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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.R_GENUS;
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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_SUBGENUS;
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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.HashSet;
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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.apache.poi.hssf.record.formula.functions.Isblank;
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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.common.ICdmIO;
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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.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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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.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.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 FaunaEuropaeaTaxonNameImport 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(FaunaEuropaeaTaxonNameImport.class);
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/* Max number of taxa to retrieve (for test purposes) */
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private int maxTaxa = 0;
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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 taxa from FauEU DB
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*/
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protected boolean doInvoke(FaunaEuropaeaImportState state) {
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boolean success = true;
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if(logger.isInfoEnabled()) { logger.info("Start making taxa..."); }
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success = processTaxa(state);
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logger.info("End making taxa...");
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return success;
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}
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/** Retrieve taxa from FauEu DB, process in blocks */
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private boolean processTaxa(FaunaEuropaeaImportState state) {
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int limit = state.getConfig().getLimitSave();
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TransactionStatus txStatus = null;
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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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Map<Integer, TaxonBase<?>> taxonMap = null;
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Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = null;
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/* Store for heterotypic synonyms to be save separately */
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Set<Synonym> synonymSet = null;
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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ReferenceBase<?> sourceRef = fauEuConfig.getSourceReference();
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Source source = fauEuConfig.getSource();
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int i = 0;
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boolean success = true;
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String selectCount =
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" SELECT count(*) ";
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String selectColumns =
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" SELECT Parent.TAX_NAME AS P2Name, Parent.TAX_RNK_ID AS P2RankId, " +
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" GrandParent.TAX_ID AS GP3Id, GrandParent.TAX_NAME AS GP3Name, GrandParent.TAX_RNK_ID AS GP3RankId, " +
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" GreatGrandParent.TAX_ID AS GGP4Id, GreatGrandParent.TAX_NAME AS GGP4Name, GreatGrandParent.TAX_RNK_ID AS GGP4RankId, " +
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" GreatGreatGrandParent.TAX_ID AS GGGP5Id, GreatGreatGrandParent.TAX_NAME AS GGGP5Name, OriginalGenusTaxon.TAX_NAME AS OGenusName, " +
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" Taxon.*, rank.*, author.* ";
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String fromClause =
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" FROM Taxon LEFT OUTER JOIN " +
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" Taxon AS Parent ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID LEFT OUTER JOIN " +
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" Taxon AS GrandParent ON Parent.TAX_TAX_IDPARENT = GrandParent.TAX_ID LEFT OUTER JOIN " +
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" Taxon AS GreatGrandParent ON GrandParent.TAX_TAX_IDPARENT = GreatGrandParent.TAX_ID LEFT OUTER JOIN " +
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" Taxon AS GreatGreatGrandParent ON GreatGrandParent.TAX_TAX_IDPARENT = GreatGreatGrandParent.TAX_ID LEFT OUTER JOIN " +
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" Taxon AS OriginalGenusTaxon ON Taxon.TAX_TAX_IDGENUS = OriginalGenusTaxon.TAX_ID LEFT OUTER JOIN " +
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" author ON Taxon.TAX_AUT_ID = author.aut_id LEFT OUTER JOIN " +
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" rank ON Taxon.TAX_RNK_ID = rank.rnk_id ";
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String countQuery =
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selectCount + fromClause;
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String selectQuery =
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selectColumns + fromClause;
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try {
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ResultSet rs = source.getResultSet(countQuery);
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rs.next();
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int count = rs.getInt(1);
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rs = source.getResultSet(selectQuery);
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if (logger.isInfoEnabled()) {
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logger.info("Number of rows: " + count);
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logger.info("Count Query: " + countQuery);
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logger.info("Select Query: " + selectQuery);
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}
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while (rs.next()) {
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if ((i++ % limit) == 0) {
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txStatus = startTransaction();
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taxonMap = new HashMap<Integer, TaxonBase<?>>(limit);
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fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);
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synonymSet = new HashSet<Synonym>();
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Transaction started");
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}
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}
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String localName = rs.getString("TAX_NAME");
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String parentName = rs.getString("P2Name");
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int grandParentId = rs.getInt("GP3Id");
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String grandParentName = rs.getString("GP3Name");
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int greatGrandParentId = rs.getInt("GGP4Id");
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String greatGrandParentName = rs.getString("GGP4Name");
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int greatGreatGrandParentId = rs.getInt("GGGP5Id");
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String greatGreatGrandParentName = rs.getString("GGGP5Name");
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String originalGenusName = rs.getString("OGenusName");
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String autName = rs.getString("aut_name");
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int taxonId = rs.getInt("TAX_ID");
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int rankId = rs.getInt("TAX_RNK_ID");
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int parentId = rs.getInt("TAX_TAX_IDPARENT");
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int parentRankId = rs.getInt("P2RankId");
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int grandParentRankId = rs.getInt("GP3RankId");
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int greatGrandParentRankId = rs.getInt("GGP4RankId");
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int originalGenusId = rs.getInt("TAX_TAX_IDGENUS");
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int autId = rs.getInt("TAX_AUT_ID");
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int status = rs.getInt("TAX_VALID");
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// Avoid publication year 0 for NULL values in database.
