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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.HashMap;
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import java.util.List;
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import java.util.Map;
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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.facade.DerivedUnitFacade;
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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.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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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.SpecimenTypeDesignationStatus;
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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.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;
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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 02.02.2023
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*/
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@Component
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public class CaryoSileneaeNameImport extends CaryoSileneaeImportBase {
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private static final long serialVersionUID = 8931253645038029899L;
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private static final Logger logger = LogManager.getLogger();
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private static final String NOMEN_ID = "nomen_id";
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private static final String RANK = "rank";
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private static final String GENUS = "Genus";
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private static final String INFRAGEN_NAME = "Infragen_name";
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private static final String SPECIES = "Species";
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private static final String INFRASP_EPITHET = "Infrasp_epithet";
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private static final String AUTHORS = "Authors";
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private static final String BASIONYM_LINK = "Basionym_link";
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private static final String IPNI_ID = "IPNI_ID";
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private static final String NOTES = "Notes";
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private static final String NOMINVAL_FLAG = "NomInval_Flag";
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private static final String TYPE_SPECIMEN = "Type_specimen";
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private static final String TYPE_SPECIES_LINK = "TypeSpecies_link";
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//maybe not used
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private static final String PUBLICATION = "Publication";
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private static final String PUBL_DATE = "PublDate";
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//not used
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@SuppressWarnings("unused")
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private static final String HOMONYM_FLAG = "Homonym_Flag";
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@SuppressWarnings("unused")
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private static final String MISAPPLIED_FLAG = "Misapplied_Flag";
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@SuppressWarnings("unused")
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private static final String SynonymyReference_link = "SynonymyReference_link";
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private Map<Integer, UUID> nameMapping = new HashMap<>();
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private SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state;
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@Override
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protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> 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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Integer nomenId = Integer.valueOf(getValue(record, NOMEN_ID));
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String rankStr = getValue(record, RANK);
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String genusStr = getValue(record, GENUS);
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String infragenStr = getValue(record, INFRAGEN_NAME);
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String speciesStr = getValue(record, SPECIES);
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String infraspStr = getValue(record, INFRASP_EPITHET);
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String authorsStr = getValue(record, AUTHORS);
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String ipniId = getValue(record, IPNI_ID);
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String notes = getValue(record, NOTES);
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String nomInvalFlag = getValue(record, NOMINVAL_FLAG);
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String typeSpecimenStr = getValue(record, TYPE_SPECIMEN);
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String row = String.valueOf(line) + "("+nomenId+"): ";
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try {
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//create name
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Rank rank = state.getTransformer().getRankByKey(rankStr);
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TaxonName name = TaxonNameFactory.NewBotanicalInstance(rank);
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//fill simple
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name.setGenusOrUninomial(Ne(genusStr));
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name.setInfraGenericEpithet(Ne(infragenStr));
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name.setSpecificEpithet(Ne(speciesStr));
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name.setInfraSpecificEpithet(Ne(infraspStr));
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NonViralNameParserImpl.NewInstance().parseAuthors(name, authorsStr);
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//TODO ??publication + PublDate
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//ipni ID
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if (isNotBlank(ipniId)) {
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name.addIdentifier(ipniId, DefinedTerm.IDENTIFIER_NAME_IPNI());
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}
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//notes
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if (isNotBlank(notes)) {
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Annotation annotation = Annotation.NewDefaultLanguageInstance(notes);
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annotation.setAnnotationType(AnnotationType.TECHNICAL());
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name.addAnnotation(annotation);
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}
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//nominval flag
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if (nomInvalFlag != null && nomInvalFlag.trim().equalsIgnoreCase("yes")) {
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Reference ref = null;
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name.addStatus(NomenclaturalStatusType.INVALID(), ref, null);
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}
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//type specimen
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if (isNotBlank(typeSpecimenStr)) {
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
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facade.setCollector(null); //just to create field unit and gathering event
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facade.innerDerivedUnit().setTitleCache(typeSpecimenStr, true);
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SpecimenTypeDesignationStatus status = null; //TODO
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Reference ref = null;
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String originalInfo = null;
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name.addSpecimenTypeDesignation(facade.innerDerivedUnit(), status, ref, null, originalInfo, false, false);
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// save ??
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}
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} catch (UndefinedTransformerMethodException | StringNotParsableException e) {
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e.printStackTrace();
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}
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}
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private String Ne(String genusStr) {
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return CdmUtils.Ne(genusStr);
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}
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private TaxonName dedupliateNameParts(TaxonName name) {
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if (state.getConfig().isDoDeduplicate()){
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state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(name);
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}
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return name;
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}
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private String getOtherAuthors(List<TaxonName> otherNames) {
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String result = "";
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for (TaxonName name : otherNames){
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result = CdmUtils.concat(";", result, name.getAuthorshipCache());
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}
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return result;
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}
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private 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(state), 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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@Override
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protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
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Map<String, String> record = state.getOriginalRecord();
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int line = state.getCurrentLine();
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Integer nomenId = Integer.valueOf(getValue(record, NOMEN_ID));
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Integer basionymId = getInt(getValue(record, BASIONYM_LINK));
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Integer typeSpeciesId = getInt(getValue(record, TYPE_SPECIES_LINK));
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String row = String.valueOf(line) + "("+nomenId+"): ";
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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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TaxonName name = getName(state, nomenId);
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if (name == null) {
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logger.warn(row + "Name does not exist");
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return;
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}
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//basionym
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if (basionymId != null) {
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TaxonName basionym = getName(state, basionymId);
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if (basionym == null) {
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logger.warn(row + "basionym does not exist");
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}else {
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name.addBasionym(basionym);
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}
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}
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//type name
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if (typeSpeciesId != null) {
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TaxonName typeSpecies = getName(state, typeSpeciesId);
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if (typeSpecies == null) {
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logger.warn(row + "typeSpecies does not exist");
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}else {
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Reference ref = null;
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NameTypeDesignationStatus status = null; //TODO
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name.addNameTypeDesignation(typeSpecies, ref, null, null, status, false);
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}
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}
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}
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}
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