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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.ArrayList;
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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.io.pesi.out.PesiTransformer;
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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.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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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.SynonymRelationship;
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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 final String parentPluralString = "Taxa";
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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() || state.getConfig().isDoInferredSynonyms());
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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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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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if (state.getConfig().isDoInferredSynonyms()){
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processInferredSynonyms(state);
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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, taxonSpecialistMap, taxonGroupCoordinatorMap);
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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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305
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commitTransaction(txStatus);
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return childParentMap;
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}
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310
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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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313
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int limit = state.getConfig().getLimitSave();
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315
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TransactionStatus txStatus = null;
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317
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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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321
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int i = 0;
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322
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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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332
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333
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334
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335
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String countQuery =
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selectCount + fromClause;
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338
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String selectQuery =
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selectColumns + fromClause + orderClause;
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341
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if(logger.isInfoEnabled()) { logger.info("Start making misapplied name relationships..."); }
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343
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344
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try {
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345
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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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349
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350
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rs = source.getResultSet(selectQuery);
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351
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352
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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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355
|
logger.info("Select Query: " + selectQuery);
|
|
356
|
}
|
|
357
|
|
|
358
|
while (rs.next()) {
|
|
359
|
|
|
360
|
if ((i++ % limit) == 0) {
|
|
361
|
|
|
362
|
txStatus = startTransaction();
|
|
363
|
childParentMap = new HashMap<UUID, UUID>(limit);
|
|
364
|
|
|
365
|
if(logger.isInfoEnabled()) {
|
|
366
|
logger.info("Misapplied names retrieved: " + (i-1) );
|
|
367
|
}
|
|
368
|
}
|
|
369
|
|
|
370
|
String childUuidStr = rs.getString("MisappliedUuid");
|
|
371
|
String parentUuidStr = rs.getString("AcceptedUuid");
|
|
372
|
UUID childUuid = UUID.fromString(childUuidStr);
|
|
373
|
UUID parentUuid = UUID.fromString(parentUuidStr);
|
|
374
|
|
|
375
|
if (!childParentMap.containsKey(childUuid)) {
|
|
376
|
|
|
377
|
childParentMap.put(childUuid, parentUuid);
|
|
378
|
|
|
379
|
} else {
|
|
380
|
if(logger.isDebugEnabled()) {
|
|
381
|
logger.debug("Duplicated child UUID (" + childUuid + ")");
