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/**
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* Copyright (C) 2009 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.pesi.out;
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import java.sql.Connection;
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import java.sql.PreparedStatement;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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/**
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* The export class for relations between {@link eu.etaxonomy.cdm.model.taxon.TaxonBase TaxonBases}.<p>
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* Inserts into DataWarehouse database table <code>RelTaxon</code>.
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* @author e.-m.lee
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* @since 23.02.2010
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*
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*/
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@Component
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public class PesiRelTaxonExport extends PesiExportBase {
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private static final long serialVersionUID = 67808745337549629L;
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private static final Logger logger = Logger.getLogger(PesiRelTaxonExport.class);
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private static final Class<? extends CdmBase> standardMethodParameter = RelationshipBase.class;
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private static int modCount = 1000;
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private static final String dbTableName = "RelTaxon";
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private static final String pluralString = "Relationships";
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private static PreparedStatement synonymsStmt;
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private final HashMap<Rank, Rank> rank2endRankMap = new HashMap<Rank, Rank>();
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private final List<Rank> rankList = new ArrayList<Rank>();
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private PesiExportMapping mapping;
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private int count = 0;
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public PesiRelTaxonExport() {
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super();
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}
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@Override
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public Class<? extends CdmBase> getStandardMethodParameter() {
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return standardMethodParameter;
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}
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@Override
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protected boolean doCheck(PesiExportState state) {
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boolean result = true;
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return result;
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}
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@Override
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protected void doInvoke(PesiExportState state) {
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try {
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logger.info("*** Started Making " + pluralString + " ...");
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Connection connection = state.getConfig().getDestination().getConnection();
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String synonymsSql = "UPDATE Taxon SET KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?";
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synonymsStmt = connection.prepareStatement(synonymsSql);
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// Stores whether this invoke was successful or not.
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boolean success = true;
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// PESI: Clear the database table RelTaxon.
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//doDelete(state); -> done by stored procedure
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// Get specific mappings: (CDM) Relationship -> (PESI) RelTaxon
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mapping = getMapping();
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// Initialize the db mapper
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mapping.initialize(state);
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//Export taxon relations
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success &= doPhase01(state, mapping);
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// Export name relations
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success &= doPhase02(state, mapping);
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if (! success){
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state.getResult().addError("An unknown error occurred in PesiRelTaxonExport");
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}
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} catch (SQLException e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.getResult().addException(e);
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return;
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}
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}
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private boolean doPhase01(PesiExportState state, PesiExportMapping mapping2) throws SQLException {
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logger.info("PHASE 1: Taxon Relationships ...");
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boolean success = true;
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int limit = state.getConfig().getLimitSave();
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// Start transaction
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TransactionStatus txStatus = startTransaction(true);
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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List<RelationshipBase> list;
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//taxon relations
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int partitionCount = 0;
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int totalCount = 0;
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while ((list = getNextTaxonRelationshipPartition( limit, partitionCount++, null)) != null ) {
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totalCount = totalCount + list.size();
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logger.info("Read " + list.size() + " PESI relations. Limit: " + limit + ". Total: " + totalCount );
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// if (list.size() > 0){
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// logger.warn("First relation type is " + list.get(0).getType().getTitleCache());
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// }
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for (RelationshipBase rel : list){
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try {
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mapping.invoke(rel);
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} catch (Exception e) {
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logger.error(e.getMessage() + ". Relationship: " + rel.getUuid());
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e.printStackTrace();
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}
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}
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commitTransaction(txStatus);
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txStatus = startTransaction();
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}
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list = null;
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commitTransaction(txStatus);
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return success;
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}
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private boolean doPhase02(PesiExportState state, PesiExportMapping mapping2) throws SQLException {
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logger.info("PHASE 2: Name Relationships ...");
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boolean success = true;
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int limit = state.getConfig().getLimitSave();
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// Start transaction
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TransactionStatus txStatus = startTransaction(true);
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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List<RelationshipBase> list;
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//name relations
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int partitionCount = 0;
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while ((list = getNextNameRelationshipPartition(null, limit, partitionCount++, null)) != null ) {
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for (RelationshipBase rel : list){
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try {
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TaxonName name1;
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TaxonName name2;
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if (rel.isInstanceOf(HybridRelationship.class)){
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HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class);
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name1 = hybridRel.getParentName();
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name2 = hybridRel.getHybridName();
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hybridRel = null;
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}else if (rel.isInstanceOf(NameRelationship.class)){
