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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.casearia;
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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.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.common.Language;
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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.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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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* Taxon import for Casearia from Kew world checklist of plants.
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*
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* @author a.mueller
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* @since 12.05.2020
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*/
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@Component
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public class CaseariaTaxonImport extends SimpleExcelTaxonImport<CaseariaImportConfigurator>{
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private static final long serialVersionUID = 7686154384296707819L;
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private static final Logger logger = LogManager.getLogger();
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protected static final String TAXON_MAPPING = "TaxonMapping";
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private static final String NAME_CIT = "NameCit";
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private static final String IPNI_ID = "ipni_id";
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private static final String PLANT_NAME_ID = "plant_name_id";
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private static final String TAXON_RANK = "taxon_rank";
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private static final String TAXON_STATUS = "taxon_status";
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private static final String NOMENCLATURAL_REMARKS = "nomenclatural_remarks";
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private static final String ACCEPTED_PLANT_NAME_ID = "accepted_plant_name_id";
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private static final String TAXON_NAME = "taxon_name";
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private static final String TAXON_AUTHORS = "taxon_authors";
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private static final String FAMILY = "family";
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private static final String FIRST_PUBLISHED = "first_published";
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private static final String PUB_TYPE = "PubType";
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private static final String VOLUME_AND_PAGE = "volume_and_page";
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private static final String PLACE_OF_PUBLICATION = "place_of_publication";
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private static final String PRIMARY_AUTHOR = "primary_author";
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private static final String PARENTHETICAL_AUTHOR = "parenthetical_author";
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private static final String INFRASPECIFIC_RANK = "infraspecific_rank";
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private static final String INFRASPECIES = "infraspecies";
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private static final String SPECIES = "species";
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private static final String GENUS = "genus";
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private static final int RECORDS_PER_TRANSACTION = 500;
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private static boolean logMissingIpniId = false;
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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<UUID> createdNames = new HashSet<>();
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private SimpleExcelTaxonImportState<CaseariaImportConfigurator> state;
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private NonViralNameParserImpl parser = new NonViralNameParserImpl();
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<CaseariaImportConfigurator> state) {
