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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.commons.lang.StringUtils;
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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.hibernate.HibernateProxyHelper;
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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.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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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.model.taxon.TaxonNode;
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//import eu.etaxonomy.cdm.profiler.ProfilerController;
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import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
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/**
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* @author a.babadshanjan
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* @created 12.05.2009
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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 = "bab7642e-f733-4a21-848d-a15250d2f4ed"; //for faunEu (2.4)
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private static final String acceptedTaxonUUID = "DADA6F44-B7B5-4C0A-9F32-980F54B02C36"; // for MfNFaunaEuropaea
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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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@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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@Override
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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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@Override
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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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if (!state.getConfig().isDoTaxonomicallyIncluded()){
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return;
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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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logger.warn("Before processParentsChildren" + state.getConfig().isDoTaxonomicallyIncluded());
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//ProfilerController.memorySnapshot();
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if (state.getConfig().isDoTaxonomicallyIncluded()) {
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processParentsChildren(state);
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}
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if (state.getConfig().isDoAssociatedSpecialists()){
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processAssociatedSpecialists(state);
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}
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logger.warn("Before processMissappliedNames" + state.getConfig().isDoMisappliedNames());
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//ProfilerController.memorySnapshot();
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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 relationships......");
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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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Map<UUID, UUID> taxonSpecialistMap = null;
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Map<UUID, UUID> taxonGroupCoordinatorMap = 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, Taxon.tax_usr_idgc as group_coordinator, Taxon.tax_usr_idsp as specialist, Parent.UUID AS ParentUuid, Parent.tax_usr_idgc as parent_group_coordinator, Parent.tax_usr_idsp as parent_specialist";
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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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taxonSpecialistMap = new HashMap<UUID,UUID>(limit);
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taxonGroupCoordinatorMap = 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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int group_coordinator_id = rs.getInt("group_coordinator");
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int specialist_id = rs.getInt("specialist");
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int parent_group_coordinator_id = rs.getInt("parent_group_coordinator");
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int parent_specialist_id = rs.getInt("parent_specialist");
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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 (!taxonSpecialistMap.containsKey(childUuid)) {
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taxonSpecialistMap.put(childUuid, state.getAgentMap().get(specialist_id));
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}
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if (!taxonSpecialistMap.containsKey(parentUuid)) {
