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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 BerlinModelTaxonRelationImportValidator implements IOValidator<BerlinModelImportState> {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonRelationImportValidator.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 &= checkInActivatedStatus(state);
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result &= checkSynonymRelationsWithAcceptedTaxa(state);
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result &= checkConceptRelationsWithSynonymTaxa(state);
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result &= checkRelPTaxonWithNotes(state);
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result &= checkTaxaWithNoRelations(state);
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return result;
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}
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private boolean checkInActivatedStatus(BerlinModelImportState state){
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try {
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boolean result = true;
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BerlinModelImportConfigurator config = state.getConfig();
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Source source = state.getConfig().getSource();
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String strSQL =
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" SELECT RelPTaxon.RelPTaxonId, RelPTaxon.RelQualifierFk, FromName.FullNameCache AS FromName, RelPTaxon.PTNameFk1 AS FromNameID, " +
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" Status.Status AS FromStatus, ToName.FullNameCache AS ToName, RelPTaxon.PTNameFk2 AS ToNameId, ToStatus.Status AS ToStatus, FromTaxon.DoubtfulFlag AS doubtfulFrom, ToTaxon.DoubtfulFlag AS doubtfulTo" +
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" FROM PTaxon AS FromTaxon " +
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" INNER JOIN RelPTaxon ON FromTaxon.PTNameFk = RelPTaxon.PTNameFk1 AND FromTaxon.PTRefFk = RelPTaxon.PTRefFk1 " +
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" INNER JOIN PTaxon AS ToTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk " +
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" INNER JOIN Name AS ToName ON ToTaxon.PTNameFk = ToName.NameId " +
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" INNER JOIN Name AS FromName ON FromTaxon.PTNameFk = FromName.NameId " +
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" INNER JOIN Status ON FromTaxon.StatusFk = Status.StatusId AND FromTaxon.StatusFk = Status.StatusId " +
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" INNER JOIN Status AS ToStatus ON ToTaxon.StatusFk = ToStatus.StatusId AND ToTaxon.StatusFk = ToStatus.StatusId " +
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" WHERE (RelPTaxon.RelQualifierFk = - 99) ";
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if (StringUtils.isNotBlank(config.getRelTaxaIdQuery())){
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strSQL += String.format(" AND (RelPTaxon.RelPTaxonId IN " +
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" ( %s ) )" , config.getRelTaxaIdQuery()) ;
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}
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// System.out.println(strSQL);
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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 TaxonRelationships with status 'inactivated'(-99)!");
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System.out.println("========================================================");
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}
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int relPTaxonId = rs.getInt("RelPTaxonId");
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String fromName = rs.getString("FromName");
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int fromNameID = rs.getInt("FromNameID");
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String fromStatus = rs.getString("FromStatus");
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String toName = rs.getString("ToName");
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int toNameId = rs.getInt("ToNameId");
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String toStatus = rs.getString("ToStatus");
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String doubtfulFrom = String.valueOf(rs.getObject("doubtfulFrom"));
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String doubtfulTo = String.valueOf(rs.getObject("doubtfulTo"));
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System.out.println("RelPTaxonId:" + relPTaxonId +
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"\n FromName: " + fromName + "\n FromNameID: " + fromNameID + "\n FromStatus: " + fromStatus + "\n FromDoubtful: " + doubtfulFrom +
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"\n ToName: " + toName + "\n ToNameId: " + toNameId + "\n ToStatus: " + toStatus + "\n ToDoubtful: " + doubtfulTo );
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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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* @param state
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* @return
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*/
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private boolean checkRelPTaxonWithNotes(BerlinModelImportState state) {
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boolean success = true;
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try {
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BerlinModelImportConfigurator config = state.getConfig();
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Source source = config.getSource();
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String strQuery =
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"SELECT count(*) AS n FROM RelPTaxon " +
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" WHERE (Notes IS NOT NULL) AND (RTRIM(LTRIM(Notes)) <> '') ";
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if (StringUtils.isNotBlank(config.getRelTaxaIdQuery())){
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strQuery += String.format(" AND (RelPTaxon.RelPTaxonId IN " +
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" ( %s ) ) " , config.getRelTaxaIdQuery()) ;
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}
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ResultSet rs = source.getResultSet(strQuery);
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rs.next();
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int n;
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n = rs.getInt("n");
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if (n > 0){
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System.out.println("========================================================");
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System.out.println("There are " + n + " RelPTaxa with a note. Notes for RelPTaxa are not imported!");
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System.out.println("========================================================");
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success = false;
