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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.pesi.faunaEuropaea;
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import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.A_AUCT;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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.SynonymRelationshipType;
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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.profiler.ProfilerController;
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/**
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* @author a.babadshanjan
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* @created 12.05.2009
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* @version 1.0
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*/
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@Component
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public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase {
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public static final String OS_NAMESPACE_TAXON = "Taxon";
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaRelTaxonIncludeImport.class);
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//private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database
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//private static final String acceptedTaxonUUID = "E23E6295-836A-4332-BF72-7D29949C7C60"; //faunaEu_1_3
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private static final String acceptedTaxonUUID = "BB9CDF6C-BBA3-4AC7-A3FD-648A14F518A0"; //for faunEu (2.4)
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private Reference<?> sourceRef;
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private static String ALL_SYNONYM_FROM_CLAUSE = " FROM Taxon INNER JOIN Taxon AS Parent " +
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" ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +
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" WHERE (Taxon.TAX_VALID = 0) " +
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" AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL)";
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean doCheck(FaunaEuropaeaImportState state) {
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boolean result = true;
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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logger.warn("Checking for Taxa not yet fully implemented");
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result &= checkTaxonStatus(fauEuConfig);
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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protected boolean isIgnore(FaunaEuropaeaImportState state) {
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return ! (state.getConfig().isDoTaxonomicallyIncluded() ||
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state.getConfig().isDoMisappliedNames() || state.getConfig().isDoHeterotypicSynonyms());
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}
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private boolean checkTaxonStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
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boolean result = true;
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// try {
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Source source = fauEuConfig.getSource();
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String sqlStr = "";
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ResultSet rs = source.getResultSet(sqlStr);
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return result;
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// } catch (SQLException e) {
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// e.printStackTrace();
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// return false;
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// }
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}
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protected void doInvoke(FaunaEuropaeaImportState state) {
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/*logger.warn("Start RelTaxon doInvoke");
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ProfilerController.memorySnapshot();
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*/
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Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
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MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);
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authorStore.makeEmpty();
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if(logger.isInfoEnabled()) { logger.info("Start making relationships..."); }
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TransactionStatus txStatus = startTransaction();
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// the uuid of an accepted taxon is needed here. any accepted taxon will do.
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TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
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sourceRef = taxon.getSec();
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Classification tree = getClassificationFor(state, sourceRef);
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commitTransaction(txStatus);
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/*
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logger.warn("Before processParentsChildren");
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ProfilerController.memorySnapshot();
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*/
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if (state.getConfig().isDoTaxonomicallyIncluded()) {
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processParentsChildren(state);
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}
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/*
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logger.warn("Before processMissappliedNames");
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ProfilerController.memorySnapshot();
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*/
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if (state.getConfig().isDoMisappliedNames()) {
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processMisappliedNames(state);
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}
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/*
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logger.warn("Before heterotypic synonyms");
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ProfilerController.memorySnapshot();
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*/
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if (state.getConfig().isDoHeterotypicSynonyms()) {
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if(logger.isInfoEnabled()) {
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logger.info("Start making heterotypic synonym relationships...");
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}
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processHeterotypicSynonyms(state, ALL_SYNONYM_FROM_CLAUSE);
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}
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/*
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logger.warn("End RelTaxon doInvoke");
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ProfilerController.memorySnapshot();
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*/
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logger.info("End making taxa...");
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return;
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}
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/** Retrieve child-parent uuid map from CDM DB */
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private void processParentsChildren(FaunaEuropaeaImportState state) {
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int limit = state.getConfig().getLimitSave();
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TransactionStatus txStatus = null;
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Map<UUID, UUID> childParentMap = null;
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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Source source = fauEuConfig.getSource();
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int i = 0;
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String selectCount =
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" SELECT count(*) ";
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String selectColumns = " SELECT Taxon.UUID AS ChildUuid, Parent.UUID AS ParentUuid ";
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String fromClause = " FROM Taxon INNER JOIN Taxon AS Parent " +
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" ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +
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" WHERE (Taxon.TAX_VALID <> 0) AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL )";
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String orderClause = " ORDER BY Taxon.TAX_RNK_ID ASC";
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String countQuery =
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selectCount + fromClause;
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String selectQuery =
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selectColumns + fromClause + orderClause;
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if(logger.isInfoEnabled()) { logger.info("Start making taxonomically included relationships..."); }
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try {
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ResultSet rs = source.getResultSet(countQuery);
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rs.next();
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int count = rs.getInt(1);
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rs = source.getResultSet(selectQuery);