|
|
382
|
}
|
|
383
|
}
|
|
384
|
|
|
385
|
if (((i % limit) == 0 && i != 1 ) || i == count) {
|
|
386
|
|
|
387
|
createAndCommitMisappliedNameRelationships(state, txStatus,
|
|
388
|
childParentMap);
|
|
389
|
childParentMap = null;
|
|
390
|
|
|
391
|
|
|
392
|
if(logger.isInfoEnabled()) {
|
|
393
|
logger.info("i = " + i + " - Transaction committed");
|
|
394
|
}
|
|
395
|
}
|
|
396
|
}
|
|
397
|
if (childParentMap != null){
|
|
398
|
logger.info("processMisappliedNames... last commit");
|
|
399
|
createAndCommitMisappliedNameRelationships(state, txStatus,
|
|
400
|
childParentMap);
|
|
401
|
childParentMap = null;
|
|
402
|
}
|
|
403
|
|
|
404
|
} catch (SQLException e) {
|
|
405
|
logger.error("SQLException:" + e);
|
|
406
|
state.setUnsuccessfull();
|
|
407
|
}
|
|
408
|
return;
|
|
409
|
}
|
|
410
|
|
|
411
|
private void createAndCommitMisappliedNameRelationships(
|
|
412
|
FaunaEuropaeaImportState state, TransactionStatus txStatus,
|
|
413
|
Map<UUID, UUID> childParentMap) {
|
|
414
|
createMisappliedNameRelationships(state, childParentMap);
|
|
415
|
commitTransaction(txStatus);
|
|
416
|
}
|
|
417
|
|
|
418
|
|
|
419
|
|
|
420
|
/** Retrieve synonyms from FauEuDB DB */
|
|
421
|
private void processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {
|
|
422
|
|
|
423
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
424
|
Source source = fauEuConfig.getSource();
|
|
425
|
|
|
426
|
String selectCount =
|
|
427
|
" SELECT count(*) ";
|
|
428
|
|
|
429
|
String selectColumns = " SELECT Taxon.UUID AS SynonymUuid, Parent.UUID AS AcceptedUuid ";
|
|
430
|
|
|
431
|
String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";
|
|
432
|
|
|
433
|
String countQuery =
|
|
434
|
selectCount + fromClause;
|
|
435
|
|
|
436
|
String selectQuery =
|
|
437
|
selectColumns + fromClause + orderClause;
|
|
438
|
logger.debug(selectQuery);
|
|
439
|
|
|
440
|
try {
|
|
441
|
|
|
442
|
ResultSet rs = source.getResultSet(countQuery);
|
|
443
|
rs.next();
|
|
444
|
int count = rs.getInt(1);
|
|
445
|
|
|
446
|
rs = source.getResultSet(selectQuery);
|
|
447
|
|
|
448
|
if (logger.isInfoEnabled()) {
|
|
449
|
logger.info("Number of rows: " + count);
|
|
450
|
logger.info("Count Query: " + countQuery);
|
|
451
|
logger.info("Select Query: " + selectQuery);
|
|
452
|
}
|
|
453
|
|
|
454
|
storeSynonymRelationships(rs, count, state);
|
|
455
|
rs = null;
|
|
456
|
} catch (SQLException e) {
|
|
457
|
logger.error("SQLException:" + e);
|
|
458
|
state.setUnsuccessfull();
|
|
459
|
}
|
|
460
|
return;
|
|
461
|
}
|
|
462
|
|
|
463
|
|
|
464
|
|
|
465
|
|
|
466
|
private void storeSynonymRelationships(ResultSet rs, int count, FaunaEuropaeaImportState state)
|
|
467
|
throws SQLException {
|
|
468
|
|
|
469
|
TransactionStatus txStatus = null;
|
|
470
|
Map<UUID, UUID> synonymAcceptedMap = null;
|
|
471
|
int i = 0;
|
|
472
|
int limit = state.getConfig().getLimitSave();
|
|
473
|
|
|
474
|
while (rs.next()) {
|
|
475
|
|
|
476
|
if ((i++ % limit) == 0) {
|
|
477
|
|
|
478
|
txStatus = startTransaction();
|
|
479
|
synonymAcceptedMap = new HashMap<UUID, UUID>(limit);
|
|
480
|
|
|
481
|
if(logger.isInfoEnabled()) {
|
|
482
|
logger.info("Synonyms retrieved: " + (i-1));
|
|
483
|
}
|
|
484
|
}
|
|
485
|
|
|
486
|
String synonymUuidStr = rs.getString("SynonymUuid");
|
|
487
|
String acceptedUuidStr = rs.getString("AcceptedUuid");
|
|
488
|
UUID synonymUuid = UUID.fromString(synonymUuidStr);
|
|
489
|
UUID acceptedUuid = UUID.fromString(acceptedUuidStr);
|
|
490
|
|
|
491
|
if (!synonymAcceptedMap.containsKey(synonymUuid)) {
|
|
492
|
|
|
493
|
synonymAcceptedMap.put(synonymUuid, acceptedUuid);
|
|
494
|
|
|
495
|
} else {
|
|
496
|
if(logger.isDebugEnabled()) {
|
|
497
|
logger.debug("Duplicated synonym UUID (" + synonymUuid + ")");
|
|
498
|
}
|
|
499
|
}
|
|
500
|
|
|
501
|
if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
|
502
|
|
|
503
|
synonymAcceptedMap = createAndCommitHeterotypicSynonyms(state,
|
|
504
|
txStatus, synonymAcceptedMap);
|
|
505
|
|
|
506
|
if(logger.isInfoEnabled()) {
|
|
507
|
logger.info("i = " + i + " - Transaction committed");
|
|
508
|
}
|
|
509
|
}
|
|
510
|
}
|
|
511
|
if (synonymAcceptedMap != null){
|
|
512
|
logger.info("processHeterotypicSynonyms... last commit");
|
|
513
|
synonymAcceptedMap = createAndCommitHeterotypicSynonyms(state,
|
|
514
|
txStatus, synonymAcceptedMap);
|
|
515
|
}
|
|
516
|
return;
|
|
517
|
}
|
|
518
|
|
|
519
|
private Map<UUID, UUID> createAndCommitHeterotypicSynonyms(
|
|
520
|
FaunaEuropaeaImportState state, TransactionStatus txStatus,
|
|
521
|
Map<UUID, UUID> synonymAcceptedMap) {
|
|
522
|
createHeterotypicSynonyms(state, synonymAcceptedMap);
|
|
523
|
|
|
524
|
synonymAcceptedMap = null;
|
|
525
|
commitTransaction(txStatus);
|
|
526
|
return synonymAcceptedMap;
|
|
527
|
}
|
|
528
|
|
|
529
|
|
|
530
|
|
|
531
|
|
|
532
|
|
|
533
|
/* Creates parent-child relationships.
|
|
534
|
* Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
|
535
|
*/
|
|
536
|
private void createParentChildRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> childParentMap, Map<UUID, UUID> taxonSpecialistMap, Map<UUID, UUID> taxonGroupCoordinatorMap) {