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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return success;
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}
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/**
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* @param state
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* @return
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*/
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private boolean checkSynonymRelationsWithAcceptedTaxa(BerlinModelImportState state) {
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boolean success = true;
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try {
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BerlinModelImportConfigurator config = state.getConfig();
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Source source = config.getSource();
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String strQuery =
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"SELECT RelPTaxon.RelPTaxonId, RelPTQualifier, PTaxon.RIdentifier, Name.FullNameCache fromName, PTaxon.PTRefFk, Name.NameId as fromNameId, AcceptedName.FullNameCache acceptedName" +
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" FROM RelPTaxon INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
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" INNER JOIN RelPTQualifier ON RelPTaxon.RelQualifierFk = RelPTQualifier.RelPTQualifierId " +
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" LEFT OUTER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
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" LEFT OUTER JOIN Name AS AcceptedName ON RelPTaxon.PTNameFk2 = AcceptedName.NameId " +
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" WHERE (PTaxon.StatusFk = 1) AND (RelPTaxon.RelQualifierFk IN (2, 4, 5, 6, 7)) ";
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if (StringUtils.isNotBlank(config.getRelTaxaIdQuery())){
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strQuery += String.format(" AND (RelPTaxon.RelPTaxonId IN " +
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" ( %s ) )" , config.getRelTaxaIdQuery()) ;
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}
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ResultSet rs = source.getResultSet(strQuery);
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boolean firstRow = true;
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while (rs.next()){
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if (firstRow){
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System.out.println("========================================================");
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System.out.println("There are accepted taxa having synonym role in a synonym relationship!");
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System.out.println("========================================================");
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}
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int relPTaxonId = rs.getInt("RelPTaxonId");
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String relType = rs.getString("RelPTQualifier");
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int fromIdentifier = rs.getInt("RIdentifier");
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String fromName = rs.getString("fromName");
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int fromRefFk = rs.getInt("PTRefFk");
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int fromNameId = rs.getInt("fromNameId");
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String toName = rs.getString("acceptedName");
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System.out.println("RelPTaxonId:" + relPTaxonId +
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"\n TaxonRIdentifier: " + fromIdentifier + "\n name: " + fromName + "\n nameId: " + fromNameId + "\n RefFk: " + fromRefFk + "\n RelType: " + relType
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+ "\n acceptedName: " + toName //+ "\n ToNameId: " + toNameId + "\n ToStatus: " + toStatus + "\n ToDoubtful: " + doubtfulTo )
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);
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success = (firstRow = false);
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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return success;
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}
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/**
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* @param state
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* @return
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*/
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private boolean checkConceptRelationsWithSynonymTaxa(BerlinModelImportState state) {
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boolean success = true;
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try {
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BerlinModelImportConfigurator config = state.getConfig();
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Source source = config.getSource();
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String strQuery =
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"SELECT RelPTaxon.RelPTaxonId, RelPTQualifier, PTaxon.RIdentifier,PTaxon.StatusFk as fromStatus, Name.FullNameCache fromName, PTaxon.PTRefFk, Name.NameId as fromNameId, AcceptedName.FullNameCache acceptedName" +
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" FROM RelPTaxon INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
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" INNER JOIN RelPTQualifier ON RelPTaxon.RelQualifierFk = RelPTQualifier.RelPTQualifierId " +
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" LEFT OUTER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
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" LEFT OUTER JOIN Name AS AcceptedName ON RelPTaxon.PTNameFk2 = AcceptedName.NameId " +
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" WHERE (PTaxon.StatusFk IN (2,3,4)) AND (RelPTaxon.RelQualifierFk NOT IN (2, 4, 5, 6, 7, 101, 102, 103, 104, -99)) ";
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if (StringUtils.isNotBlank(config.getRelTaxaIdQuery())){
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strQuery += String.format(" AND (RelPTaxon.RelPTaxonId IN " +
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" ( %s ) )" , config.getRelTaxaIdQuery()) ;
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}
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ResultSet rs = source.getResultSet(strQuery);
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boolean firstRow = true;
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while (rs.next()){
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if (firstRow){
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System.out.println("========================================================");
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System.out.println("There are synonyms being part of an accepted taxon relationship!");
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System.out.println("--------------------------------------------------------");
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System.out.println(strQuery);