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taxonSpecialistMap.put(parentUuid, state.getAgentMap().get(parent_specialist_id));
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}
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if (taxonGroupCoordinatorMap.containsKey(childUuid)) {
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taxonGroupCoordinatorMap.put(childUuid, state.getAgentMap().get(group_coordinator_id));
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}
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if (!taxonGroupCoordinatorMap.containsKey(parentUuid)) {
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taxonGroupCoordinatorMap.put(parentUuid, state.getAgentMap().get(parent_group_coordinator_id));
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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, taxonGroupCoordinatorMap, taxonSpecialistMap);
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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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rs = null;
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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,taxonSpecialistMap, taxonGroupCoordinatorMap);
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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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childParentMap = null;
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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, Map<UUID, UUID> taxonSpecialistMap, Map<UUID, UUID> taxonGroupCoordinatorMap) {
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createParentChildRelationships(state, childParentMap, taxonSpecialistMap, taxonGroupCoordinatorMap);
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293
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commitTransaction(txStatus);
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return childParentMap;
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}
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298
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/** Retrieve misapplied name / accepted taxon uuid map from CDM DB */
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300
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private void processMisappliedNames(FaunaEuropaeaImportState state) {
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301
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int limit = state.getConfig().getLimitSave();
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TransactionStatus txStatus = null;
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305
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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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310
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311
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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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320
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321
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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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345
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346
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while (rs.next()) {
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347
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348
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if ((i++ % limit) == 0) {
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349
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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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357
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String childUuidStr = rs.getString("MisappliedUuid");
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String parentUuidStr = rs.getString("AcceptedUuid");
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360
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UUID childUuid = UUID.fromString(childUuidStr);
|
|
361
|
UUID parentUuid = UUID.fromString(parentUuidStr);
|
|
362
|
|
|
363
|
if (!childParentMap.containsKey(childUuid)) {
|
|
364
|
|
|
365
|
childParentMap.put(childUuid, parentUuid);
|
|
366
|
|
|
367
|
} else {
|
|
368
|
if(logger.isDebugEnabled()) {
|
|
369
|
logger.debug("Duplicated child UUID (" + childUuid + ")");
|
|
370
|
}
|
|
371
|
}
|
|
372
|
|
|
373
|
if (((i % limit) == 0 && i != 1 ) || i == count) {
|
|
374
|
|
|
375
|
createAndCommitMisappliedNameRelationships(state, txStatus,
|
|
376
|
childParentMap);
|
|
377
|
childParentMap = null;
|
|
378
|
|
|
379
|
|
|
380
|
if(logger.isInfoEnabled()) {
|
|
381
|
logger.info("i = " + i + " - Transaction committed");
|
|
382
|
}
|
|
383
|
}
|
|
384
|
}
|
|
385
|