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NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class);
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name1 = nameRel.getFromName();
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name2 = nameRel.getToName();
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nameRel = null;
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}else{
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logger.warn ("Only hybrid- and name-relationships alowed here");
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continue;
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}
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List<IdentifiableEntity> fromList = new ArrayList<IdentifiableEntity>();
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List<IdentifiableEntity> toList = new ArrayList<IdentifiableEntity>();
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makeList(name1, fromList);
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makeList(name2, toList);
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for (IdentifiableEntity fromEntity : fromList){
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for (IdentifiableEntity toEntity : toList){
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//TODO set entities to state
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state.setCurrentFromObject(fromEntity);
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state.setCurrentToObject(toEntity);
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mapping.invoke(rel);
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}
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}
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fromList = null;
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toList = null;
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name1 = null;
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name2 = null;
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rel = null;
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} catch (Exception e) {
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logger.error(e.getMessage() + ". Relationship: " + rel.getUuid());
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e.printStackTrace();
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}
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}
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commitTransaction(txStatus);
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txStatus = startTransaction();
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}
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commitTransaction(txStatus);
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list = null;
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logger.info("End PHASE 2: Name Relationships ...");
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state.setCurrentFromObject(null);
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state.setCurrentToObject(null);
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return success;
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}
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private void makeList(TaxonName name, List<IdentifiableEntity> list) {
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if (! hasPesiTaxon(name)){
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list.add(name);
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}else{
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for (TaxonBase taxon: getPesiTaxa(name)){
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list.add(taxon);
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}
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)
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*/
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protected void doInvoke_Old(PesiExportState state) {
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try {
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logger.info("*** Started Making " + pluralString + " ...");
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Connection connection = state.getConfig().getDestination().getConnection();
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String synonymsSql = "UPDATE Taxon SET KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?";
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synonymsStmt = connection.prepareStatement(synonymsSql);
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// Stores whether this invoke was successful or not.
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boolean success = true;
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// PESI: Clear the database table RelTaxon.
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doDelete(state);
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// Get specific mappings: (CDM) Relationship -> (PESI) RelTaxon
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mapping = getMapping();
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// Initialize the db mapper
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mapping.initialize(state);
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TransactionStatus txStatus = null;
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List<Classification> classificationList = null;
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// Specify starting ranks for tree traversing
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rankList.add(Rank.KINGDOM());
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rankList.add(Rank.GENUS());
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// Specify where to stop traversing (value) when starting at a specific Rank (key)
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rank2endRankMap.put(Rank.GENUS(), null); // Since NULL does not match an existing Rank, traverse all the way down to the leaves
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rank2endRankMap.put(Rank.KINGDOM(), Rank.GENUS()); // excludes rank genus
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// Retrieve list of classifications
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txStatus = startTransaction(true);
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logger.info("Started transaction. Fetching all classifications...");
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classificationList = getClassificationService().listClassifications(null, 0, null, null);
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commitTransaction(txStatus);
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logger.debug("Committed transaction.");
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logger.info("Fetched " + classificationList.size() + " classification(s).");
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for (Classification classification : classificationList) {
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for (Rank rank : rankList) {
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txStatus = startTransaction(true);
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logger.info("Started transaction to fetch all rootNodes specific to Rank " + rank.getLabel() + " ...");
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List<TaxonNode> rankSpecificRootNodes = getClassificationService().listRankSpecificRootNodes(classification, rank, null, null, null);
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logger.info("Fetched " + rankSpecificRootNodes.size() + " RootNodes for Rank " + rank.getLabel());
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commitTransaction(txStatus);
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logger.debug("Committed transaction.");
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for (TaxonNode rootNode : rankSpecificRootNodes) {
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txStatus = startTransaction(false);
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Rank endRank = rank2endRankMap.get(rank);
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logger.debug("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till " + (endRank == null ? "leaves are reached ..." : "Rank " + endRank.getLabel() + " ..."));
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TaxonNode newNode = getTaxonNodeService().load(rootNode.getUuid());
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if (isPesiTaxon(newNode.getTaxon())){
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TaxonNode parentNode = newNode.getParent();
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success &=traverseTree(newNode, parentNode, endRank, state);
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commitTransaction(txStatus);
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logger.debug("Committed transaction.");
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}else{
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logger.debug("Taxon is not in PESI");
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}
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}
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}
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}
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logger.warn("*** Finished Making " + pluralString + " ..." + getSuccessString(success));
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if (!success){
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state.getResult().addError("An unknown error occurred in PesiRelTaxonExport");
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}
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return;
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} catch (SQLException e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.getResult().addException(e);
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return;
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}
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}
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/**
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* Traverses the classification recursively and stores determined values for every Taxon.