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Integer year = rs.getInt("TAX_YEAR");
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if (year != null && year.intValue() == 0) {
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year = null;
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}
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//int familyId = rs.getInt("TAX_TAX_IDFAMILY");
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Rank rank = null;
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int parenthesis = rs.getInt("TAX_PARENTHESIS");
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UUID taxonBaseUuid = null;
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if (resultSetHasColumn(rs,"UUID")){
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taxonBaseUuid = UUID.fromString(rs.getString("UUID"));
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} else {
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taxonBaseUuid = UUID.randomUUID();
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}
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FaunaEuropaeaTaxon fauEuTaxon = new FaunaEuropaeaTaxon();
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fauEuTaxon.setUuid(taxonBaseUuid);
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fauEuTaxon.setId(taxonId);
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fauEuTaxon.setRankId(rankId);
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fauEuTaxon.setLocalName(localName);
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fauEuTaxon.setParentId(parentId);
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fauEuTaxon.setParentRankId(parentRankId);
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fauEuTaxon.setParentName(parentName);
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fauEuTaxon.setGrandParentId(grandParentId);
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fauEuTaxon.setGrandParentRankId(grandParentRankId);
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fauEuTaxon.setGrandParentName(grandParentName);
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fauEuTaxon.setGreatGrandParentId(greatGrandParentId);
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fauEuTaxon.setGreatGrandParentName(greatGrandParentName);
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fauEuTaxon.setGreatGreatGrandParentId(greatGreatGrandParentId);
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fauEuTaxon.setGreatGrandParentRankId(greatGrandParentRankId);
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fauEuTaxon.setGreatGreatGrandParentName(greatGreatGrandParentName);
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fauEuTaxon.setOriginalGenusId(originalGenusId);
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fauEuTaxon.setYear(year);
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fauEuTaxon.setOriginalGenusName(originalGenusName);
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fauEuTaxon.setAuthorName(autName);
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if (parenthesis == P_PARENTHESIS) {
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fauEuTaxon.setParenthesis(true);
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} else {
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fauEuTaxon.setParenthesis(false);
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}
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if (status == T_STATUS_ACCEPTED) {
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fauEuTaxon.setValid(true);
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} else {
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fauEuTaxon.setValid(false);
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}
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// fauEuTaxon.setAuthorId(autId);
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try {
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rank = FaunaEuropaeaTransformer.rankId2Rank(rs, false);
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} catch (UnknownCdmTypeException e) {
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logger.warn("Taxon (" + taxonId + ") has unknown rank (" + rankId + ") and could not be saved.");
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continue;
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} catch (NullPointerException e) {
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logger.warn("Taxon (" + taxonId + ") has rank null and can not be saved.");
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continue;
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}
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ReferenceBase<?> sourceReference = fauEuConfig.getSourceReference();
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ReferenceBase<?> auctReference = fauEuConfig.getAuctReference();
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ZoologicalName zooName = ZoologicalName.NewInstance(rank);
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TeamOrPersonBase<?> author = authorStore.get(autId);
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285
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zooName.setCombinationAuthorTeam(author);
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zooName.setPublicationYear(year);
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289
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TaxonBase<?> taxonBase;
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290
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291
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Synonym synonym;
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Taxon taxon;
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try {
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if ((status == T_STATUS_ACCEPTED) || (autId == A_AUCT)) { // taxon
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if (autId == A_AUCT) { // misapplied name
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zooName.setCombinationAuthorTeam(null);
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zooName.setPublicationYear(null);
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taxon = Taxon.NewInstance(zooName, auctReference);
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299
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if (logger.isDebugEnabled()) {
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300
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logger.debug("Misapplied name created (" + taxonId + ")");
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}
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} else { // accepted taxon
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taxon = Taxon.NewInstance(zooName, sourceReference);
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if (logger.isDebugEnabled()) {