if (childParentMap != null){
|
|
386
|
logger.info("processMisappliedNames... last commit");
|
|
387
|
createAndCommitMisappliedNameRelationships(state, txStatus,
|
|
388
|
childParentMap);
|
|
389
|
childParentMap = null;
|
|
390
|
}
|
|
391
|
|
|
392
|
} catch (SQLException e) {
|
|
393
|
logger.error("SQLException:" + e);
|
|
394
|
state.setUnsuccessfull();
|
|
395
|
}
|
|
396
|
return;
|
|
397
|
}
|
|
398
|
|
|
399
|
private void createAndCommitMisappliedNameRelationships(
|
|
400
|
FaunaEuropaeaImportState state, TransactionStatus txStatus,
|
|
401
|
Map<UUID, UUID> childParentMap) {
|
|
402
|
createMisappliedNameRelationships(state, childParentMap);
|
|
403
|
commitTransaction(txStatus);
|
|
404
|
}
|
|
405
|
|
|
406
|
|
|
407
|
|
|
408
|
/** Retrieve synonyms from FauEuDB DB */
|
|
409
|
private void processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {
|
|
410
|
|
|
411
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
412
|
Source source = fauEuConfig.getSource();
|
|
413
|
|
|
414
|
String selectCount =
|
|
415
|
" SELECT count(*) ";
|
|
416
|
|
|
417
|
String selectColumns = " SELECT Taxon.UUID AS SynonymUuid, Parent.UUID AS AcceptedUuid ";
|
|
418
|
|
|
419
|
String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";
|
|
420
|
|
|
421
|
String countQuery =
|
|
422
|
selectCount + fromClause;
|
|
423
|
|
|
424
|
String selectQuery =
|
|
425
|
selectColumns + fromClause + orderClause;
|
|
426
|
logger.debug(selectQuery);
|
|
427
|
|
|
428
|
try {
|
|
429
|
|
|
430
|
ResultSet rs = source.getResultSet(countQuery);
|
|
431
|
rs.next();
|
|
432
|
int count = rs.getInt(1);
|
|
433
|
|
|
434
|
rs = source.getResultSet(selectQuery);
|
|
435
|
|
|
436
|
if (logger.isInfoEnabled()) {
|
|
437
|
logger.info("Number of rows: " + count);
|
|
438
|
logger.info("Count Query: " + countQuery);
|
|
439
|
logger.info("Select Query: " + selectQuery);
|
|
440
|
}
|
|
441
|
|
|
442
|
storeSynonymRelationships(rs, count, state);
|
|
443
|
rs = null;
|
|
444
|
} catch (SQLException e) {
|
|
445
|
logger.error("SQLException:" + e);
|
|
446
|
state.setUnsuccessfull();
|
|
447
|
}
|
|
448
|
return;
|
|
449
|
}
|
|
450
|
|
|
451
|
|
|
452
|
|
|
453
|
|
|
454
|
private void storeSynonymRelationships(ResultSet rs, int count, FaunaEuropaeaImportState state)
|
|
455
|
throws SQLException {
|
|
456
|
|
|
457
|
TransactionStatus txStatus = null;
|
|
458
|
Map<UUID, UUID> synonymAcceptedMap = null;
|
|
459
|
int i = 0;
|
|
460
|
int limit = state.getConfig().getLimitSave();
|
|
461
|
|
|
462
|
while (rs.next()) {
|
|
463
|
|
|
464
|
if ((i++ % limit) == 0) {
|
|
465
|
|
|
466
|
txStatus = startTransaction();
|
|
467
|
synonymAcceptedMap = new HashMap<UUID, UUID>(limit);
|
|
468
|
|
|
469
|
if(logger.isInfoEnabled()) {
|
|
470
|
logger.info("Synonyms retrieved: " + (i-1));
|
|
471
|
}
|
|
472
|
}
|
|
473
|
|
|
474
|
String synonymUuidStr = rs.getString("SynonymUuid");
|
|
475
|
String acceptedUuidStr = rs.getString("AcceptedUuid");
|
|
476
|
UUID synonymUuid = UUID.fromString(synonymUuidStr);
|
|
477
|
UUID acceptedUuid = UUID.fromString(acceptedUuidStr);
|
|
478
|
|
|
479
|
if (!synonymAcceptedMap.containsKey(synonymUuid)) {
|
|
480
|
|
|
481
|
synonymAcceptedMap.put(synonymUuid, acceptedUuid);
|
|
482
|
|
|
483
|
} else {
|
|
484
|
if(logger.isDebugEnabled()) {
|
|
485
|
logger.debug("Duplicated synonym UUID (" + synonymUuid + ")");
|
|
486
|
}
|
|
487
|
}
|
|
488
|
|
|
489
|
if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
|
490
|
|
|
491
|
synonymAcceptedMap = createAndCommitHeterotypicSynonyms(state,
|
|
492
|
txStatus, synonymAcceptedMap);
|
|
493
|
|
|
494
|
if(logger.isInfoEnabled()) {
|
|
495
|
logger.info("i = " + i + " - Transaction committed");
|
|
496
|
}
|
|
497
|
}
|
|
498
|
}
|
|
499
|
if (synonymAcceptedMap != null){
|
|
500
|
logger.info("processHeterotypicSynonyms... last commit");
|
|
501
|
synonymAcceptedMap = createAndCommitHeterotypicSynonyms(state,
|
|
502
|
txStatus, synonymAcceptedMap);
|
|
503
|
}
|
|
504
|
return;
|
|
505
|
}
|
|
506
|
|
|
507
|
private Map<UUID, UUID> createAndCommitHeterotypicSynonyms(
|
|
508
|
FaunaEuropaeaImportState state, TransactionStatus txStatus,
|
|
509
|
Map<UUID, UUID> synonymAcceptedMap) {
|
|
510
|
createHeterotypicSynonyms(state, synonymAcceptedMap);
|
|
511
|
|
|
512
|
synonymAcceptedMap = null;
|
|
513
|
commitTransaction(txStatus);
|
|
514
|
return synonymAcceptedMap;
|
|
515
|
}
|
|
516
|
|
|
517
|
|
|
518
|
|
|
519
|
|
|
520
|
|
|
521
|
/* Creates parent-child relationships.
|
|
522
|
* Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
|
523
|
*/
|
|
524
|
private void createParentChildRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> childParentMap, Map<UUID, UUID> taxonSpecialistMap, Map<UUID, UUID> taxonGroupCoordinatorMap) {
|
|
525
|
//gets the taxon "Hydroscaphidae"(family)
|
|
526
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
|
527
|
sourceRef = taxon.getSec();
|
|
528
|
int limit = state.getConfig().getLimitSave();