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* @param childNode
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* @param parentNode
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* @param treeIndex
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* @param fetchLevel
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* @param state
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*/
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private boolean traverseTree(TaxonNode childNode, TaxonNode parentNode, Rank fetchLevel, PesiExportState state) {
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boolean success = true;
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// Traverse all branches from this childNode until specified fetchLevel is reached.
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TaxonBase<?> childTaxon = childNode.getTaxon();
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if (childTaxon != null) {
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if (isPesiTaxon(childTaxon)){
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if (childTaxon.getName() != null) {
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Rank childTaxonNameRank = childTaxon.getName().getRank();
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if (childTaxonNameRank != null) {
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if (! childTaxonNameRank.equals(fetchLevel)) {
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success &= saveData(childNode, parentNode, state);
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for (TaxonNode newNode : childNode.getChildNodes()) {
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success &= traverseTree(newNode, childNode, fetchLevel, state);
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}
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} else {
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// logger.error("Target Rank " + fetchLevel.getLabel() + " reached");
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return success;
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}
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} else {
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logger.warn("Rank is NULL. FetchLevel can not be checked: " + childTaxon.getUuid() + " (" + childTaxon.getTitleCache() + ")");
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}
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} else {
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logger.error("TaxonName is NULL for taxon: " + childTaxon.getUuid());
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}
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}else{
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logger.debug("Taxon is not a PESI taxon: " + childTaxon.getUuid());
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}
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} else {
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logger.error("Taxon is NULL for TaxonNode: " + childNode.getUuid());
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}
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return success;
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}
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/**
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* Stores values in database for every recursive round.
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* @param childNode
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* @param parentNode
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* @param treeIndex
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* @param state
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* @param currentTaxonFk
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*/
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private boolean saveData(TaxonNode childNode, TaxonNode parentNode, PesiExportState state) {
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boolean success = true;
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Taxon childNodeTaxon = childNode.getTaxon();
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if (childNodeTaxon != null) {
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// TaxonRelationships
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success &= saveTaxonRelationships(state, childNodeTaxon);
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// TaxonNameRelationships
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success &= saveNameRelationships(state, childNodeTaxon);
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// SynonymRelationships
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success &= saveSynonymAndSynNameRelationships(state, childNodeTaxon);
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}
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return success;
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}
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395
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396
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private boolean saveSynonymAndSynNameRelationships(PesiExportState state, Taxon childNodeTaxon) {
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boolean success = true;
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for (Synonym synonym : childNodeTaxon.getSynonyms()) { // synonyms of accepted taxon
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TaxonName synonymTaxonName = synonym.getName();
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if (! isPesiTaxon(synonym)){
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logger.warn("Synonym " + synonym.getId() + " is not a PESI taxon. Can't export relationship");
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continue;
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}