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if (logger.isInfoEnabled()) {
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logger.info("Number of rows: " + count);
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logger.info("Count Query: " + countQuery);
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logger.info("Select Query: " + selectQuery);
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}
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while (rs.next()) {
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if ((i++ % limit) == 0) {
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txStatus = startTransaction();
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childParentMap = new HashMap<UUID, UUID>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("Taxonomically included retrieved: " + (i-1));
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}
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}
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String childUuidStr = rs.getString("ChildUuid");
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String parentUuidStr = rs.getString("ParentUuid");
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UUID childUuid = UUID.fromString(childUuidStr);
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UUID parentUuid = UUID.fromString(parentUuidStr);
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if (!childParentMap.containsKey(childUuid)) {
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childParentMap.put(childUuid, parentUuid);
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} else {
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if(logger.isDebugEnabled()) {
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logger.debug("Duplicated child UUID (" + childUuid + ")");
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}
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}
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if (((i % limit) == 0 && i != 1 ) || i == count ) {
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createAndCommitParentChildRelationships(
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state, txStatus, childParentMap);
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childParentMap = null;
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Transaction committed");
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}
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}
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}
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if (childParentMap != null){
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logger.info("processParentsChildren... last commit");
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createAndCommitParentChildRelationships(
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state, txStatus, childParentMap);
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childParentMap = null;
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}
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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state.setUnsuccessfull();
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}
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return;
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}
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private Map<UUID, UUID> createAndCommitParentChildRelationships(
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FaunaEuropaeaImportState state, TransactionStatus txStatus,
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Map<UUID, UUID> childParentMap) {
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createParentChildRelationships(state, childParentMap);
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commitTransaction(txStatus);
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return childParentMap;
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}
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/** Retrieve misapplied name / accepted taxon uuid map from CDM DB */
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private void processMisappliedNames(FaunaEuropaeaImportState state) {
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int limit = state.getConfig().getLimitSave();
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TransactionStatus txStatus = null;
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Map<UUID, UUID> childParentMap = null;
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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Source source = fauEuConfig.getSource();
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int i = 0;
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String selectCount =
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" SELECT count(*) ";
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String selectColumns = " SELECT Taxon.UUID AS MisappliedUuid, Parent.UUID AS AcceptedUuid ";
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String fromClause = " FROM Taxon INNER JOIN Taxon AS Parent " +
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" ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +
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" WHERE (Taxon.TAX_VALID = 0) AND (Taxon.TAX_AUT_ID = " + A_AUCT + ")";
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String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";
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String countQuery =
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selectCount + fromClause;
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String selectQuery =
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selectColumns + fromClause + orderClause;
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if(logger.isInfoEnabled()) { logger.info("Start making misapplied name relationships..."); }
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try {
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ResultSet rs = source.getResultSet(countQuery);
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rs.next();
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int count = rs.getInt(1);
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rs = source.getResultSet(selectQuery);
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if (logger.isInfoEnabled()) {
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logger.info("Number of rows: " + count);
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logger.info("Count Query: " + countQuery);
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logger.info("Select Query: " + selectQuery);
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}
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while (rs.next()) {
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if ((i++ % limit) == 0) {
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txStatus = startTransaction();
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childParentMap = new HashMap<UUID, UUID>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("Misapplied names retrieved: " + (i-1) );
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}
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}
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String childUuidStr = rs.getString("MisappliedUuid");
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String parentUuidStr = rs.getString("AcceptedUuid");
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UUID childUuid = UUID.fromString(childUuidStr);
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UUID parentUuid = UUID.fromString(parentUuidStr);
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if (!childParentMap.containsKey(childUuid)) {
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childParentMap.put(childUuid, parentUuid);
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} else {
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if(logger.isDebugEnabled()) {
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logger.debug("Duplicated child UUID (" + childUuid + ")");
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}
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}
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if (((i % limit) == 0 && i != 1 ) || i == count) {
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createAndCommitMisappliedNameRelationships(state, txStatus,
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childParentMap);
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childParentMap = null;
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339
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Transaction committed");
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}
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}
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}
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if (childParentMap != null){
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logger.info("processMisappliedNames... last commit");
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createAndCommitMisappliedNameRelationships(state, txStatus,
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childParentMap);
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childParentMap = null;
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}
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351
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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state.setUnsuccessfull();
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}
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356
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return;
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357
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}
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358
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359
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private void createAndCommitMisappliedNameRelationships(
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FaunaEuropaeaImportState state, TransactionStatus txStatus,