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int line = state.getCurrentLine();
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if ((line % RECORDS_PER_TRANSACTION) == 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 ipniId = getValue(record, IPNI_ID);
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String sourceId = getValue(record, PLANT_NAME_ID);
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String rankStr = getValue(record, TAXON_RANK);
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String status = getValue(record, TAXON_STATUS);
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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 taxonNameStr = getValue(record, TAXON_NAME);
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String taxonAuthors = getValue(record, TAXON_AUTHORS);
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String fullNameStr = CdmUtils.concat(" ", taxonNameStr,taxonAuthors);
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String row = String.valueOf(line) + "("+fullNameStr+"): ";
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boolean isNewName = true;
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try {
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List<NomenclaturalStatusType> statusTypes = new ArrayList<>();
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Class<? extends CdmBase> taxonClazz = makeStatus(status, sourceId, accId, row, statusTypes);
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Rank rank = state.getTransformer().getRankByKey(rankStr);
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TaxonName name = parser.parseReferencedName(fullCitation, state.getConfig().getNomenclaturalCode(), 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(fullNameStr, true);
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name.setNameCache(taxonNameStr, 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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createdNames.add(name.getUuid());
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handleNomenclRemarkAndNameStatus(nomenclaturalRemarks, row, isNewName, name, statusTypes);
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TaxonBase<?> taxonBase;
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if (taxonClazz == 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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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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if(logMissingIpniId){
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logger.warn(row + "IPNI id is missing.");
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}
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}
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UUID uuid = taxonMapping.put(sourceId, taxonBase.getUuid());{
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if (uuid != null){
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logger.warn(row + "sourceId already existed in taxonMapping: " + sourceId);
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}
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}
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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 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) || "Misapplied".equals(status)){
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clazz = Taxon.class;
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}else if ("Synonym".equals(status)){
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clazz = (accId == null)? Taxon.class : Synonym.class;
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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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}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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}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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}
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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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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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}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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}else if (", nom. rej.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.REJECTED();