|
|
529
|
|
|
530
|
Classification tree = getClassificationFor(state, sourceRef);
|
|
531
|
|
|
532
|
Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);
|
|
533
|
|
|
534
|
Set<UUID> childKeysSet = childParentMap.keySet();
|
|
535
|
Set<UUID> parentValuesSet = new HashSet<UUID>(childParentMap.values());
|
|
536
|
|
|
537
|
if (logger.isTraceEnabled()) {
|
|
538
|
logger.trace("Start reading children and parents");
|
|
539
|
}
|
|
540
|
List<TaxonBase> children = getTaxonService().find(childKeysSet);
|
|
541
|
List<TaxonBase> parents = getTaxonService().find(parentValuesSet);
|
|
542
|
Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>(parents.size());
|
|
543
|
|
|
544
|
for (TaxonBase taxonBase : parents){
|
|
545
|
parentsMap.put(taxonBase.getUuid(), taxonBase);
|
|
546
|
}
|
|
547
|
|
|
548
|
if (logger.isTraceEnabled()) {
|
|
549
|
logger.debug("End reading children and parents");
|
|
550
|
for (UUID uuid : childKeysSet) {
|
|
551
|
logger.trace("child uuid query: " + uuid);
|
|
552
|
}
|
|
553
|
for (UUID uuid : parentValuesSet) {
|
|
554
|
logger.trace("parent uuid query: " + uuid);
|
|
555
|
}
|
|
556
|
for (TaxonBase tb : children) {
|
|
557
|
logger.trace("child uuid result: " + tb.getUuid());
|
|
558
|
}
|
|
559
|
for (TaxonBase tb : parents) {
|
|
560
|
logger.trace("parent uuid result: " + tb.getUuid());
|
|
561
|
}
|
|
562
|
}
|
|
563
|
|
|
564
|
UUID mappedParentUuid = null;
|
|
565
|
UUID childUuid = null;
|
|
566
|
TaxonNode childNode;
|
|
567
|
TeamOrPersonBase taxonomicSpecialist = null;
|
|
568
|
TeamOrPersonBase groupCoordinator = null;
|
|
569
|
UUID agentUuid = null;
|
|
570
|
for (TaxonBase child : children) {
|
|
571
|
|
|
572
|
try {
|
|
573
|
Taxon childTaxon = child.deproxy(child, Taxon.class);
|
|
574
|
childUuid = childTaxon.getUuid();
|
|
575
|
mappedParentUuid = childParentMap.get(childUuid);
|
|
576
|
TaxonBase parent = null;
|
|
577
|
|
|
578
|
TaxonBase potentialParent = parentsMap.get(mappedParentUuid);
|
|
579
|
// for (TaxonBase potentialParent : parents ) {
|
|
580
|
// parentUuid = potentialParent.getUuid();
|
|
581
|
// if(parentUuid.equals(mappedParentUuid)) {
|
|
582
|
parent = potentialParent;
|
|
583
|
if (logger.isDebugEnabled()) {
|
|
584
|
logger.debug("Parent (" + mappedParentUuid + ") found for child (" + childUuid + ")");
|
|
585
|
}
|
|
586
|
// break;
|
|
587
|
// }
|
|
588
|
// }
|
|
589
|
|
|
590
|
Taxon parentTaxon = parent.deproxy(parent, Taxon.class);
|
|
591
|
|
|
592
|
if (childTaxon != null && parentTaxon != null) {
|
|
593
|
|
|
594
|
childNode = tree.addParentChild(parentTaxon, childTaxon, sourceRef, null);
|
|
595
|
agentUuid = taxonSpecialistMap.get(childTaxon.getUuid());
|
|
596
|
taxonomicSpecialist = null;
|
|
597
|
if (agentUuid != null){
|
|
598
|
taxonomicSpecialist = (TeamOrPersonBase) getAgentService().find(agentUuid);
|
|
599
|
|
|
600
|
if (taxonomicSpecialist != null){
|
|
601
|
childNode.addAgentRelation(FaunaEuropaeaTransformer.getTaxonomicSpecialistType(getTermService()), taxonomicSpecialist);
|
|
602
|
}
|
|
603
|
}
|
|
604
|
|
|
605
|
agentUuid = taxonGroupCoordinatorMap.get(childTaxon.getUuid());
|
|
606
|
groupCoordinator = (TeamOrPersonBase) getAgentService().find(agentUuid);
|
|
607
|
if (groupCoordinator != null){
|
|
608
|
childNode.addAgentRelation(FaunaEuropaeaTransformer.getGroupCoordinatorType(getTermService()), groupCoordinator);
|
|
609
|
}
|
|
610
|
|
|
611
|
//TODO: add the specialist and the group coordinator to the node!!
|
|
612
|
if (logger.isDebugEnabled()) {
|
|
613
|
logger.debug("Parent-child (" + mappedParentUuid + "-" + childUuid +
|
|
614
|
") relationship created");
|
|
615
|
}
|
|
616
|
if (childTaxon != null && !childSet.contains(childTaxon)) {
|
|
617
|
|
|
618
|
childSet.add(childTaxon);
|
|
619
|
|
|
620
|
if (logger.isTraceEnabled()) {
|
|
621
|
logger.trace("Child taxon (" + childUuid + ") added to Set");
|
|
622
|
}
|
|
623
|
|
|
624
|
} else {
|
|
625
|
if (logger.isDebugEnabled()) {
|
|
626
|
logger.debug("Duplicated child taxon (" + childUuid + ")");
|
|
627
|
}
|
|
628
|
}
|
|
629
|
} else {
|
|
630
|
if (logger.isDebugEnabled()) {
|
|
631
|
logger.debug("Parent(" + mappedParentUuid + ") or child (" + childUuid + " is null");
|
|
632
|
}
|
|
633
|
}
|
|
634
|
|
|
635
|
} catch (Exception e) {
|
|
636
|
logger.error("Error creating taxonomically included relationship parent-child (" +
|
|
637
|
mappedParentUuid + " <----> " + childUuid + ")", e);
|
|
638
|
}
|
|
639
|
|
|
640
|
}
|
|
641
|
if (logger.isTraceEnabled()) {
|
|
642
|
logger.trace("Start saving childSet");
|
|
643
|
}
|
|
644
|
getTaxonService().save(childSet);
|
|
645
|
if (logger.isTraceEnabled()) {
|
|
646
|
logger.trace("End saving childSet");
|
|
647
|
}
|
|
648
|
|
|
649
|
parentValuesSet = null;
|
|
650
|
childSet = null;
|
|
651
|
children = null;
|
|
652
|
parents = null;
|
|
653
|
tree = null;
|
|
654
|
|
|
655
|
return;
|
|
656
|
}
|
|
657
|
|
|
658
|
/* Creates misapplied name relationships.