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// Store synonym data in Taxon table
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invokeSynonyms(state, synonymTaxonName);
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407
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408
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try {
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if (neededValuesNotNull(synonym, state)) {
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doCount(count++, modCount, pluralString);
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success &= mapping.invoke(synonym);
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}
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} catch (SQLException e) {
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logger.error("Synonym (" + synonym.getUuid() + ") could not be stored : " + e.getMessage());
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}
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418
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419
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// SynonymNameRelationship
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success &= saveNameRelationships(state, synonym);
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}
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state.setCurrentFromObject(null);
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return success;
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}
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426
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427
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private boolean saveNameRelationships(PesiExportState state, TaxonBase taxonBase) {
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428
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boolean success = true;
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TaxonName childNodeTaxonName = taxonBase.getName();
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430
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431
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//from relations
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432
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Set<NameRelationship> nameRelations = childNodeTaxonName.getRelationsFromThisName();
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433
|
state.setCurrentFromObject(taxonBase);
|
434
|
boolean isFrom = true;
|
435
|
success &= saveOneSideNameRelation(state, isFrom, nameRelations);
|
436
|
|
437
|
//toRelations
|
438
|
nameRelations = childNodeTaxonName.getRelationsToThisName();
|
439
|
state.setCurrentToObject(taxonBase);
|
440
|
isFrom = false;
|
441
|
success &= saveOneSideNameRelation(state, isFrom, nameRelations);
|
442
|
state.setCurrentToObject(null);
|
443
|
return success;
|
444
|
}
|
445
|
|
446
|
private boolean saveOneSideNameRelation(PesiExportState state, boolean isFrom, Set<NameRelationship> nameRelations) {
|
447
|
boolean success = true;
|
448
|
for (NameRelationship nameRelation : nameRelations) {
|
449
|
try {
|
450
|
TaxonName relatedName = isFrom ? nameRelation.getToName(): nameRelation.getFromName();
|
451
|
if ( isPurePesiName(relatedName)){
|
452
|
success &= checkAndInvokeNameRelation(state, nameRelation, relatedName, isFrom);
|
453
|
}else{
|
454
|
for (TaxonBase<?> relatedTaxon : getPesiTaxa(relatedName)){
|
455
|
success &= checkAndInvokeNameRelation(state, nameRelation, relatedTaxon, isFrom);
|
456
|
}
|
457
|
}
|
458
|
} catch (SQLException e) {
|
459
|
logger.error("NameRelationship " + nameRelation.getUuid() + " for " + nameRelation.getFromName().getTitleCache() + " and " + nameRelation.getToName().getTitleCache() + " could not be created: " + e.getMessage());
|
460
|
success = false;
|
461
|
}
|
462
|
}
|
463
|
return success;
|
464
|
}
|
465
|
|
466
|
private boolean checkAndInvokeNameRelation(PesiExportState state, NameRelationship nameRelation, IdentifiableEntity<?> relatedObject, boolean isFrom) throws SQLException {
|
467
|
boolean success = true;
|
468
|
if (isFrom){
|
469
|
state.setCurrentToObject(relatedObject);
|
470
|
}else{
|
471
|
state.setCurrentFromObject(relatedObject);
|
472
|
}
|
473
|
if (neededValuesNotNull(nameRelation, state)) {
|
474
|
doCount(count++, modCount, pluralString);
|
475
|
success &= mapping.invoke(nameRelation);
|
476
|
}
|
477
|
state.setCurrentFromObject(null);
|
478
|
state.setCurrentToObject(null);
|
479
|
return success;
|
480
|
}
|
481
|
|
482
|
private boolean saveTaxonRelationships(PesiExportState state, Taxon childNodeTaxon) {
|
483
|
boolean success = true;
|
484
|
Taxon taxon = childNodeTaxon;
|
485
|
Set<TaxonRelationship> taxonRelations = taxon.getRelationsToThisTaxon();
|
486
|
for (TaxonRelationship taxonRelationship : taxonRelations) {
|
487
|
try {
|
488
|
if (neededValuesNotNull(taxonRelationship, state)) {
|
489
|
doCount(count++, modCount, pluralString);
|
490
|
success &= mapping.invoke(taxonRelationship);
|
491
|
}
|
492
|
} catch (SQLException e) {
|
493
|
logger.error("TaxonRelationship could not be created for this TaxonRelation (" + taxonRelationship.getUuid() + "): " + e.getMessage());
|
494
|
}
|
495
|
}
|
496
|
return success;
|
497
|
}
|
498
|
|
499
|
/**
|
500
|
* Determines synonym related data and saves them.
|
501
|
* @param state
|
502
|
* @param sr
|
503
|
*/
|
504
|
private void invokeSynonyms(PesiExportState state, TaxonName synonymTaxonName) {
|
505
|
// Store KingdomFk and Rank information in Taxon table
|
506
|
Integer kingdomFk = PesiTransformer.nomenClaturalCode2Kingdom(synonymTaxonName.getNomenclaturalCode());
|
507
|
Integer synonymFk = state.getDbId(synonymTaxonName);
|
508
|
|
509
|
saveSynonymData(state, synonymTaxonName, synonymTaxonName.getNomenclaturalCode(), kingdomFk, synonymFk);
|
510
|
}
|
511
|
|
512
|
/**
|
513
|
* Stores synonym data.