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}else if (", nom. subnud.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.SUBNUDUM();
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}else if (", nom. superfl.".equals(nomenclaturalRemarks)){
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remarkType = NomenclaturalStatusType.SUPERFLUOUS();
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}else if (", not validly publ.".equals(nomenclaturalRemarks)){
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statusTypes.add(NomenclaturalStatusType.INVALID());
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}else if (", opus utique oppr.".equals(nomenclaturalRemarks)){
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statusTypes.add(NomenclaturalStatusType.OPUS_UTIQUE_OPPR());
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}else {
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logger.warn(row + "Unhandled nomenclatural remark: " + nomenclaturalRemarks);
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}
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NomenclaturalStatusType kewType = remarkType != null? remarkType : statusType;
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if (isNewName){
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if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
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logger.warn(row + "Kew suggests 2 different nom. status. types for new name. The status from nomenclatural_remarks was taken.");
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}
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if (kewType != null){
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name.addStatus(kewType, getSecRef(), null);
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}
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}else{
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NomenclaturalStatusType existingType = null;
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if (!name.getStatus().isEmpty()){
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existingType = name.getStatus().iterator().next().getType();
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}
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if (existingType != null && kewType != null){
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if (!existingType.equals(kewType)){
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logger.warn(row + "Existing name status "+existingType.getTitleCache()+" differs from Kew status " + kewType.getTitleCache() + ". Key status ignored");
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}
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}else if (existingType != null && kewType == null){
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logger.warn(row + "Info: Existing name has a name status "+existingType.getTitleCache()+" but Kew name has no status. Existing status kept.");
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}else if (existingType == null && kewType != null){
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if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
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logger.warn(row + "Existing name has no status while Kew name suggests a status (but 2 different status form status and nomenclatural_remarks field).");
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}else{
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logger.warn(row + "Existing name has no status while Kew name suggests a status ("+kewType.getTitleCache()+"). Kew status ignored.");
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}
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}
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}
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}
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private void newTransaction(SimpleExcelTaxonImportState<CaseariaImportConfigurator> state) {
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commitTransaction(state.getTransactionStatus());
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secRef = null;
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state.getDeduplicationHelper().reset();
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state.setSourceReference(null);