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Map<UUID, UUID> childParentMap) {
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362
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createMisappliedNameRelationships(state, childParentMap);
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commitTransaction(txStatus);
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364
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}
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365
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366
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367
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368
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/** Retrieve synonyms from FauEuDB DB */
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369
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private void processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {
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370
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371
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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372
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Source source = fauEuConfig.getSource();
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373
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374
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String selectCount =
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375
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" SELECT count(*) ";
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376
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377
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String selectColumns = " SELECT Taxon.UUID AS SynonymUuid, Parent.UUID AS AcceptedUuid ";
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378
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379
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String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";
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380
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381
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String countQuery =
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382
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selectCount + fromClause;
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383
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384
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String selectQuery =
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385
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selectColumns + fromClause + orderClause;
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386
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logger.debug(selectQuery);
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387
|
|
388
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try {
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389
|
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390
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ResultSet rs = source.getResultSet(countQuery);
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391
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rs.next();
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392
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int count = rs.getInt(1);
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393
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394
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rs = source.getResultSet(selectQuery);
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395
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|
396
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if (logger.isInfoEnabled()) {
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397
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logger.info("Number of rows: " + count);
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398
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logger.info("Count Query: " + countQuery);
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399
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logger.info("Select Query: " + selectQuery);
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400
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}
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401
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402
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storeSynonymRelationships(rs, count, state);
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403
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404
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} catch (SQLException e) {
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405
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logger.error("SQLException:" + e);
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406
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state.setUnsuccessfull();
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407
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}
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408
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return;
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409
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}
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410
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|
411
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412
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413
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414
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private void storeSynonymRelationships(ResultSet rs, int count, FaunaEuropaeaImportState state)
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415
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throws SQLException {
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416
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417
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TransactionStatus txStatus = null;
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418
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Map<UUID, UUID> synonymAcceptedMap = null;
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419
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int i = 0;
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420
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int limit = state.getConfig().getLimitSave();
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421
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422
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while (rs.next()) {
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423
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424
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if ((i++ % limit) == 0) {
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425
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426
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txStatus = startTransaction();
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427
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synonymAcceptedMap = new HashMap<UUID, UUID>(limit);
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428
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429
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if(logger.isInfoEnabled()) {
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430
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logger.info("Synonyms retrieved: " + (i-1));
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431
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}
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432
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}
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433
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434
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String synonymUuidStr = rs.getString("SynonymUuid");
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435
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String acceptedUuidStr = rs.getString("AcceptedUuid");
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436
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UUID synonymUuid = UUID.fromString(synonymUuidStr);
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437
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UUID acceptedUuid = UUID.fromString(acceptedUuidStr);
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438
|
|
439
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if (!synonymAcceptedMap.containsKey(synonymUuid)) {
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440
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441
|
synonymAcceptedMap.put(synonymUuid, acceptedUuid);
|
442
|
|
443
|
} else {
|
444
|
if(logger.isDebugEnabled()) {
|
445
|
logger.debug("Duplicated synonym UUID (" + synonymUuid + ")");
|
446
|
}
|
447
|
}
|
448
|
|
449
|
if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
450
|
|
451
|
synonymAcceptedMap = createAndCommitHeterotypicSynonyms(state,
|
452
|
txStatus, synonymAcceptedMap);
|
453
|
|
454
|
if(logger.isInfoEnabled()) {
|
455
|
logger.info("i = " + i + " - Transaction committed");
|
456
|
}
|
457
|
}
|
458
|
}
|
459
|
if (synonymAcceptedMap != null){
|
460
|
logger.info("processHeterotypicSynonyms... last commit");
|
461
|
synonymAcceptedMap = createAndCommitHeterotypicSynonyms(state,
|
462
|
txStatus, synonymAcceptedMap);
|
463
|
}
|
464
|
return;
|
465
|
}
|
466
|
|
467
|
private Map<UUID, UUID> createAndCommitHeterotypicSynonyms(
|
468
|
FaunaEuropaeaImportState state, TransactionStatus txStatus,
|
469
|
Map<UUID, UUID> synonymAcceptedMap) {
|
470
|
createHeterotypicSynonyms(state, synonymAcceptedMap);
|
471
|
|
472
|
synonymAcceptedMap = null;
|
473
|
commitTransaction(txStatus);
|
474
|
return synonymAcceptedMap;
|
475
|
}
|
476
|
|
477
|
|
478
|
|
479
|
|
480
|
|
481
|
/* Creates parent-child relationships.
