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/**
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* Copyright (C) 2009 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.pesi.out;
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import java.sql.Connection;
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import java.sql.PreparedStatement;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.sql.Types;
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import java.util.ArrayList;
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import java.util.EnumSet;
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import java.util.HashMap;
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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 java.util.regex.Matcher;
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import java.util.regex.Pattern;
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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.api.service.TaxonServiceImpl;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbConstantMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbStringMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.ObjectChangeMapper;
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import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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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.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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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.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.strategy.cache.HTMLTagRules;
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import eu.etaxonomy.cdm.strategy.cache.TagEnum;
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import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.ZooNameNoMarkerCacheStrategy;
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/**
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* The export class for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase TaxonNames}.<p>
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* Inserts into DataWarehouse database table <code>Taxon</code>.
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* It is divided into four phases:<p><ul>
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* <li>Phase 1: Export of all {@link eu.etaxonomy.cdm.model.name.TaxonName TaxonNames} except some data exported in the following phases.
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* <li>Phase 2: Export of additional data: ParentTaxonFk and TreeIndex.
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* <li>Phase 3: Export of additional data: Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk.
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* <li>Phase 4: Export of Inferred Synonyms.</ul>
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*
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* @author e.-m.lee
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* @since 23.02.2010
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*/
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@Component
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public class PesiTaxonExport extends PesiExportBase {
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private static final long serialVersionUID = -3412722058790200078L;
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private static final Logger logger = Logger.getLogger(PesiTaxonExport.class);
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private static final Class<? extends CdmBase> standardMethodParameter = TaxonBase.class;
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private static int modCount = 1000;
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private static final String dbTableName = "Taxon";
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private static final String dbTableNameSynRel = "RelTaxon";
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private static final String dbTableAdditionalSourceRel = "AdditionalTaxonSource";
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private static final String pluralString = "Taxa";
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private static final String parentPluralString = "Taxa";
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private static final String pluralStringNames = "Names";
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// private PreparedStatement parentTaxonFk_TreeIndex_KingdomFkStmts;
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private PreparedStatement parentTaxonFkStmt;
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private PreparedStatement rankTypeExpertsUpdateStmt;
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private PreparedStatement rankUpdateStmt;
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private Integer kingdomFk;
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private static ExtensionType lastActionExtensionType;
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private static ExtensionType lastActionDateExtensionType;
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private static ExtensionType expertNameExtensionType;
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private static ExtensionType speciesExpertNameExtensionType;
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private static ExtensionType cacheCitationExtensionType;
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public static TaxonNameDefaultCacheStrategy zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();
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public static TaxonNameDefaultCacheStrategy nonViralNameStrategy = TaxonNameDefaultCacheStrategy.NewInstance();
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private static int currentTaxonId;
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enum NamePosition {
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beginning,
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end,
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between,
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alone,
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nowhere
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}
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public PesiTaxonExport() {
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super();
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}
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@Override
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public Class<? extends CdmBase> getStandardMethodParameter() {
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return standardMethodParameter;
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}
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@Override
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protected void doInvoke(PesiExportState state) {
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try {
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logger.info("*** Started Making " + pluralString + " ...");
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initPreparedStatements(state);
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// Stores whether this invoke was successful or not.
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boolean success = true;
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// PESI: Clear the database table Taxon.
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doDelete(state);
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// Get specific mappings: (CDM) Taxon -> (PESI) Taxon
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PesiExportMapping mapping = getMapping();
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PesiExportMapping synonymRelMapping = getSynRelMapping();
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PesiExportMapping additionalSourceMapping = getAdditionalSourceMapping(state);
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// Initialize the db mapper
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mapping.initialize(state);
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synonymRelMapping.initialize(state);
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additionalSourceMapping.initialize(state);
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// Find extensionTypes
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lastActionExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtLastAction);
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lastActionDateExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtLastActionDate);
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expertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtExpertName);
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speciesExpertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtSpeciesExpertName);
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cacheCitationExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtCacheCitation);
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//Export Taxa..
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success &= doPhase01(state, mapping, additionalSourceMapping);
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//"PHASE 1b: Handle names without taxa ...
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success &= doPhase01b_Names(state, additionalSourceMapping);
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// 2nd Round: Add ParentTaxonFk to each taxon
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success &= doPhase02(state);
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//PHASE 3: Add Rank data, KingdomFk, TypeNameFk ...
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success &= doPhase03(state);
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// 4nd Round: Add TreeIndex to each taxon
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success &= doPhase04(state);
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//"PHASE 5: Creating Inferred Synonyms...
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success &= doPhase05(state, mapping, synonymRelMapping);
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logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success));
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if (!success){
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state.getResult().addError("An error occurred in PesiTaxonExport.doInvoke. Success = false");
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}
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return;
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} catch (Exception e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.getResult().addException(e);
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}
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}
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private void initPreparedStatements(PesiExportState state) throws SQLException {
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// initTreeIndexStatement(state);
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initRankExpertsUpdateStmt(state);
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initRankUpdateStatement(state);
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initParentFkStatement(state);
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}
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// // Prepare TreeIndex-And-KingdomFk-Statement
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// private void initTreeIndexStatement(PesiExportState state) throws SQLException {
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// Connection connection = state.getConfig().getDestination().getConnection();
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// String parentTaxonFk_TreeIndex_KingdomFkSql = "UPDATE Taxon SET ParentTaxonFk = ?, TreeIndex = ? WHERE TaxonId = ?";
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// parentTaxonFk_TreeIndex_KingdomFkStmt = connection.prepareStatement(parentTaxonFk_TreeIndex_KingdomFkSql);
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// }
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// Prepare TreeIndex-And-KingdomFk-Statement
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private void initParentFkStatement(PesiExportState state) throws SQLException {
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Connection connection = state.getConfig().getDestination().getConnection();
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String parentTaxonFkSql = "UPDATE Taxon SET ParentTaxonFk = ? WHERE TaxonId = ?";
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parentTaxonFkStmt = connection.prepareStatement(parentTaxonFkSql);
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}
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private void initRankUpdateStatement(PesiExportState state) throws SQLException {
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Connection connection = state.getConfig().getDestination().getConnection();
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String rankSql = "UPDATE Taxon SET RankFk = ?, RankCache = ?, KingdomFk = ? WHERE TaxonId = ?";
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rankUpdateStmt = connection.prepareStatement(rankSql);
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}
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private void initRankExpertsUpdateStmt(PesiExportState state) throws SQLException {
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// String sql_old = "UPDATE Taxon SET RankFk = ?, RankCache = ?, TypeNameFk = ?, KingdomFk = ?, " +
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// "ExpertFk = ?, SpeciesExpertFk = ? WHERE TaxonId = ?";
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//TODO handle experts GUIDs
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Connection connection = state.getConfig().getDestination().getConnection();
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String sql = "UPDATE Taxon SET RankFk = ?, RankCache = ?, TypeNameFk = ?, KingdomFk = ? " +
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" WHERE TaxonId = ?";
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rankTypeExpertsUpdateStmt = connection.prepareStatement(sql);
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}
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private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping){
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int count = 0;
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int pastCount = 0;
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boolean success = true;
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// Get the limit for objects to save within a single transaction.
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int limit = state.getConfig().getLimitSave();
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logger.info("PHASE 1: Export Taxa...limit is " + limit);
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// Start transaction
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TransactionStatus txStatus = startTransaction(true);
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if (logger.isDebugEnabled()) {
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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logger.info("Taking snapshot at the beginning of phase 1 of taxonExport");
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//ProfilerController.memorySnapshot();
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}
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int partitionCount = 0;
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List<TaxonBase<?>> list;
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while ((list = getNextTaxonPartition(null, limit, partitionCount++, null)) != null ) {
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logger.debug("Fetched " + list.size() + " " + pluralString + ". Exporting...");
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for (TaxonBase<?> taxon : list) {
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doCount(count++, modCount, pluralString);
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TaxonName taxonName = taxon.getName();
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TaxonName nvn = CdmBase.deproxy(taxonName);
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if (! nvn.isProtectedTitleCache()){
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nvn.setTitleCache(null, false);
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}
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if (! nvn.isProtectedNameCache()){
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nvn.setNameCache(null, false);
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}
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if (! nvn.isProtectedFullTitleCache()){
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nvn.setFullTitleCache(null, false);
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}
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if (! nvn.isProtectedAuthorshipCache()){
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nvn.setAuthorshipCache(null, false);
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}
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try{
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if (nvn.getRank().equals(Rank.KINGDOM())){
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if(taxon.isInstanceOf(Taxon.class)){
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String treeIndex = ((Taxon)taxon).getTaxonNodes().iterator().next().treeIndex();
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Integer kingdomId = PesiTransformer.pesiKingdomId(nvn.getGenusOrUninomial());
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state.getTreeIndexKingdomMap().put(treeIndex, kingdomId);
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}else{
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logger.warn("Kingdom taxon is not of class Taxon but " + taxon.getClass().getSimpleName() + ": " + nvn.getGenusOrUninomial());
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}
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}
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}catch(NullPointerException e){
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logger.error(nvn.getTitleCache() + " has no Rank!");
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System.err.println(nvn.getTitleCache() + " has no Rank!");
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}
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//core mapping
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success &= mapping.invoke(taxon);
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//additional source
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if (nvn.getNomenclaturalReference() != null || StringUtils.isNotBlank(nvn.getNomenclaturalMicroReference() )){
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additionalSourceMapping.invoke(taxon);
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}
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//TODO switch on again, leads to some warnings in ERMS for taxa of not correctly handled kingdoms
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validatePhaseOne(taxon, nvn);
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}
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// Commit transaction
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commitTransaction(txStatus);
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logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count + " (Phase 01)");
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pastCount = count;
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// Start new transaction
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txStatus = startTransaction(true);
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if (logger.isDebugEnabled()) {
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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}
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}
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logger.debug("No " + pluralString + " left to fetch.");
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// Commit transaction
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commitTransaction(txStatus);
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txStatus = null;
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return success;
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}
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private void validatePhaseOne(TaxonBase<?> taxon, TaxonName taxonName) {
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// Check whether some rules are violated
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String genusOrUninomial = taxonName.getGenusOrUninomial();
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String specificEpithet = taxonName.getSpecificEpithet();
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String infraSpecificEpithet = taxonName.getInfraSpecificEpithet();
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String infraGenericEpithet = taxonName.getInfraGenericEpithet();
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Rank rank = taxonName.getRank();
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//as kingdomFk can not be defined in Phase 01 the below code was switched to use the CDM rank.
