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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.berlinModel.in.validation;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.Source;
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/**
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* @author a.mueller
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* @since 17.02.2010
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*/
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public class BerlinModelCommonNamesImportValidator implements IOValidator<BerlinModelImportState> {
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private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImportValidator.class);
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@Override
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public boolean validate(BerlinModelImportState state) {
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boolean result = true;
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result &= checkNameUsedInSourceMinusOne(state.getConfig());
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result &= checkUnreferredNameUsedInSource(state.getConfig());
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result &= checkUnreferredLanguageRefFk(state.getConfig());
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result &= checkTaxonIsAccepted(state.getConfig());
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return result;
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}
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private boolean checkNameUsedInSourceMinusOne(BerlinModelImportConfigurator config){
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try {
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boolean result = true;
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Source source = config.getSource();
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String strQuery = "SELECT Count(*) as n " +
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" FROM emCommonName " +
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" WHERE (emCommonName.NameInSourceFk = - 1) ";
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if (StringUtils.isNotBlank(config.getCommonNameFilter())){
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strQuery += String.format(" AND (%s) ", config.getCommonNameFilter()) ;
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}
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ResultSet rs = source.getResultSet(strQuery);
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rs.next();
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int count = rs.getInt("n");
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if (count > 0){
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System.out.println("========================================================");
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System.out.println("There are " + count + " common names that have a name usedInSourceFk = -1.");
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System.out.println("========================================================");
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}
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String sql =
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" SELECT DISTINCT emCommonName.CommonNameId, emCommonName.NameInSourceFk, emCommonName.CommonName, PTaxon.PTNameFk, PTaxon.PTRefFk," +
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" Name.FullNameCache, PTaxon.RIdentifier " +
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" FROM emCommonName INNER JOIN " +
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" PTaxon ON emCommonName.PTNameFk = PTaxon.PTNameFk AND emCommonName.PTRefFk = PTaxon.PTRefFk INNER JOIN " +
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" Name ON PTaxon.PTNameFk = Name.NameId " +
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" WHERE (emCommonName.NameInSourceFk = - 1) ";
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if (StringUtils.isNotBlank(config.getCommonNameFilter())){
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sql += String.format(" AND (%s) ", config.getCommonNameFilter()) ;
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}
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rs = source.getResultSet(sql);
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int i = 0;
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while (rs.next()){
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i++;
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int commonNameId = rs.getInt("CommonNameId");
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String fullNameCache = rs.getString("FullNameCache");
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String commonName = rs.getString("CommonName");
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int rIdentifier = rs.getInt("RIdentifier");
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int nameFk = rs.getInt("PTNameFk");
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int refFk = rs.getInt("PTRefFk");
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int nameInSourceFk = rs.getInt("NameInSourceFk");
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System.out.println("CommonName: " + commonName + "\n CommonNameId: " + commonNameId + "\n Taxon Name:" + fullNameCache + "\n TaxonNameFk: " + nameFk +
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"\n TaxonRefFk: " + refFk + "\n TaxonId" + rIdentifier + "\n NameInSourceFk: " + nameInSourceFk + "\n");
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}
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if (i > 0){
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System.out.println(" ");
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}
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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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private boolean checkUnreferredNameUsedInSource(BerlinModelImportConfigurator config){
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try {
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boolean result = true;
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Source source = config.getSource();
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String strQuery = "SELECT Count(*) as n " +
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" FROM emCommonName " +
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" WHERE (emCommonName.NameInSourceFk NOT IN " +
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"(SELECT NameId FROM Name AS Name_1)) AND " +
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"(emCommonName.NameInSourceFk <> - 1) ";
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if (StringUtils.isNotBlank(config.getCommonNameFilter())){
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strQuery += String.format(" AND (%s) ", config.getCommonNameFilter()) ;
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}
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ResultSet rs = source.getResultSet(strQuery);
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rs.next();
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int count = rs.getInt("n");
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if (count > 0){
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System.out.println("========================================================");
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System.out.println("There are " + count + " common names that have a name used in source which can not be found in the database.");
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System.out.println("========================================================");
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}
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String sql =