|
|
537
|
//gets the taxon "Hydroscaphidae"(family)
|
|
538
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
|
539
|
sourceRef = taxon.getSec();
|
|
540
|
int limit = state.getConfig().getLimitSave();
|
|
541
|
|
|
542
|
Classification tree = getClassificationFor(state, sourceRef);
|
|
543
|
|
|
544
|
Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);
|
|
545
|
|
|
546
|
Set<UUID> childKeysSet = childParentMap.keySet();
|
|
547
|
Set<UUID> parentValuesSet = new HashSet<UUID>(childParentMap.values());
|
|
548
|
|
|
549
|
if (logger.isTraceEnabled()) {
|
|
550
|
logger.trace("Start reading children and parents");
|
|
551
|
}
|
|
552
|
List<TaxonBase> children = getTaxonService().find(childKeysSet);
|
|
553
|
List<TaxonBase> parents = getTaxonService().find(parentValuesSet);
|
|
554
|
Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>(parents.size());
|
|
555
|
|
|
556
|
for (TaxonBase taxonBase : parents){
|
|
557
|
parentsMap.put(taxonBase.getUuid(), taxonBase);
|
|
558
|
}
|
|
559
|
|
|
560
|
if (logger.isTraceEnabled()) {
|
|
561
|
logger.debug("End reading children and parents");
|
|
562
|
for (UUID uuid : childKeysSet) {
|
|
563
|
logger.trace("child uuid query: " + uuid);
|
|
564
|
}
|
|
565
|
for (UUID uuid : parentValuesSet) {
|
|
566
|
logger.trace("parent uuid query: " + uuid);
|
|
567
|
}
|
|
568
|
for (TaxonBase tb : children) {
|
|
569
|
logger.trace("child uuid result: " + tb.getUuid());
|
|
570
|
}
|
|
571
|
for (TaxonBase tb : parents) {
|
|
572
|
logger.trace("parent uuid result: " + tb.getUuid());
|
|
573
|
}
|
|
574
|
}
|
|
575
|
|
|
576
|
UUID mappedParentUuid = null;
|
|
577
|
UUID childUuid = null;
|
|
578
|
TaxonNode childNode;
|
|
579
|
TeamOrPersonBase taxonomicSpecialist = null;
|
|
580
|
TeamOrPersonBase groupCoordinator = null;
|
|
581
|
UUID agentUuid = null;
|
|
582
|
for (TaxonBase child : children) {
|
|
583
|
|
|
584
|
try {
|
|
585
|
Taxon childTaxon = child.deproxy(child, Taxon.class);
|
|
586
|
childUuid = childTaxon.getUuid();
|
|
587
|
mappedParentUuid = childParentMap.get(childUuid);
|
|
588
|
TaxonBase parent = null;
|
|
589
|
|
|
590
|
TaxonBase potentialParent = parentsMap.get(mappedParentUuid);
|
|
591
|
// for (TaxonBase potentialParent : parents ) {
|
|
592
|
// parentUuid = potentialParent.getUuid();
|
|
593
|
// if(parentUuid.equals(mappedParentUuid)) {
|
|
594
|
parent = potentialParent;
|
|
595
|
if (logger.isDebugEnabled()) {
|
|
596
|
logger.debug("Parent (" + mappedParentUuid + ") found for child (" + childUuid + ")");
|
|
597
|
}
|
|
598
|
// break;
|
|
599
|
// }
|
|
600
|
// }
|
|
601
|
|
|
602
|
Taxon parentTaxon = parent.deproxy(parent, Taxon.class);
|
|
603
|
|
|
604
|
if (childTaxon != null && parentTaxon != null) {
|
|
605
|
|
|
606
|
childNode = tree.addParentChild(parentTaxon, childTaxon, sourceRef, null);
|
|
607
|
agentUuid = taxonSpecialistMap.get(childTaxon.getUuid());
|
|
608
|
taxonomicSpecialist = null;
|
|
609
|
if (agentUuid != null){
|
|
610
|
taxonomicSpecialist = (TeamOrPersonBase) getAgentService().find(agentUuid);
|
|
611
|
|
|
612
|
if (taxonomicSpecialist != null){
|
|
613
|
childNode.addAgentRelation(FaunaEuropaeaTransformer.getTaxonomicSpecialistType(getTermService()), taxonomicSpecialist);
|
|
614
|
}
|
|
615
|
}
|
|
616
|
|
|
617
|
agentUuid = taxonGroupCoordinatorMap.get(childTaxon.getUuid());
|
|
618
|
groupCoordinator = (TeamOrPersonBase) getAgentService().find(agentUuid);
|
|
619
|
if (groupCoordinator != null){
|
|
620
|
childNode.addAgentRelation(FaunaEuropaeaTransformer.getGroupCoordinatorType(getTermService()), groupCoordinator);
|
|
621
|
}
|
|
622
|
|
|
623
|
//TODO: add the specialist and the group coordinator to the node!!
|
|
624
|
if (logger.isDebugEnabled()) {
|
|
625
|
logger.debug("Parent-child (" + mappedParentUuid + "-" + childUuid +
|
|
626
|
") relationship created");
|
|
627
|
}
|
|
628
|
if (childTaxon != null && !childSet.contains(childTaxon)) {
|
|
629
|
|
|
630
|
childSet.add(childTaxon);
|
|
631
|
|
|
632
|
if (logger.isTraceEnabled()) {
|
|
633
|
logger.trace("Child taxon (" + childUuid + ") added to Set");
|
|
634
|
}
|
|
635
|
|
|
636
|
} else {
|
|
637
|
if (logger.isDebugEnabled()) {
|
|
638
|
logger.debug("Duplicated child taxon (" + childUuid + ")");
|
|
639
|
}
|
|
640
|
}
|
|
641
|
} else {
|
|
642
|
if (logger.isDebugEnabled()) {
|
|
643
|
logger.debug("Parent(" + mappedParentUuid + ") or child (" + childUuid + " is null");
|
|
644
|
}
|
|
645
|
}
|
|
646
|
|
|
647
|
} catch (Exception e) {
|
|
648
|
logger.error("Error creating taxonomically included relationship parent-child (" +
|
|
649
|
mappedParentUuid + " <----> " + childUuid + ")", e);
|
|
650
|
}
|
|
651
|
|
|
652
|
}
|
|
653
|
if (logger.isTraceEnabled()) {
|
|
654
|
logger.trace("Start saving childSet");
|
|
655
|
}
|
|
656
|
getTaxonService().save(childSet);
|
|
657
|
if (logger.isTraceEnabled()) {
|
|
658
|
logger.trace("End saving childSet");
|
|
659
|
}
|
|
660
|
|
|
661
|
parentValuesSet = null;
|
|
662
|
childSet = null;
|
|
663
|
children = null;
|
|
664
|
parents = null;
|
|
665
|
tree = null;
|
|
666
|
|
|
667
|
return;
|
|
668
|
}
|
|
669
|
|
|
670
|
/* Creates misapplied name relationships.