|
514
|
* @param state
|
515
|
* @param taxonName
|
516
|
* @param nomenclaturalCode
|
517
|
* @param kingdomFk
|
518
|
* @param synonymParentTaxonFk
|
519
|
* @param currentTaxonFk
|
520
|
*/
|
521
|
private boolean saveSynonymData(PesiExportState state, TaxonName taxonName,
|
522
|
NomenclaturalCode nomenclaturalCode, Integer kingdomFk,
|
523
|
Integer currentSynonymFk) {
|
524
|
try {
|
525
|
if (kingdomFk != null) {
|
526
|
synonymsStmt.setInt(1, kingdomFk);
|
527
|
} else {
|
528
|
synonymsStmt.setObject(1, null);
|
529
|
}
|
530
|
|
531
|
Integer rankFk = getRankFk(taxonName, nomenclaturalCode);
|
532
|
if (rankFk != null) {
|
533
|
synonymsStmt.setInt(2, rankFk);
|
534
|
} else {
|
535
|
synonymsStmt.setObject(2, null);
|
536
|
}
|
537
|
synonymsStmt.setString(3, getRankCache(taxonName, nomenclaturalCode, state));
|
538
|
|
539
|
if (currentSynonymFk != null) {
|
540
|
synonymsStmt.setInt(4, currentSynonymFk);
|
541
|
} else {
|
542
|
synonymsStmt.setObject(4, null);
|
543
|
}
|
544
|
synonymsStmt.executeUpdate();
|
545
|
return true;
|
546
|
} catch (SQLException e) {
|
547
|
logger.error("SQLException during invoke for taxonName - " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + "): " + e.getMessage());
|
548
|
e.printStackTrace();
|
549
|
return false;
|
550
|
}
|
551
|
}
|
552
|
|
553
|
private boolean neededValuesNotNull(Synonym synonym, PesiExportState state) {
|
554
|
boolean result = true;
|
555
|
if (getTaxonFk1(synonym, state) == null) {
|
556
|
logger.warn("TaxonFk1 is NULL, but is not allowed to be. Therefore no record was written to export database for this relationship: " + synonym.getUuid());
|
557
|
result = false;
|
558
|
}
|
559
|
return result;
|
560
|
}
|
561
|
|
562
|
|
563
|
/**
|
564
|
* Checks whether needed values for an entity are NULL.
|
565
|
* @return
|
566
|
*/
|
567
|
private boolean neededValuesNotNull(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
568
|
boolean result = true;
|
569
|
if (getTaxonFk1(relationship, state) == null) {
|
570
|
logger.warn("TaxonFk1 is NULL, but is not allowed to be. Therefore no record was written to export database for this relationship: " + relationship.getUuid());
|
571
|
result = false;
|
572
|
}
|
573
|
if (getTaxonFk2(relationship, state) == null) {
|
574
|
logger.warn("TaxonFk2 is NULL, but is not allowed to be. Therefore no record was written to export database for this relationship: " + relationship.getUuid());
|
575
|
result = false;
|
576
|
}
|
577
|
return result;
|
578
|
}
|
579
|
|
580
|
/**
|
581
|
* Deletes all entries of database tables related to <code>RelTaxon</code>.
|
582
|
* @param state The {@link PesiExportState PesiExportState}.
|
583
|
* @return Whether the delete operation was successful or not.
|
584
|
*/
|
585
|
protected boolean doDelete(PesiExportState state) {
|
586
|
PesiExportConfigurator pesiConfig = state.getConfig();
|
587
|
|
588
|
String sql;
|
589
|
Source destination = pesiConfig.getDestination();
|
590
|
|
591
|
// Clear RelTaxon
|
592
|
sql = "DELETE FROM " + dbTableName;
|
593
|
destination.setQuery(sql);
|
594
|
destination.update(sql);
|
595
|
return true;
|
596
|
}
|
597
|
|
598
|
@Override
|
599
|
protected boolean isIgnore(PesiExportState state) {
|
600
|
return ! state.getConfig().isDoRelTaxa();
|
601
|
}
|
602
|
|
603
|
/**
|
604
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.
|
605
|
* @param relationship The {@link RelationshipBase Relationship}.
|
606
|
* @param state The {@link PesiExportState PesiExportState}.
|
607
|
* @return The <code>TaxonFk1</code> attribute.
|
608
|
* @see MethodMapper
|
609
|
*/
|
610
|
private static Integer getTaxonFk1(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
611
|
return getObjectFk(relationship, state, true);
|
612
|
}
|
613
|
|
614
|
/**
|
615
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.
|
616
|
* @param relationship The {@link RelationshipBase Relationship}.
|
617
|
* @param state The {@link PesiExportState PesiExportState}.
|
618
|
* @return The <code>TaxonFk1</code> attribute.
