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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.faunaEuropaea;
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import static eu.etaxonomy.cdm.io.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.io.profiler.ProfilerController;
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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.ReferenceBase;
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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.model.taxon.TaxonomicTree;
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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 = "EC765B43-E909-4D32-8822-34DA186424E8"; // any accepted taxon uuid, taken from original fauna europaea database
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private ReferenceBase<?> 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 boolean doInvoke(FaunaEuropaeaImportState state) {
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boolean success = true;
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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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TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);
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commitTransaction(txStatus);
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//ProfilerController.memorySnapshot();
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if (state.getConfig().isDoTaxonomicallyIncluded()) {
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success = processParentsChildren(state);
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}
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//ProfilerController.memorySnapshot();
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if (state.getConfig().isDoMisappliedNames()) {
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success = processMisappliedNames(state);
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}
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//ProfilerController.memorySnapshot();
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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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success = processHeterotypicSynonyms(state, ALL_SYNONYM_FROM_CLAUSE);
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}
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//ProfilerController.memorySnapshot();
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logger.info("End making taxa...");
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return success;
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}
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/** Retrieve child-parent uuid map from CDM DB */
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private boolean 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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boolean success = true;
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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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success = createParentChildRelationships(state, childParentMap);
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childParentMap = null;
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commitTransaction(txStatus);
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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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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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success = false;
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}
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return success;
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}
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/** Retrieve misapplied name / accepted taxon uuid map from CDM DB */
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private boolean 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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boolean success = true;
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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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success = createMisappliedNameRelationships(state, childParentMap);
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childParentMap = null;
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commitTransaction(txStatus);
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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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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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success = false;
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}
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return success;
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}
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/** Retrieve synonyms from FauEuDB DB */
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private boolean processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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Source source = fauEuConfig.getSource();
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boolean success = true;
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String selectCount =
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" SELECT count(*) ";
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String selectColumns = " SELECT Taxon.UUID AS SynonymUuid, Parent.UUID AS AcceptedUuid ";
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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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logger.debug(selectQuery);
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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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success = storeSynonymRelationships(rs, count, state);
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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success = false;
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}
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return success;
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}
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private boolean storeSynonymRelationships(ResultSet rs, int count, FaunaEuropaeaImportState state)
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throws SQLException {
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TransactionStatus txStatus = null;
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Map<UUID, UUID> synonymAcceptedMap = null;
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int i = 0;
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boolean success = true;
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int limit = state.getConfig().getLimitSave();
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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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synonymAcceptedMap = new HashMap<UUID, UUID>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("Synonyms retrieved: " + (i-1));
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}
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}
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String synonymUuidStr = rs.getString("SynonymUuid");
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String acceptedUuidStr = rs.getString("AcceptedUuid");
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UUID synonymUuid = UUID.fromString(synonymUuidStr);
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UUID acceptedUuid = UUID.fromString(acceptedUuidStr);
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if (!synonymAcceptedMap.containsKey(synonymUuid)) {
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synonymAcceptedMap.put(synonymUuid, acceptedUuid);
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} else {
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if(logger.isDebugEnabled()) {
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logger.debug("Duplicated synonym UUID (" + synonymUuid + ")");
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}
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}
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if (((i % limit) == 0 && i != 1 ) || i == count) {
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success = createHeterotypicSynonyms(state, synonymAcceptedMap);
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synonymAcceptedMap = null;
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commitTransaction(txStatus);
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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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return success;
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}
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/* Creates parent-child relationships.