|
|
671
|
* Misapplied name-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
|
672
|
*/
|
|
673
|
private void createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
|
674
|
|
|
675
|
//gets the taxon "Hydroscaphidae" (family)
|
|
676
|
|
|
677
|
TaxonBase taxon = getTaxonService().find(UUID.fromString(acceptedTaxonUUID));
|
|
678
|
sourceRef = taxon.getSec();
|
|
679
|
int limit = state.getConfig().getLimitSave();
|
|
680
|
|
|
681
|
Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);
|
|
682
|
|
|
683
|
Set<UUID> misappliedNamesSet = fromToMap.keySet();
|
|
684
|
Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());
|
|
685
|
|
|
686
|
if (logger.isTraceEnabled()) {
|
|
687
|
logger.trace("Start reading misapplied names and accepted taxa");
|
|
688
|
}
|
|
689
|
List<TaxonBase> misappliedNames = getTaxonService().find(misappliedNamesSet);
|
|
690
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaSet);
|
|
691
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
|
692
|
for (TaxonBase taxonBase : acceptedTaxa){
|
|
693
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
|
694
|
}
|
|
695
|
|
|
696
|
if (logger.isTraceEnabled()) {
|
|
697
|
logger.info("End reading misapplied names and accepted taxa");
|
|
698
|
for (UUID uuid : misappliedNamesSet) {
|
|
699
|
logger.trace("misapplied name uuid query: " + uuid);
|
|
700
|
}
|
|
701
|
for (UUID uuid : acceptedTaxaSet) {
|
|
702
|
logger.trace("accepted taxon uuid query: " + uuid);
|
|
703
|
}
|
|
704
|
for (TaxonBase tb : misappliedNames) {
|
|
705
|
logger.trace("misapplied name uuid result: " + tb.getUuid());
|
|
706
|
}
|
|
707
|
for (TaxonBase tb : acceptedTaxa) {
|
|
708
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
|
709
|
}
|
|
710
|
}
|
|
711
|
|
|
712
|
UUID mappedAcceptedTaxonUuid = null;
|
|
713
|
UUID misappliedNameUuid = null;
|
|
714
|
Taxon misappliedNameTaxon = null;
|
|
715
|
TaxonBase acceptedTaxonBase = null;
|
|
716
|
Taxon acceptedTaxon = null;
|
|
717
|
|
|
718
|
for (TaxonBase misappliedName : misappliedNames) {
|
|
719
|
|
|
720
|
try {
|
|
721
|
misappliedNameTaxon = misappliedName.deproxy(misappliedName, Taxon.class);
|
|
722
|
misappliedNameUuid = misappliedNameTaxon.getUuid();
|
|
723
|
mappedAcceptedTaxonUuid = fromToMap.get(misappliedNameUuid);
|
|
724
|
acceptedTaxonBase = null;
|
|
725
|
|
|
726
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
|
727
|
if (logger.isDebugEnabled()) {
|
|
728
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + misappliedNameUuid + ")");
|
|
729
|
}
|
|
730
|
|
|
731
|
acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);
|
|
732
|
|
|
733
|
if (misappliedNameTaxon != null && acceptedTaxon != null) {
|
|
734
|
|
|
735
|
acceptedTaxon.addMisappliedName(misappliedNameTaxon, sourceRef, null);
|
|
736
|
|
|
737
|
if (logger.isDebugEnabled()) {
|
|
738
|
logger.debug("Accepted taxon / misapplied name (" + mappedAcceptedTaxonUuid + "-" + misappliedNameUuid +
|
|
739
|
") relationship created");
|
|
740
|
}
|
|
741
|
if (!misappliedNameSet.contains(misappliedNameTaxon)) {
|
|
742
|
|
|
743
|
misappliedNameSet.add(misappliedNameTaxon);
|
|
744
|
|
|
745
|
if (logger.isTraceEnabled()) {
|
|
746
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
|
747
|
}
|
|
748
|
|
|
749
|
} else {
|
|
750
|
if (logger.isDebugEnabled()) {
|
|
751
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
|
752
|
}
|
|
753
|
}
|
|
754
|
} else {
|
|
755
|
if (logger.isDebugEnabled()) {
|
|
756
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + misappliedNameUuid + " is null");
|
|
757
|
}
|
|
758
|
}
|
|
759
|
|
|
760
|
if (misappliedNameTaxon != null && !misappliedNameSet.contains(misappliedNameTaxon)) {
|
|
761
|
misappliedNameSet.add(misappliedNameTaxon);
|
|
762
|
if (logger.isTraceEnabled()) {
|
|
763
|
logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");
|
|
764
|
}
|
|
765
|
} else {
|
|
766
|
if (logger.isDebugEnabled()) {
|
|
767
|
logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");
|
|
768
|
}
|
|
769
|
}
|
|
770
|
|
|
771
|
} catch (Exception e) {
|
|
772
|
logger.error("Error creating misapplied name relationship accepted taxon-misapplied name (" +
|
|
773
|
mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + ")", e);
|
|
774
|
}
|
|
775
|
|
|
776
|
}
|
|
777
|
if (logger.isTraceEnabled()) {
|
|
778
|
logger.trace("Start saving misappliedNameSet");
|
|
779
|
}
|
|
780
|
getTaxonService().save(misappliedNameSet);
|
|
781
|
if (logger.isTraceEnabled()) {
|
|
782
|
logger.trace("End saving misappliedNameSet");
|
|
783
|
}
|
|
784
|
|
|
785
|
acceptedTaxaSet = null;
|
|
786
|
misappliedNameSet = null;
|
|
787
|
misappliedNames = null;
|
|
788
|
acceptedTaxa = null;
|
|
789
|
|
|
790
|
return;
|
|
791
|
}
|
|
792
|
|
|
793
|
|
|
794
|
/* Creates heterotypic synonym relationships.
|
|
795
|
* Synonym-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB.