|
482
|
* Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
483
|
*/
|
484
|
private void createParentChildRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> childParentMap) {
|
485
|
//gets the taxon "Hydroscaphidae"(family)
|
486
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
487
|
sourceRef = taxon.getSec();
|
488
|
int limit = state.getConfig().getLimitSave();
|
489
|
|
490
|
Classification tree = getClassificationFor(state, sourceRef);
|
491
|
|
492
|
Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);
|
493
|
|
494
|
Set<UUID> childKeysSet = childParentMap.keySet();
|
495
|
Set<UUID> parentValuesSet = new HashSet<UUID>(childParentMap.values());
|
496
|
|
497
|
if (logger.isTraceEnabled()) {
|
498
|
logger.trace("Start reading children and parents");
|
499
|
}
|
500
|
List<TaxonBase> children = getTaxonService().find(childKeysSet);
|
501
|
List<TaxonBase> parents = getTaxonService().find(parentValuesSet);
|
502
|
Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>(parents.size());
|
503
|
|
504
|
for (TaxonBase taxonBase : parents){
|
505
|
parentsMap.put(taxonBase.getUuid(), taxonBase);
|
506
|
}
|
507
|
|
508
|
if (logger.isTraceEnabled()) {
|
509
|
logger.debug("End reading children and parents");
|
510
|
for (UUID uuid : childKeysSet) {
|
511
|
logger.trace("child uuid query: " + uuid);
|
512
|
}
|
513
|
for (UUID uuid : parentValuesSet) {
|
514
|
logger.trace("parent uuid query: " + uuid);
|
515
|
}
|
516
|
for (TaxonBase tb : children) {
|
517
|
logger.trace("child uuid result: " + tb.getUuid());
|
518
|
}
|
519
|
for (TaxonBase tb : parents) {
|
520
|
logger.trace("parent uuid result: " + tb.getUuid());
|
521
|
}
|
522
|
}
|
523
|
|
524
|
UUID mappedParentUuid = null;
|
525
|
UUID childUuid = null;
|
526
|
|
527
|
for (TaxonBase child : children) {
|
528
|
|
529
|
try {
|
530
|
Taxon childTaxon = child.deproxy(child, Taxon.class);
|
531
|
childUuid = childTaxon.getUuid();
|
532
|
mappedParentUuid = childParentMap.get(childUuid);
|
533
|
TaxonBase parent = null;
|
534
|
|
535
|
TaxonBase potentialParent = parentsMap.get(mappedParentUuid);
|
536
|
// for (TaxonBase potentialParent : parents ) {
|
537
|
// parentUuid = potentialParent.getUuid();
|
538
|
// if(parentUuid.equals(mappedParentUuid)) {
|
539
|
parent = potentialParent;
|
540
|
if (logger.isDebugEnabled()) {
|
541
|
logger.debug("Parent (" + mappedParentUuid + ") found for child (" + childUuid + ")");
|
542
|
}
|
543
|
// break;
|
544
|
// }
|
545
|
// }
|
546
|
|
547
|
Taxon parentTaxon = parent.deproxy(parent, Taxon.class);
|
548
|
|
549
|
if (childTaxon != null && parentTaxon != null) {
|
550
|
|
551
|
tree.addParentChild(parentTaxon, childTaxon, sourceRef, null);
|
552
|
|
553
|
if (logger.isDebugEnabled()) {
|
554
|
logger.debug("Parent-child (" + mappedParentUuid + "-" + childUuid +
|
555
|
") relationship created");
|
556
|
}
|
557