|
619
|
* @see MethodMapper
|
620
|
*/
|
621
|
private static Integer getTaxonFk1(Synonym synonym, PesiExportState state) {
|
622
|
return synonym.getAcceptedTaxon().getId();
|
623
|
}
|
624
|
|
625
|
|
626
|
/**
|
627
|
* Returns the <code>TaxonFk2</code> attribute. It corresponds to a CDM <code>SynonymRelationship</code>.
|
628
|
* @param relationship The {@link RelationshipBase Relationship}.
|
629
|
* @param state The {@link PesiExportState PesiExportState}.
|
630
|
* @return The <code>TaxonFk2</code> attribute.
|
631
|
* @see MethodMapper
|
632
|
*/
|
633
|
private static Integer getTaxonFk2(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
634
|
return getObjectFk(relationship, state, false);
|
635
|
}
|
636
|
|
637
|
/**
|
638
|
* Returns the <code>RelTaxonQualifierFk</code> attribute.
|
639
|
* @param relationship The {@link RelationshipBase Relationship}.
|
640
|
* @return The <code>RelTaxonQualifierFk</code> attribute.
|
641
|
* @see MethodMapper
|
642
|
*/
|
643
|
@SuppressWarnings("unused")
|
644
|
private static Integer getRelTaxonQualifierFk(RelationshipBase<?, ?, ?> relationship) {
|
645
|
return PesiTransformer.taxonRelation2RelTaxonQualifierFk(relationship);
|
646
|
}
|
647
|
|
648
|
/**
|
649
|
* Returns the <code>RelQualifierCache</code> attribute.
|
650
|
* @param relationship The {@link RelationshipBase Relationship}.
|
651
|
* @return The <code>RelQualifierCache</code> attribute.
|
652
|
* @see MethodMapper
|
653
|
*/
|
654
|
@SuppressWarnings("unused")
|
655
|
private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
656
|
String result = null;
|
657
|
NomenclaturalCode code = null;
|
658
|
Taxon taxon = null;
|
659
|
TaxonName name= null;
|
660
|
if (relationship.isInstanceOf(TaxonRelationship.class)){
|
661
|
TaxonRelationship rel = CdmBase.deproxy(relationship, TaxonRelationship.class);
|
662
|
taxon = rel.getToTaxon();
|
663
|
name = taxon.getName();
|
664
|
code = name.getNomenclaturalCode();
|
665
|
rel = null;
|
666
|
|
667
|
// }else if (relationship.isInstanceOf(SynonymRelationship.class)){
|
668
|
// SynonymRelationship rel = CdmBase.deproxy(relationship, SynonymRelationship.class);
|
669
|
// taxon = rel.getAcceptedTaxon();
|
670
|
// name = taxon.getName();
|
671
|
// code = name.getNomenclaturalCode();
|
672
|
// rel = null;
|
673
|
|
674
|
}else if (relationship.isInstanceOf(NameRelationship.class)){
|
675
|
NameRelationship rel = CdmBase.deproxy(relationship, NameRelationship.class);
|
676
|
name = rel.getFromName();
|
677
|
code =name.getNomenclaturalCode();
|
678
|
rel = null;
|
679
|
|
680
|
}else if (relationship.isInstanceOf(HybridRelationship.class)){
|
681
|
HybridRelationship rel = CdmBase.deproxy(relationship, HybridRelationship.class);
|
682
|
name = rel.getParentName();
|
683
|
code = name.getNomenclaturalCode();
|
684
|
rel = null;
|
685
|
}
|
686
|
taxon = null;
|
687
|
name = null;
|
688
|
if (code != null) {
|
689
|
result = state.getConfig().getTransformer().getCacheByRelationshipType(relationship, code);
|
690
|
} else {
|
691
|
logger.error("NomenclaturalCode is NULL while creating the following relationship: " + relationship.getUuid());
|
692
|
}
|
693
|
return result;
|
694
|
}
|
695
|
|
696
|
/**
|
697
|
* Returns the <code>Notes</code> attribute.
|
698
|
* @param relationship The {@link RelationshipBase Relationship}.
|
699
|
* @return The <code>Notes</code> attribute.
|
700
|
* @see MethodMapper
|
701
|
*/
|
702
|
@SuppressWarnings("unused")
|
703
|
private static String getNotes(RelationshipBase<?, ?, ?> relationship) {
|
704
|
// TODO
|
705
|
return null;
|
706
|
}
|
707
|
|
708
|
/**
|
709
|
* Returns the database key of an object in the given relationship.
