 |
|
|
}
|
622 |
|
|
}
|
623 |
|
|
}else if ("Synonym".equals(status)){
|
624 |
|
|
if(accTaxon == null){
|
625 |
|
|
if(isSynonymAccepted){
|
626 |
|
|
logger.warn(row + "Synonym added to 'unresolved' as accepted taxon is synonym itself.");
|
627 |
|
|
}else if (accId != null){
|
628 |
|
|
logger.warn(row + "Accepted taxon for synonym unexpectedly does not exist (it seems not to be a synonym itself). Synonym moved to 'unresolved'");
|
629 |
|
|
}else{
|
630 |
|
|
logger.warn(row + "No accepted taxon given for synonym. Therefore taxon moved to 'unresolved'");
|
631 |
|
|
}
|
632 |
|
|
if(accId != null){
|
633 |
|
|
child = Taxon.NewInstance(syn.getName(), syn.getSec());
|
634 |
26f92af1
|
Andreas Müller
|
child.addImportSource(sourceId, PLANT_NAME_ID, getSourceReference(state), "line " + state.getCurrentLine());
|
635 |
721766b0
|
Andreas Müller
|
}
|
636 |
|
|
addChild(unresolvedParent(), child, row);
|
637 |
|
|
getTaxonService().deleteSynonym(syn, new SynonymDeletionConfigurator());
|
638 |
|
|
}else{
|
639 |
|
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF());
|
640 |
|
|
}
|
641 |
|
|
}else if ("Unplaced".equals(status)){
|
642 |
|
|
parent = unresolvedParent();
|
643 |
|
|
addChild(parent, child, row);
|
644 |
|
|
}else if ("Artificial Hybrid".equals(status)){
|
645 |
|
|
parent = hybridParent();
|
646 |
|
|
addChild(parent, child, row);
|
647 |
|
|
}else if ("Orthographic".equals(status)){
|
648 |
|
|
if(accTaxon == null){
|
649 |
|
|
logger.warn(row + "'Orthographic' taxon has no acc taxon");
|
650 |
|
|
}else{
|
651 |
|
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF());
|
652 |
|
|
}
|
653 |
|
|
}else if("Illegitimate".equals(status) || "Invalid".equals(status)){
|
654 |
|
|
if (hasAccepted){
|
655 |
|
|
if(accTaxon == null){
|
656 |
|
|
logger.warn(row + "accepted taxon for illegitimate or invalid taxon not found");
|
657 |
|
|
}else{
|
658 |
|
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF());
|
659 |
|
|
}
|
660 |
|
|
}else{
|
661 |
|
|
addChild(unresolvedParent(), child, row);
|
662 |
|
|
}
|
663 |
|
|
}else{
|
664 |
|
|
logger.warn(row + "Unhandled status: " + status);
|
665 |
|
|
}
|
666 |
|
|
|
667 |
26f92af1
|
Andreas Müller
|
if (basionymId != null && false){
|
668 |
721766b0
|
Andreas Müller
|
UUID basionymUuid = taxonMapping.get(basionymId);
|
669 |
|
|
TaxonBase<?> basionymTaxon = getTaxonService().find(basionymUuid);
|
670 |
|
|
if (basionymTaxon != null){
|
671 |
|
|
if (hasSameAcceptedTaxon(taxonBase, basionymTaxon)){
|
672 |
|
|
if (taxonBase.getName().getBasionym() == null){
|
673 |
|
|
taxonBase.getName().addBasionym(basionymTaxon.getName());
|
674 |
|
|
}
|
675 |
|
|
}else{
|
676 |
|
|
logger.warn(row + "Basionym has not same accepted taxon and therefore was ignored.");
|
677 |
|
|
}
|
678 |
|
|
}else{
|
679 |
|
|
logger.warn(row + "Basionym "+basionymId+" not found.");
|
680 |
|
|
}
|
681 |
|
|
}
|
682 |
|
|
} catch (Exception e) {
|
683 |
|
|
logger.error(row + "Error.");
|
684 |
|
|
e.printStackTrace();
|
685 |
|
|
}
|
686 |
|
|
}
|
687 |
|
|
|
688 |
|
|
private boolean hasSameAcceptedTaxon(TaxonBase<?> taxonBase, TaxonBase<?> basionymTaxon) {
|
689 |
|
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
690 |