|
|
796
|
*/
|
|
797
|
private void createHeterotypicSynonyms(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {
|
|
798
|
|
|
799
|
int limit = state.getConfig().getLimitSave();
|
|
800
|
|
|
801
|
Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);
|
|
802
|
|
|
803
|
Set<UUID> synonymUuidSet = fromToMap.keySet();
|
|
804
|
Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());
|
|
805
|
|
|
806
|
if (logger.isTraceEnabled()) {
|
|
807
|
logger.trace("Reading synonym names and accepted taxa...");
|
|
808
|
}
|
|
809
|
List<TaxonBase> synonyms = getTaxonService().find(synonymUuidSet);
|
|
810
|
List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaUuidSet);
|
|
811
|
Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());
|
|
812
|
for (TaxonBase taxonBase : acceptedTaxa){
|
|
813
|
acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);
|
|
814
|
}
|
|
815
|
|
|
816
|
if (logger.isTraceEnabled()) {
|
|
817
|
logger.trace("End reading synonyms names and accepted taxa");
|
|
818
|
for (UUID uuid : synonymUuidSet) {
|
|
819
|
logger.trace("synonym uuid query: " + uuid);
|
|
820
|
}
|
|
821
|
for (UUID uuid : acceptedTaxaUuidSet) {
|
|
822
|
logger.trace("accepted taxon uuid query: " + uuid);
|
|
823
|
}
|
|
824
|
for (TaxonBase tb : synonyms) {
|
|
825
|
logger.trace("synonym uuid result: " + tb.getUuid());
|
|
826
|
}
|
|
827
|
for (TaxonBase tb : acceptedTaxa) {
|
|
828
|
logger.trace("accepted taxon uuid result: " + tb.getUuid());
|
|
829
|
}
|
|
830
|
}
|
|
831
|
|
|
832
|
UUID mappedAcceptedTaxonUuid = null;
|
|
833
|
UUID synonymUuid = null;
|
|
834
|
Synonym synonym = null;
|
|
835
|
TaxonBase acceptedTaxonBase = null;
|
|
836
|
Taxon acceptedTaxon = null;
|
|
837
|
|
|
838
|
for (TaxonBase synonymTaxonBase : synonyms) {
|
|
839
|
|
|
840
|
try {
|
|
841
|
//check for misapplied names with nec (in Fauna Europaea they have a synonym relationship to the accepted taxon)
|
|
842
|
if (synonymTaxonBase instanceof Taxon ){
|
|
843
|
if (((Taxon)synonymTaxonBase).isMisapplication()){
|
|
844
|
if (logger.isDebugEnabled()) {
|
|
845
|
logger.debug("misapplied name with exclusion" + synonymTaxonBase.getTitleCache());
|
|
846
|
}
|
|
847
|
}
|
|
848
|
continue;
|
|
849
|
}
|
|
850
|
synonym = HibernateProxyHelper.deproxy(synonymTaxonBase, Synonym.class);
|
|
851
|
synonymUuid = synonym.getUuid();
|
|
852
|
mappedAcceptedTaxonUuid = fromToMap.get(synonymUuid);
|
|
853
|
acceptedTaxonBase = null;
|
|
854
|
|
|
855
|
acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);
|
|
856
|
if (logger.isDebugEnabled()) {
|
|
857
|
logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + synonymUuid + ")");
|
|
858
|
}
|
|
859
|
acceptedTaxon = CdmBase.deproxy(acceptedTaxonBase, Taxon.class);
|
|
860
|
|
|
861
|
if (synonym != null && acceptedTaxon != null) {
|
|
862
|
|
|
863
|
//TODO: in case original genus exists must add synonym to original genus instead of to accepted taxon
|
|
864
|
acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
|
|
865
|
|
|
866
|
if (logger.isDebugEnabled()) {
|
|
867
|
logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid +
|
|
868
|
") relationship created");
|
|
869
|
}
|
|
870
|
if (synonym != null && !synonymSet.contains(synonym)) {
|
|
871
|
|
|
872
|
synonymSet.add(synonym);
|
|
873
|
|
|
874
|
if (logger.isTraceEnabled()) {
|
|
875
|
logger.trace("Synonym (" + synonymUuid + ") added to Set");
|
|
876
|
}
|
|
877
|
|
|
878
|
} else {
|
|
879
|
if (logger.isDebugEnabled()) {
|
|
880
|
logger.debug("Duplicated synonym (" + synonymUuid + ")");
|
|
881
|
}
|
|
882
|
}
|
|
883
|
} else {
|
|
884
|
if (logger.isDebugEnabled()) {
|
|
885
|
logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + synonymUuid + " is null");
|
|
886
|
}
|
|
887
|
}
|
|
888
|
} catch (Exception e) {
|
|
889
|
logger.error("Error creating synonym relationship: accepted taxon-synonym (" +
|
|
890
|
mappedAcceptedTaxonUuid + "-" + synonymUuid + ": "+ synonymTaxonBase.getTitleCache() +")", e);
|
|
891
|
}
|
|
892
|
}
|
|
893
|
if (logger.isTraceEnabled()) {
|
|
894
|
logger.trace("Start saving synonymSet");
|
|
895
|
}
|
|
896
|
getTaxonService().save(synonymSet);
|
|
897
|
if (logger.isTraceEnabled()) {
|
|
898