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305
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logger.debug("Taxon created (" + taxonId + ")");
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}
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307
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}
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taxonBase = taxon;
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} else if ((status == T_STATUS_NOT_ACCEPTED) && (autId != A_AUCT)) { // synonym
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synonym = Synonym.NewInstance(zooName, sourceReference);
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//logger.info("Synonym created: " + synonym.getTitleCache() + " taxonName: " + zooName.getTitleCache());
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312
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if (logger.isDebugEnabled()) {
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logger.debug("Synonym created (" + taxonId + ")");
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}
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taxonBase = synonym;
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} else {
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logger.warn("Unknown taxon status " + status + ". Taxon (" + taxonId + ") ignored.");
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continue;
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319
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}
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320
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321
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taxonBase.setUuid(taxonBaseUuid);
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322
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323
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ImportHelper.setOriginalSource(taxonBase, fauEuConfig.getSourceReference(), taxonId, OS_NAMESPACE_TAXON);
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ImportHelper.setOriginalSource(zooName, fauEuConfig.getSourceReference(), taxonId, "TaxonName");
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325
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326
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327
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if (!taxonMap.containsKey(taxonId)) {
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328
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if (taxonBase == null) {
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329
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if (logger.isDebugEnabled()) {
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logger.debug("Taxon base is null. Taxon (" + taxonId + ") ignored.");
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331
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}
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332
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continue;
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333
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}
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taxonMap.put(taxonId, taxonBase);
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335
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fauEuTaxonMap.put(taxonId, fauEuTaxon);
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336
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|
|
337
|
// if (logger.isDebugEnabled()) {
|
|
338
|
// logger.debug("Stored taxon base (" + taxonId + ") " + localName);
|
|
339
|
// }
|
|
340
|
} else {
|
|
341
|
logger.warn("Not imported taxon base with duplicated TAX_ID (" + taxonId +
|
|
342
|
") " + localName);
|
|
343
|
}
|
|
344
|
} catch (Exception e) {
|
|
345
|
logger.warn("An exception occurred when creating taxon base with id " + taxonId +
|
|
346
|
". Taxon base could not be saved.");
|
|
347
|
e.printStackTrace();
|
|
348
|
}
|
|
349
|
|
|
350
|
if (((i % limit) == 0 && i != 1 ) || i == count) {
|
|
351
|
|
|
352
|
success = processTaxaSecondPass(state, taxonMap, fauEuTaxonMap, synonymSet);
|
|
353
|
if(logger.isDebugEnabled()) { logger.debug("Saving taxa ..."); }
|
|
354
|
getTaxonService().save((Collection)taxonMap.values());
|
|
355
|
getTaxonService().save((Collection)synonymSet);
|
|
356
|
|
|
357
|
taxonMap = null;
|
|
358
|
synonymSet = null;
|
|
359
|
fauEuTaxonMap = null;
|
|
360
|
commitTransaction(txStatus);
|
|
361
|
|
|
362
|
if(logger.isInfoEnabled()) {
|
|
363
|
logger.info("i = " + i + " - Transaction committed");
|
|
364
|
}
|
|
365
|
}
|
|
366
|
|
|
367
|
}
|
|
368
|
} catch (SQLException e) {
|
|
369
|
logger.error("SQLException:" + e);
|
|
370
|
success = false;
|
|
371
|
}
|
|
372
|
|
|
373
|
return success;
|
|
374
|
}
|
|
375
|
|
|
376
|
|
|
377
|
/**
|
|
378
|
* Processes taxa from complete taxon store
|
|
379
|
*/
|
|
380
|
private boolean processTaxaSecondPass(FaunaEuropaeaImportState state, Map<Integer, TaxonBase<?>> taxonMap,
|
|
381
|
Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, Set<Synonym> synonymSet) {
|
|
382
|
|
|
383
|
if(logger.isDebugEnabled()) { logger.debug("Processing taxa second pass..."); }
|
|
384
|
|
|
385
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
386
|
|
|
387
|
boolean success = true;
|
|
388
|
|
|
389
|
for (int id : taxonMap.keySet())
|
|
390
|
{
|
|
391
|
if (logger.isDebugEnabled()) { logger.debug("Taxon # " + id); }
|
|
392
|
|
|
393
|
TaxonBase<?> taxonBase = taxonMap.get(id);
|
|
394
|
TaxonNameBase<?,?> taxonName = taxonBase.getName();
|
|
395
|
FaunaEuropaeaTaxon fauEuTaxon = fauEuTaxonMap.get(id);
|
|
396
|
boolean useOriginalGenus = false;
|
|
397
|
if (taxonBase instanceof Synonym){
|
|
398
|
useOriginalGenus = true;
|
|
399
|
}
|
|
400
|
String nameString =
|
|
401
|
buildTaxonName(fauEuTaxon, taxonBase, taxonName, useOriginalGenus, fauEuConfig);
|
|
402
|
|
|
403
|
if (taxonBase instanceof Synonym){
|
|
404
|
logger.info("Name of Synonym: " + nameString);
|
|
405
|
}
|
|
406
|
|
|
407
|
|
|
408
|
if (fauEuConfig.isDoBasionyms()
|
|
409
|
&& fauEuTaxon.getRankId() > R_SUBGENUS
|
|
410
|
&& (fauEuTaxon.getOriginalGenusId() != 0)) {
|
|
411
|
|
|
412
|
int originalGenusId = fauEuTaxon.getOriginalGenusId();
|
|
413
|
int actualGenusId = getActualGenusId(fauEuTaxon);
|
|
414
|
|
|
415
|
if (logger.isDebugEnabled()) {
|
|
416
|
logger.debug("actual genus id = " + actualGenusId + ", original genus id = " + originalGenusId);
|
|
417
|
}
|
|
418
|
|
|
419
|
if (actualGenusId != originalGenusId && taxonBase.isInstanceOf(Taxon.class)) {
|
|
420
|
success = createBasionym(fauEuTaxon, taxonBase, taxonName, fauEuConfig, synonymSet);
|
|
421
|
} else if (fauEuTaxon.isParenthesis()){
|
|
422
|
//the authorteam should be set in parenthesis because there should be a basionym, but we do not know it?