|
|
659
|
* Misapplied name-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
|
660
|
*/
|
|
661
|
private void createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
|
662
|
|
|
663
|
//gets the taxon "Hydroscaphidae" (family)
|
|
664
|
|
|
665
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
|
666
|
sourceRef = taxon.getSec();
|
|
667
|
int limit = state.getConfig().getLimitSave();
|
|
668
|
|
|
669
|
Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);
|
|
670
|
|
|
671
|
Set<UUID> misappliedNamesSet = fromToMap.keySet();
|
|
672
|
Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());
|
|
673
|
|
|
674
|
if (logger.isTraceEnabled()) {
|
|
675
|
logger.trace("Start reading misapplied names and accepted taxa");
|
|
676
|
}
|
|
677
|
List<TaxonBase> misappliedNames = getTaxonService().find(misappliedNamesSet);
|
|
678
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaSet);
|
|
679
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
|
680
|
for (TaxonBase taxonBase : acceptedTaxa){
|
|
681
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
|
682
|
}
|
|
683
|
|
|
684
|
if (logger.isTraceEnabled()) {
|
|
685
|
logger.info("End reading misapplied names and accepted taxa");
|
|
686
|
for (UUID uuid : misappliedNamesSet) {
|
|
687
|
logger.trace("misapplied name uuid query: " + uuid);
|
|
688
|
}
|
|
689
|
for (UUID uuid : acceptedTaxaSet) {
|
|
690
|
logger.trace("accepted taxon uuid query: " + uuid);
|
|
691
|
}
|
|
692
|
for (TaxonBase tb : misappliedNames) {
|
|
693
|
logger.trace("misapplied name uuid result: " + tb.getUuid());
|
|
694
|
}
|
|
695
|
for (TaxonBase tb : acceptedTaxa) {
|
|
696
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
|
697
|
}
|
|
698
|
}
|
|
699
|
|
|
700
|
UUID mappedAcceptedTaxonUuid = null;
|
|
701
|
UUID misappliedNameUuid = null;
|
|
702
|
Taxon misappliedNameTaxon = null;
|
|
703
|
TaxonBase acceptedTaxonBase = null;
|
|
704
|
Taxon acceptedTaxon = null;
|
|
705
|
|
|
706
|
for (TaxonBase misappliedName : misappliedNames) {
|
|
707
|
|
|
708
|
try {
|
|
709
|
misappliedNameTaxon = misappliedName.deproxy(misappliedName, Taxon.class);
|
|
710
|
misappliedNameUuid = misappliedNameTaxon.getUuid();
|
|
711
|
mappedAcceptedTaxonUuid = fromToMap.get(misappliedNameUuid);
|
|
712
|
acceptedTaxonBase = null;
|
|
713
|
|
|
714
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
|
715
|
if (logger.isDebugEnabled()) {
|
|
716
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + misappliedNameUuid + ")");
|
|
717
|
}
|
|
718
|
|
|
719
|
acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);
|
|
720
|
|
|
721
|
if (misappliedNameTaxon != null && acceptedTaxon != null) {
|
|
722
|
|
|
723
|
acceptedTaxon.addMisappliedName(misappliedNameTaxon, sourceRef, null);
|
|
724
|
|
|
725
|
if (logger.isDebugEnabled()) {
|
|
726
|
logger.debug("Accepted taxon / misapplied name (" + mappedAcceptedTaxonUuid + "-" + misappliedNameUuid +
|
|
727
|
") relationship created");
|
|
728
|
}
|
|
729
|
if (!misappliedNameSet.contains(misappliedNameTaxon)) {
|
|
730
|
|
|
731
|
misappliedNameSet.add(misappliedNameTaxon);
|
|
732
|
|
|
733
|
if (logger.isTraceEnabled()) {
|
|
734
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
|
735
|
}
|
|
736
|
|
|
737
|
} else {
|
|
738