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* Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
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*/
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private boolean createParentChildRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> childParentMap) {
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//gets the taxon "Hydroscaphidae"(family)
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TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
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sourceRef = taxon.getSec();
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boolean success = true;
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int limit = state.getConfig().getLimitSave();
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TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);
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Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);
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Set<UUID> childKeysSet = childParentMap.keySet();
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Set<UUID> parentValuesSet = new HashSet<UUID>(childParentMap.values());
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442
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443
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if (logger.isTraceEnabled()) {
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444
|
logger.trace("Start reading children and parents");
|
445
|
}
|
446
|
List<TaxonBase> children = getTaxonService().find(childKeysSet);
|
447
|
List<TaxonBase> parents = getTaxonService().find(parentValuesSet);
|
448
|
Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>(parents.size());
|
449
|
for (TaxonBase taxonBase : parents){
|
450
|
parentsMap.put(taxonBase.getUuid(), taxonBase);
|
451
|
}
|
452
|
|
453
|
if (logger.isTraceEnabled()) {
|
454
|
logger.debug("End reading children and parents");
|
455
|
for (UUID uuid : childKeysSet) {
|
456
|
logger.trace("child uuid query: " + uuid);
|
457
|
}
|
458
|
for (UUID uuid : parentValuesSet) {
|
459
|
logger.trace("parent uuid query: " + uuid);
|
460
|
}
|
461
|
for (TaxonBase tb : children) {
|
462
|
logger.trace("child uuid result: " + tb.getUuid());
|
463
|
}
|
464
|
for (TaxonBase tb : parents) {
|
465
|
logger.trace("parent uuid result: " + tb.getUuid());
|
466
|
}
|
467
|
}
|
468
|
|
469
|
UUID mappedParentUuid = null;
|
470
|
UUID childUuid = null;
|
471
|
|
472
|
for (TaxonBase child : children) {
|
473
|
|
474
|
try {
|
475
|
Taxon childTaxon = child.deproxy(child, Taxon.class);
|
476
|
childUuid = childTaxon.getUuid();
|
477
|
mappedParentUuid = childParentMap.get(childUuid);
|
478
|
TaxonBase parent = null;
|
479
|
|
480
|
TaxonBase potentialParent = parentsMap.get(mappedParentUuid);
|
481
|
// for (TaxonBase potentialParent : parents ) {
|
482
|
// parentUuid = potentialParent.getUuid();
|
483
|
// if(parentUuid.equals(mappedParentUuid)) {
|
484
|
parent = potentialParent;
|
485
|
if (logger.isDebugEnabled()) {
|
486
|
logger.debug("Parent (" + mappedParentUuid + ") found for child (" + childUuid + ")");
|
487
|
}
|
488
|
// break;
|
489
|
// }
|
490
|
// }
|
491
|
|
492
|
Taxon parentTaxon = parent.deproxy(parent, Taxon.class);
|
493
|
|
494
|
if (childTaxon != null && parentTaxon != null) {
|
495
|
|
496
|
tree.addParentChild(parentTaxon, childTaxon, sourceRef, null);
|
497
|
|
498
|
if (logger.isDebugEnabled()) {
|
499
|
logger.debug("Parent-child (" + mappedParentUuid + "-" + childUuid +
|
500
|
") relationship created");
|
501
|
}
|
502
|
if (childTaxon != null && !childSet.contains(childTaxon)) {
|
503
|
|
504
|
childSet.add(childTaxon);
|
505
|
|
506
|
if (logger.isTraceEnabled()) {
|
507
|
logger.trace("Child taxon (" + childUuid + ") added to Set");
|
508
|
}
|
509
|
|
510
|
} else {
|
511
|
if (logger.isDebugEnabled()) {
|
512
|
logger.debug("Duplicated child taxon (" + childUuid + ")");
|
513
|
}
|
514
|
}
|
515
|
} else {
|
516
|
if (logger.isDebugEnabled()) {
|
517
|
logger.debug("Parent(" + mappedParentUuid + ") or child (" + childUuid + " is null");
|
518
|
}
|
519
|
}
|
520
|
|
521
|
} catch (Exception e) {
|
522
|
logger.error("Error creating taxonomically included relationship parent-child (" +
|
523
|
mappedParentUuid + "-" + childUuid + ")", e);
|
524
|
}
|
525
|
|
526
|
}
|
527
|
if (logger.isTraceEnabled()) {
|
528
|
logger.trace("Start saving childSet");
|
529
|
}
|
530
|
getTaxonService().save(childSet);
|
531
|
if (logger.isTraceEnabled()) {
|
532
|
logger.trace("End saving childSet");
|
533
|
}
|
534
|
|
535
|
parentValuesSet = null;
|
536
|
childSet = null;
|
537
|
children = null;
|
538
|
parents = null;
|
539
|
tree = null;
|
540
|
|
541
|
return success;
|
542
|
}
|
543
|
|
544
|
/* Creates misapplied name relationships.