|
|
423
|
ZoologicalName zooName = taxonName.deproxy(taxonName, ZoologicalName.class);
|
|
424
|
zooName.setBasionymAuthorTeam(zooName.getCombinationAuthorTeam());
|
|
425
|
zooName.setCombinationAuthorTeam(null);
|
|
426
|
zooName.setOriginalPublicationYear(zooName.getPublicationYear());
|
|
427
|
zooName.setPublicationYear(null);
|
|
428
|
}
|
|
429
|
|
|
430
|
}
|
|
431
|
}
|
|
432
|
return success;
|
|
433
|
}
|
|
434
|
|
|
435
|
|
|
436
|
private boolean createBasionym(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase,
|
|
437
|
TaxonNameBase<?,?>taxonName, FaunaEuropaeaImportConfigurator fauEuConfig, Set<Synonym> synonymSet) {
|
|
438
|
|
|
439
|
boolean success = true;
|
|
440
|
|
|
441
|
try {
|
|
442
|
ZoologicalName zooName = taxonName.deproxy(taxonName, ZoologicalName.class);
|
|
443
|
|
|
444
|
// create basionym
|
|
445
|
ZoologicalName basionym = ZoologicalName.NewInstance(taxonName.getRank());
|
|
446
|
basionym.setCombinationAuthorTeam(zooName.getCombinationAuthorTeam());
|
|
447
|
|
|
448
|
zooName.setOriginalPublicationYear(zooName.getPublicationYear());
|
|
449
|
basionym.setPublicationYear(zooName.getPublicationYear());
|
|
450
|
|
|
451
|
// add originalGenusId as source
|
|
452
|
String originalGenusIdString = "" + fauEuTaxon.getOriginalGenusId();
|
|
453
|
IdentifiableSource basionymSource = IdentifiableSource.NewInstance(originalGenusIdString, "originalGenusId");
|
|
454
|
basionym.addSource(basionymSource);
|
|
455
|
|
|
456
|
zooName.addBasionym(basionym, fauEuConfig.getSourceReference(), null, null);
|
|
457
|
zooName.setBasionymAuthorTeam(zooName.getCombinationAuthorTeam());
|
|
458
|
zooName.setCombinationAuthorTeam(null);
|
|
459
|
zooName.setPublicationYear(null);
|
|
460
|
zooName.setTitleCache(null); // This should (re)generate the titleCache automagically
|
|
461
|
if (logger.isDebugEnabled()) {
|
|
462
|
logger.debug("Basionym created (" + fauEuTaxon.getId() + ")");
|
|
463
|
}
|
|
464
|
|
|
465
|
// create synonym
|
|
466
|
Synonym synonym = Synonym.NewInstance(basionym, fauEuConfig.getSourceReference());
|
|
467
|
|
|
468
|
if (fauEuTaxon.isValid()) { // Taxon
|
|
469
|
|
|
470
|
// homotypic synonym
|
|
471
|
Taxon taxon = taxonBase.deproxy(taxonBase, Taxon.class);
|
|
472
|
taxon.addHomotypicSynonym(synonym, fauEuConfig.getSourceReference(), null);
|
|
473
|
if (logger.isDebugEnabled()) {
|
|
474
|
logger.debug("Homotypic synonym created (" + fauEuTaxon.getId() + ")");
|
|
475
|
}
|
|
476
|
|
|
477
|
} else { // Synonym
|
|
478
|
|
|
479
|
// heterotypic synonym
|
|
480
|
// synonym relationship to the accepted taxon is created later
|
|
481
|
synonymSet.add(synonym);
|
|
482
|
|
|
483
|
if (logger.isDebugEnabled()) {
|
|
484
|
logger.debug("Heterotypic synonym stored (" + fauEuTaxon.getId() + ")");
|
|
485
|
}
|
|
486
|
}
|
|
487
|
|
|
488
|
buildTaxonName(fauEuTaxon, synonym, basionym, true, fauEuConfig);
|
|
489
|
|
|
490
|
} catch (Exception e) {
|
|
491
|
logger.warn("Exception occurred when creating basionym for " + fauEuTaxon.getId());
|
|
492
|
e.printStackTrace();
|
|
493
|
}
|
|
494
|
|
|
495
|
|
|
496
|
return success;
|
|
497
|
}
|
|
498
|
|
|
499
|
|
|
500
|
/* Build name title cache */
|
|
501
|
private String buildNameTitleCache(String nameString, boolean useOriginalGenus, FaunaEuropaeaTaxon fauEuTaxon) {
|
|
502
|
|
|
503
|
StringBuilder titleCacheStringBuilder = new StringBuilder(nameString);
|
|
504
|
Integer year = fauEuTaxon.getYear();
|
|
505
|
if (year != null) { // TODO: Ignore authors like xp, xf, etc?