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System.gc();
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state.setTransactionStatus(startTransaction());
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}
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private Reference getSecRef() {
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if (secRef == null){
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secRef = getReferenceService().find(state.getConfig().getSecUuid());
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if (secRef == null){
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secRef = ReferenceFactory.newDatabase();
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secRef.setTitle("Casearia Database");
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}
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}
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return secRef;
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}
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private Class<? extends CdmBase> getIllegInvalidStatus(String sourceId, String accId) {
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if (sourceId.equals(accId)){
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return Taxon.class;
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}else if(accId != null){
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return Synonym.class;
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}
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return null;
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}
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private void testParsedName(SimpleExcelTaxonImportState<CaseariaImportConfigurator> state, TaxonName name,
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String row, String fullCitation) throws UndefinedTransformerMethodException {
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Map<String, String> record = state.getOriginalRecord();
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// publication_author
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String rankStr = getValue(record, TAXON_RANK);
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String nameCache = getValue(record, TAXON_NAME);
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String authorshipCache = getValue(record, TAXON_AUTHORS);
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String genus = getValue(record, GENUS);
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String species = getValue(record, SPECIES);
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String infraspecies = getValue(record, INFRASPECIES);
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String infraSpecRank = getValue(record, INFRASPECIFIC_RANK);
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String basionymAuthor = getValue(record, PARENTHETICAL_AUTHOR);
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String combinationAuthor = getValue(record, PRIMARY_AUTHOR);
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String place_of_publication = getValue(record, PLACE_OF_PUBLICATION);
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String volume_and_page = getValue(record, VOLUME_AND_PAGE);
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String pubType = getValue(record, PUB_TYPE);
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String yearPublished = getValue(record, FIRST_PUBLISHED);
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String fullName = CdmUtils.concat(" ", nameCache, authorshipCache);
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if (!CdmUtils.nullSafeEqual(name.getNameCache(), nameCache)){
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logger.warn(row + "Unexpected nameCache: " + nameCache);
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}
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if (!CdmUtils.nullSafeEqual(name.getTitleCache(), fullName)){
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logger.warn(row + "Unexpected titleCache: <->" + name.getTitleCache());
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}
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if (!CdmUtils.nullSafeEqual(name.getGenusOrUninomial(),genus)){
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logger.warn(row + "Unexpected genus: " + genus);
|
|
325
|
}
|
|
326
|