|
710
|
* @param relationship {@link RelationshipBase RelationshipBase}.
|
711
|
* @param state {@link PesiExportState PesiExportState}.
|
712
|
* @param isFrom A boolean value indicating whether the database key of the parent or child in this relationship is searched. <code>true</code> means the child is searched. <code>false</code> means the parent is searched.
|
713
|
* @return The database key of an object in the given relationship.
|
714
|
*/
|
715
|
private static Integer getObjectFk(RelationshipBase<?, ?, ?> relationship, PesiExportState state, boolean isFrom) {
|
716
|
TaxonBase<?> taxonBase = null;
|
717
|
if (relationship.isInstanceOf(TaxonRelationship.class)) {
|
718
|
TaxonRelationship tr = (TaxonRelationship)relationship;
|
719
|
taxonBase = (isFrom) ? tr.getFromTaxon(): tr.getToTaxon();
|
720
|
|
721
|
// } else if (relationship.isInstanceOf(SynonymRelationship.class)) {
|
722
|
// SynonymRelationship sr = (SynonymRelationship)relationship;
|
723
|
// taxonBase = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon();
|
724
|
} else if (relationship.isInstanceOf(NameRelationship.class) || relationship.isInstanceOf(HybridRelationship.class)) {
|
725
|
if (isFrom){
|
726
|
return state.getDbId(state.getCurrentFromObject());
|
727
|
}else{
|
728
|
return state.getDbId(state.getCurrentToObject());
|
729
|
}
|
730
|
}
|
731
|
if (taxonBase != null) {
|
732
|
if (! isPesiTaxon(taxonBase)){
|
733
|
logger.warn("Related taxonBase is not a PESI taxon. Taxon: " + taxonBase.getId() + "/" + taxonBase.getUuid() + "; TaxonRel: " + relationship.getId() + "(" + relationship.getType().getTitleCache() + ")");
|
734
|
return null;
|
735
|
}else{
|
736
|
return state.getDbId(taxonBase);
|
737
|
}
|
738
|
|
739
|
}
|
740
|
logger.warn("No taxon found in state for relationship: " + relationship.toString());
|
741
|
return null;
|
742
|
}
|
743
|
|
744
|
/**
|
745
|
* Returns the <code>RankFk</code> attribute.
|
746
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
747
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
748
|
* @return The <code>RankFk</code> attribute.
|
749
|
* @see MethodMapper
|
750
|
*/
|
751
|
private static Integer getRankFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode) {
|
752
|
Integer result = null;
|
753
|
if (nomenclaturalCode != null) {
|
754
|
if (taxonName != null && taxonName.getRank() == null) {
|
755
|
logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
756
|
}
|
757
|
result = PesiTransformer.rank2RankId(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));
|
758
|
if (result == null) {
|
759
|
logger.warn("Rank could not be determined for PESI-Kingdom-Id " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode) + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
760
|
}
|
761
|
}
|
762
|
return result;
|
763
|
}
|
764
|
|
765
|
/**
|
766
|
* Returns the <code>RankCache</code> attribute.
|
767
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
768
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
769
|
* @param state
|
770
|
* @return The <code>RankCache</code> attribute.
|
771
|
* @see MethodMapper
|
772
|
*/
|
773
|
private static String getRankCache(TaxonName taxonName, NomenclaturalCode nomenclaturalCode, PesiExportState state) {
|
774
|
if (nomenclaturalCode != null) {
|
775
|
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));
|
776
|
}else{
|
777
|
logger.warn("No nomenclatural code defined for rank cache search");
|
778
|
return null;
|
779
|
}
|
780
|
}
|
781
|
|
782
|
/**
|
783
|
* Returns the CDM to PESI specific export mappings.
|
784
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
785
|
*/
|
786
|
PesiExportMapping getMapping() {
|
787
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
788
|
|
789
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getTaxonFk1", standardMethodParameter, PesiExportState.class));
|
790
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getTaxonFk2", standardMethodParameter, PesiExportState.class));
|
791
|
mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this));
|
792
|
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this, RelationshipBase.class, PesiExportState.class));
|
793
|
mapping.addMapper(MethodMapper.NewInstance("Notes", this));
|
794
|
|
795
|
return mapping;
|
796
|
}
|
797
|
|
798
|
}
|