|
if (logger.isDebugEnabled()) {
|
|
739
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
|
740
|
}
|
|
741
|
}
|
|
742
|
} else {
|
|
743
|
if (logger.isDebugEnabled()) {
|
|
744
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + misappliedNameUuid + " is null");
|
|
745
|
}
|
|
746
|
}
|
|
747
|
|
|
748
|
if (misappliedNameTaxon != null && !misappliedNameSet.contains(misappliedNameTaxon)) {
|
|
749
|
misappliedNameSet.add(misappliedNameTaxon);
|
|
750
|
if (logger.isTraceEnabled()) {
|
|
751
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
|
752
|
}
|
|
753
|
} else {
|
|
754
|
if (logger.isDebugEnabled()) {
|
|
755
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
|
756
|
}
|
|
757
|
}
|
|
758
|
|
|
759
|
} catch (Exception e) {
|
|
760
|
logger.error("Error creating misapplied name relationship accepted taxon-misapplied name (" +
|
|
761
|
mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + ")", e);
|
|
762
|
}
|
|
763
|
|
|
764
|
}
|
|
765
|
if (logger.isTraceEnabled()) {
|
|
766
|
logger.trace("Start saving misappliedNameSet");
|
|
767
|
}
|
|
768
|
getTaxonService().save(misappliedNameSet);
|
|
769
|
if (logger.isTraceEnabled()) {
|
|
770
|
logger.trace("End saving misappliedNameSet");
|
|
771
|
}
|
|
772
|
|
|
773
|
acceptedTaxaSet = null;
|
|
774
|
misappliedNameSet = null;
|
|
775
|
misappliedNames = null;
|
|
776
|
acceptedTaxa = null;
|
|
777
|
|
|
778
|
return;
|
|
779
|
}
|
|
780
|
|
|
781
|
|
|
782
|
/* Creates heterotypic synonym relationships.
|
|
783
|
* Synonym-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
|
784
|
*/
|
|
785
|
private void createHeterotypicSynonyms(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
|
786
|
|
|
787
|
int limit = state.getConfig().getLimitSave();
|
|
788
|
|
|
789
|
Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);
|
|
790
|
|
|
791
|
Set<UUID> synonymUuidSet = fromToMap.keySet();
|
|
792
|
Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());
|
|
793
|
|
|
794
|
if (logger.isTraceEnabled()) {
|
|
795
|
logger.trace("Reading synonym names and accepted taxa...");
|
|
796
|
}
|
|
797
|
List<TaxonBase> synonyms = getTaxonService().find(synonymUuidSet);
|
|
798
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaUuidSet);
|
|
799
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
|
800
|
for (TaxonBase taxonBase : acceptedTaxa){
|
|
801
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
|
802
|
}
|
|
803
|
|
|
804
|
if (logger.isTraceEnabled()) {
|
|
805
|
logger.trace("End reading synonyms names and accepted taxa");
|
|
806
|
for (UUID uuid : synonymUuidSet) {
|
|
807
|
logger.trace("synonym uuid query: " + uuid);
|
|
808
|
}
|
|
809
|
for (UUID uuid : acceptedTaxaUuidSet) {
|
|
810
|
logger.trace("accepted taxon uuid query: " + uuid);
|
|
811
|
}
|
|
812
|
for (TaxonBase tb : synonyms) {
|
|
813
|
logger.trace("synonym uuid result: " + tb.getUuid());
|
|
814
|
}
|
|
815
|
for (TaxonBase tb : acceptedTaxa) {
|
|
816
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
|
817
|
}
|
|
818
|
}
|
|
819
|
|
|
820
|
UUID mappedAcceptedTaxonUuid = null;
|
|
821
|
UUID synonymUuid = null;
|
|
822
|
Synonym synonym = null;
|
|
823
|
TaxonBase acceptedTaxonBase = null;
|
|
824
|
Taxon acceptedTaxon = null;
|
|
825
|
|
|