|
logger.trace("End saving synonymSet");
|
|
899
|
}
|
|
900
|
|
|
901
|
acceptedTaxaUuidSet = null;
|
|
902
|
synonymSet = null;
|
|
903
|
synonyms = null;
|
|
904
|
acceptedTaxa = null;
|
|
905
|
|
|
906
|
return;
|
|
907
|
}
|
|
908
|
|
|
909
|
private void processAssociatedSpecialists(FaunaEuropaeaImportState state){
|
|
910
|
int limit = state.getConfig().getLimitSave();
|
|
911
|
|
|
912
|
TransactionStatus txStatus = null;
|
|
913
|
|
|
914
|
Map<UUID, UUID> childParentMap = null;
|
|
915
|
|
|
916
|
|
|
917
|
TaxonNode taxonNode = null;
|
|
918
|
TeamOrPersonBase associatedSpecialist = null;
|
|
919
|
TaxonNodeAgentRelation agentRel = null;
|
|
920
|
UUID agentUuid = null;
|
|
921
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
922
|
Source source = fauEuConfig.getSource();
|
|
923
|
int i = 0;
|
|
924
|
|
|
925
|
String selectCount =
|
|
926
|
" SELECT count(*) ";
|
|
927
|
|
|
928
|
|
|
929
|
|
|
930
|
String selectColumns = "SELECT u.USR_GROUPNAME as groupName, u.USR_GROUPNOTE groupNote, u.USR_USR_ID as user_user_id, "
|
|
931
|
+ " u.usr_id user_id, user2.USR_ID as user2_id, taxon.UUID as tax_uuid ";
|
|
932
|
|
|
933
|
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 "
|
|
934
|
+ " left join TAXON taxon on (taxon.TAX_USR_IDSP= user2.USR_ID or taxon.TAX_USR_IDGC= user2.USR_ID) "
|
|
935
|
+ " where USERROLE.URL_ROL_ID = 7 order by taxon.TAX_ID";
|
|
936
|
String orderClause = " ORDER BY taxon.TAX_ID";
|
|
937
|
|
|
938
|
String countQuery =
|
|
939
|
selectCount + fromClause;
|
|
940
|
|
|
941
|
String selectQuery =
|
|
942
|
selectColumns + fromClause + orderClause;
|
|
943
|
|
|
944
|
if(logger.isInfoEnabled()) { logger.info("Start making associated specialists..."); }
|
|
945
|
|
|
946
|
try {
|
|
947
|
|
|
948
|
ResultSet rs = source.getResultSet(countQuery);
|
|
949
|
rs.next();
|
|
950
|
int count = rs.getInt(1);
|
|
951
|
|
|
952
|
rs = source.getResultSet(selectQuery);
|
|
953
|
|
|
954
|
if (logger.isInfoEnabled()) {
|
|
955
|
logger.info("Number of rows: " + count);
|
|
956
|
logger.info("Count Query: " + countQuery);
|
|
957
|
logger.info("Select Query: " + selectQuery);
|
|
958
|
}
|
|
959
|
|
|
960
|
while (rs.next()) {
|
|
961
|
String taxonUUID = rs.getString("taxUuid");
|
|
962
|
String oldTaxonUuidString = null;
|
|
963
|
int userId = rs.getInt("user_id");
|
|
964
|
int user2Id = rs.getInt("user2_id");
|
|
965
|
String groupName = rs.getString("groupName");
|
|
966
|
Taxon taxon = null;
|
|
967
|
if (!taxonUUID.equals(oldTaxonUuidString)){
|
|
968
|
if (taxonNode != null){
|
|
969
|
getTaxonNodeService().saveOrUpdate(taxonNode);
|
|
970
|
}
|
|
971
|
commitTransaction(txStatus);
|
|
972
|
txStatus = startTransaction();
|
|
973
|
taxon = HibernateProxyHelper.deproxy(getTaxonService().find(UUID.fromString(taxonUUID)), Taxon.class);
|
|
974
|
oldTaxonUuidString = taxonUUID;
|
|
975
|
if (!taxon.getTaxonNodes().isEmpty()){
|
|
976
|
taxonNode = taxon.getTaxonNodes().iterator().next();
|
|
977
|
} else {
|
|
978
|
taxonNode = null;
|
|
979
|
logger.info("There is an associated specialist for a taxon which has no taxonnode.");
|
|
980
|
}
|
|
981
|
}
|
|
982
|
|
|
983
|
agentUuid = state.getAgentMap().get(userId);
|
|
984
|
|
|
985
|
|
|
986
|
associatedSpecialist = (TeamOrPersonBase) getAgentService().find(agentUuid);
|
|
987
|
if (associatedSpecialist != null && taxonNode != null){
|
|
988
|
agentRel =taxonNode.addAgentRelation(FaunaEuropaeaTransformer.getAssociateSpecialistType(getTermService()), associatedSpecialist);
|
|
989
|
if (!StringUtils.isBlank(groupName)) {
|
|
990
|
agentRel.addAnnotation(Annotation.NewInstance(groupName, Language.DEFAULT()));
|
|
991
|
}
|
|
992
|
}
|
|
993
|
|
|
994
|
|
|
995
|
}
|
|
996
|
getTaxonNodeService().saveOrUpdate(taxonNode);
|
|
997
|
commitTransaction(txStatus);
|
|
998
|
}catch(SQLException e){
|
|
999
|
logger.info("Problems during creating associated specialists.", e);
|
|
1000
|
}
|
|
1001
|
}
|
|
1002
|
|
|
1003
|
private void processInferredSynonyms(FaunaEuropaeaImportState state){
|
|
1004
|
|
|
1005
|
int count;
|
|
1006
|
int pastCount;
|
|
1007
|
boolean success = true;
|
|
1008
|
// Get the limit for objects to save within a single transaction.