if (!CdmUtils.nullSafeEqual(name.getSpecificEpithet(), species)){
|
|
327
|
logger.warn(row + "Unexpected species epithet: " + name.getSpecificEpithet() +"<->"+ species);
|
|
328
|
}
|
|
329
|
if (!CdmUtils.nullSafeEqual(name.getInfraSpecificEpithet(), infraspecies)){
|
|
330
|
logger.warn(row + "Unexpected infraspecific epithet: " + name.getInfraSpecificEpithet() +"<->"+ infraspecies);
|
|
331
|
}
|
|
332
|
if (!CdmUtils.nullSafeEqual(name.getAuthorshipCache(), authorshipCache)){
|
|
333
|
logger.warn(row + "Unexpected authors: " + name.getAuthorshipCache() +"<->"+ authorshipCache);
|
|
334
|
}
|
|
335
|
String combinationAndExAuthor = authorTitle(name.getCombinationAuthorship(), name.getExCombinationAuthorship());
|
|
336
|
if (!CdmUtils.nullSafeEqual(combinationAndExAuthor, combinationAuthor)){
|
|
337
|
logger.warn(row + "Unexpected combination author: " + combinationAndExAuthor +"<->"+ combinationAuthor);
|
|
338
|
}
|
|
339
|
String basionymAndExAuthor = authorTitle(name.getBasionymAuthorship(), name.getExBasionymAuthorship());
|
|
340
|
if (!CdmUtils.nullSafeEqual(basionymAndExAuthor, basionymAuthor)){
|
|
341
|
logger.warn(row + "Unexpected basionym author: " + basionymAndExAuthor +"<->"+ basionymAuthor);
|
|
342
|
}
|
|
343
|
Rank rank = state.getTransformer().getRankByKey(rankStr);
|
|
344
|
if (!rank.equals(name.getRank())){
|
|
345
|
logger.warn(row + "Unexpected rank: " + rankStr);
|
|
346
|
}
|
|
347
|
|
|
348
|
Reference nomRef = name.getNomenclaturalReference();
|
|
349
|
if (nomRef == null){
|
|
350
|
if (fullCitation != null){
|
|
351
|
NonViralNameParserImpl parser = new NonViralNameParserImpl();
|
|
352
|
TaxonName parsedName = parser.parseReferencedName(fullCitation, NomenclaturalCode.ICNAFP, rank);
|
|
353
|
if (parsedName.getNomenclaturalReference() != null){
|
|
354
|
name.setNomenclaturalReference(parsedName.getNomenclaturalReference());
|
|
355
|
logger.warn(row + "Nom.ref. was missing. Taken from Kew");
|
|
356
|
}else{
|
|
357
|
logger.warn(row + "Nom. ref. is missing or can not be parsed");
|
|
358
|
}
|
|
359
|
}else{
|
|
360
|
logger.warn(row + "NomRef is missing.");
|
|
361
|
}
|
|
362
|
}else{
|
|
363
|
if ("A".equals(pubType) && nomRef.getType() != ReferenceType.Article){
|
|
364
|
logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString());
|
|
365
|
}
|
|
366
|
if ("B".equals(pubType) && nomRef.getType() != ReferenceType.Book){
|
|
367
|
logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString());
|
|
368
|
}
|
|
369
|
String year = normalizeYear(yearPublished);
|
|
370
|
if (!CdmUtils.nullSafeEqual(year, nomRef.getDatePublishedString())){
|
|
371
|
logger.warn(row + "Unexpected year: " + year + "<->" + nomRef.getDatePublishedString());
|
|
372
|
}
|
|
373
|
if (volume_and_page != null && !name.getFullTitleCache().contains(volume_and_page)){
|
|
374
|
logger.warn(row + "volume_and_page not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ volume_and_page);
|
|
375
|
}
|
|
376
|
if (place_of_publication != null && !name.getFullTitleCache().contains(place_of_publication)){
|
|
377
|
logger.warn(row + "place_of_publication not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ place_of_publication);
|
|
378
|
}
|
|
379
|
}
|
|
380
|
if (isBlank(infraSpecRank)){
|
|
381
|
if (rank.isLowerThan(RankClass.Species)){
|
|
382
|
logger.warn(row + "No infraspce marker given but rank is lower than species");
|
|
383
|
}
|
|
384
|
}else if ("subsp.".equals(infraSpecRank)){
|
|
385
|
if(!rank.equals(Rank.SUBSPECIES())){
|
|
386
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
387
|
}
|
|
388
|
}else if ("var.".equals(infraSpecRank)){
|
|
389
|
if (!rank.equals(Rank.VARIETY())){
|
|
390
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
391
|
}
|
|
392
|
}else if ("subvar.".equals(infraSpecRank)){
|
|
393
|
if (!rank.equals(Rank.SUBVARIETY())){
|
|
394
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
395
|
}
|
|
396
|
}else if ("f.".equals(infraSpecRank)){
|
|
397
|
if (!rank.equals(Rank.FORM())){
|
|
398
|
logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank);
|
|
399
|
}
|
|
400
|
}else{
|
|
401
|
logger.warn(row + "Unhandled infraspec marker: " + infraSpecRank);
|
|
402
|
}
|
|
403
|
}
|
|
404
|
|
|
405
|
private String authorTitle(TeamOrPersonBase<?> author, TeamOrPersonBase<?> exAuthor) {
|
|
406
|
String authorStr = author == null? null: author.getNomenclaturalTitleCache();
|
|
407
|