|
|
506
|
titleCacheStringBuilder.append(" ");
|
|
507
|
if ((fauEuTaxon.isParenthesis() == true) && !useOriginalGenus) {
|
|
508
|
titleCacheStringBuilder.append("(");
|
|
509
|
}
|
|
510
|
titleCacheStringBuilder.append(fauEuTaxon.getAuthor());
|
|
511
|
titleCacheStringBuilder.append(" ");
|
|
512
|
titleCacheStringBuilder.append(year);
|
|
513
|
if ((fauEuTaxon.isParenthesis() == true) && !useOriginalGenus) {
|
|
514
|
titleCacheStringBuilder.append(")");
|
|
515
|
}
|
|
516
|
}
|
|
517
|
return titleCacheStringBuilder.toString();
|
|
518
|
}
|
|
519
|
|
|
520
|
|
|
521
|
/* Build taxon title cache */
|
|
522
|
private String buildTaxonTitleCache(String nameCache, ReferenceBase<?> reference) {
|
|
523
|
|
|
524
|
StringBuilder titleCacheStringBuilder = new StringBuilder(nameCache);
|
|
525
|
titleCacheStringBuilder.append(" sec. ");
|
|
526
|
titleCacheStringBuilder.append(reference.getTitleCache());
|
|
527
|
return titleCacheStringBuilder.toString();
|
|
528
|
}
|
|
529
|
|
|
530
|
|
|
531
|
/* Build name full title cache */
|
|
532
|
private String buildNameFullTitleCache(String titleCache, FaunaEuropaeaImportConfigurator fauEuConfig) {
|
|
533
|
|
|
534
|
StringBuilder fullTitleCacheStringBuilder = new StringBuilder(titleCache);
|
|
535
|
fullTitleCacheStringBuilder.append(" ");
|
|
536
|
fullTitleCacheStringBuilder.append(fauEuConfig.getSourceReferenceTitle());
|
|
537
|
return fullTitleCacheStringBuilder.toString();
|
|
538
|
}
|
|
539
|
|
|
540
|
|
|
541
|
private String genusPart(StringBuilder originalGenusName, boolean useOriginalGenus,
|
|
542
|
StringBuilder genusOrUninomial) {
|
|
543
|
|
|
544
|
StringBuilder stringBuilder = new StringBuilder();
|
|
545
|
|
|
546
|
if(useOriginalGenus == true) {
|
|
547
|
stringBuilder.append(originalGenusName);
|
|
548
|
genusOrUninomial.delete(0, genusOrUninomial.length());
|
|
549
|
genusOrUninomial.append(originalGenusName);
|
|
550
|
} else {
|
|
551
|
stringBuilder.append(genusOrUninomial);
|
|
552
|
}
|
|
553
|
stringBuilder.append(" ");
|
|
554
|
|
|
555
|
return stringBuilder.toString();
|
|
556
|
}
|
|
557
|
|
|
558
|
|
|
559
|
private String genusSubGenusPart(StringBuilder originalGenusName, boolean useOriginalGenus,
|
|
560
|
StringBuilder genusOrUninomial,
|
|
561
|
StringBuilder infraGenericEpithet) {
|
|
562
|
|
|
563
|
StringBuilder stringBuilder = new StringBuilder();
|
|
564
|
|
|
565
|
stringBuilder.append(genusPart(originalGenusName, useOriginalGenus, genusOrUninomial));
|
|
566
|
|
|
567
|
if (useOriginalGenus == true) {
|
|
568
|
infraGenericEpithet.delete(0, infraGenericEpithet.length());
|
|
569
|
stringBuilder.append(" ");
|
|
570
|
return stringBuilder.toString();
|
|
571
|
}
|
|
572
|
|
|
573
|
stringBuilder.append("(");
|
|
574
|
stringBuilder.append(infraGenericEpithet);
|
|
575
|
stringBuilder.append(")");
|
|
576
|
stringBuilder.append(" ");
|
|
577
|
|
|
578
|
return stringBuilder.toString();
|
|
579
|
}
|
|
580
|
|
|
581
|
/** Get actual genus id **/
|
|
582
|
private int getActualGenusId(FaunaEuropaeaTaxon fauEuTaxon) {
|
|
583
|
|
|
584
|
int actualGenusId = -1;
|
|
585
|
int rank = fauEuTaxon.getRankId();
|
|
586
|
int parentRankId = fauEuTaxon.getParentRankId();
|
|
587
|
int grandParentRankId = fauEuTaxon.getGrandParentRankId();
|
|
588
|
int greatGrandParentRankId = fauEuTaxon.getGreatGrandParentRankId();
|
|
589
|
|
|
590
|
if (fauEuTaxon.isValid()) { // Taxon
|
|
591
|
|
|
592
|
if (rank == R_SPECIES) {
|
|
593
|
|
|
594
|
if(parentRankId == R_SUBGENUS) {
|
|
595
|
|
|
596
|
actualGenusId = fauEuTaxon.getGrandParentId();
|
|
597
|
|
|
598
|
} else if(parentRankId == R_GENUS) {
|
|
599
|
|
|
600
|
actualGenusId = fauEuTaxon.getParentId();
|
|
601
|
}
|
|
602
|
|
|
603
|
} else if (rank == R_SUBSPECIES) {
|
|
604
|
|
|
605
|
if(grandParentRankId == R_SUBGENUS) {
|
|
606
|
|
|
607
|
actualGenusId = fauEuTaxon.getGreatGrandParentId();
|
|
608
|
|
|
609
|
} else if (grandParentRankId == R_GENUS) {
|
|
610
|
|
|
611
|
actualGenusId = fauEuTaxon.getGrandParentId();
|
|
612
|
|
|
613
|
}
|
|
614
|
}
|
|
615
|
} else { // Synonym
|
|