|
545
|
* Misapplied name-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
546
|
*/
|
547
|
private boolean createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
548
|
|
549
|
//gets the taxon "Hydroscaphidae" (family)
|
550
|
|
551
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
552
|
sourceRef = taxon.getSec();
|
553
|
boolean success = true;
|
554
|
int limit = state.getConfig().getLimitSave();
|
555
|
|
556
|
Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);
|
557
|
|
558
|
Set<UUID> misappliedNamesSet = fromToMap.keySet();
|
559
|
Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());
|
560
|
|
561
|
if (logger.isTraceEnabled()) {
|
562
|
logger.trace("Start reading misapplied names and accepted taxa");
|
563
|
}
|
564
|
List<TaxonBase> misappliedNames = getTaxonService().find(misappliedNamesSet);
|
565
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaSet);
|
566
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
567
|
for (TaxonBase taxonBase : acceptedTaxa){
|
568
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
569
|
}
|
570
|
|
571
|
if (logger.isTraceEnabled()) {
|
572
|
logger.info("End reading misapplied names and accepted taxa");
|
573
|
for (UUID uuid : misappliedNamesSet) {
|
574
|
logger.trace("misapplied name uuid query: " + uuid);
|
575
|
}
|
576
|
for (UUID uuid : acceptedTaxaSet) {
|
577
|
logger.trace("accepted taxon uuid query: " + uuid);
|
578
|
}
|
579
|
for (TaxonBase tb : misappliedNames) {
|
580
|
logger.trace("misapplied name uuid result: " + tb.getUuid());
|
581
|
}
|
582
|
for (TaxonBase tb : acceptedTaxa) {
|
583
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
584
|
}
|
585
|
}
|
586
|
|
587
|
UUID mappedAcceptedTaxonUuid = null;
|
588
|
UUID misappliedNameUuid = null;
|
589
|
Taxon misappliedNameTaxon = null;
|
590
|
TaxonBase acceptedTaxonBase = null;
|
591
|
Taxon acceptedTaxon = null;
|
592
|
|
593
|
for (TaxonBase misappliedName : misappliedNames) {
|
594
|
|
595
|
try {
|
596
|
misappliedNameTaxon = misappliedName.deproxy(misappliedName, Taxon.class);
|
597
|
misappliedNameUuid = misappliedNameTaxon.getUuid();
|
598
|
mappedAcceptedTaxonUuid = fromToMap.get(misappliedNameUuid);
|
599
|
acceptedTaxonBase = null;
|
600
|
|
601
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
602
|
if (logger.isDebugEnabled()) {
|
603
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + misappliedNameUuid + ")");
|
604
|
}
|
605
|
|
606
|
acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);
|
607
|
|
608
|
if (misappliedNameTaxon != null && acceptedTaxon != null) {
|
609
|
|
610
|
acceptedTaxon.addMisappliedName(misappliedNameTaxon, sourceRef, null);
|
611
|
|
612
|
if (logger.isDebugEnabled()) {
|
613
|
logger.debug("Accepted taxon / misapplied name (" + mappedAcceptedTaxonUuid + "-" + misappliedNameUuid +
|
614
|
") relationship created");
|
615
|
}
|
616
|
if (!misappliedNameSet.contains(misappliedNameTaxon)) {
|
617
|
|
618
|
misappliedNameSet.add(misappliedNameTaxon);
|
619
|
|
620
|
if (logger.isTraceEnabled()) {
|
621
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
622
|
}
|
623
|
|
624
|
} else {
|
625
|
if (logger.isDebugEnabled()) {
|
626
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
627
|
}
|
628
|
}
|
629
|
} else {
|
630
|
if (logger.isDebugEnabled()) {
|
631
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + misappliedNameUuid + " is null");
|
632
|
}
|
633
|
}
|
634
|
|
635
|
if (misappliedNameTaxon != null && !misappliedNameSet.contains(misappliedNameTaxon)) {
|
636
|
misappliedNameSet.add(misappliedNameTaxon);
|
637
|
if (logger.isTraceEnabled()) {
|
638
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
639
|
}
|
640
|
} else {
|
641
|
if (logger.isDebugEnabled()) {
|
642
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
643
|
}
|
644
|
}
|
645
|
|
646
|
} catch (Exception e) {
|
647
|
logger.error("Error creating misapplied name relationship accepted taxon-misapplied name (" +
|
648
|
mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + ")", e);
|
649
|
}
|
650
|
|
651
|
}
|
652
|
if (logger.isTraceEnabled()) {
|
653
|
logger.trace("Start saving misappliedNameSet");
|
654
|
}
|
655
|
getTaxonService().save(misappliedNameSet);
|
656
|
if (logger.isTraceEnabled()) {
|
657
|
logger.trace("End saving misappliedNameSet");
|
658
|
}
|
659
|
|
660
|
acceptedTaxaSet = null;
|
661
|
misappliedNameSet = null;
|
662
|
misappliedNames = null;
|
663
|
acceptedTaxa = null;
|
664
|
|
665
|
return success;
|
666
|
}
|
667
|
|
668
|
|
669
|
/* Creates heterotypic synonym relationships.