String exAuthorStr = exAuthor == null? null: exAuthor.getNomenclaturalTitleCache();
|
|
408
|
return CdmUtils.concat(" ex ", exAuthorStr, authorStr);
|
|
409
|
}
|
|
410
|
|
|
411
|
private String normalizeYear(String year) {
|
|
412
|
if (year == null){
|
|
413
|
return null;
|
|
414
|
}else{
|
|
415
|
year = year.substring(1, year.length() - 1);
|
|
416
|
}
|
|
417
|
if (year.contains("\" [")){
|
|
418
|
String[] split = year.split("\" \\[");
|
|
419
|
year = split[1].replace("]","") + " [" + split[0]+"\"]";
|
|
420
|
}else if ("?".equals(year)){
|
|
421
|
return null;
|
|
422
|
}
|
|
423
|
return year;
|
|
424
|
}
|
|
425
|
|
|
426
|
@Override
|
|
427
|
protected void secondPass(SimpleExcelTaxonImportState<CaseariaImportConfigurator> state) {
|
|
428
|
state.putStatusItem(TAXON_MAPPING, taxonMapping);
|
|
429
|
|
|
430
|
|
|
431
|
Map<String, String> record = state.getOriginalRecord();
|
|
432
|
int line = state.getCurrentLine();
|
|
433
|
// String fullName = getValue(record, KEW_F_NAME4CDM_LINK);
|
|
434
|
String status = getValue(record, TAXON_STATUS);
|
|
435
|
String sourceId = getValue(record, PLANT_NAME_ID);
|
|
436
|
String accId = getValue(record, ACCEPTED_PLANT_NAME_ID);
|
|
437
|
String family = getValue(record, FAMILY);
|
|
438
|
|
|
439
|
String accName = getValue(record, "AcceptedName");
|
|
440
|
String basionymId = getValue(record, "basionym_plant_name_id");
|
|
441
|
String homotypicSynonym = getValue(record, "homotypic_synonym");
|
|
442
|
|
|
443
|
// AcceptedName, Basionym, taxon_name_hybcorr, genus_hybrid, species_hybrid, homotypic_synonym,
|
|
444
|
// basionym_plant_name_id
|
|
445
|
|
|
446
|
String taxonNameStr = getValue(record, TAXON_NAME);
|
|
447
|
String taxonAuthors = getValue(record, TAXON_AUTHORS);
|
|
448
|
String fullNameStr = CdmUtils.concat(" ", taxonNameStr,taxonAuthors);
|
|
449
|
String row = String.valueOf(line) + "("+fullNameStr+"): ";
|
|
450
|
|
|
451
|
try {
|
|
452
|
if ((line % RECORDS_PER_TRANSACTION) == 0){
|
|
453
|
newTransaction(state);
|
|
454
|
System.out.println(line);
|
|
455
|
}
|
|
456
|
|
|
457
|
UUID uuid = taxonMapping.get(sourceId);
|
|
458
|
TaxonBase<?> taxonBase = getTaxonService().find(uuid);
|
|
459
|
if (taxonBase == null){
|
|
460
|
logger.warn(row + "taxonBase not found: " + sourceId);
|
|
461
|
return;
|
|
462
|
}
|
|
463
|
|
|
464
|
UUID accUuid = taxonMapping.get(accId);
|
|
465
|
boolean hasAccepted = !sourceId.equals(accId);
|
|
466
|
|
|
467
|
Taxon accTaxon = null;
|
|
468
|
TaxonNode parent = null;
|
|
469
|
Taxon child = null;
|
|
470
|
Synonym syn = null;
|
|
471
|
boolean isSynonymAccepted = false;
|
|
472
|
|
|
473
|
if(accId == null){
|
|
474
|
logger.info(row + "accID is null");
|
|
475
|
child = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
476
|
//synonyms
|
|
477
|
}else if(hasAccepted){
|
|
478
|
TaxonBase<?> accTaxonBase = getTaxonService().find(accUuid);
|
|
479
|
if (accTaxonBase == null){
|
|
480
|
// logger.warn(row + "acctaxon not found: " + accId + "; " + accName);
|
|
481
|
}else if(!accTaxonBase.isInstanceOf(Taxon.class)){
|
|
482
|
logger.warn(row + "acctaxon is synonym: " + accId + "; " + accName);
|
|
483
|
isSynonymAccepted = true;
|
|
484
|
}else{
|
|
485
|
accTaxon = CdmBase.deproxy(accTaxonBase, Taxon.class);
|
|
486
|
if (!accTaxon.getName().getTitleCache().equals(accName)){
|
|
487
|
logger.warn(row + "Accepted name differs: " + accName +" <-> "+ accTaxon.getName().getTitleCache());
|
|
488
|
}
|
|
489
|
}
|
|
490
|
//accepted taxa
|
|
491
|
}else if (sourceId.equals(accId)){
|
|
492
|
if (!taxonBase.isInstanceOf(Taxon.class)){
|
|
493
|
logger.warn(row + "child not of class Taxon: " + sourceId);
|
|
494
|
}else{
|
|
495
|
Rank rank = taxonBase.getName().getRank();
|
|
496
|
child = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
497
|
if(rank.equals(Rank.GENUS())){
|
|
498
|
parent = getFamily(row, family);
|
|
499
|
}else if (rank.equals(Rank.SPECIES())){
|
|
500
|
String genus = child.getName().getGenusOrUninomial();
|
|
501
|
UUID parentUuid = taxonMapping.get(genus);
|
|
502
|
parent = getParent(parentUuid, row);
|
|
503
|
}else if (rank.isLowerThan(RankClass.Species)){
|
|
504
|
String speciesName = child.getName().getGenusOrUninomial() + " " + child.getName().getSpecificEpithet();
|
|
505
|
UUID parentUuid = taxonMapping.get(speciesName);
|
|
506
|
parent = getParent(parentUuid, row);
|
|
507
|
}
|
|
508
|
}
|
|
509
|
}
|
|
510