|
if (childTaxon != null && !childSet.contains(childTaxon)) {
|
558
|
|
559
|
childSet.add(childTaxon);
|
560
|
|
561
|
if (logger.isTraceEnabled()) {
|
562
|
logger.trace("Child taxon (" + childUuid + ") added to Set");
|
563
|
}
|
564
|
|
565
|
} else {
|
566
|
if (logger.isDebugEnabled()) {
|
567
|
logger.debug("Duplicated child taxon (" + childUuid + ")");
|
568
|
}
|
569
|
}
|
570
|
} else {
|
571
|
if (logger.isDebugEnabled()) {
|
572
|
logger.debug("Parent(" + mappedParentUuid + ") or child (" + childUuid + " is null");
|
573
|
}
|
574
|
}
|
575
|
|
576
|
} catch (Exception e) {
|
577
|
logger.error("Error creating taxonomically included relationship parent-child (" +
|
578
|
mappedParentUuid + " <----> " + childUuid + ")", e);
|
579
|
}
|
580
|
|
581
|
}
|
582
|
if (logger.isTraceEnabled()) {
|
583
|
logger.trace("Start saving childSet");
|
584
|
}
|
585
|
getTaxonService().save(childSet);
|
586
|
if (logger.isTraceEnabled()) {
|
587
|
logger.trace("End saving childSet");
|
588
|
}
|
589
|
|
590
|
parentValuesSet = null;
|
591
|
childSet = null;
|
592
|
children = null;
|
593
|
parents = null;
|
594
|
tree = null;
|
595
|
|
596
|
return;
|
597
|
}
|
598
|
|
599
|
/* Creates misapplied name relationships.
|
600
|
* Misapplied name-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
601
|
*/
|
602
|
private void createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
603
|
|
604
|
//gets the taxon "Hydroscaphidae" (family)
|
605
|
|
606
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
607
|
sourceRef = taxon.getSec();
|
608
|
int limit = state.getConfig().getLimitSave();
|
609
|
|
610
|
Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);
|
611
|
|
612
|
Set<UUID> misappliedNamesSet = fromToMap.keySet();
|
613
|
Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());
|
614
|
|
615
|
if (logger.isTraceEnabled()) {
|
616
|
logger.trace("Start reading misapplied names and accepted taxa");
|
617
|
}
|
618
|
List<TaxonBase> misappliedNames = getTaxonService().find(misappliedNamesSet);
|
619
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaSet);
|
620
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
621
|
for (TaxonBase taxonBase : acceptedTaxa){
|
622
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
623
|
}
|
624
|
|
625
|
if (logger.isTraceEnabled()) {
|
626
|
logger.info("End reading misapplied names and accepted taxa");
|
627
|
for (UUID uuid : misappliedNamesSet) {
|
628
|
logger.trace("misapplied name uuid query: " + uuid);
|
629
|
}
|
630
|
for (UUID uuid : acceptedTaxaSet) {
|
631
|
logger.trace("accepted taxon uuid query: " + uuid);
|
632
|
}
|
633
|
for (TaxonBase tb : misappliedNames) {
|
634
|
logger.trace("misapplied name uuid result: " + tb.getUuid());
|
635
|
}
|
636
|
for (TaxonBase tb : acceptedTaxa) {
|
637
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
638
|
}
|
639
|
}
|