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//This may be changed if we move validation to Phase03 or later
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// Integer rankFk = getRankFk(taxonName, taxonName.getNameType());
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|
335
|
// if (rankFk == null) {
|
|
336
|
// logger.error("Rank was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
337
|
// } else {
|
|
338
|
|
|
339
|
// Check whether infraGenericEpithet is set correctly
|
|
340
|
// 1. Childs of an accepted taxon of rank subgenus that are accepted taxa of rank species have to have an infraGenericEpithet
|
|
341
|
// 2. Grandchilds of an accepted taxon of rank subgenus that are accepted taxa of rank subspecies have to have an infraGenericEpithet
|
|
342
|
|
|
343
|
int ancestorLevel = 0;
|
|
344
|
if (rank == null){
|
|
345
|
logger.warn("PhaseOne validation: Taxon name has no rank: " + taxonName.getTitleCache());
|
|
346
|
}else if (rank.equals(Rank.SUBSPECIES())) {
|
|
347
|
// The accepted taxon two rank levels above should be of rank subgenus
|
|
348
|
ancestorLevel = 2;
|
|
349
|
}else if (rank.equals(Rank.SPECIES())) {
|
|
350
|
// The accepted taxon one rank level above should be of rank subgenus
|
|
351
|
ancestorLevel = 1;
|
|
352
|
}
|
|
353
|
if (ancestorLevel > 0) {
|
|
354
|
if (validateAncestorOfSpecificRank(taxon, ancestorLevel, Rank.SUBGENUS())) {
|
|
355
|
// The child (species or subspecies) of this parent (subgenus) has to have an infraGenericEpithet
|
|
356
|
if (infraGenericEpithet == null) {
|
|
357
|
logger.warn("InfraGenericEpithet for (sub)species of infrageneric taxon does not exist even though it should (also valid for Botanical Names?) for: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
358
|
// maybe the taxon could be named here
|
|
359
|
}
|
|
360
|
}
|
|
361
|
}
|
|
362
|
|
|
363
|
if (rank != null){
|
|
364
|
if (infraGenericEpithet == null && rank.isInfraGenericButNotSpeciesGroup()) {
|
|
365
|
logger.warn("InfraGenericEpithet was not determined although it should exist for infra generic names: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
366
|
}
|
|
367
|
if (specificEpithet != null && (rank.isInfraGenericButNotSpeciesGroup()||rank.isGenus()||rank.isSupraGeneric())) {
|
|
368
|
logger.warn("SpecificEpithet was determined for rank " + rank.getTitleCache() + " although it should only exist for species aggregates, species or infraspecific taxa: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
369
|
}
|
|
370
|
if (infraSpecificEpithet != null && !rank.isInfraSpecific()) {
|
|
371
|
String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rank.getTitleCache() + " although it should only exist for rank species and higher: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";
|
|
372
|
if (StringUtils.isNotBlank(infraSpecificEpithet)){
|
|
373
|
logger.warn(message);
|
|
374
|
}else{
|
|
375
|
logger.warn(message);
|
|
376
|
}
|
|
377
|
}
|
|
378
|
}
|
|
379
|
// }
|
|
380
|
if (infraSpecificEpithet != null && specificEpithet == null) {
|
|
381
|
logger.warn("An infraSpecificEpithet was determined, but a specificEpithet was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
382
|
}
|
|
383
|
if (genusOrUninomial == null) {
|
|
384
|
logger.warn("GenusOrUninomial was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
385
|
}
|
|
386
|
}
|
|
387
|
|
|
388
|
/**
|
|
389
|
* 2nd Round: Add ParentTaxonFk to each taxon and add Biota if not exists
|
|
390
|
*/
|
|
391
|
private boolean doPhase02(PesiExportState state) {
|
|
392
|
int count = 0;
|
|
393
|
int pastCount = 0;
|
|
394
|
boolean success = true;
|
|
395
|
if (! state.getConfig().isDoParentAndBiota()){
|
|
396
|
logger.info ("Ignore PHASE 2: Make ParentFk and Biota...");
|
|
397
|
return success;
|
|
398
|
}
|
|
399
|
|
|
400
|
// Get the limit for objects to save within a single transaction.
|
|
401
|
int limit = state.getConfig().getLimitSave();
|
|
402
|
|
|
403
|
insertBiota(state);
|
|
404
|
|
|
405
|
logger.info("PHASE 2: Make ParentFk and Biota ... limit is " + limit);
|
|
406
|
// Start transaction
|
|
407
|
TransactionStatus txStatus = startTransaction(true);
|
|
408
|
int partitionCount = 0;
|
|
409
|
|
|
410
|
// ProfilerController.memorySnapshot();
|
|
411
|
List<Taxon> list;
|
|
412
|
while ((list = getNextTaxonPartition(Taxon.class, limit, partitionCount++, null)) != null ) {
|
|
413
|
|
|
414
|
if(logger.isDebugEnabled()) {
|
|
415
|
logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");
|
|
416
|
}
|
|
417
|
for (Taxon taxon : list) {
|
|
418
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
419
|
doCount(count++, modCount, pluralString);
|
|
420
|
TaxonNode parentNode = node.getParent();
|
|
421
|
if (parentNode != null && isPesiTaxon(parentNode.getTaxon())){ //exclude root taxa and unpublished parents (relevant for "Valueless" parent for E+M Rubus taxa). Usually a parent should not be unpublished
|
|
422
|
int childId = state.getDbId( taxon);
|
|
423
|
int parentId = state.getDbId(parentNode.getTaxon());
|
|
424
|
success &= invokeParentTaxonFk(parentId, childId);
|
|
425
|
}
|
|
426
|
}
|
|
427
|
}
|
|
428
|
|
|
429
|
// Commit transaction
|
|
430
|
commitTransaction(txStatus);
|
|
431
|
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count + " (Phase 2)");
|
|
432
|
pastCount = count;
|
|
433
|
// Start transaction
|
|
434
|
txStatus = startTransaction(true);
|
|
435
|
if (logger.isDebugEnabled()){
|
|
436
|
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
437
|
}
|
|
438
|
}
|
|
439
|
logger.debug("No " + pluralString + " left to fetch.");
|
|
440
|
|
|
441
|
// Commit transaction
|
|
442
|
commitTransaction(txStatus);
|
|
443
|
|
|
444
|
return success;
|
|
445
|
}
|
|
446
|
|
|
447
|
/**
|
|
448
|
* Inserts the Biota Taxon if not yet exists.
|
|
449
|
*/
|
|
450
|
private void insertBiota(PesiExportState state) {
|
|
451
|
try {
|
|
452
|
ResultSet rs = state.getConfig().getDestination().getResultSet("SELECT * FROM Taxon WHERE GenusOrUninomial = 'Biota' ");
|
|
453
|
if (rs.next() == false){
|
|
454
|
int biotaId = state.getConfig().getNameIdStart() -1 ;
|
|
455
|
String sqlInsertBiota = "INSERT INTO Taxon (TaxonId, KingdomFk, RankFk, RankCache, GenusOrUninomial, WebSearchName, WebShowName, FullName, DisplayName, TaxonStatusFk, TaxonStatusCache) " +
|
|
456
|
" VALUES (" + biotaId + ", 0, 0, 'Superdomain', 'Biota', 'Biota', '<i>Biota</i>', 'Biota', '<i>Biota</i>', 1 , 'accepted')";
|
|
457
|
state.getConfig().getDestination().update(sqlInsertBiota);
|
|
458
|
}
|
|
459
|
rs = null;
|
|
460
|
} catch (SQLException e) {
|
|
461
|
logger.warn ("Biota could not be requested or inserted");
|
|
462
|
}
|
|
463
|
}
|
|
464
|
|
|
465
|
//PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...
|
|
466
|
private boolean doPhase03(PesiExportState state) {
|
|
467
|
int count = 0;
|
|
468
|
int pastCount = 0;
|
|
469
|
boolean success = true;
|
|
470
|
if (! state.getConfig().isDoTreeIndex()){
|
|
471
|
logger.info ("Ignore PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...");
|
|
472
|
return success;
|
|
473
|
}
|
|
474
|
|
|
475
|
addValuelessTaxonToKingdomMap(state);
|
|
476
|
|
|
477
|
// Get the limit for objects to save within a single transaction.