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" SELECT DISTINCT emCommonName.CommonNameId, emCommonName.NameInSourceFk, emCommonName.CommonName, PTaxon.PTNameFk, PTaxon.PTRefFk," +
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" Name.FullNameCache, PTaxon.RIdentifier " +
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" FROM emCommonName INNER JOIN " +
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" PTaxon ON emCommonName.PTNameFk = PTaxon.PTNameFk AND emCommonName.PTRefFk = PTaxon.PTRefFk INNER JOIN " +
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" Name ON PTaxon.PTNameFk = Name.NameId " +
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" WHERE (emCommonName.NameInSourceFk NOT IN " +
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"(SELECT NameId FROM Name AS Name_1)) AND " +
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"(emCommonName.NameInSourceFk <> - 1)";
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rs = source.getResultSet(sql);
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int i = 0;
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while (rs.next()){
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i++;
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int commonNameId = rs.getInt("CommonNameId");
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String fullNameCache = rs.getString("FullNameCache");
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String commonName = rs.getString("CommonName");
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int rIdentifier = rs.getInt("RIdentifier");
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int nameFk = rs.getInt("PTNameFk");
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int refFk = rs.getInt("PTRefFk");
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int nameInSourceFk = rs.getInt("NameInSourceFk");
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System.out.println("CommonName: " + commonName + "\n CommonNameId: " + commonNameId + "\n Taxon Name:" + fullNameCache + "\n TaxonNameFk: " + nameFk +
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"\n TaxonRefFk: " + refFk + "\n TaxonId" + rIdentifier + "\n NameInSourceFk: " + nameInSourceFk + "\n");
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}
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if (i > 0){
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System.out.println(" ");
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}
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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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private boolean checkUnreferredLanguageRefFk(BerlinModelImportConfigurator config){
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try {
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boolean result = true;
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Source source = config.getSource();
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String strQueryArticlesWithoutJournal = "SELECT Count(*) as n " +
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" FROM emCommonName " +
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" WHERE (emCommonName.LanguageRefFk NOT IN " +
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"(SELECT ReferenceId FROM emLanguageReference)) AND " +
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"(emCommonName.LanguageRefFk is NOT NULL)";
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ResultSet rs = source.getResultSet(strQueryArticlesWithoutJournal);
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rs.next();
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int count = rs.getInt("n");
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if (count > 0){
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System.out.println("========================================================");
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logger.warn("There are " + count + " common names that have a languageRefFk which can not be found in the emLanguageRefernce table.");
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System.out.println("========================================================");
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}
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if (count > 0){
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System.out.println(" ");
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}
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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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private static boolean checkTaxonIsAccepted(BerlinModelImportConfigurator config){
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try {
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boolean result = true;
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Source source = config.getSource();
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String strQuery = "SELECT cn.CommonNameId, cn.CommonName, pt.StatusFk, n.FullNameCache, s.Status, pt.PTRefFk, r.RefCache " +
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" FROM emCommonName cn " +
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" INNER JOIN PTaxon pt ON cn.PTNameFk = pt.PTNameFk AND cn.PTRefFk = pt.PTRefFk " +
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" INNER JOIN Name n ON pt.PTNameFk = n.NameId " +
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" INNER JOIN Status s ON pt.StatusFk = s.StatusId " +
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" LEFT OUTER JOIN Reference r ON pt.PTRefFk = r.RefId " +
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" WHERE (pt.StatusFk NOT IN ( 1, 5)) ";
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if (StringUtils.isNotBlank(config.getOccurrenceFilter())){
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strQuery += String.format(" AND (%s) ", config.getCommonNameFilter()) ;
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}
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ResultSet resulSet = source.getResultSet(strQuery);
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boolean firstRow = true;
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while (resulSet.next()){
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if (firstRow){
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System.out.println("========================================================");
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System.out.println("There are Common Names for a taxon that is not accepted!");
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System.out.println("========================================================");
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}
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int commonNameId = resulSet.getInt("CommonNameId");
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String commonName = resulSet.getString("CommonName");
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String status = resulSet.getString("Status");
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String fullNameCache = resulSet.getString("FullNameCache");
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String ptRefFk = resulSet.getString("PTRefFk");
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String ptRef = resulSet.getString("RefCache");
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System.out.println("CommonNameId: " + commonNameId + "\n CommonName: " + commonName +
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"\n Status: " + status +
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"\n FullNameCache: " + fullNameCache + "\n ptRefFk: " + ptRefFk +
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"\n sec: " + ptRef );
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result = firstRow = false;
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}
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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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