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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.Map;
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import java.util.UUID;
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import java.util.stream.Collectors;
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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.dto.IdentifiedEntityDTO;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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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.TaxonNode;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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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 CaryoSileneaeSynonymSynonymCleanupImport extends CaryoSileneaeImportBase {
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private static final long serialVersionUID = -3721982716275962061L;
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private static final Logger logger = LogManager.getLogger();
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private static final UUID uuidSileneaeInfoNameIdType = UUID.fromString("95ecbf6d-521d-447f-bae5-d82585ff3617");
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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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@Override
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protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
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return "Synonyms";
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}
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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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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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//find synonym name
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TaxonName synonymName = getNameFromDb(state, nameLinkID, row);
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if (synonymName == 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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Integer accNameId = accIdMap.get(taxonLinkId);
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if (accNameId == null) {
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logger.warn(row + "Taxon not found in taxon map: " + taxonLinkId);
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return;
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}
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TaxonName accName = getNameFromDb(state, accNameId, row);
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if (accName == null) {
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logger.warn(row + "Accepeted taxon name for synonym " + synonymName.getTitleCache() + " not found. Keep as unresolved.");
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return;
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}
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Taxon newAccTaxon;
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//add as synonym
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if (accName.getTaxa().size() != 1) {
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if (accName.getTaxa().isEmpty()){
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logger.warn(row + "Accepted taxon name "+accName.getTitleCache()+" has no taxon attached. Keep synonynm " + synonymName.getTitleCache() + "as unresolved");
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return;
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}else {
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String names = accName.getTaxa().stream().map(t->t.getTitleCache()).collect(Collectors.toList()).toString();
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logger.warn(row + "Acc taxon name has "+accName.getTaxa().size()+" taxa attached: n=" + accName.getTaxa().size() + " (" + names +")" );
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newAccTaxon = accName.getTaxa().iterator().next();
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logger.warn(row + " used: " + newAccTaxon.getTitleCache());
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}
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}else {
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newAccTaxon = accName.getTaxa().iterator().next();
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}
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Synonym synonym = Synonym.NewInstance(synonymName, getSecRef(state));
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newAccTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF);
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getTaxonService().saveOrUpdate(newAccTaxon);
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//remove from parent
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if (synonymName.getTaxa().size() != 1) {
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logger.warn(row + "syn taxon name "+ synonymName.getTitleCache() + " has "+synonymName.getTaxa().size()+" taxa attached");
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return;
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}
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Taxon accTaxon = synonymName.getTaxa().iterator().next();
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if (accTaxon.getTaxonNodes().size() != 1) {
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logger.warn(row + "syn taxon has "+accTaxon.getTaxonNodes().size()+" taxon nodes attached");
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return;
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}
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TaxonNode node = accTaxon.getTaxonNodes().iterator().next();
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//boolean success = node.getParent().deleteChildNode(node);
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node.setTaxon(null);
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// if (!success) {
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// logger.warn(row + "deleteChildNode not successful");
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// }
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accTaxon.setName(null);
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getTaxonService().delete(accTaxon);
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// getTaxonNodeService().delete(node);
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}
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private TaxonName getNameFromDb(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state, Integer nameId, String row) {
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try {
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DefinedTerm sileneaeInfoNameIdType = getIdentiferType(state,
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uuidSileneaeInfoNameIdType, null, null, null, null);
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Pager<IdentifiedEntityDTO<TaxonName>> list = getNameService().findByIdentifier(TaxonName.class, nameId.toString(),
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sileneaeInfoNameIdType, MatchMode.EXACT, true, null, null, null);
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return list.getRecords().get(0).getCdmEntity().getEntity();
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} catch (Exception e) {
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logger.warn(row + "Error when getting name from DB. nameID = " + nameId);
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e.printStackTrace();
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return null;
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}
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}
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boolean first = true;
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@Override
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protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
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// if (first) {
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// for (TaxonName taxonName : orphanedNameMap.values()) {
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// Taxon taxon = Taxon.NewInstance(taxonName, getSecRef(state));
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// TaxonNode node = getUnresolvedNode(state).addChildTaxon(taxon, null);
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// getTaxonNodeService().saveOrUpdate(node);
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// }
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// first = false;
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// }
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}
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//
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// private TaxonNode unresolvedNode;
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// private TaxonNode getUnresolvedNode(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
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// if (unresolvedNode == null) {
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// unresolvedNode = getTaxonNodeService().find(state.getConfig().getUnresolvedNodeUuid());
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// }
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// return unresolvedNode;
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// }
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}
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