|
|
478
|
int limit = state.getConfig().getLimitSave();
|
|
479
|
|
|
480
|
logger.info("PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...");
|
|
481
|
// Be sure to add rank information, KingdomFk, TypeNameFk, expertFk and speciesExpertFk to every taxonName
|
|
482
|
|
|
483
|
// Start transaction
|
|
484
|
TransactionStatus txStatus = startTransaction(true);
|
|
485
|
if (logger.isDebugEnabled()) {
|
|
486
|
logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
487
|
}
|
|
488
|
int partitionCount = 0;
|
|
489
|
@SuppressWarnings("rawtypes")
|
|
490
|
List<TaxonBase> list;
|
|
491
|
while ((list = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, null)) != null) {
|
|
492
|
|
|
493
|
if (logger.isDebugEnabled()) {
|
|
494
|
logger.debug("Fetched " + list.size() + " " + pluralString + ". Exporting...");
|
|
495
|
}
|
|
496
|
for (TaxonBase<?> taxon : list) {
|
|
497
|
TaxonName taxonName = CdmBase.deproxy(taxon.getName());
|
|
498
|
// Determine expertFk
|
|
499
|
// Integer expertFk = makeExpertFk(state, taxonName);
|
|
500
|
//
|
|
501
|
// // Determine speciesExpertFk
|
|
502
|
// Integer speciesExpertFk = makeSpeciesExpertFk(state, taxonName);
|
|
503
|
|
|
504
|
doCount(count++, modCount, pluralString);
|
|
505
|
Integer typeNameFk = getTypeNameFk(taxonName, state);
|
|
506
|
Integer kingdomFk = findKingdomIdFromTreeIndex(taxon, state);
|
|
507
|
Integer rankFk = getRankFk(taxonName, kingdomFk);
|
|
508
|
|
|
509
|
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, state.getDbId(taxon),
|
|
510
|
typeNameFk, kingdomFk, rankFk, state);
|
|
511
|
}
|
|
512
|
|
|
513
|
// Commit transaction
|
|
514
|
commitTransaction(txStatus);
|
|
515
|
if (logger.isDebugEnabled()){logger.debug("Committed transaction.");}
|
|
516
|
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count + " (Phase 3)");
|
|
517
|
pastCount = count;
|
|
518
|
|
|
519
|
// Start transaction
|
|
520
|
txStatus = startTransaction(true);
|
|
521
|
if (logger.isDebugEnabled()) {
|
|
522
|
logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
523
|
}
|
|
524
|
}
|
|
525
|
logger.debug("No " + pluralString + " left to fetch.");
|
|
526
|
|
|
527
|
// Commit transaction
|
|
528
|
commitTransaction(txStatus);
|
|
529
|
|
|
530
|
if (logger.isDebugEnabled()){
|
|
531
|
logger.debug("Committed transaction.");
|
|
532
|
logger.debug("Try to take snapshot at the end of phase 3 of taxonExport, number of partitions: " + partitionCount);
|
|
533
|
//ProfilerController.memorySnapshot();
|
|
534
|
}
|
|
535
|
return success;
|
|
536
|
}
|
|
537
|
|
|
538
|
private void addValuelessTaxonToKingdomMap(PesiExportState state) {
|
|
539
|
TransactionStatus txStatus = startTransaction();
|
|
540
|
Taxon valuelessTaxon = (Taxon)getTaxonService().find(PesiTransformer.uuidTaxonValuelessEuroMed);
|
|
541
|
if (valuelessTaxon != null){
|
|
542
|
String treeIndex = valuelessTaxon.getTaxonNodes().iterator().next().treeIndex();
|
|
543
|
Integer kingdomId = PesiTransformer.pesiKingdomId("Plantae");
|
|
544
|
state.getTreeIndexKingdomMap().put(treeIndex, kingdomId);
|
|
545
|
}
|
|
546
|
commitTransaction(txStatus);
|
|
547
|
}
|
|
548
|
|
|
549
|
// 4th round: Add TreeIndex to each taxon
|
|
550
|
private boolean doPhase04(PesiExportState state) {
|
|
551
|
boolean success = true;
|
|
552
|
|
|
553
|
logger.info("PHASE 4: Make TreeIndex ... ");
|
|
554
|
|
|
555
|
//TODO test if possible to move to phase 02
|
|
556
|
String sql = " UPDATE Taxon SET ParentTaxonFk = (SELECT TaxonId FROM Taxon WHERE RankFk = 0) " +
|
|
557
|
" WHERE (RankFk = 10) and TaxonStatusFk = 1 ";
|
|
558
|
state.getConfig().getDestination().update(sql);
|
|
559
|
|
|
560
|
state.getConfig().getDestination().update("EXEC dbo.recalculateallstoredpaths");
|
|
561
|
|
|
562
|
logger.info("PHASE 4: Make TreeIndex DONE");
|
|
563
|
|
|
564
|
return success;
|
|
565
|
}
|
|
566
|
|
|
567
|
private static Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxonBase, PesiExportState state) {
|
|
568
|
Taxon taxon;
|
|
569
|
if (taxonBase instanceof Synonym){
|
|
570
|
taxon = ((Synonym) taxonBase).getAcceptedTaxon();
|
|
571
|
}else{
|
|
572
|
taxon = checkPseudoOrRelatedTaxon((Taxon)taxonBase);
|
|
573
|
}
|
|
574
|
if (taxon == null){
|
|
575
|
NomenclaturalCode nomenclaturalCode = taxonBase.getName().getNameType();
|
|
576
|
logger.warn("Taxon is synonym with no accepted taxon attached: " + taxonBase.getTitleCache() + ". The kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode) );
|
|
577
|
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode);
|
|
578
|
} else{
|
|
579
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
580
|
if (nodes.isEmpty()){
|
|
581
|
NomenclaturalCode nomenclaturalCode = taxon.getName().getNameType();
|
|
582
|
logger.warn("The taxon has no nodes: " + taxon.getTitleCache() + ". The kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode));
|
|
583
|
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode);
|
|
584
|
} else {
|
|
585
|
if (nodes.size()>1){
|
|
586
|
logger.warn("The taxon has more then 1 taxon node: " + taxon.getTitleCache() + ". Take arbitrary one.");
|
|
587
|
}
|
|
588
|
String treeIndex = nodes.iterator().next().treeIndex();
|
|
589
|
|
|
590
|
Pattern pattern = Pattern.compile("#t[0-9]+#([0-9]+#){3}");
|
|
591
|
Matcher matcher = pattern.matcher(treeIndex);
|
|
592
|
Integer kingdomID = null;
|
|
593
|
if(matcher.find()) {
|
|
594
|
String treeIndexKingdom = matcher.group(0);
|
|
595
|
kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom);
|
|
596
|
}
|
|
597
|
if (kingdomID == null){
|
|
598
|
pattern = Pattern.compile("#t[0-9]+#([0-9]+#){2}");
|
|
599
|
matcher = pattern.matcher(treeIndex);
|
|
600
|
if(matcher.find()) {
|
|
601
|
String treeIndexKingdom = matcher.group(0);
|
|
602
|
Map<String, Integer> map = state.getTreeIndexKingdomMap();
|
|
603
|
kingdomID = map.get(treeIndexKingdom);
|
|
604
|
}
|
|
605
|
}
|
|
606
|
if(Rank.DOMAIN().equals(taxon.getName().getRank())){
|
|
607
|
return 0;
|
|
608
|
}
|
|
609
|
if(kingdomID == null){
|
|
610
|
logger.warn("Kingdom could not be defined for treeindex " + treeIndex);
|
|
611
|
}
|
|
612
|
return kingdomID;
|
|
613
|
}
|
|
614
|
}
|
|
615
|
}
|
|
616
|
|
|
617
|
private static Taxon checkPseudoOrRelatedTaxon(Taxon taxon) {
|
|
618
|
if (!taxon.getTaxonNodes().isEmpty()){
|
|
619
|
return taxon;
|
|
620
|
}else if(hasPseudoTaxonRelationship(taxon)){
|
|
621
|
return acceptedPseudoTaxon(taxon);
|
|
622
|
}else if(isMisappliedNameOrProParteSynonym(taxon)){
|
|
623
|
return acceptedTaxonConcept(taxon);
|
|
624
|
}else{
|
|
625
|
return taxon;
|
|
626
|
}
|
|
627
|
}
|
|
628
|
|
|
629
|
private static Taxon acceptedPseudoTaxon(Taxon taxon) {
|
|
630
|
for (TaxonRelationship rel : taxon.getRelationsFromThisTaxon()){
|
|
631
|
if (TaxonRelationshipType.pseudoTaxonUuids().contains(rel.getType().getUuid())){
|
|
632
|
return rel.getToTaxon();
|
|
633
|
}
|
|
634
|
}
|
|
635
|
return taxon;
|
|
636
|
}
|
|
637
|
|
|
638
|
private static Taxon acceptedTaxonConcept(Taxon taxon) {
|
|
639
|
for (TaxonRelationship rel : taxon.getRelationsFromThisTaxon()){
|
|
640
|
if (TaxonRelationshipType.misappliedNameUuids().contains(rel.getType().getUuid())||
|
|
641
|
TaxonRelationshipType.proParteOrPartialSynonymUuids().contains(rel.getType().getUuid())){
|
|
642
|
return rel.getToTaxon();
|
|
643
|
}
|
|
644
|
}
|
|
645
|
return taxon;
|
|
646
|
}
|
|
647
|
|
|
648
|
private static boolean hasPseudoTaxonRelationship(Taxon taxon) {
|
|
649
|
for (TaxonRelationship rel : taxon.getRelationsFromThisTaxon()){
|
|
650
|
if (TaxonRelationshipType.pseudoTaxonUuids().contains(rel.getType().getUuid())){
|
|
651
|
return true;
|
|
652
|
}
|
|
653
|
}
|
|
654
|
return false;
|
|
655
|
}
|
|
656
|
|
|
657
|
private static boolean isMisappliedNameOrProParteSynonym(Taxon taxon) {
|
|
658
|
for (TaxonRelationship rel : taxon.getRelationsFromThisTaxon()){
|
|
659
|
if (TaxonRelationshipType.misappliedNameUuids().contains(rel.getType().getUuid())||
|
|
660
|
TaxonRelationshipType.proParteOrPartialSynonymUuids().contains(rel.getType().getUuid())){
|
|
661
|
return true;
|
|
662
|
}
|
|
663
|
}
|
|
664
|
return false;
|
|
665
|
}
|
|
666
|
|
|
667
|
// "PHASE 5: Creating Inferred Synonyms..."