|
|
|
511
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
512
|
syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
513
|
}
|
|
514
|
|
|
515
|
if ("Accepted".equals(status)){
|
|
516
|
if (parent == null){
|
|
517
|
logger.warn(row + "Parent is missing. Taxon is moved to 'unresolved' instead'");
|
|
518
|
parent = unresolvedParent();
|
|
519
|
}
|
|
520
|
if (child == null){
|
|
521
|
logger.warn(row + "Child is missing. Taxon not imported.");
|
|
522
|
}else{
|
|
523
|
if (!child.getTaxonNodes().isEmpty()){
|
|
524
|
if(!child.getName().getRank().equals(Rank.GENUS())){
|
|
525
|
logger.warn(row + "Taxon already has a parent. Taxon not attached to any further parent taxon.");
|
|
526
|
}
|
|
527
|
}else{
|
|
528
|
addChild(parent, child, row);
|
|
529
|
}
|
|
530
|
}
|
|
531
|
}else if ("Synonym".equals(status)){
|
|
532
|
if(accTaxon == null){
|
|
533
|
if(isSynonymAccepted){
|
|
534
|
logger.warn(row + "Synonym added to 'unresolved' as accepted taxon is synonym itself.");
|
|
535
|
}else if (accId != null){
|
|
536
|
logger.warn(row + "Accepted taxon "+accName+" for synonym unexpectedly does not exist. Synonym was moved to 'unresolved'");
|
|
537
|
}else{
|
|
538
|
logger.warn(row + "No accepted taxon given for synonym. Therefore taxon was moved to 'unresolved'");
|
|
539
|
}
|
|
540
|
if(accId != null){
|
|
541
|
child = Taxon.NewInstance(syn.getName(), syn.getSec());
|
|
542
|
taxonMapping.put(sourceId, child.getUuid());
|
|
543
|
child.addImportSource(sourceId, PLANT_NAME_ID, getSourceReference(state), "line " + state.getCurrentLine());
|
|
544
|
}
|
|
545
|
addChild(unresolvedParent(), child, row);
|
|
546
|
getTaxonService().deleteSynonym(syn, new SynonymDeletionConfigurator());
|
|
547
|
}else{
|
|
548
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF);
|
|
549
|
}
|
|
550
|
}else if ("Misapplied".equals(status)){
|
|
551
|
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
552
|
if(accTaxon == null){
|
|
553
|
if(isSynonymAccepted){
|
|
554
|
logger.warn(row + "Misapplication added to 'unresolved' as accepted taxon is synonym itself.");
|
|
555
|
}else if (accId != null){
|
|
556
|
logger.warn(row + "Accepted taxon "+accName+" for misapplication unexpectedly does not exist. Misapplication was moved to 'unresolved'");
|
|
557
|
}else{
|
|
558
|
logger.warn(row + "No accepted taxon given for misapplication. Therefore taxon was moved to 'unresolved'");
|
|
559
|
}
|
|
560
|
addChild(unresolvedParent(), taxon, row);
|
|
561
|
}else{
|
|
562
|
accTaxon.addMisappliedName(taxon, null, null);
|
|
563
|
}
|
|
564
|
}else if ("Unplaced".equals(status)){
|
|
565
|
parent = unresolvedParent();
|
|
566
|
addChild(parent, child, row);
|
|
567
|
}else if("Illegitimate".equals(status) || "Invalid".equals(status)){
|
|
568
|
if (hasAccepted){
|
|
569
|
if(accTaxon == null){
|
|
570
|
logger.warn(row + "accepted taxon for illegitimate or invalid taxon not found. Illeg/inval taxon was moved to 'unresolved'");
|
|
571
|
child = Taxon.NewInstance(syn.getName(), syn.getSec());
|
|
572
|
addChild(unresolvedParent(), child, row);
|
|
573
|
}else{
|
|
574
|
accTaxon.addSynonym(syn, SynonymType.SYNONYM_OF);
|
|
575
|
}
|
|
576
|
}else{
|
|
577
|
addChild(unresolvedParent(), child, row);
|
|
578
|
}
|
|
579
|
}else{
|
|
580
|
logger.warn(row + "Unhandled status: " + status);
|
|
581
|
}
|
|
582
|
|
|
583
|
if (basionymId != null && false){
|
|
584
|
UUID basionymUuid = taxonMapping.get(basionymId);
|
|
585
|
TaxonBase<?> basionymTaxon = getTaxonService().find(basionymUuid);
|
|
586
|
if (basionymTaxon != null){
|
|
587
|
if (hasSameAcceptedTaxon(taxonBase, basionymTaxon)){
|
|
588
|
if (taxonBase.getName().getBasionym() == null){
|
|
589
|
taxonBase.getName().addBasionym(basionymTaxon.getName());
|
|
590
|
}
|
|
591
|
}else{
|
|
592
|
logger.warn(row + "Basionym has not same accepted taxon and therefore was ignored.");
|
|
593
|
}
|
|
594
|
}else{
|
|
595
|
logger.warn(row + "Basionym "+basionymId+" not found.");
|
|
596
|
}
|
|
597
|
}
|
|
598
|
} catch (Exception e) {
|
|
599
|
logger.error(row + "Error.");
|
|
600
|
e.printStackTrace();
|
|
601
|
}
|
|
602
|
}
|
|
603
|
|
|
604
|
private boolean hasSameAcceptedTaxon(TaxonBase<?> taxonBase, TaxonBase<?> basionymTaxon) {
|
|
605
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
606
|
taxonBase = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
|
|
607
|
}
|
|
608
|