|
|
1009
|
if (! state.getConfig().isDoInferredSynonyms()){
|
|
1010
|
logger.info ("Ignore Creating Inferred Synonyms...");
|
|
1011
|
return;
|
|
1012
|
}
|
|
1013
|
|
|
1014
|
int limit = state.getConfig().getLimitSave();
|
|
1015
|
// Create inferred synonyms for accepted taxa
|
|
1016
|
logger.info("Creating Inferred Synonyms...");
|
|
1017
|
|
|
1018
|
|
|
1019
|
count = 0;
|
|
1020
|
pastCount = 0;
|
|
1021
|
int pageSize = limit/10;
|
|
1022
|
int pageNumber = 1;
|
|
1023
|
String inferredSynonymPluralString = "Inferred Synonyms";
|
|
1024
|
|
|
1025
|
// Start transaction
|
|
1026
|
TransactionStatus txStatus = startTransaction(true);
|
|
1027
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
1028
|
List<TaxonBase> taxonList = null;
|
|
1029
|
Set<TaxonBase> synonymList = new HashSet<TaxonBase>();
|
|
1030
|
|
|
1031
|
|
|
1032
|
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", Rank.SPECIES(), pageSize, pageNumber)).size() > 0) {
|
|
1033
|
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
|
|
1034
|
|
|
1035
|
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Importing...");
|
|
1036
|
synonymList = createInferredSynonymsForTaxonList(state, taxonList);
|
|
1037
|
getTaxonService().save(synonymList);
|
|
1038
|
|
|
1039
|
// getTaxonService().saveOrUpdate(taxonList);
|
|
1040
|
// Commit transaction
|
|
1041
|
commitTransaction(txStatus);
|
|
1042
|
logger.debug("Committed transaction.");
|
|
1043
|
logger.info("Imported " + (taxonList.size()) + " " + inferredSynonymPluralString + ". Total: " + count);
|
|
1044
|
//pastCount = count;
|
|
1045
|
|
|
1046
|
|
|
1047
|
|
|
1048
|
// Start transaction
|
|
1049
|
txStatus = startTransaction(true);
|
|
1050
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
1051
|
|
|
1052
|
// Increment pageNumber
|
|
1053
|
pageNumber++;
|
|
1054
|
}
|
|
1055
|
taxonList = null;
|
|
1056
|
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", Rank.SUBSPECIES(), pageSize, pageNumber)).size() > 0) {
|
|
1057
|
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
|
|
1058
|
|
|
1059
|
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
1060
|
synonymList = createInferredSynonymsForTaxonList(state, taxonList);
|
|
1061
|
|
|
1062
|
getTaxonService().save(synonymList);
|
|
1063
|
// Commit transaction
|
|
1064
|
commitTransaction(txStatus);
|
|
1065
|
logger.debug("Committed transaction.");
|
|
1066
|
logger.info("Exported " + taxonList.size()+ " " + inferredSynonymPluralString + ". Total: " + count);
|
|
1067
|
//pastCount = count;
|
|
1068
|
|
|
1069
|
|
|
1070
|
|
|
1071
|
// Start transaction
|
|
1072
|
txStatus = startTransaction(true);
|
|
1073
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
1074
|
|
|
1075
|
// Increment pageNumber
|
|
1076
|
pageNumber++;
|
|
1077
|
inferredSynonymsDataToBeSaved = null;
|
|
1078
|
}
|
|
1079
|
if (taxonList.size() == 0) {
|
|
1080
|
logger.info("No " + parentPluralString + " left to fetch.");
|
|
1081
|
}
|
|
1082
|
|
|
1083
|
taxonList = null;
|
|
1084
|
|
|
1085
|
// Commit transaction
|
|
1086
|
commitTransaction(txStatus);
|
|
1087
|
System.gc();
|
|
1088
|
|
|
1089
|
//ProfilerController.memorySnapshot();
|
|
1090
|
logger.debug("Committed transaction.");
|
|
1091
|
|
|
1092
|
|
|
1093
|
}
|
|
1094
|
|
|
1095
|
/**
|
|
1096
|
* @param state
|
|
1097
|
* @param mapping
|
|
1098
|
* @param synRelMapping
|
|
1099
|
* @param currentTaxonId
|
|
1100
|
* @param taxonList
|
|
1101
|
* @param inferredSynonymsDataToBeSaved
|
|
1102
|
* @return
|
|
1103
|
*/
|
|
1104
|
private Set<TaxonBase> createInferredSynonymsForTaxonList(FaunaEuropaeaImportState state,
|
|
1105
|
List<TaxonBase> taxonList) {
|
|
1106
|
|
|
1107
|
Taxon acceptedTaxon;
|
|
1108
|
Classification classification = null;
|
|
1109
|
Set<TaxonBase> inferredSynonyms = new HashSet<TaxonBase>();
|
|
1110
|
List<Synonym> inferredSynonymsLocal= new ArrayList<Synonym>();
|
|
1111
|
boolean localSuccess = true;
|
|
1112
|
|
|
1113
|
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
|
|
1114
|
|
|
1115
|
for (TaxonBase<?> taxonBase : taxonList) {
|
|
1116
|
|
|
1117
|
if (taxonBase.isInstanceOf(Taxon.class)) { // this should always be the case since we should have fetched accepted taxon only, but you never know...
|
|
1118
|
acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
1119
|
TaxonNameBase<?,?> taxonName = acceptedTaxon.getName();
|
|
1120
|
|
|
1121
|
if (taxonName.isInstanceOf(ZoologicalName.class)) {
|
|
1122
|
Set<TaxonNode> taxonNodes = acceptedTaxon.getTaxonNodes();
|
|
1123
|
TaxonNode singleNode = null;
|
|
1124
|
|
|
1125
|
if (taxonNodes.size() > 0) {
|
|
1126
|
// Determine the classification of the current TaxonNode
|
|
1127
|
|
|
1128
|
singleNode = taxonNodes.iterator().next();
|
|
1129
|
if (singleNode != null) {
|
|
1130
|
classification = singleNode.getClassification();
|
|
1131
|
} else {
|
|
1132
|
logger.error("A TaxonNode belonging to this accepted Taxon is NULL: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache() +")");
|
|
1133
|
}
|
|
1134
|
} else {
|
|
1135
|
// Classification could not be determined directly from this TaxonNode
|
|
1136
|
// The stored classification from another TaxonNode is used. It's a simple, but not a failsafe fallback solution.