26f92af1
|
Andreas Müller
|
taxonBase = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
|
691 |
721766b0
|
Andreas Müller
|
}
|
692 |
|
|
if (basionymTaxon.isInstanceOf(Synonym.class)){
|
693 |
26f92af1
|
Andreas Müller
|
basionymTaxon = CdmBase.deproxy(basionymTaxon, Synonym.class).getAcceptedTaxon();
|
694 |
721766b0
|
Andreas Müller
|
}
|
695 |
26f92af1
|
Andreas Müller
|
return taxonBase != null && basionymTaxon != null && taxonBase.equals(basionymTaxon);
|
696 |
721766b0
|
Andreas Müller
|
}
|
697 |
|
|
|
698 |
|
|
private TaxonNode getParent(UUID parentUuid, String row) {
|
699 |
|
|
if(parentUuid == null){
|
700 |
|
|
logger.warn(row + "Parent uuid is null. No parent found.");
|
701 |
|
|
return null;
|
702 |
|
|
}
|
703 |
|
|
TaxonBase<?> pTaxon = getTaxonService().find(parentUuid);
|
704 |
|
|
if (pTaxon == null){
|
705 |
|
|
logger.warn(row + "No parent found for parent UUID. This should not happen.");
|
706 |
|
|
return null;
|
707 |
|
|
}
|
708 |
|
|
if (pTaxon.isInstanceOf(Synonym.class)){
|
709 |
|
|
logger.warn(row + "Parent is synonym");
|
710 |
|
|
return null;
|
711 |
|
|
}else{
|
712 |
|
|
Taxon ptax = CdmBase.deproxy(pTaxon, Taxon.class);
|
713 |
|
|
if(ptax.getTaxonNodes().isEmpty()){
|
714 |
|
|
logger.warn(row + "Parent has no node yet");
|
715 |
|
|
return null;
|
716 |
|
|
}else {
|
717 |
|
|
if(ptax.getTaxonNodes().size()>1){
|
718 |
|
|
logger.warn("Parent has >1 nodes. Take arbitrary one");
|
719 |
|
|
}
|
720 |
|
|
return ptax.getTaxonNodes().iterator().next();
|
721 |
|
|
}
|
722 |
|
|
}
|
723 |
|
|
}
|
724 |
|
|
|
725 |
|
|
private void addChild(TaxonNode parent, Taxon child, String row) {
|
726 |
|
|
if (parent == null){
|
727 |
|
|
logger.warn(row + "Parent is null");
|
728 |
|
|
}else if (child == null){
|
729 |
|
|
logger.warn(row + "Child is null");
|
730 |
|
|
}else{
|
731 |
|
|
if (!child.getTaxonNodes().isEmpty()){
|
732 |
|
|
TaxonNode childNode = child.getTaxonNodes().iterator().next();
|
733 |
|
|
if (childNode.getParent() != null && childNode.getParent().equals(parent)){
|
734 |
|
|
logger.info(row + "Parent-child relation exists already.");
|
735 |
|
|
}else{
|
736 |
|
|
logger.warn(row + "Child already has different parent. Parent-child relation not added.");
|
737 |
|
|
}
|
738 |
|
|
}else{
|
739 |
|
|
TaxonNode node = parent.addChildTaxon(child, null, null);
|
740 |
|
|
getTaxonNodeService().saveOrUpdate(node);
|
741 |
|
|
}
|
742 |
|
|
}
|
743 |
|
|
}
|
744 |
|
|
|
745 |
|
|
private TaxonNode getFamily(){
|
746 |
|
|
UUID uuid = UUID.fromString("0334809a-aa20-447d-add9-138194f80f56");
|
747 |
|
|
TaxonNode aizoaceae = getTaxonNodeService().find(uuid);
|
748 |
|
|
return aizoaceae;
|
749 |
|
|
}
|
750 |
|
|
|
751 |
|
|
private TaxonNode hybridParent(){
|
752 |
|
|
UUID uuid = UUID.fromString("2fae0fa1-758a-4fcb-bb6c-a2bd11f40641");
|
753 |
|
|
TaxonNode hybridParent = getTaxonNodeService().find(uuid);
|
754 |
|
|
return hybridParent;
|
755 |
|
|
}
|
756 |
|
|
private TaxonNode unresolvedParent(){
|
757 |
|
|
UUID uuid = UUID.fromString("accb1ff6-5748-4b18-b529-9368c331a38d");
|
758 |
|
|
TaxonNode unresolvedParent = getTaxonNodeService().find(uuid);
|
759 |
|
|
return unresolvedParent;
|
760 |
|
|
}
|
761 |
|
|
}
|