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/**
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* Copyright (C) 2007 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.faunaEuropaea;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.A_AUCT;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.P_PARENTHESIS;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.Q_NO_RESTRICTION;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_GENUS;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBGENUS;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SPECIES;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBSPECIES;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_ACCEPTED;
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import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_NOT_ACCEPTED;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Collection;
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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.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 org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.berlinModel.CdmOneToManyMapper;
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import eu.etaxonomy.cdm.io.berlinModel.CdmStringMapper;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
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import eu.etaxonomy.cdm.io.common.CdmAttributeMapperBase;
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import eu.etaxonomy.cdm.io.common.CdmSingleAttributeMapperBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.tcsxml.in.TcsXmlImportState;
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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.ISourceable;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.OriginalSource;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.reference.Database;
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import eu.etaxonomy.cdm.model.reference.Generic;
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import eu.etaxonomy.cdm.model.reference.PublicationBase;
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import eu.etaxonomy.cdm.model.reference.Publisher;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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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.TaxonomicTree;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.babadshanjan
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* @created 12.05.2009
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* @version 1.0
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*/
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@Component
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public class FaunaEuropaeaRelShipImport extends FaunaEuropaeaImportBase {
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public static final String OS_NAMESPACE_TAXON = "Taxon";
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaRelShipImport.class);
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean doCheck(FaunaEuropaeaImportState state) {
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boolean result = true;
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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logger.warn("Checking for Taxa not yet fully implemented");
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result &= checkTaxonStatus(fauEuConfig);
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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protected boolean isIgnore(FaunaEuropaeaImportState state) {
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return ! state.getConfig().isDoTaxa();
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}
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private boolean checkTaxonStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
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boolean result = true;
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// try {
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Source source = fauEuConfig.getSource();
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String sqlStr = "";
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ResultSet rs = source.getResultSet(sqlStr);
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return result;
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// } catch (SQLException e) {
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// e.printStackTrace();
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// return false;
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// }
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}
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/*
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* Import with complete taxon store
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*/
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protected boolean doInvoke(FaunaEuropaeaImportState state) {
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Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
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MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);
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authorStore.makeEmpty();
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Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = state.getFauEuTaxonMap();
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TransactionStatus txStatus = null;
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boolean success = true;
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if(logger.isInfoEnabled()) { logger.info("Start making taxa..."); }
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if (state.getConfig().isUseTransactions()) {
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txStatus = startTransaction();
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}
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success = processTaxa(state, fauEuTaxonMap);
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success = saveTaxa(state, state.getHighestTaxonIndex(), state.getConfig().getLimitSave());
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if (state.getConfig().isUseTransactions()) {
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commitTransaction(txStatus);
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}
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logger.info("End making taxa...");
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return success;
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}
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/*
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* Processes taxa from complete taxon store
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*/
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private boolean processTaxa(FaunaEuropaeaImportState state,
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Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap) {
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if(logger.isInfoEnabled()) { logger.info("Processing taxa second pass..."); }
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Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
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MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();
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boolean success = true;
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for (int id : fauEuTaxonMap.keySet())
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//for (int id : taxonStore.keySet())
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{
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TaxonBase<?> taxonBase = taxonStore.get(id);
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TaxonNameBase<?,?> taxonName = taxonBase.getName();
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FaunaEuropaeaTaxon fauEuTaxon = fauEuTaxonMap.get(id);
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if (logger.isDebugEnabled()) { logger.debug("Taxon # " + id); }
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createRelationships(fauEuTaxon, taxonBase, taxonName, fauEuTaxonMap, state);
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}
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return success;
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}
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/** Creates relationships for existing taxon store in memory */
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private boolean createRelationships(FaunaEuropaeaTaxon fauEuTaxon,
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TaxonBase<?> taxonBase, TaxonNameBase<?,?> taxonName,
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Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) {
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int parentId = fauEuTaxon.getParentId();
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int taxonId = fauEuTaxon.getId();
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Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
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MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
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ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();
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TaxonBase<?> parentTaxonBase = taxonStore.get(parentId);
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Taxon parentTaxon = parentTaxonBase.deproxy(parentTaxonBase, Taxon.class);
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// FaunaEuropaeaTaxon parent = fauEuTaxonMap.get(parentId);
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boolean success = true;
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if (!fauEuTaxon.isValid()) { // FauEu Synonym
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if (fauEuTaxon.getAuthor() != null && fauEuTaxon.getAuthor().equals("A_AUCT_NAME")) {
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try {
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// add misapplied name relationship from this taxon to parent
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Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);
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taxon.addMisappliedName(parentTaxon, sourceRef, null);
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if (logger.isInfoEnabled()) {
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logger.info("Misapplied name created " + taxon.getUuid());
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}
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} catch (Exception e) {
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logger.error("Error creating misapplied name relationship for taxon (" +
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parentId + ")");
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}
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}
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else if((fauEuTaxon.getAuthor() == null)
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|| (fauEuTaxon.getAuthor() != null && !fauEuTaxon.getAuthor().equals("A_AUCT_NAME"))) {
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try {
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// add this synonym as heterotypic synonym to parent
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Synonym synonym = taxonBase.deproxy(taxonBase, Synonym.class);
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parentTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
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if (logger.isDebugEnabled()) {
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logger.debug("Heterotypic synonym created " + synonym.getUuid());
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}
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} catch (Exception e) {
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logger.error("Error creating heterotypic synonym for taxon (" + parentId + ")");
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// e.printStackTrace();
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}
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}
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} else if (fauEuTaxon.isValid()) { // FauEu Taxon
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Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);
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try {
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// add this taxon as child to parent
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if (parentTaxon != null) {
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makeTaxonomicallyIncluded(state, parentTaxon, taxon, sourceRef, null);
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if (logger.isDebugEnabled()) {
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logger.debug("Parent-child (" + parentId + "-" + taxonId +
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") relationship created");
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}
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}
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} catch (Exception e) {
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logger.error("Error creating taxonomically included relationship Parent-child (" +
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parentId + "-" + taxonId + ")");
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}
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}
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return success;
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}
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private boolean makeTaxonomicallyIncluded(FaunaEuropaeaImportState state, Taxon toTaxon, Taxon fromTaxon, ReferenceBase citation, String microCitation){
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boolean success = true;
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ReferenceBase sec = toTaxon.getSec();
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TaxonomicTree tree = state.getTree(sec);
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if (tree == null){
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tree = makeTree(state, sec);
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}
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success = tree.addParentChild(toTaxon, fromTaxon, citation, microCitation);
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return success;
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}
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}
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