|
|
1137
|
if (taxonNodes.size() == 0) {
|
|
1138
|
//logger.error("Classification could not be determined directly from this Taxon: " + acceptedTaxon.getUuid() + " is misapplication? "+acceptedTaxon.isMisapplication()+ "). The classification of the last taxon is used");
|
|
1139
|
|
|
1140
|
}
|
|
1141
|
}
|
|
1142
|
|
|
1143
|
if (classification != null) {
|
|
1144
|
try{
|
|
1145
|
TaxonNameBase name = acceptedTaxon.getName();
|
|
1146
|
|
|
1147
|
//if (name.isSpecies() || name.isInfraSpecific()){
|
|
1148
|
inferredSynonymsLocal = getTaxonService().createAllInferredSynonyms(acceptedTaxon, classification, true);
|
|
1149
|
// logger.info("number of inferred synonyms: " + inferredSynonyms.size());
|
|
1150
|
//}
|
|
1151
|
// inferredSynonyms = getTaxonService().createInferredSynonyms(classification, acceptedTaxon, SynonymRelationshipType.INFERRED_GENUS_OF());
|
|
1152
|
if (inferredSynonymsLocal != null) {
|
|
1153
|
for (TaxonBase synonym : inferredSynonymsLocal) {
|
|
1154
|
// TaxonNameBase<?,?> synonymName = synonym.getName();
|
|
1155
|
MarkerType markerType =getUuidMarkerType(PesiTransformer.uuidMarkerGuidIsMissing, state);
|
|
1156
|
|
|
1157
|
synonym.addMarker(Marker.NewInstance(markerType, true));
|
|
1158
|
|
|
1159
|
|
|
1160
|
//get SynonymRelationship and export
|
|
1161
|
if (((Synonym)synonym).getSynonymRelations().isEmpty() ){
|
|
1162
|
SynonymRelationship synRel;
|
|
1163
|
IdentifiableSource source = ((Synonym)synonym).getSources().iterator().next();
|
|
1164
|
if (source.getIdNamespace().contains("Potential combination")){
|
|
1165
|
synRel = acceptedTaxon.addSynonym((Synonym)synonym, SynonymRelationshipType.POTENTIAL_COMBINATION_OF());
|
|
1166
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to potential combination");
|
|
1167
|
} else if (source.getIdNamespace().contains("Inferred Genus")){
|
|
1168
|
synRel = acceptedTaxon.addSynonym((Synonym)synonym, SynonymRelationshipType.INFERRED_GENUS_OF());
|
|
1169
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to inferred genus");
|
|
1170
|
} else if (source.getIdNamespace().contains("Inferred Epithet")){
|
|
1171
|
synRel = acceptedTaxon.addSynonym((Synonym)synonym, SynonymRelationshipType.INFERRED_EPITHET_OF());
|
|
1172
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to inferred epithet");
|
|
1173
|
} else{
|
|
1174
|
synRel = acceptedTaxon.addSynonym((Synonym)synonym, SynonymRelationshipType.INFERRED_SYNONYM_OF());
|
|
1175
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to inferred synonym");
|
|
1176
|
}
|
|
1177
|
|
|
1178
|
|
|
1179
|
|
|
1180
|
synRel = null;
|
|
1181
|
} else {
|
|
1182
|
for (SynonymRelationship synRel: ((Synonym)synonym).getSynonymRelations()){
|
|
1183
|
if (!localSuccess) {
|
|
1184
|
logger.error("Synonym relationship export failed " + synonym.getTitleCache() + " accepted taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
1185
|
} else {
|
|
1186
|
// logger.info("Synonym relationship successfully exported: " + synonym.getTitleCache() + " " +acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
1187
|
}
|
|
1188
|
synRel = null;
|
|
1189
|
}
|
|
1190
|
}
|
|
1191
|
|
|
1192
|
inferredSynonymsDataToBeSaved.put(synonym.getId(), synonym.getName());
|
|
1193
|
}
|
|
1194
|
|
|
1195
|
inferredSynonyms.addAll(inferredSynonymsLocal);
|
|
1196
|
//logger.info("inferredSet: " + inferredSet.size());
|
|
1197
|
//getTaxonService().save(inferredSynonyms);
|
|
1198
|
//commitTransaction(txStatus);
|
|
1199
|
|
|
1200
|
inferredSynonymsLocal = null;
|
|
1201
|
|
|
1202
|
}
|
|
1203
|
|
|
1204
|
|
|
1205
|
}catch(Exception e){
|
|
1206
|
logger.error(e.getMessage());
|
|
1207
|
e.printStackTrace();
|
|
1208
|
}
|
|
1209
|
} else {
|
|
1210
|
logger.error("Classification is NULL. Inferred Synonyms could not be created for this Taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache() + ")");
|
|
1211
|
}
|
|
1212
|
} else {
|
|
1213
|
// logger.error("TaxonName is not a ZoologicalName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1214
|
}
|
|
1215
|
} else {
|
|
1216
|
logger.error("This TaxonBase is not a Taxon even though it should be: " + taxonBase.getUuid() + " (" + taxonBase.getTitleCache() + ")");
|
|
1217
|
}
|
|
1218
|
}
|
|
1219
|
//getTaxonService().saveOrUpdate(taxonList);
|
|
1220
|
taxonList = null;
|
|
1221
|
return inferredSynonyms;
|
|
1222
|
}
|
|
1223
|
|
|
1224
|
|
|
1225
|
}
|