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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.HashSet;
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import java.util.Map;
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import java.util.Set;
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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.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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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 CaryoSileneaeSynonymImport extends CaryoSileneaeImportBase {
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private static final long serialVersionUID = 7967768097472488888L;
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private static final Logger logger = LogManager.getLogger();
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private static final String NOMTAX_ID = "NomTax_ID";
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private static final String NOMEN_LINK = "Nomen_link";
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private static final String TAXON_LINK = "Taxon_link";
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private Set<String> neglectedRecords = new HashSet<>();
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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 nomTaxId = Integer.valueOf(getValue(record, NOMTAX_ID));
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Integer nameLinkID = Integer.valueOf(getValue(record, NOMEN_LINK));
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Integer taxonLinkId = Integer.valueOf(getValue(record, TAXON_LINK));
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String row = String.valueOf(line) + "("+nomTaxId+"): ";
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TaxonName name = getName(state, nameLinkID);
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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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Synonym synonym = Synonym.NewInstance(name, getSecRef(state));
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Taxon taxon = getTaxon(state, taxonLinkId);
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if (taxon == null) {
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logger.warn(row + "Taxon does not exist");
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return;
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}
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//TODO type (compute homotypics)
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taxon.addSynonym(synonym, SynonymType.SYNONYM_OF);
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}
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@Override
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protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
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}
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private boolean hasSameAcceptedTaxon(TaxonBase<?> taxonBase, TaxonBase<?> basionymTaxon) {
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if (taxonBase.isInstanceOf(Synonym.class)){
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taxonBase = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
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}
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if (basionymTaxon.isInstanceOf(Synonym.class)){
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basionymTaxon = CdmBase.deproxy(basionymTaxon, Synonym.class).getAcceptedTaxon();
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}
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return taxonBase != null && basionymTaxon != null && taxonBase.equals(basionymTaxon);
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}
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}
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