826
|
for (TaxonBase synonymTaxonBase : synonyms) {
|
|
827
|
|
|
828
|
try {
|
|
829
|
//check for misapplied names with nec (in Fauna Europaea they have a synonym relationship to the accepted taxon)
|
|
830
|
if (synonymTaxonBase instanceof Taxon ){
|
|
831
|
if (((Taxon)synonymTaxonBase).isMisapplication()){
|
|
832
|
if (logger.isDebugEnabled()) {
|
|
833
|
logger.debug("misapplied name with exclusion" + synonymTaxonBase.getTitleCache());
|
|
834
|
}
|
|
835
|
}
|
|
836
|
continue;
|
|
837
|
}
|
|
838
|
synonym = HibernateProxyHelper.deproxy(synonymTaxonBase, Synonym.class);
|
|
839
|
synonymUuid = synonym.getUuid();
|
|
840
|
mappedAcceptedTaxonUuid = fromToMap.get(synonymUuid);
|
|
841
|
acceptedTaxonBase = null;
|
|
842
|
|
|
843
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
|
844
|
if (logger.isDebugEnabled()) {
|
|
845
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + synonymUuid + ")");
|
|
846
|
}
|
|
847
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxonBase, Taxon.class);
|
|
848
|
|
|
849
|
if (synonym != null && acceptedTaxon != null) {
|
|
850
|
|
|
851
|
//TODO: in case original genus exists must add synonym to original genus instead of to accepted taxon
|
|
852
|
acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
|
853
|
|
|
854
|
if (logger.isDebugEnabled()) {
|
|
855
|
logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid +
|
|
856
|
") relationship created");
|
|
857
|
}
|
|
858
|
if (synonym != null && !synonymSet.contains(synonym)) {
|
|
859
|
|
|
860
|
synonymSet.add(synonym);
|
|
861
|
|
|
862
|
if (logger.isTraceEnabled()) {
|
|
863
|
logger.trace("Synonym (" + synonymUuid + ") added to Set");
|
|
864
|
}
|
|
865
|
|
|
866
|
} else {
|
|
867
|
if (logger.isDebugEnabled()) {
|
|
868
|
logger.debug("Duplicated synonym (" + synonymUuid + ")");
|
|
869
|
}
|
|
870
|
}
|
|
871
|
} else {
|
|
872
|
if (logger.isDebugEnabled()) {
|
|
873
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + synonymUuid + " is null");
|
|
874
|
}
|
|
875
|
}
|
|
876
|
} catch (Exception e) {
|
|
877
|
logger.error("Error creating synonym relationship: accepted taxon-synonym (" +
|
|
878
|
mappedAcceptedTaxonUuid + "-" + synonymUuid + ": "+ synonymTaxonBase.getTitleCache() +")", e);
|
|
879
|
}
|
|
880
|
}
|
|
881
|
if (logger.isTraceEnabled()) {
|
|
882
|
logger.trace("Start saving synonymSet");
|
|
883
|
}
|
|
884
|
getTaxonService().save(synonymSet);
|
|
885
|
if (logger.isTraceEnabled()) {
|
|
886
|
logger.trace("End saving synonymSet");
|
|
887
|
}
|
|
888
|
|
|
889
|
acceptedTaxaUuidSet = null;
|
|
890
|
synonymSet = null;
|
|
891
|
synonyms = null;
|
|
892
|
acceptedTaxa = null;
|
|
893
|
|
|
894
|
return;
|
|
895
|
}
|
|
896
|
|
|
897
|
private void processAssociatedSpecialists(FaunaEuropaeaImportState state){
|
|
898
|
int limit = state.getConfig().getLimitSave();
|
|
899
|
|
|
900
|
TransactionStatus txStatus = null;
|
|
901
|
|
|
902
|
Map<UUID, UUID> childParentMap = null;
|
|
903
|
|
|
904
|
|
|
905
|
TaxonNode taxonNode = null;
|
|
906
|
TeamOrPersonBase associatedSpecialist = null;
|
|
907
|
TaxonNodeAgentRelation agentRel = null;
|
|
908
|
UUID agentUuid = null;
|
|
909
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
910
|
Source source = fauEuConfig.getSource();