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System.out.println("========================================================");
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}
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int relPTaxonId = rs.getInt("RelPTaxonId");
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String relType = rs.getString("RelPTQualifier");
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int fromIdentifier = rs.getInt("RIdentifier");
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String fromName = rs.getString("fromName");
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int fromRefFk = rs.getInt("PTRefFk");
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int fromNameId = rs.getInt("fromNameId");
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String toName = rs.getString("acceptedName");
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System.out.println("RelPTaxonId:" + relPTaxonId +
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"\n TaxonRIdentifier: " + fromIdentifier + "\n name: " + fromName + "\n nameId: " + fromNameId + "\n RefFk: " + fromRefFk + "\n RelType: " + relType
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+ "\n toName: " + toName //+ "\n ToNameId: " + toNameId + "\n ToStatus: " + toStatus + "\n ToDoubtful: " + doubtfulTo )
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);
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success = (firstRow = false);
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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return success;
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}
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/**
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* @param state
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* @return
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*/
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private boolean checkTaxaWithNoRelations(BerlinModelImportState state) {
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boolean success = true;
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try {
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BerlinModelImportConfigurator config = state.getConfig();
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Source source = config.getSource();
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String strSelect = " SELECT pt.PTRefFk AS secRefFk, r.RefCache AS secRef, n.FullNameCache, n.NameId, st.Status ";
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String strCount = " SELECT count(*) as n ";
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String strQueryBase =
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" FROM PTaxon AS pt LEFT OUTER JOIN " +
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" Status st ON pt.StatusFk = st.StatusId LEFT OUTER JOIN " +
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" Reference r ON pt.PTRefFk = r.RefId LEFT OUTER JOIN " +
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" Name n ON pt.PTNameFk = n.NameId LEFT OUTER JOIN " +
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" RelPTaxon rel1 ON pt.PTNameFk = rel1.PTNameFk2 AND pt.PTRefFk = rel1.PTRefFk2 LEFT OUTER JOIN " +
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" RelPTaxon AS rel2 ON pt.PTNameFk = rel2.PTNameFk1 AND pt.PTRefFk = rel2.PTRefFk1 " +
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" WHERE (rel2.RelQualifierFk IS NULL) AND (rel1.RelQualifierFk IS NULL) AND pt.statusFK <> 6 ";
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String strOrderBy = " ORDER BY r.RefCache, pt.PTRefFk, n.FullNameCache, pt.statusFK ";
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if (state.getConfig().isEuroMed()){
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strQueryBase += " AND pt.RIdentifier IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll) AND (pt.IsExcludedMarker = 0 OR pt.IsExcludedMarker IS NULL) " ;
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}
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//project filter
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// if (StringUtils.isNotBlank(config.getRelTaxaIdQuery())){
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// strQuery += String.format(" AND (RelPTaxon.RelPTaxonId IN " +
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// " ( %s ) )" , config.getRelTaxaIdQuery()) ;
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// }
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ResultSet rs = source.getResultSet(strCount + strQueryBase);
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rs.next();
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int n = rs.getInt("n");
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if (n > 0){
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System.out.println("=======================================================================");
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System.out.println("There are "+n+" taxa without any taxon relationship and not being orphaned!");
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System.out.println("=======================================================================");
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}
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287
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rs = source.getResultSet(strSelect + strQueryBase + strOrderBy);
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while (rs.next()){
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289
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290
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int secRefFk = rs.getInt("secRefFk");
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String secRef = rs.getString("secRef");
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String nameCache = rs.getString("FullNameCache");
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int nameId = rs.getInt("NameId");
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String status = rs.getString("Status");
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295
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System.out.println("SecRef:" + secRefFk +
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"\n secRef: " + secRef + "\n name: " + nameCache + "\n nameId: " + nameId
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+ "\n status: " + status
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);
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300
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}
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success = (n == 0);
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} catch (SQLException e) {
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303
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e.printStackTrace();
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success = false;
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}
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return success;
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307
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}
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310
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}
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