if (basionymTaxon.isInstanceOf(Synonym.class)){
|
|
609
|
basionymTaxon = CdmBase.deproxy(basionymTaxon, Synonym.class).getAcceptedTaxon();
|
|
610
|
}
|
|
611
|
return taxonBase != null && basionymTaxon != null && taxonBase.equals(basionymTaxon);
|
|
612
|
}
|
|
613
|
|
|
614
|
private TaxonNode getParent(UUID parentUuid, String row) {
|
|
615
|
if(parentUuid == null){
|
|
616
|
logger.warn(row + "Parent uuid is null. No parent found.");
|
|
617
|
return null;
|
|
618
|
}
|
|
619
|
TaxonBase<?> pTaxon = getTaxonService().find(parentUuid);
|
|
620
|
if (pTaxon == null){
|
|
621
|
logger.warn(row + "No parent found for parent UUID. This should not happen.");
|
|
622
|
return null;
|
|
623
|
}
|
|
624
|
if (pTaxon.isInstanceOf(Synonym.class)){
|
|
625
|
logger.warn(row + "Parent is synonym");
|
|
626
|
return null;
|
|
627
|
}else{
|
|
628
|
Taxon ptax = CdmBase.deproxy(pTaxon, Taxon.class);
|
|
629
|
if(ptax.getTaxonNodes().isEmpty()){
|
|
630
|
logger.info(row + "Parent has no node yet");
|
|
631
|
TaxonNode newParent = getClassification().addChildTaxon(ptax, null, null);
|
|
632
|
getTaxonNodeService().saveOrUpdate(newParent);
|
|
633
|
return newParent;
|
|
634
|
}else {
|
|
635
|
if(ptax.getTaxonNodes().size()>1){
|
|
636
|
logger.warn("Parent has >1 nodes. Take arbitrary one");
|
|
637
|
}
|
|
638
|
return ptax.getTaxonNodes().iterator().next();
|
|
639
|
}
|
|
640
|
}
|
|
641
|
}
|
|
642
|
|
|
643
|
private void addChild(TaxonNode parent, Taxon child, String row) {
|
|
644
|
if (parent == null){
|
|
645
|
logger.warn(row + "Parent is null");
|
|
646
|
}else if (child == null){
|
|
647
|
logger.warn(row + "Child is null");
|
|
648
|
}else{
|
|
649
|
if (!child.getTaxonNodes().isEmpty()){
|
|
650
|
TaxonNode childNode = child.getTaxonNodes().iterator().next();
|
|
651
|
if (childNode.getParent() != null && childNode.getParent().equals(parent)){
|
|
652
|
logger.info(row + "Parent-child relation exists already.");
|
|
653
|
}else{
|
|
654
|
logger.warn(row + "Child already has different parent. Parent-child relation not added.");
|
|
655
|
}
|
|
656
|
}else{
|
|
657
|
TaxonNode node = parent.addChildTaxon(child, null, null);
|
|
658
|
getTaxonNodeService().saveOrUpdate(node);
|
|
659
|
}
|
|
660
|
}
|
|
661
|
}
|
|
662
|
|
|
663
|
private TaxonNode getFamily(String line, String family){
|
|
664
|
UUID uuid;
|
|
665
|
if ("Salicaceae".equals(family)){
|
|
666
|
uuid = UUID.fromString("5432a4eb-2fbe-4494-925d-d01743ed435f");
|
|
667
|
// }else if ("Meliaceae".equals(family)){
|
|
668
|
// //Note: not needed, genus with family Meliaceae is synonym
|
|
669
|
// uuid = UUID.fromString("c8694910-bfec-45a1-8901-2a0a2a6f12b1");
|
|
670
|
}else{
|
|
671
|
logger.warn(line + "Family not yet handled: " + family);
|
|
672
|
return null;
|
|
673
|
}
|
|
674
|
TaxonNode familyNode = getTaxonNodeService().find(uuid);
|
|
675
|
if (familyNode == null){
|
|
676
|
familyNode = createFamily(family, uuid);
|
|
677
|
}
|
|
678
|
return familyNode;
|
|
679
|
}
|
|
680
|
|
|
681
|
private TaxonNode createFamily(String family, UUID uuid) {
|
|
682
|
Classification classification = getClassification();
|
|
683
|
TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
|
|
684
|
name.setGenusOrUninomial(family);
|
|
685
|
Taxon taxon = Taxon.NewInstance(name, getSecRef());
|
|
686
|
TaxonNode result = classification.addChildTaxon(taxon, null, null);
|
|
687
|
result.setUuid(uuid);
|
|
688
|
getTaxonNodeService().saveOrUpdate(result);
|
|
689
|
return result;
|
|
690
|
}
|
|
691
|
|
|
692
|
private Classification getClassification() {
|
|
693
|
Classification classification = getClassificationService().find(state.getConfig().getClassificationUuid());
|
|
694
|
if (classification == null){
|
|
695
|
classification = Classification.NewInstance(
|
|
696
|
state.getConfig().getClassificationName(), getSecRef(), Language.LATIN());
|
|
697
|
classification.setUuid(state.getConfig().getClassificationUuid());
|
|
698
|
getClassificationService().save(classification);
|
|
699
|
}
|
|
700
|
return classification;
|
|
701
|
}
|
|
702
|
|
|
703
|
private TaxonNode unresolvedParent(){
|
|
704
|
UUID uuid = UUID.fromString("1c48b8d3-077d-4aef-9e41-d4d3e0abd4c7");
|
|
705
|
TaxonNode unresolvedParent = getTaxonNodeService().find(uuid);
|
|
706
|
if (unresolvedParent == null){
|
|
707
|
unresolvedParent = createFamily("Unresolved", uuid);
|
|
708
|
}
|
|
709
|
return unresolvedParent;
|
|
710
|
}
|
|
711
|
}
|