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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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* @created 17.02.2010
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*/
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public class BerlinModelTaxonImportValidator implements IOValidator<BerlinModelImportState>{
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonImportValidator.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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BerlinModelImportConfigurator bmiConfig = state.getConfig();
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// result &= checkTaxonStatus(bmiConfig); //handled by TaxonRelationValidator
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result &= checkInactivated(bmiConfig);
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return result;
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}
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private boolean checkTaxonStatus(BerlinModelImportConfigurator bmiConfig){
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try {
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boolean result = true;
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Source source = bmiConfig.getSource();
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String strSQL = " SELECT RelPTaxon.RelQualifierFk, RelPTaxon.relPTaxonId, PTaxon.PTNameFk, PTaxon.PTRefFk, PTaxon_1.PTNameFk AS Expr1, PTaxon.RIdentifier, PTaxon_1.RIdentifier AS Expr3, Name.FullNameCache " +
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" FROM RelPTaxon " +
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" INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
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" INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk " +
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" INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
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" WHERE (dbo.PTaxon.StatusFk = 1) AND ((RelPTaxon.RelQualifierFk = 7) OR (RelPTaxon.RelQualifierFk = 6) OR (RelPTaxon.RelQualifierFk = 2)) ";
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ResultSet rs = source.getResultSet(strSQL);
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boolean firstRow = true;
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int i = 0;
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while (rs.next()){
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i++;
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if (firstRow){
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System.out.println("========================================================");
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logger.warn("There are taxa that have a 'is synonym of' - relationship but having taxon status 'accepted'!");
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System.out.println("========================================================");
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}
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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 relPTaxonId = rs.getInt("relPTaxonId");
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String taxonName = rs.getString("FullNameCache");
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System.out.println("RIdentifier:" + rIdentifier + "\n name: " + nameFk +
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"\n taxonName: " + taxonName + "\n refId: " + refFk + "\n RelPTaxonId: " + relPTaxonId );
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result = firstRow = false;
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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 checkInactivated(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 strSQL = " SELECT * " +
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" FROM PTaxon t " +
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" INNER JOIN Name n ON t.PTNameFk = n.NameId " +
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" WHERE (t.DoubtfulFlag = 'i') ";
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if (StringUtils.isNotBlank(config.getTaxonTable())){
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strSQL += String.format(" AND (t.RIdentifier IN " +
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" (SELECT RIdentifier FROM %s ))" , config.getTaxonTable()) ;
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}
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strSQL += " ORDER BY t.ptRefFk, n.FullNameCache";
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ResultSet rs = source.getResultSet(strSQL);
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boolean firstRow = true;
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int i = 0;
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while (rs.next()){
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i++;
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if (firstRow){
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System.out.println("========================================================");
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System.out.println("There are taxa that have a doubtful flag 'i'(inactivated). Inactivated is not supported by CDM!");
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System.out.println("========================================================");
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}
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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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String taxonName = rs.getString("FullNameCache");
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System.out.println("RIdentifier:" + rIdentifier + "\n nameId: " + nameFk +
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"\n taxonName: " + taxonName + "\n refId: " + refFk );
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result = firstRow = false;
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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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}
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