640
|
|
641
|
UUID mappedAcceptedTaxonUuid = null;
|
642
|
UUID misappliedNameUuid = null;
|
643
|
Taxon misappliedNameTaxon = null;
|
644
|
TaxonBase acceptedTaxonBase = null;
|
645
|
Taxon acceptedTaxon = null;
|
646
|
|
647
|
for (TaxonBase misappliedName : misappliedNames) {
|
648
|
|
649
|
try {
|
650
|
misappliedNameTaxon = misappliedName.deproxy(misappliedName, Taxon.class);
|
651
|
misappliedNameUuid = misappliedNameTaxon.getUuid();
|
652
|
mappedAcceptedTaxonUuid = fromToMap.get(misappliedNameUuid);
|
653
|
acceptedTaxonBase = null;
|
654
|
|
655
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
656
|
if (logger.isDebugEnabled()) {
|
657
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + misappliedNameUuid + ")");
|
658
|
}
|
659
|
|
660
|
acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);
|
661
|
|
662
|
if (misappliedNameTaxon != null && acceptedTaxon != null) {
|
663
|
|
664
|
acceptedTaxon.addMisappliedName(misappliedNameTaxon, sourceRef, null);
|
665
|
|
666
|
if (logger.isDebugEnabled()) {
|
667
|
logger.debug("Accepted taxon / misapplied name (" + mappedAcceptedTaxonUuid + "-" + misappliedNameUuid +
|
668
|
") relationship created");
|
669
|
}
|
670
|
if (!misappliedNameSet.contains(misappliedNameTaxon)) {
|
671
|
|
672
|
misappliedNameSet.add(misappliedNameTaxon);
|
673
|
|
674
|
if (logger.isTraceEnabled()) {
|
675
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
676
|
}
|
677
|
|
678
|
} else {
|
679
|
if (logger.isDebugEnabled()) {
|
680
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
681
|
}
|
682
|
}
|
683
|
} else {
|
684
|
if (logger.isDebugEnabled()) {
|
685
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + misappliedNameUuid + " is null");
|
686
|
}
|
687
|
}
|
688
|
|
689
|
if (misappliedNameTaxon != null && !misappliedNameSet.contains(misappliedNameTaxon)) {
|
690
|
misappliedNameSet.add(misappliedNameTaxon);
|
691
|
if (logger.isTraceEnabled()) {
|
692
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
693
|
}
|
694
|
} else {
|
695
|
if (logger.isDebugEnabled()) {
|
696
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
697
|
}
|
698
|
}
|
699
|
|
700
|
} catch (Exception e) {
|
701
|
logger.error("Error creating misapplied name relationship accepted taxon-misapplied name (" +
|
702
|
mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + ")", e);
|
703
|
}
|
704
|
|
705
|
}
|
706
|
if (logger.isTraceEnabled()) {
|
707
|
logger.trace("Start saving misappliedNameSet");
|
708
|
}
|
709
|
getTaxonService().save(misappliedNameSet);
|
710
|
if (logger.isTraceEnabled()) {
|
711
|
logger.trace("End saving misappliedNameSet");
|
712
|
}
|
713
|
|
714
|
acceptedTaxaSet = null;
|
715
|
misappliedNameSet = null;
|
716
|
misappliedNames = null;
|
717
|
acceptedTaxa = null;
|
718
|
|
719
|
return;
|
720
|
}
|
721
|
|
722
|
|
723
|
/* Creates heterotypic synonym relationships.