|
|
668
|
private boolean doPhase05(PesiExportState state, PesiExportMapping mapping, PesiExportMapping synRelMapping) {
|
|
669
|
int count;
|
|
670
|
int pastCount;
|
|
671
|
boolean success = true;
|
|
672
|
// Get the limit for objects to save within a single transaction.
|
|
673
|
if (! state.getConfig().isDoInferredSynonyms()){
|
|
674
|
logger.info ("Ignore PHASE 5: Creating Inferred Synonyms...");
|
|
675
|
return success;
|
|
676
|
}
|
|
677
|
|
|
678
|
int limit = state.getConfig().getLimitSave();
|
|
679
|
// Create inferred synonyms for accepted taxa
|
|
680
|
logger.info("PHASE 5: Creating Inferred Synonyms...");
|
|
681
|
|
|
682
|
// Determine the count of elements in data warehouse database table Taxon
|
|
683
|
currentTaxonId = determineTaxonCount(state);
|
|
684
|
currentTaxonId++;
|
|
685
|
|
|
686
|
count = 0;
|
|
687
|
pastCount = 0;
|
|
688
|
int pageSize = limit/10;
|
|
689
|
int pageNumber = 1;
|
|
690
|
String inferredSynonymPluralString = "Inferred Synonyms";
|
|
691
|
|
|
692
|
// Start transaction
|
|
693
|
TransactionStatus txStatus = startTransaction(true);
|
|
694
|
if (logger.isDebugEnabled()) {
|
|
695
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
696
|
}
|
|
697
|
|
|
698
|
List<TaxonBase> taxonList = null;
|
|
699
|
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", "*", Rank.SPECIES(), pageSize, pageNumber, null)).size() > 0) {
|
|
700
|
|
|
701
|
Map<Integer, TaxonName> inferredSynonymsDataToBeSaved = new HashMap<>();
|
|
702
|
|
|
703
|
if (logger.isDebugEnabled()) {
|
|
704
|
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
705
|
}
|
|
706
|
inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,
|
|
707
|
synRelMapping, taxonList));
|
|
708
|
|
|
709
|
doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);
|
|
710
|
// Commit transaction
|
|
711
|
commitTransaction(txStatus);
|
|
712
|
if (logger.isDebugEnabled()){logger.debug("Committed transaction.");}
|
|
713
|
logger.info("Exported " + (taxonList.size()) + " " + inferredSynonymPluralString + ". Total: " + count);
|
|
714
|
//pastCount = count;
|
|
715
|
|
|
716
|
// Save Rank Data and KingdomFk for inferred synonyms
|
|
717
|
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
|
718
|
TaxonName taxonName = inferredSynonymsDataToBeSaved.get(taxonFk);
|
|
719
|
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), taxonFk, kingdomFk, state);
|
|
720
|
}
|
|
721
|
|
|
722
|
// Start transaction
|
|
723
|
txStatus = startTransaction(true);
|
|
724
|
if (logger.isDebugEnabled()) {
|
|
725
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
726
|
}
|
|
727
|
|
|
728
|
// Increment pageNumber
|
|
729
|
pageNumber++;
|
|
730
|
}
|
|
731
|
taxonList = null;
|
|
732
|
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", "*", Rank.SUBSPECIES(), pageSize, pageNumber, null)).size() > 0) {
|
|
733
|
Map<Integer, TaxonName> inferredSynonymsDataToBeSaved = new HashMap<>();
|
|
734
|
|
|
735
|
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
736
|
inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,
|
|
737
|
synRelMapping, taxonList));
|
|
738
|
|
|
739
|
doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);
|
|
740
|
// Commit transaction
|
|
741
|
commitTransaction(txStatus);
|
|
742
|
logger.debug("Committed transaction.");
|
|
743
|
logger.info("Exported " + taxonList.size()+ " " + inferredSynonymPluralString + ". Total: " + count);
|
|
744
|
//pastCount = count;
|
|
745
|
|
|
746
|
// Save Rank Data and KingdomFk for inferred synonyms
|
|
747
|
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
|
748
|
TaxonName taxonName = inferredSynonymsDataToBeSaved.get(taxonFk);
|
|
749
|
invokeRankDataAndKingdomFk(taxonName, taxonFk, kingdomFk, state);
|
|
750
|
}
|
|
751
|
|
|
752
|
// Start transaction
|
|
753
|
txStatus = startTransaction(true);
|
|
754
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
755
|
|
|
756
|
// Increment pageNumber
|
|
757
|
pageNumber++;
|
|
758
|
inferredSynonymsDataToBeSaved = null;
|
|
759
|
}
|
|
760
|
if (taxonList.size() == 0) {
|
|
761
|
logger.info("No " + parentPluralString + " left to fetch.");
|
|
762
|
}
|
|
763
|
|
|
764
|
taxonList = null;
|
|
765
|
// logger.warn("Taking snapshot at the end of phase 5 of taxonExport");
|
|
766
|
// ProfilerController.memorySnapshot();
|
|
767
|
|
|
768
|
// Commit transaction
|
|
769
|
commitTransaction(txStatus);
|
|
770
|
System.gc();
|
|
771
|
logger.debug("Taking snapshot at the end of phase 5 after gc() of taxonExport");
|
|
772
|
//ProfilerController.memorySnapshot();
|
|
773
|
logger.debug("Committed transaction.");
|
|
774
|
return success;
|
|
775
|
}
|
|
776
|
|
|
777
|
private Map<Integer, TaxonName> createInferredSynonymsForTaxonList(PesiExportState state,
|
|
778
|
PesiExportMapping mapping, PesiExportMapping synRelMapping, List<TaxonBase> taxonList) {
|
|
779
|
|
|
780
|
Taxon acceptedTaxon;
|
|
781
|
Classification classification = null;
|
|
782
|
List<Synonym> inferredSynonyms = null;
|
|
783
|
boolean localSuccess = true;
|
|
784
|
|
|
785
|
Map<Integer, TaxonName> inferredSynonymsDataToBeSaved = new HashMap<>();
|
|
786
|
|
|
787
|
for (TaxonBase<?> taxonBase : taxonList) {
|
|
788
|
|
|
789
|
if (taxonBase.isInstanceOf(Taxon.class)) { // this should always be the case since we should have fetched accepted taxon only, but you never know...
|
|
790
|
acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
791
|
TaxonName taxonName = acceptedTaxon.getName();
|
|
792
|
|
|
793
|
if (taxonName.isZoological()) {
|
|
794
|
kingdomFk = findKingdomIdFromTreeIndex(taxonBase, state);
|
|
795
|
|
|
796
|
Set<TaxonNode> taxonNodes = acceptedTaxon.getTaxonNodes();
|
|
797
|
TaxonNode singleNode = null;
|
|
798
|
|
|
799
|
if (taxonNodes.size() > 0) {
|
|
800
|
// Determine the classification of the current TaxonNode
|
|
801
|
|
|
802
|
singleNode = taxonNodes.iterator().next();
|
|
803
|
if (singleNode != null) {
|
|
804
|
classification = singleNode.getClassification();
|
|
805
|
} else {
|
|
806
|
logger.error("A TaxonNode belonging to this accepted Taxon is NULL: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache() +")");
|
|
807
|
}
|
|
808
|
} else {
|
|
809
|
// Classification could not be determined directly from this TaxonNode
|
|
810
|
// The stored classification from another TaxonNode is used. It's a simple, but not a failsafe fallback solution.