616
|
|
|
617
|
if (rank == R_SPECIES) {
|
|
618
|
|
|
619
|
if(grandParentRankId == R_SUBGENUS) {
|
|
620
|
|
|
621
|
actualGenusId = fauEuTaxon.getGreatGrandParentId();
|
|
622
|
|
|
623
|
} else if (grandParentRankId == R_GENUS) {
|
|
624
|
|
|
625
|
actualGenusId = fauEuTaxon.getGrandParentId();
|
|
626
|
|
|
627
|
}
|
|
628
|
|
|
629
|
} else if (rank == R_SUBSPECIES) {
|
|
630
|
|
|
631
|
if(greatGrandParentRankId == R_SUBGENUS) {
|
|
632
|
|
|
633
|
actualGenusId = fauEuTaxon.getGreatGreatGrandParentId();
|
|
634
|
|
|
635
|
} else if (greatGrandParentRankId == R_GENUS) {
|
|
636
|
|
|
637
|
actualGenusId = fauEuTaxon.getGreatGrandParentId();
|
|
638
|
}
|
|
639
|
}
|
|
640
|
}
|
|
641
|
return actualGenusId;
|
|
642
|
}
|
|
643
|
|
|
644
|
|
|
645
|
/** Build species and subspecies names */
|
|
646
|
private String buildLowerTaxonName(StringBuilder originalGenus, boolean useOriginalGenus,
|
|
647
|
StringBuilder genusOrUninomial, StringBuilder infraGenericEpithet,
|
|
648
|
StringBuilder specificEpithet, StringBuilder infraSpecificEpithet,
|
|
649
|
FaunaEuropaeaTaxon fauEuTaxon) {
|
|
650
|
|
|
651
|
String localName = fauEuTaxon.getLocalName();
|
|
652
|
int taxonId = fauEuTaxon.getId();
|
|
653
|
int parentId = fauEuTaxon.getParentId();
|
|
654
|
StringBuilder nameCacheStringBuilder = new StringBuilder();
|
|
655
|
|
|
656
|
// FaunaEuropaeaTaxon parent = fauEuTaxonMap.get(parentId);
|
|
657
|
if (parentId == 0) {
|
|
658
|
nameCacheStringBuilder.append(localName);
|
|
659
|
if (logger.isInfoEnabled()) {
|
|
660
|
logger.info("Parent of (" + taxonId + ") is null");
|
|
661
|
}
|
|
662
|
return nameCacheStringBuilder.toString();
|
|
663
|
}
|
|
664
|
|
|
665
|
String parentName = fauEuTaxon.getParentName();
|
|
666
|
String grandParentName = fauEuTaxon.getGrandParentName();
|
|
667
|
String greatGrandParentName = fauEuTaxon.getGreatGrandParentName();
|
|
668
|
int rank = fauEuTaxon.getRankId();
|
|
669
|
int parentRankId = fauEuTaxon.getParentRankId();
|
|
670
|
int grandParentRankId = fauEuTaxon.getGrandParentRankId();
|
|
671
|
int greatGrandParentRankId = fauEuTaxon.getGreatGrandParentRankId();
|
|
672
|
// int grandParentId = fauEuTaxon.getGrandParentId();
|
|
673
|
// int greatGrandParentId = grandParent.getParentId();
|
|
674
|
|
|
675
|
|
|
676
|
if (fauEuTaxon.isValid()) { // Taxon
|
|
677
|
|
|
678
|
if (rank == R_SPECIES) {
|
|
679
|
|
|
680
|
if(parentRankId == R_SUBGENUS) {
|
|
681
|
//differ between isParanthesis= true and false
|
|
682
|
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus,
|
|
683
|
genusOrUninomial.append(grandParentName),
|
|
684
|
infraGenericEpithet.append(parentName));
|
|
685
|
nameCacheStringBuilder.append(genusSubGenusPart);
|
|
686
|
|
|
687
|
|
|
688
|
} else if(parentRankId == R_GENUS) {
|
|
689
|
|
|
690
|
String genusPart = genusPart(originalGenus, useOriginalGenus,
|
|
691
|
genusOrUninomial.append(parentName));
|
|
692
|
nameCacheStringBuilder.append(genusPart);
|
|
693
|
}
|
|
694
|
nameCacheStringBuilder.append(localName);
|
|
695
|
specificEpithet.append(localName);
|
|
696
|
|
|
697
|
} else if (rank == R_SUBSPECIES) {
|
|
698
|
|
|
699
|
if(grandParentRankId == R_SUBGENUS) {
|
|
700
|
|
|
701
|
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus,
|
|
702
|
genusOrUninomial.append(greatGrandParentName),
|
|
703
|
infraGenericEpithet.append(grandParentName));
|
|
704
|
nameCacheStringBuilder.append(genusSubGenusPart);
|
|
705
|
|
|
706
|
} else if (grandParentRankId == R_GENUS) {
|
|
707
|
|
|
708
|
String genusPart = genusPart(originalGenus, useOriginalGenus,
|
|
709
|
genusOrUninomial.append(grandParentName));
|
|
710
|
nameCacheStringBuilder.append(genusPart);
|
|
711
|
|
|
712
|
}
|
|
713
|
nameCacheStringBuilder.append(parentName);
|
|
714
|
nameCacheStringBuilder.append(" ");
|
|
715
|
nameCacheStringBuilder.append(localName);
|
|
716
|
specificEpithet.append(parentName);
|
|
717
|
infraSpecificEpithet.append(localName);
|
|
718
|
}
|
|
719
|
} else { // Synonym
|
|
720
|
|
|
721
|
if (rank == R_SPECIES) {
|
|
722
|
|
|
723
|
if(grandParentRankId == R_SUBGENUS) {