|
670
|
* Synonym-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
671
|
*/
|
672
|
private boolean createHeterotypicSynonyms(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
673
|
|
674
|
int limit = state.getConfig().getLimitSave();
|
675
|
boolean success = true;
|
676
|
|
677
|
Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);
|
678
|
|
679
|
Set<UUID> synonymUuidSet = fromToMap.keySet();
|
680
|
Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());
|
681
|
|
682
|
if (logger.isTraceEnabled()) {
|
683
|
logger.trace("Reading synonym names and accepted taxa...");
|
684
|
}
|
685
|
List<TaxonBase> synonyms = getTaxonService().find(synonymUuidSet);
|
686
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaUuidSet);
|
687
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
688
|
for (TaxonBase taxonBase : acceptedTaxa){
|
689
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
690
|
}
|
691
|
|
692
|
if (logger.isTraceEnabled()) {
|
693
|
logger.trace("End reading synonyms names and accepted taxa");
|
694
|
for (UUID uuid : synonymUuidSet) {
|
695
|
logger.trace("synonym uuid query: " + uuid);
|
696
|
}
|
697
|
for (UUID uuid : acceptedTaxaUuidSet) {
|
698
|
logger.trace("accepted taxon uuid query: " + uuid);
|
699
|
}
|
700
|
for (TaxonBase tb : synonyms) {
|
701
|
logger.trace("synonym uuid result: " + tb.getUuid());
|
702
|
}
|
703
|
for (TaxonBase tb : acceptedTaxa) {
|
704
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
705
|
}
|
706
|
}
|
707
|
|
708
|
UUID mappedAcceptedTaxonUuid = null;
|
709
|
UUID synonymUuid = null;
|
710
|
Synonym synonym = null;
|
711
|
TaxonBase acceptedTaxonBase = null;
|
712
|
Taxon acceptedTaxon = null;
|
713
|
|
714
|
for (TaxonBase synonymTaxonBase : synonyms) {
|
715
|
|
716
|
try {
|
717
|
synonym = synonymTaxonBase.deproxy(synonymTaxonBase, Synonym.class);
|
718
|
synonymUuid = synonym.getUuid();
|
719
|
mappedAcceptedTaxonUuid = fromToMap.get(synonymUuid);
|
720
|
acceptedTaxonBase = null;
|
721
|
|
722
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
723
|
if (logger.isDebugEnabled()) {
|
724
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + synonymUuid + ")");
|
725
|
}
|
726
|
acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);
|
727
|
|
728
|
if (synonym != null && acceptedTaxon != null) {
|
729
|
|
730
|
//TODO: in case original genus exists must add synonym to original genus instead of to accepted taxon
|
731
|
acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
732
|
|
733
|
if (logger.isDebugEnabled()) {
|
734
|
logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid +
|
735
|
") relationship created");
|
736
|
}
|
737
|
if (synonym != null && !synonymSet.contains(synonym)) {
|
738
|
|
739
|
synonymSet.add(synonym);
|
740
|
|
741
|
if (logger.isTraceEnabled()) {
|
742
|
logger.trace("Synonym (" + synonymUuid + ") added to Set");
|
743
|
}
|
744
|
|
745
|
} else {
|
746
|
if (logger.isDebugEnabled()) {
|
747
|
logger.debug("Duplicated synonym (" + synonymUuid + ")");
|
748
|
}
|
749
|
}
|
750
|
} else {
|
751
|
if (logger.isDebugEnabled()) {
|
752
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + synonymUuid + " is null");
|
753
|
}
|
754
|
}
|
755
|
} catch (Exception e) {
|
756
|
logger.error("Error creating synonym relationship: accepted taxon-synonym (" +
|
757
|
mappedAcceptedTaxonUuid + "-" + synonymUuid + ")", e);
|
758
|
}
|
759
|
}
|
760
|
if (logger.isTraceEnabled()) {
|
761
|
logger.trace("Start saving synonymSet");
|
762
|
}
|
763
|
getTaxonService().save(synonymSet);
|
764
|
if (logger.isTraceEnabled()) {
|
765
|
logger.trace("End saving synonymSet");
|
766
|
}
|
767
|
|
768
|
acceptedTaxaUuidSet = null;
|
769
|
synonymSet = null;
|
770
|
synonyms = null;
|
771
|
acceptedTaxa = null;
|
772
|
|
773
|
return success;
|
774
|
}
|
775
|
|
776
|
}
|