|
|
811
|
if (taxonNodes.size() == 0) {
|
|
812
|
//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");
|
|
813
|
}
|
|
814
|
}
|
|
815
|
|
|
816
|
if (classification != null) {
|
|
817
|
try{
|
|
818
|
TaxonName name = acceptedTaxon.getName();
|
|
819
|
//if (name.isSpecies() || name.isInfraSpecific()){
|
|
820
|
inferredSynonyms = getTaxonService().createAllInferredSynonyms(acceptedTaxon, classification, true);
|
|
821
|
//}
|
|
822
|
// inferredSynonyms = getTaxonService().createInferredSynonyms(classification, acceptedTaxon, SynonymType.INFERRED_GENUS_OF());
|
|
823
|
if (inferredSynonyms != null) {
|
|
824
|
for (Synonym synonym : inferredSynonyms) {
|
|
825
|
// TaxonName synonymName = synonym.getName();
|
|
826
|
MarkerType markerType =getUuidMarkerType(PesiTransformer.uuidMarkerGuidIsMissing, state);
|
|
827
|
synonym.addMarker(Marker.NewInstance(markerType, true));
|
|
828
|
// Both Synonym and its TaxonName have no valid Id yet
|
|
829
|
synonym.setId(currentTaxonId++);
|
|
830
|
|
|
831
|
|
|
832
|
localSuccess &= mapping.invoke(synonym);
|
|
833
|
//get SynonymRelationship and export
|
|
834
|
if (synonym.getAcceptedTaxon() == null ){
|
|
835
|
IdentifiableSource source = synonym.getSources().iterator().next();
|
|
836
|
if (source.getIdNamespace().contains("Potential combination")){
|
|
837
|
acceptedTaxon.addSynonym(synonym, SynonymType.POTENTIAL_COMBINATION_OF());
|
|
838
|
logger.error(synonym.getTitleCache() + " is not attached to " + acceptedTaxon.getTitleCache() + " type is set to potential combination");
|
|
839
|
} else if (source.getIdNamespace().contains("Inferred Genus")){
|
|
840
|
acceptedTaxon.addSynonym(synonym, SynonymType.INFERRED_GENUS_OF());
|
|
841
|
logger.error(synonym.getTitleCache() + " is not attached to " + acceptedTaxon.getTitleCache() + " type is set to inferred genus");
|
|
842
|
} else if (source.getIdNamespace().contains("Inferred Epithet")){
|
|
843
|
acceptedTaxon.addSynonym(synonym, SynonymType.INFERRED_EPITHET_OF());
|
|
844
|
logger.error(synonym.getTitleCache() + " is not attached to " + acceptedTaxon.getTitleCache() + " type is set to inferred epithet");
|
|
845
|
} else{
|
|
846
|
acceptedTaxon.addSynonym(synonym, SynonymType.INFERRED_SYNONYM_OF());
|
|
847
|
logger.error(synonym.getTitleCache() + " is not attached to " + acceptedTaxon.getTitleCache() + " type is set to inferred synonym");
|
|
848
|
}
|
|
849
|
|
|
850
|
localSuccess &= synRelMapping.invoke(synonym);
|
|
851
|
if (!localSuccess) {
|
|
852
|
logger.error("Synonym relationship export failed " + synonym.getTitleCache() + " accepted taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
853
|
}
|
|
854
|
} else {
|
|
855
|
localSuccess &= synRelMapping.invoke(synonym);
|
|
856
|
if (!localSuccess) {
|
|
857
|
logger.error("Synonym relationship export failed " + synonym.getTitleCache() + " accepted taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
858
|
} else {
|
|
859
|
logger.info("Synonym relationship successfully exported: " + synonym.getTitleCache() + " " +acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
860
|
}
|
|
861
|
}
|
|
862
|
|
|
863
|
inferredSynonymsDataToBeSaved.put(synonym.getId(), synonym.getName());
|
|
864
|
}
|
|
865
|
}
|
|
866
|
}catch(Exception e){
|
|
867
|
logger.error(e.getMessage());
|
|
868
|
e.printStackTrace();
|
|
869
|
}
|
|
870
|
} else {
|
|
871
|
logger.error("Classification is NULL. Inferred Synonyms could not be created for this Taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache() + ")");
|
|
872
|
}
|
|
873
|
} else {
|
|
874
|
// logger.error("TaxonName is not a ZoologicalName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
875
|
}
|
|
876
|
} else {
|
|
877
|
logger.error("This TaxonBase is not a Taxon even though it should be: " + taxonBase.getUuid() + " (" + taxonBase.getTitleCache() + ")");
|
|
878
|
}
|
|
879
|
}
|
|
880
|
return inferredSynonymsDataToBeSaved;
|
|
881
|
}
|
|
882
|
|
|
883
|
/**
|
|
884
|
* Handles names that do not appear in taxa.
|
|
885
|
*/
|
|
886
|
private boolean doPhase01b_Names(PesiExportState state, PesiExportMapping additionalSourceMapping) {
|
|
887
|
|
|
888
|
boolean success = true;
|
|
889
|
if (! state.getConfig().isDoPureNames()){
|
|
890
|
logger.info ("Ignore PHASE 1b: PureNames");
|
|
891
|
return success;
|
|
892
|
}
|
|
893
|
|
|
894
|
try {
|
|
895
|
PesiExportMapping mapping = getPureNameMapping(state);
|
|
896
|
mapping.initialize(state);
|
|
897
|
int count = 0;
|
|
898
|
int pastCount = 0;
|
|
899
|
success = true;
|
|
900
|
// Get the limit for objects to save within a single transaction.
|
|
901
|
int limit = state.getConfig().getLimitSave();
|
|
902
|
|
|
903
|
logger.info("PHASE 1b: Export Pure Names ...");
|
|
904
|
// Start transaction
|
|
905
|
TransactionStatus txStatus = startTransaction(true);
|
|
906
|
logger.info("Started new transaction for Pure Names. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
907
|
|
|
908
|
int partitionCount = 0;
|
|
909
|
List<TaxonName> list;
|
|
910
|
while ((list = getNextPureNamePartition(null, limit, partitionCount++)) != null ) {
|
|
911
|
|
|
912
|
logger.debug("Fetched " + list.size() + pluralStringNames + " without taxa. Exporting...");
|
|
913
|
for (TaxonName taxonName : list) {
|
|
914
|
doCount(count++, modCount, pluralString);
|
|
915
|
success &= mapping.invoke(taxonName);
|
|
916
|
//additional source
|
|
917
|
if (taxonName.getNomenclaturalReference() != null || StringUtils.isNotBlank(taxonName.getNomenclaturalMicroReference() )){
|
|
918
|
additionalSourceMapping.invoke(taxonName);
|
|
919
|
}
|
|
920
|
}
|
|
921
|
|
|
922
|
// Commit transaction
|
|
923
|
commitTransaction(txStatus);
|
|
924
|
logger.debug("Committed transaction.");
|
|
925
|
logger.info("Exported " + (count - pastCount) + " " + pluralStringNames + ". Total: " + count + ". Partition: " + partitionCount);
|
|
926
|
pastCount = count;
|
|
927
|
|
|
928
|
// Start transaction
|
|
929
|
txStatus = startTransaction(true);
|
|
930
|
logger.debug("Started new transaction for PureNames. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
931
|
}
|
|
932
|
logger.debug("No " + pluralString + " left to fetch.");
|
|
933
|
|
|
934
|
// Commit transaction
|
|
935
|
commitTransaction(txStatus);
|
|
936
|
logger.debug("Committed transaction.");
|
|
937
|
} catch (Exception e) {
|
|
938
|
logger.error("Error occurred in pure name export");
|
|
939
|
e.printStackTrace();
|
|
940
|
success = false;
|
|
941
|
}
|
|
942
|
return success;
|
|
943
|
}
|
|
944
|
|
|
945
|
/**
|
|
946
|
* Determines the current number of entries in the DataWarehouse database table <code>Taxon</code>.
|
|
947
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
948
|
* @return The count.
|
|
949
|
*/
|
|
950
|
private Integer determineTaxonCount(PesiExportState state) {
|
|
951
|
Integer result = null;
|
|
952
|
PesiExportConfigurator pesiConfig = state.getConfig();
|
|
953
|
|
|
954
|
String sql;
|
|
955
|
Source destination = pesiConfig.getDestination();
|
|
956
|
sql = "SELECT max(taxonId) FROM Taxon";
|
|
957
|
destination.setQuery(sql);
|
|
958
|
ResultSet resultSet = destination.getResultSet();
|
|
959
|
try {
|
|
960
|
resultSet.next();
|
|
961
|
result = resultSet.getInt(1);
|
|
962
|
} catch (SQLException e) {
|
|
963
|
logger.error("TaxonCount could not be determined: " + e.getMessage());
|
|
964
|
e.printStackTrace();
|
|
965
|
}
|
|
966
|
resultSet = null;
|
|
967
|
return result;
|
|
968
|
}
|
|
969
|
|
|
970
|
/**
|
|
971
|
* Checks whether a parent at specific level has a specific Rank.
|
|
972
|
* @param taxonName A {@link TaxonNameBase TaxonName}.
|
|
973
|
* @param level The ancestor level.
|
|
974
|
* @param ancestorRank The ancestor rank.
|
|
975
|
* @return Whether a parent at a specific level has a specific Rank.