|
|
724
|
|
|
725
|
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus,
|
|
726
|
genusOrUninomial.append(greatGrandParentName),
|
|
727
|
infraGenericEpithet.append(grandParentName));
|
|
728
|
nameCacheStringBuilder.append(genusSubGenusPart);
|
|
729
|
|
|
730
|
} else if (grandParentRankId == R_GENUS) {
|
|
731
|
|
|
732
|
String genusPart = genusPart(originalGenus, useOriginalGenus,
|
|
733
|
genusOrUninomial.append(grandParentName));
|
|
734
|
nameCacheStringBuilder.append(genusPart);
|
|
735
|
|
|
736
|
}
|
|
737
|
nameCacheStringBuilder.append(localName);
|
|
738
|
specificEpithet.append(localName);
|
|
739
|
|
|
740
|
} else if (rank == R_SUBSPECIES) {
|
|
741
|
|
|
742
|
String greatGreatGrandParentName = fauEuTaxon.getGreatGreatGrandParentName();
|
|
743
|
|
|
744
|
if(greatGrandParentRankId == R_SUBGENUS) {
|
|
745
|
|
|
746
|
String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus,
|
|
747
|
genusOrUninomial.append(greatGreatGrandParentName),
|
|
748
|
infraGenericEpithet.append(greatGrandParentName));
|
|
749
|
nameCacheStringBuilder.append(genusSubGenusPart);
|
|
750
|
|
|
751
|
} else if (greatGrandParentRankId == R_GENUS) {
|
|
752
|
|
|
753
|
String genusPart = genusPart(originalGenus, useOriginalGenus,
|
|
754
|
genusOrUninomial.append(greatGreatGrandParentName));
|
|
755
|
nameCacheStringBuilder.append(genusPart);
|
|
756
|
}
|
|
757
|
|
|
758
|
nameCacheStringBuilder.append(grandParentName);
|
|
759
|
nameCacheStringBuilder.append(" ");
|
|
760
|
specificEpithet.append(grandParentName);
|
|
761
|
nameCacheStringBuilder.append(localName);
|
|
762
|
infraSpecificEpithet.append(localName);
|
|
763
|
}
|
|
764
|
|
|
765
|
|
|
766
|
|
|
767
|
}
|
|
768
|
|
|
769
|
return nameCacheStringBuilder.toString();
|
|
770
|
}
|
|
771
|
|
|
772
|
|
|
773
|
/** Build taxon's name parts and caches */
|
|
774
|
private String buildTaxonName(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, TaxonNameBase<?,?>taxonName,
|
|
775
|
boolean useOriginalGenus, FaunaEuropaeaImportConfigurator fauEuConfig) {
|
|
776
|
|
|
777
|
/* Local taxon name string */
|
|
778
|
String localString = "";
|
|
779
|
/* Concatenated taxon name string */
|
|
780
|
String completeString = "";
|
|
781
|
|
|
782
|
StringBuilder originalGenus = null;
|
|
783
|
|
|
784
|
|
|
785
|
StringBuilder genusOrUninomial = new StringBuilder();
|
|
786
|
StringBuilder infraGenericEpithet = new StringBuilder();
|
|
787
|
StringBuilder specificEpithet = new StringBuilder();
|
|
788
|
StringBuilder infraSpecificEpithet = new StringBuilder();
|
|
789
|
|
|
790
|
localString = fauEuTaxon.getLocalName();
|
|
791
|
|
|
792
|
int rank = fauEuTaxon.getRankId();
|
|
793
|
|
|
794
|
String originalGenusString = null;
|
|
795
|
//rank is subgenus and the taxon is accepted -> the genusepithet is the parentName
|
|
796
|
if (rank == R_SUBGENUS && fauEuTaxon.isValid()){
|
|
797
|
originalGenusString = fauEuTaxon.getParentName();
|
|
798
|
|
|
799
|
} else if (rank == R_SUBGENUS && !fauEuTaxon.isValid()){
|
|
800
|
//the rank is subgenus and not accepted -> the parent is the accepted taxon and the grandparent name is the genusepithet
|
|
801
|
originalGenusString = fauEuTaxon.getGrandParentName();
|
|
802
|
}else{
|
|
803
|
// parent of species can be subgenus, so the grandparent is genus
|
|
804
|
int parentRankId = fauEuTaxon.getParentRankId();
|
|
805
|
if (parentRankId == R_SUBGENUS) {
|
|
806
|
originalGenusString = fauEuTaxon.getGrandParentName();
|
|
807
|
} else {
|
|
808
|
originalGenusString = fauEuTaxon.getParentName();
|
|
809
|
}
|
|
810
|
}
|
|
811
|
if (originalGenusString != null) {
|
|
812
|
originalGenus = new StringBuilder(originalGenusString);
|
|
813
|
}
|
|
814
|
|
|
815
|
if(logger.isDebugEnabled()) {
|
|
816
|
logger.debug("Local taxon name (rank = " + rank + "): " + localString);
|
|
817
|
}
|
|
818
|
|
|
819
|
if (rank < R_SPECIES) {
|
|
820
|
|
|
821
|
completeString = localString;
|
|
822
|
if (rank == R_SUBGENUS) {
|
|
823
|
infraGenericEpithet.append(localString);
|
|
824
|
genusOrUninomial.append(originalGenus);