|
|
911
|
int i = 0;
|
|
912
|
|
|
913
|
String selectCount =
|
|
914
|
" SELECT count(*) ";
|
|
915
|
|
|
916
|
|
|
917
|
|
|
918
|
String selectColumns = "SELECT u.USR_GROUPNAME as groupName, u.USR_GROUPNOTE groupNote, u.USR_USR_ID as user_user_id, "
|
|
919
|
+ " u.usr_id user_id, user2.USR_ID as user2_id, taxon.UUID as tax_uuid ";
|
|
920
|
|
|
921
|
String fromClause = " FROM USERROLE as userrole left join USERS u on userrole.URL_USR_ID = u.USR_ID left join USERS user2 on user2.USR_ID = u.USR_USR_ID "
|
|
922
|
+ " left join TAXON taxon on (taxon.TAX_USR_IDSP= user2.USR_ID or taxon.TAX_USR_IDGC= user2.USR_ID) "
|
|
923
|
+ " where USERROLE.URL_ROL_ID = 7 order by taxon.TAX_ID";
|
|
924
|
String orderClause = " ORDER BY taxon.TAX_ID";
|
|
925
|
|
|
926
|
String countQuery =
|
|
927
|
selectCount + fromClause;
|
|
928
|
|
|
929
|
String selectQuery =
|
|
930
|
selectColumns + fromClause + orderClause;
|
|
931
|
|
|
932
|
if(logger.isInfoEnabled()) { logger.info("Start making associated specialists..."); }
|
|
933
|
|
|
934
|
try {
|
|
935
|
|
|
936
|
ResultSet rs = source.getResultSet(countQuery);
|
|
937
|
rs.next();
|
|
938
|
int count = rs.getInt(1);
|
|
939
|
|
|
940
|
rs = source.getResultSet(selectQuery);
|
|
941
|
|
|
942
|
if (logger.isInfoEnabled()) {
|
|
943
|
logger.info("Number of rows: " + count);
|
|
944
|
logger.info("Count Query: " + countQuery);
|
|
945
|
logger.info("Select Query: " + selectQuery);
|
|
946
|
}
|
|
947
|
|
|
948
|
while (rs.next()) {
|
|
949
|
String taxonUUID = rs.getString("taxUuid");
|
|
950
|
String oldTaxonUuidString = null;
|
|
951
|
int userId = rs.getInt("user_id");
|
|
952
|
int user2Id = rs.getInt("user2_id");
|
|
953
|
String groupName = rs.getString("groupName");
|
|
954
|
Taxon taxon = null;
|
|
955
|
if (!taxonUUID.equals(oldTaxonUuidString)){
|
|
956
|
if (taxonNode != null){
|
|
957
|
getTaxonNodeService().saveOrUpdate(taxonNode);
|
|
958
|
}
|
|
959
|
commitTransaction(txStatus);
|
|
960
|
txStatus = startTransaction();
|
|
961
|
taxon = HibernateProxyHelper.deproxy(getTaxonService().find(UUID.fromString(taxonUUID)), Taxon.class);
|
|
962
|
oldTaxonUuidString = taxonUUID;
|
|
963
|
if (!taxon.getTaxonNodes().isEmpty()){
|
|
964
|
taxonNode = taxon.getTaxonNodes().iterator().next();
|
|
965
|
} else {
|
|
966
|
taxonNode = null;
|
|
967
|
logger.info("There is an associated specialist for a taxon which has no taxonnode.");
|
|
968
|
}
|
|
969
|
}
|
|
970
|
|
|
971
|
agentUuid = state.getAgentMap().get(userId);
|
|
972
|
|
|
973
|
|
|
974
|
associatedSpecialist = (TeamOrPersonBase) getAgentService().find(agentUuid);
|
|
975
|
if (associatedSpecialist != null && taxonNode != null){
|
|
976
|
agentRel =taxonNode.addAgentRelation(FaunaEuropaeaTransformer.getAssociateSpecialistType(getTermService()), associatedSpecialist);
|
|
977
|
if (!StringUtils.isBlank(groupName))
|
|
978
|
agentRel.addAnnotation(Annotation.NewInstance(groupName, Language.DEFAULT()));
|
|
979
|
}
|
|
980
|
|
|
981
|
|
|
982
|
}
|
|
983
|
getTaxonNodeService().saveOrUpdate(taxonNode);
|
|
984
|
commitTransaction(txStatus);
|
|
985
|
}catch(SQLException e){
|
|
986
|
logger.info("Problems during creating associated specialists.", e);
|
|
987
|
}
|
|
988
|
}
|
|
989
|
|
|
990
|
|
|
991
|
}
|