|
|
976
|
*/
|
|
977
|
private boolean validateAncestorOfSpecificRank(TaxonBase<?> taxonBase, int level, Rank ancestorRank) {
|
|
978
|
boolean result = false;
|
|
979
|
TaxonNode parentNode = null;
|
|
980
|
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
981
|
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
982
|
// Get ancestor Taxon via TaxonNode
|
|
983
|
Set<TaxonNode> taxonNodes = taxon.getTaxonNodes();
|
|
984
|
if (taxonNodes.size() == 1) {
|
|
985
|
TaxonNode taxonNode = taxonNodes.iterator().next();
|
|
986
|
if (taxonNode != null) {
|
|
987
|
for (int i = 0; i < level; i++) {
|
|
988
|
if (taxonNode != null) {
|
|
989
|
taxonNode = taxonNode.getParent();
|
|
990
|
}
|
|
991
|
}
|
|
992
|
parentNode = taxonNode;
|
|
993
|
}
|
|
994
|
} else if (taxonNodes.size() > 1) {
|
|
995
|
logger.error("This taxon has " + taxonNodes.size() + " taxonNodes: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
996
|
}
|
|
997
|
}
|
|
998
|
//compare
|
|
999
|
if (parentNode != null) {
|
|
1000
|
TaxonNode node = CdmBase.deproxy(parentNode, TaxonNode.class);
|
|
1001
|
Taxon parentTaxon = node.getTaxon();
|
|
1002
|
if (parentTaxon != null) {
|
|
1003
|
TaxonName parentTaxonName = parentTaxon.getName();
|
|
1004
|
if (parentTaxonName != null && parentTaxonName.getRank().equals(ancestorRank)) {
|
|
1005
|
result = true;
|
|
1006
|
}
|
|
1007
|
} else if (parentNode.treeIndex().matches("#t\\d+#\\d+#")) {
|
|
1008
|
//do nothing (is root node)
|
|
1009
|
} else {
|
|
1010
|
logger.error("This TaxonNode has no Taxon: " + node.getUuid());
|
|
1011
|
}
|
|
1012
|
}
|
|
1013
|
return result;
|
|
1014
|
}
|
|
1015
|
|
|
1016
|
/**
|
|
1017
|
* Returns the AnnotationType for a given UUID.
|
|
1018
|
* @param uuid The Annotation UUID.
|
|
1019
|
* @param label The Annotation label.
|
|
1020
|
* @param text The Annotation text.
|
|
1021
|
* @param labelAbbrev The Annotation label abbreviation.
|
|
1022
|
* @return The AnnotationType.
|
|
1023
|
*/
|
|
1024
|
protected AnnotationType getAnnotationType(UUID uuid, String label, String text, String labelAbbrev){
|
|
1025
|
AnnotationType annotationType = (AnnotationType)getTermService().find(uuid);
|
|
1026
|
if (annotationType == null) {
|
|
1027
|
annotationType = AnnotationType.NewInstance(label, text, labelAbbrev);
|
|
1028
|
annotationType.setUuid(uuid);
|
|
1029
|
// annotationType.setVocabulary(AnnotationType.EDITORIAL().getVocabulary());
|
|
1030
|
getTermService().save(annotationType);
|
|
1031
|
}
|
|
1032
|
return annotationType;
|
|
1033
|
}
|
|
1034
|
|
|
1035
|
private boolean invokeParentTaxonFk(Integer parentId, Integer childId) {
|
|
1036
|
try {
|
|
1037
|
parentTaxonFkStmt.setInt(1, parentId);
|
|
1038
|
parentTaxonFkStmt.setInt(2, childId);
|
|
1039
|
parentTaxonFkStmt.executeUpdate();
|
|
1040
|
return true;
|
|
1041
|
} catch (SQLException e) {
|
|
1042
|
logger.warn("ParentTaxonFk (" + (parentId ==null? "-":parentId) + ") could not be inserted into database "
|
|
1043
|
+ "for taxon "+ (childId == null? "-" :childId) + ": " + e.getMessage());
|
|
1044
|
e.printStackTrace();
|
|
1045
|
return false;
|
|
1046
|
}
|
|
1047
|
}
|
|
1048
|
|
|
1049
|
|
|
1050
|
/**
|
|
1051
|
* Inserts Rank data and KingdomFk into the Taxon database table.
|
|
1052
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1053
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1054
|
* @param taxonFk The TaxonFk to store the values for.
|
|
1055
|
* @param state
|
|
1056
|
* @param kindomFk The KingdomFk.
|
|
1057
|
* @return Whether save was successful or not.
|
|
1058
|
*/
|
|
1059
|
private boolean invokeRankDataAndKingdomFk(TaxonName taxonName,
|
|
1060
|
Integer taxonFk, Integer kingdomFk, PesiExportState state) {
|
|
1061
|
|
|
1062
|
try {
|
|
1063
|
Integer rankFk = getRankFk(taxonName, kingdomFk);
|
|
1064
|
if (rankFk != null) {
|
|
1065
|
rankUpdateStmt.setInt(1, rankFk);
|
|
1066
|
} else {
|
|
1067
|
rankUpdateStmt.setObject(1, null);
|
|
1068
|
}
|
|
1069
|
|
|
1070
|
String rankCache = getRankCache(taxonName, kingdomFk, state);
|
|
1071
|
if (rankCache != null) {
|
|
1072
|
rankUpdateStmt.setString(2, rankCache);
|
|
1073
|
} else {
|
|
1074
|
rankUpdateStmt.setObject(2, null);
|
|
1075
|
}
|
|
1076
|
|
|
1077
|
if (kingdomFk != null) {
|
|
1078
|
|
|
1079
|
rankUpdateStmt.setInt(3, kingdomFk);
|
|
1080
|
} else {
|
|
1081
|
rankUpdateStmt.setObject(3, null);
|
|
1082
|
}
|
|
1083
|
|
|
1084
|
if (taxonFk != null) {
|
|
1085
|
rankUpdateStmt.setInt(4, taxonFk);
|
|
1086
|
} else {
|
|
1087
|
rankUpdateStmt.setObject(4, null);
|
|
1088
|
}
|
|
1089
|
|
|
1090
|
rankUpdateStmt.executeUpdate();
|
|
1091
|
return true;
|
|
1092
|
} catch (SQLException e) {
|
|
1093
|
logger.error("Data (RankFk, RankCache, KingdomFk) could not be inserted into database: " + e.getMessage());
|
|
1094
|
e.printStackTrace();
|
|
1095
|
return false;
|
|
1096
|
}
|
|
1097
|
}
|
|
1098
|
|
|
1099
|
/**
|
|
1100
|
* Inserts Rank data, TypeNameFk, KingdomFk, expertFk and speciesExpertFk into the Taxon database table.
|
|
1101
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1102
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1103
|
* @param taxonFk The TaxonFk to store the values for.
|
|
1104
|
* @param typeNameFk The TypeNameFk.
|
|
1105
|
* @param rankFk
|
|
1106
|
* @param state
|
|
1107
|
* @param kindomFk The KingdomFk.
|
|
1108
|
* @param expertFk The ExpertFk.
|
|
1109
|
* @param speciesExpertFk The SpeciesExpertFk.
|
|
1110
|
* @return Whether save was successful or not.
|
|
1111
|
*/
|
|
1112
|
private boolean invokeRankDataAndTypeNameFkAndKingdomFk(TaxonName taxonName,
|
|
1113
|
Integer taxonFk, Integer typeNameFk, Integer kingdomFk, Integer rankFk, PesiExportState state) {
|
|
1114
|
|
|
1115
|
try {
|
|
1116
|
int index = 1;
|
|
1117
|
if (rankFk != null) {
|
|
1118
|
rankTypeExpertsUpdateStmt.setInt(index++, rankFk);
|
|
1119
|
} else {
|
|
1120
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1121
|
}
|
|
1122
|
|
|
1123
|
String rankCache = getRankCache(taxonName, kingdomFk, state);
|
|
1124
|
if (rankCache != null) {
|
|
1125
|
rankTypeExpertsUpdateStmt.setString(index++, rankCache);
|
|
1126
|
} else {
|
|
1127
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1128
|
}
|
|
1129
|
|
|
1130
|
if (typeNameFk != null) {
|
|
1131
|
rankTypeExpertsUpdateStmt.setInt(index++, typeNameFk);
|
|
1132
|
} else {
|
|
1133
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1134
|
}
|
|
1135
|
|
|
1136
|
if (kingdomFk != null) {
|
|
1137
|
rankTypeExpertsUpdateStmt.setInt(index++, kingdomFk);
|
|
1138
|
} else {
|
|
1139
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1140
|
}
|
|
1141
|
|
|
1142
|
// if (expertFk != null) {
|
|
1143
|
// rankTypeExpertsUpdateStmt.setInt(5, expertFk);
|
|
1144
|
// } else {
|
|
1145
|
// rankTypeExpertsUpdateStmt.setObject(5, null);
|
|
1146
|
// }
|
|
1147
|
//
|
|
1148
|
// //TODO handle experts GUIDS
|
|
1149
|
// if (speciesExpertFk != null) {
|
|
1150
|
// rankTypeExpertsUpdateStmt.setInt(6, speciesExpertFk);
|
|
1151
|
// } else {
|
|
1152
|
// rankTypeExpertsUpdateStmt.setObject(6, null);
|
|
1153
|
// }
|
|
1154
|
//
|
|
1155
|
if (taxonFk != null) {
|
|
1156
|
rankTypeExpertsUpdateStmt.setInt(index++, taxonFk);
|
|
1157
|
} else {
|
|
1158
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1159
|
}
|
|
1160
|
|
|
1161
|
rankTypeExpertsUpdateStmt.executeUpdate();
|
|
1162
|
return true;
|
|
1163
|
} catch (SQLException e) {
|
|
1164
|
String name = taxonName == null? null:taxonName.getTitleCache();
|
|
1165
|
logger.error("Data could not be inserted into database: " + e.getMessage() + "; rankFk = " + rankFk + "; kingdomFk = " + kingdomFk + "; taxonFk = "+ taxonFk + "; typeNameFk = " + typeNameFk + "; name = " + name);
|
|
1166
|
e.printStackTrace();
|
|
1167
|
return false;
|
|
1168
|
} catch (Exception e) {
|
|
1169
|
String name = taxonName == null? null:taxonName.getTitleCache();
|
|
1170
|
logger.error("Some exception occurred: " + e.getMessage() + "; rankFk = " + rankFk + "; kingdomFk = " + kingdomFk + "; taxonFk = "+ taxonFk + "; typeNameFk = " + typeNameFk + "; name = " + name);
|
|
1171
|
e.printStackTrace();
|
|
1172
|
return false;
|
|
1173
|
}
|
|
1174
|
}
|
|
1175
|
|
|
1176
|
/**
|
|
1177
|
* Deletes all entries of database tables related to <code>Taxon</code>.