|
|
825
|
completeString = originalGenus + " ("+ localString + ")";
|
|
826
|
} else {
|
|
827
|
genusOrUninomial.append(localString);
|
|
828
|
}
|
|
829
|
|
|
830
|
} else {
|
|
831
|
|
|
832
|
taxonBase = taxonBase.deproxy(taxonBase, TaxonBase.class);
|
|
833
|
|
|
834
|
completeString =
|
|
835
|
buildLowerTaxonName(originalGenus, useOriginalGenus,
|
|
836
|
genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet,
|
|
837
|
fauEuTaxon);
|
|
838
|
|
|
839
|
completeString = (String) CdmUtils.removeDuplicateWhitespace(completeString.trim());
|
|
840
|
|
|
841
|
}
|
|
842
|
return setCompleteTaxonName(completeString, useOriginalGenus,
|
|
843
|
genusOrUninomial.toString(), infraGenericEpithet.toString(),
|
|
844
|
specificEpithet.toString(), infraSpecificEpithet.toString(),
|
|
845
|
fauEuTaxon, taxonBase, fauEuConfig);
|
|
846
|
|
|
847
|
}
|
|
848
|
|
|
849
|
|
|
850
|
/** Sets name parts and caches */
|
|
851
|
private String setCompleteTaxonName(String concatString, boolean useOriginalGenus,
|
|
852
|
String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet,
|
|
853
|
FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase, FaunaEuropaeaImportConfigurator fauEuConfig) {
|
|
854
|
|
|
855
|
boolean success = true;
|
|
856
|
|
|
857
|
TaxonNameBase<?,?> taxonName = taxonBase.getName();
|
|
858
|
ZoologicalName zooName = (ZoologicalName)taxonName;
|
|
859
|
|
|
860
|
if (!genusOrUninomial.equals("")) {
|
|
861
|
zooName.setGenusOrUninomial(emptyToNull(genusOrUninomial));
|
|
862
|
if (logger.isDebugEnabled()) {
|
|
863
|
logger.debug("genusOrUninomial: " + genusOrUninomial);
|
|
864
|
}
|
|
865
|
}
|
|
866
|
|
|
867
|
//if ((!infraGenericEpithet.equals("") && fauEuTaxon.isParenthesis()) || (!infraGenericEpithet.equals("") && fauEuTaxon.)) {
|
|
868
|
if (fauEuTaxon.getParentRankId() == R_SUBGENUS || (fauEuTaxon.getRankId() == R_SUBGENUS)){
|
|
869
|
zooName.setInfraGenericEpithet(emptyToNull(infraGenericEpithet));
|
|
870
|
if (logger.isDebugEnabled()) {
|
|
871
|
logger.debug("infraGenericEpithet: " + infraGenericEpithet);
|
|
872
|
}
|
|
873
|
}
|
|
874
|
if ((fauEuTaxon.getRankId() == R_SPECIES || fauEuTaxon.getRankId() == R_SUBSPECIES)) {
|
|
875
|
zooName.setSpecificEpithet(emptyToNull(specificEpithet));
|
|
876
|
if (logger.isDebugEnabled()) {
|
|
877
|
logger.debug("specificEpithet: " + specificEpithet);
|
|
878
|
}
|
|
879
|
}
|
|
880
|
if (fauEuTaxon.getRankId() == R_SUBSPECIES) {
|
|
881
|
zooName.setInfraSpecificEpithet(emptyToNull(infraSpecificEpithet));
|
|
882
|
if (logger.isDebugEnabled()) {
|
|
883
|
logger.debug("infraSpecificEpithet: " + infraSpecificEpithet);
|
|
884
|
}
|
|
885
|
}
|
|
886
|
//TODO: use generate NameCache
|
|
887
|
//zooName.setNameCache(concatString);
|
|
888
|
String result = zooName.getNameCache();
|
|
889
|
// zooName.generateTitle();
|
|
890
|
//String titleCache = buildNameTitleCache(concatString, useOriginalGenus, fauEuTaxon);
|
|
891
|
//zooName.setTitleCache(titleCache);
|
|
892
|
//titleCache = buildNameFullTitleCache(concatString, fauEuConfig);
|
|
893
|
// zooName.generateFullTitle();
|
|
894
|
//zooName.setFullTitleCache(titleCache); // TODO: Add reference, NC status
|
|
895
|
|
|
896
|
// ImportHelper.setOriginalSource(taxonName, fauEuConfig.getSourceReference(),
|
|
897
|
// fauEuTaxon.getId(), "TaxonName");
|
|
898
|
// taxonBase.setSec(fauEuConfig.getSourceReference());
|
|
899
|
// taxonBase.generateTitle();
|
|
900
|
//titleCache = buildTaxonTitleCache(concatString, fauEuConfig.getSourceReference());
|
|
901
|
//taxonBase.setTitleCache(titleCache);
|
|
902
|
|
|
903
|
if (logger.isDebugEnabled()) {
|
|
904
|
logger.debug("Name stored: " + result);
|
|
905
|
}
|
|
906
|
return result;
|
|
907
|
}
|
|
908
|
|
|
909
|
/**
|
|
910
|
* Ensures that empty strings are translated to null.
|
|
911
|
* @param genusOrUninomial
|
|
912
|
* @return
|
|
913
|
*/
|
|
914
|
private String emptyToNull(String text) {
|
|
915
|
if (CdmUtils.isEmpty(text)) {
|
|
916
|
return null;
|
|
917
|
} else {
|
|
918
|
return text;
|
|
919
|
}
|
|
920
|
}
|
|
921
|
|
|
922
|
}
|