|
724
|
* Synonym-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
725
|
*/
|
726
|
private void createHeterotypicSynonyms(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
727
|
|
728
|
int limit = state.getConfig().getLimitSave();
|
729
|
|
730
|
Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);
|
731
|
|
732
|
Set<UUID> synonymUuidSet = fromToMap.keySet();
|
733
|
Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());
|
734
|
|
735
|
if (logger.isTraceEnabled()) {
|
736
|
logger.trace("Reading synonym names and accepted taxa...");
|
737
|
}
|
738
|
List<TaxonBase> synonyms = getTaxonService().find(synonymUuidSet);
|
739
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaUuidSet);
|
740
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
741
|
for (TaxonBase taxonBase : acceptedTaxa){
|
742
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
743
|
}
|
744
|
|
745
|
if (logger.isTraceEnabled()) {
|
746
|
logger.trace("End reading synonyms names and accepted taxa");
|
747
|
for (UUID uuid : synonymUuidSet) {
|
748
|
logger.trace("synonym uuid query: " + uuid);
|
749
|
}
|
750
|
for (UUID uuid : acceptedTaxaUuidSet) {
|
751
|
logger.trace("accepted taxon uuid query: " + uuid);
|
752
|
}
|
753
|
for (TaxonBase tb : synonyms) {
|
754
|
logger.trace("synonym uuid result: " + tb.getUuid());
|
755
|
}
|
756
|
for (TaxonBase tb : acceptedTaxa) {
|
757
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
758
|
}
|
759
|
}
|
760
|
|
761
|
UUID mappedAcceptedTaxonUuid = null;
|
762
|
UUID synonymUuid = null;
|
763
|
Synonym synonym = null;
|
764
|
TaxonBase acceptedTaxonBase = null;
|
765
|
Taxon acceptedTaxon = null;
|
766
|
|
767
|
for (TaxonBase synonymTaxonBase : synonyms) {
|
768
|
|
769
|
try {
|
770
|
//check for misapplied names with nec (in Fauna Europaea they have a synonym relationship to the accepted taxon)
|
771
|
if (synonymTaxonBase instanceof Taxon ){
|
772
|
if (((Taxon)synonymTaxonBase).isMisapplication()){
|
773
|
if (logger.isDebugEnabled()) {
|
774
|
logger.debug("misapplied name with exclusion" + synonymTaxonBase.getTitleCache());
|
775
|
}
|
776
|
}
|
777
|
continue;
|
778
|
}
|
779
|
synonym = CdmBase.deproxy(synonymTaxonBase, Synonym.class);
|
780
|
synonymUuid = synonym.getUuid();
|
781
|
mappedAcceptedTaxonUuid = fromToMap.get(synonymUuid);
|
782
|
acceptedTaxonBase = null;
|
783
|
|
784
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
785
|
if (logger.isDebugEnabled()) {
|
786
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + synonymUuid + ")");
|
787
|
}
|
788
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxonBase, Taxon.class);
|
789
|
|
790
|
if (synonym != null && acceptedTaxon != null) {
|
791
|
|
792
|
//TODO: in case original genus exists must add synonym to original genus instead of to accepted taxon
|
793
|
acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
794
|
|
795
|
if (logger.isDebugEnabled()) {
|
796
|
logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid +
|
797
|
") relationship created");
|
798
|
}
|
799
|
if (synonym != null && !synonymSet.contains(synonym)) {
|
800
|
|
801
|
synonymSet.add(synonym);
|
802
|
|
803
|
if (logger.isTraceEnabled()) {
|
804
|
logger.trace("Synonym (" + synonymUuid + ") added to Set");
|
805
|
}
|
806
|
|
807
|
} else {
|
808
|
if (logger.isDebugEnabled()) {
|
809
|
logger.debug("Duplicated synonym (" + synonymUuid + ")");
|
810
|
}
|
811
|
}
|
812
|
} else {
|
813
|
if (logger.isDebugEnabled()) {
|
814
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + synonymUuid + " is null");
|
815
|
}
|
816
|
}
|
817
|
} catch (Exception e) {
|
818
|
logger.error("Error creating synonym relationship: accepted taxon-synonym (" +
|
819
|
mappedAcceptedTaxonUuid + "-" + synonymUuid + ": "+ synonymTaxonBase.getTitleCache() +")", e);
|
820
|
}
|
821
|
}
|
822
|
if (logger.isTraceEnabled()) {
|
823
|
logger.trace("Start saving synonymSet");
|
824
|
}
|
825
|
getTaxonService().save(synonymSet);
|
826
|
if (logger.isTraceEnabled()) {
|
827
|
logger.trace("End saving synonymSet");
|
828
|
}
|
829
|
|
830
|
acceptedTaxaUuidSet = null;
|
831
|
synonymSet = null;
|
832
|
synonyms = null;
|
833
|
acceptedTaxa = null;
|
834
|
|
835
|
return;
|
836
|
}
|
837
|
|
838
|
}
|