|
|
1178
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1179
|
* @return Whether the delete operation was successful or not.
|
|
1180
|
*/
|
|
1181
|
protected boolean doDelete(PesiExportState state) {
|
|
1182
|
|
|
1183
|
Source destination = state.getConfig().getDestination();
|
|
1184
|
|
|
1185
|
String[] tables = new String[]{"AdditionalTaxonSource","CommonNameSource","CommonName",
|
|
1186
|
"Image","NoteSource","Note","OccurrenceSource","Occurrence","RelTaxon","Taxon"};
|
|
1187
|
|
|
1188
|
for(String table : tables){
|
|
1189
|
String sql = "DELETE FROM " + table;
|
|
1190
|
destination.update(sql);
|
|
1191
|
}
|
|
1192
|
|
|
1193
|
return true;
|
|
1194
|
}
|
|
1195
|
|
|
1196
|
private static Integer getRankFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode) {
|
|
1197
|
Integer kingdomId = PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode);
|
|
1198
|
return getRankFk(taxonName, kingdomId);
|
|
1199
|
}
|
|
1200
|
|
|
1201
|
/**
|
|
1202
|
* Returns the <code>RankFk</code> attribute.
|
|
1203
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1204
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1205
|
* @return The <code>RankFk</code> attribute.
|
|
1206
|
* @see MethodMapper
|
|
1207
|
*/
|
|
1208
|
private static Integer getRankFk(TaxonName taxonName, Integer kingdomId) {
|
|
1209
|
Integer result = null;
|
|
1210
|
try {
|
|
1211
|
if (taxonName != null) {
|
|
1212
|
if (taxonName.getRank() == null) {
|
|
1213
|
logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1214
|
} else {
|
|
1215
|
result = PesiTransformer.rank2RankId(taxonName.getRank(), kingdomId);
|
|
1216
|
}
|
|
1217
|
if (result == null) {
|
|
1218
|
logger.warn("Rank could not be determined for PESI-Kingdom-Id " + kingdomId + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1219
|
}
|
|
1220
|
}
|
|
1221
|
} catch (Exception e) {
|
|
1222
|
e.printStackTrace();
|
|
1223
|
}
|
|
1224
|
return result;
|
|
1225
|
}
|
|
1226
|
|
|
1227
|
@SuppressWarnings("unused") //used by mapper
|
|
1228
|
private static String getRankCache(TaxonName taxonName, PesiExportState state) {
|
|
1229
|
List<TaxonNode> nodes = getTaxonNodes(taxonName);
|
|
1230
|
Integer kingdomId;
|
|
1231
|
if (nodes == null||nodes.isEmpty()){
|
|
1232
|
kingdomId = getKingdomFk(taxonName);
|
|
1233
|
}else{
|
|
1234
|
//should not happen, method exists only pure names
|
|
1235
|
kingdomId = findKingdomIdFromTreeIndex(nodes.iterator().next().getTaxon(), state);
|
|
1236
|
}
|
|
1237
|
return getRankCache(taxonName, kingdomId, state);
|
|
1238
|
}
|
|
1239
|
|
|
1240
|
private static String getRankCache(TaxonName taxonName, Integer kingdomFk, PesiExportState state) {
|
|
1241
|
if (Rank.DOMAIN().equals(taxonName.getRank())){
|
|
1242
|
return state.getTransformer().getCacheByRankAndKingdom(Rank.DOMAIN(), null);
|
|
1243
|
}else if (kingdomFk != null) {
|
|
1244
|
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), kingdomFk);
|
|
1245
|
}else if (taxonName.getNameType() != null){
|
|
1246
|
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenclaturalCode2Kingdom(taxonName.getNameType()));
|
|
1247
|
}else{
|
|
1248
|
logger.warn("No kingdom ID could be defined for name " + taxonName.getUuid());
|
|
1249
|
return null;
|
|
1250
|
}
|
|
1251
|
}
|
|
1252
|
|
|
1253
|
private static List<TaxonNode> getTaxonNodes(TaxonName taxonName) {
|
|
1254
|
List<TaxonNode> result = new ArrayList<>();
|
|
1255
|
for (TaxonBase<?> tb:taxonName.getTaxonBases()){
|
|
1256
|
Taxon taxon;
|
|
1257
|
//TODO handle ERMS taxon relationships
|
|
1258
|
if (tb.isInstanceOf(Taxon.class)){
|
|
1259
|
taxon = CdmBase.deproxy(tb, Taxon.class);
|
|
1260
|
}else{
|
|
1261
|
taxon = CdmBase.deproxy(tb, Synonym.class).getAcceptedTaxon();
|
|
1262
|
}
|
|
1263
|
if (isPesiTaxon(taxon)){
|
|
1264
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
1265
|
result.add(node);
|
|
1266
|
}
|
|
1267
|
}
|
|
1268
|
}
|
|
1269
|
return result;
|
|
1270
|
}
|
|
1271
|
|
|
1272
|
// @SuppressWarnings("unused") //used by pure name mapper and by getRankFk
|
|
1273
|
private static Integer getKingdomFk(TaxonName taxonName){
|
|
1274
|
EnumSet<PesiSource> origin = getSources(taxonName);
|
|
1275
|
if (origin.size() == 1 && origin.contains(PesiSource.EM)){
|
|
1276
|
//maybe simply replace by
|
|
1277
|
//return PesiTransformer.KINGDOM_PLANTAE;
|
|
1278
|
return PesiTransformer.nomenclaturalCode2Kingdom(taxonName.getNameType());
|
|
1279
|
}else{
|
|
1280
|
logger.warn("getKingdomFk not yet implemented for non-EuroMed pure names");
|
|
1281
|
return null;
|
|
1282
|
}
|
|
1283
|
}
|
|
1284
|
|
|
1285
|
/**
|
|
1286
|
* Returns the rankFk for the taxon name based on the names nomenclatural code.
|
|
1287
|
* You may not use this method for kingdoms other then Animalia, Plantae and Bacteria.
|
|
1288
|
*/
|
|
1289
|
@SuppressWarnings("unused") //used by pure name mapper
|
|
1290
|
private static Integer getRankFk(TaxonName taxonName) {
|
|
1291
|
EnumSet<PesiSource> origin = getSources(taxonName);
|
|
1292
|
if (origin.size() == 1 && origin.contains(PesiSource.EM)){
|
|
1293
|
return getRankFk(taxonName, getKingdomFk(taxonName));
|
|
1294
|
}else{
|
|
1295
|
logger.warn("getRankFk not yet implemented for non-EuroMed pure names");
|
|
1296
|
return null;
|
|
1297
|
}
|
|
1298
|
}
|
|
1299
|
|
|
1300
|
/**
|
|
1301
|
* Returns the <code>AuthorString</code> attribute.
|
|
1302
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1303
|
* @return The <code>AuthorString</code> attribute.
|
|
1304
|
* @see MethodMapper
|
|
1305
|
*/
|
|
1306
|
//used by mapper
|
|
1307
|
protected static String getAuthorString(TaxonBase<?> taxon) {
|
|
1308
|
try {
|
|
1309
|
// For misapplied names there are special rules
|
|
1310
|
if (isMisappliedName(taxon)){
|
|
1311
|
return getMisappliedNameAuthorship(taxon);
|
|
1312
|
}else{
|
|
1313
|
boolean isNonViralName = false;
|
|
1314
|
String authorshipCache = null;
|
|
1315
|
TaxonName taxonName = taxon.getName();
|
|
1316
|
if (taxonName != null && taxonName.isNonViral()){
|
|
1317
|
authorshipCache = taxonName.getAuthorshipCache();
|
|
1318
|
isNonViralName = true;
|
|
1319
|
}
|
|
1320
|
String result = authorshipCache;
|
|
1321
|
|
|
1322
|
if (taxonName == null){
|
|
1323
|
logger.warn("TaxonName does not exist for taxon: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
1324
|
}else if (! isNonViralName){
|
|
1325
|
logger.warn("TaxonName is not of instance NonViralName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1326
|
}
|
|
1327
|
|
|
1328
|
if (StringUtils.isBlank(result)) {
|
|
1329
|
return null;
|
|
1330
|
} else {
|
|
1331
|
return result;
|
|
1332
|
}
|
|
1333
|
}
|
|
1334
|
} catch (Exception e) {
|
|
1335
|
e.printStackTrace();
|
|
1336
|
return null;
|
|
1337
|
}
|
|
1338
|
}
|
|
1339
|
|
|
1340
|
private static String getMisappliedNameAuthorship(TaxonBase<?> taxon){
|
|
1341
|
String result;
|
|
1342
|
String relAppendedPhrase = taxon.getAppendedPhrase();
|
|
1343
|
Reference sec = taxon.getSec();
|
|
1344
|
String secTitle = sec != null ? sec.getTitleCache(): null;
|
|
1345
|
if(relAppendedPhrase == null && sec == null) {
|
|
1346
|
result = "auct.";
|
|
1347
|
}else if (relAppendedPhrase != null && sec == null){
|
|
1348
|
result = relAppendedPhrase;
|
|
1349
|
}else if (relAppendedPhrase == null && sec != null){
|
|
1350
|
result = "sensu " + secTitle;
|
|
1351
|
}else{ //append!=null && sec!=null
|
|
1352
|
result = relAppendedPhrase + " " + secTitle;
|
|
1353
|
}
|
|
1354
|
String authorship = taxon.getName().getAuthorshipCache();
|
|
1355
|
if (isNotBlank(authorship)){
|
|
1356
|
result += ", non " + authorship;
|
|
1357
|
}
|
|
1358
|
return result;
|
|
1359
|
}
|
|
1360
|
|
|
1361
|
/**
|
|
1362
|
* Returns the <code>DisplayName</code> attribute.
|
|
1363
|
* @param taxon The {@link TaxonBase Taxon}.
|
|
1364
|
* @return The <code>DisplayName</code> attribute.
|
|
1365
|
* @see MethodMapper
|
|
1366
|
*/
|
|
1367
|
//used by Mapper
|
|
1368
|
private static String getDisplayName(TaxonBase<?> taxon) {
|
|
1369
|
boolean isMisapplied = isMisappliedName(taxon);
|
|
1370
|
TaxonName taxonName = taxon.getName();
|
|
1371
|
String result = getDisplayName(taxonName, isMisapplied);
|
|
1372
|
if (isMisapplied){
|
|
1373
|
result = result + " " + getMisappliedNameAuthorship(taxon);
|
|
1374
|
}
|
|
1375
|
return result;
|
|
1376
|
}
|
|
1377
|
|
|
1378
|
/**
|
|
1379
|
* Returns the <code>DisplayName</code> attribute.
|
|
1380
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1381
|
* @return The <code>DisplayName</code> attribute.
|
|
1382
|
* @see MethodMapper
|
|
1383
|
*/
|
|
1384
|
@SuppressWarnings("unused") //used by Mapper
|
|
1385
|
private static String getDisplayName(TaxonName taxonName) {
|
|
1386
|
return getDisplayName(taxonName, false);
|
|
1387
|
}
|
|
1388
|
|
|
1389
|
private static String getDisplayName(TaxonName taxonName, boolean useNameCache) {
|
|
1390
|
if (taxonName == null) {
|
|
1391
|
return null;
|
|
1392
|
}else{
|
|
1393
|
taxonName = CdmBase.deproxy(taxonName);
|
|
1394
|
INonViralNameCacheStrategy cacheStrategy = getCacheStrategy(taxonName);
|
|
1395
|
HTMLTagRules tagRules = new HTMLTagRules().
|
|
1396
|
addRule(TagEnum.name, "i").
|
|
1397
|
addRule(TagEnum.nomStatus, "@status@");
|
|
1398
|
|
|
1399
|
String result;
|
|
1400
|
if (useNameCache){
|
|
1401
|
result = cacheStrategy.getNameCache(taxonName, tagRules);
|
|
1402
|
}else{
|
|
1403
|
EnumSet<PesiSource> sources = getSources(taxonName);
|
|
1404
|
if (sources.contains(PesiSource.ERMS)){
|
|
1405
|
result = cacheStrategy.getTitleCache(taxonName, tagRules); //according to SQL script (also in ERMS sources are not abbreviated)
|
|
1406
|
}else if (sources.contains(PesiSource.FE) || sources.contains(PesiSource.IF)){
|
|
1407
|
//TODO define for FE + IF and for multiple sources
|
|
1408
|
result = cacheStrategy.getFullTitleCache(taxonName, tagRules);
|
|
1409
|
}else if (sources.contains(PesiSource.EM)){
|
|
1410
|
result = cacheStrategy.getFullTitleCache(taxonName, tagRules);
|
|
1411
|
}else{
|
|
1412
|
logger.warn("Source not yet handled");
|
|
1413
|
result = cacheStrategy.getTitleCache(taxonName, tagRules);
|
|
1414
|
}
|
|
1415
|
result = replaceTagForInfraSpecificMarkerForProtectedTitleCache(taxonName, result);
|
|
1416
|
result = result.replaceAll("(, ?)?\\<@status@\\>.*\\</@status@\\>", "").trim();
|
|
1417
|
}
|
|
1418
|
return result;
|
|
1419
|
}
|
|
1420
|
}
|
|
1421
|
|
|
1422
|
/**
|
|
1423
|
* Returns the <code>WebShowName</code> attribute for a taxon.
|
|
1424
|
* See {@link #getWebShowName(TaxonName)} for further explanations.
|
|
1425
|
* @param taxon The {@link TaxonBase taxon}.
|
|
1426
|
* @return The <code>WebShowName</code> attribute.
|
|
1427
|
* @see #getWebShowName(TaxonName)
|
|
1428
|
* @see #getDisplayName(TaxonBase)
|
|
1429
|
* @see #getFullName(TaxonBase)
|
|
1430
|
* @see MethodMapper
|
|
1431
|
*/
|
|
1432
|
@SuppressWarnings("unused")
|
|
1433
|
private static String getWebShowName(TaxonBase<?> taxon) {
|
|
1434
|
if (isMisappliedName(taxon)){
|
|
1435
|
//for misapplications the webshowname is the same as the displayname as they do not show the nom.ref. in displayname
|
|
1436
|
return getDisplayName(taxon);
|
|
1437
|
}else{
|
|
1438
|
TaxonName taxonName = taxon.getName();
|
|
1439
|
return getWebShowName(taxonName);
|
|
1440
|
}
|
|
1441
|
}
|
|
1442
|
|
|
1443
|
/**
|
|
1444
|
* Returns the <code>WebShowName</code> attribute for a name. The
|
|
1445
|
* <code>WebShowName</code> is like fullName but with
|
|
1446
|
* tagged (<i>) name part. It is also similar to
|
|
1447
|
* <code>DisplayName</code> but for titleCache not fullTitleCache.
|
|
1448
|
* For misapplications it slightly differs (see {@link #getWebShowName(TaxonBase)} )
|
|
1449
|
*
|
|
1450
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1451
|
* @return The <code>WebShowName</code> attribute.
|
|
1452
|
* @see #getDisplayName(TaxonName)
|
|
1453
|
* @see #getFullName(TaxonName)
|
|
1454
|
* @see #getWebShowName(TaxonBase)
|
|
1455
|
* @see MethodMapper
|
|
1456
|
*/
|
|
1457
|
private static String getWebShowName(TaxonName taxonName) {
|
|
1458
|
if (taxonName == null) {
|
|
1459
|
return null;
|
|
1460
|
}else{
|
|
1461
|
taxonName = CdmBase.deproxy(taxonName);
|
|
1462
|
INonViralNameCacheStrategy cacheStrategy = getCacheStrategy(taxonName);
|
|
1463
|
|
|
1464
|
HTMLTagRules tagRules = new HTMLTagRules().addRule(TagEnum.name, "i");
|
|
1465
|
String result = cacheStrategy.getTitleCache(taxonName, tagRules);
|
|
1466
|
result = replaceTagForInfraSpecificMarkerForProtectedTitleCache(taxonName, result);
|
|
1467
|
return result;
|
|
1468
|
}
|
|
1469
|
}
|
|
1470
|
|
|
1471
|
private static String replaceTagForInfraSpecificMarkerForProtectedTitleCache(TaxonName taxonName, String result) {
|
|
1472
|
if (taxonName.isProtectedTitleCache()||taxonName.isProtectedNameCache()){
|
|
1473
|
if (!taxonName.isAutonym()){
|
|
1474
|
result = result
|
|
1475
|
.replace(" subsp. ", "</i> subsp. <i>")
|
|
1476
|
.replace(" var. ", "</i> var. <i>")
|
|
1477
|
.replace(" subvar. ", "</i> subvar. <i>")
|
|
1478
|
.replace(" f. ", "</i> f. <i>")
|
|
1479
|
.replace(" subf. ", "</i> subf. <i>") //does this exist?
|
|
1480
|
;
|
|
1481
|
}
|
|
1482
|
}
|
|
1483
|
return result;
|
|
1484
|
}
|
|
1485
|
|
|
1486
|
/**
|
|
1487
|
* Returns the <code>WebSearchName</code> attribute.
|
|
1488
|
* @param taxonName The {@link NonViralName NonViralName}.
|
|
1489
|
* @return The <code>WebSearchName</code> attribute.
|
|
1490
|
* @see MethodMapper
|
|
1491
|
*/
|
|
1492
|
@SuppressWarnings("unused")
|
|
1493
|
private static String getWebSearchName(TaxonName taxonName) {
|
|
1494
|
//TODO extensions?
|
|
1495
|
TaxonNameDefaultCacheStrategy strategy = getCacheStrategy(taxonName);
|
|
1496
|
String result = strategy.getNameCache(taxonName);
|
|
1497
|
return result;
|
|
1498
|
}
|
|
1499
|
|
|
1500
|
@SuppressWarnings("unused") //used by mapper
|
|
1501
|
private static String getFullName(TaxonBase<?> taxon) {
|
|
1502
|
if (isMisappliedName(taxon)){
|
|
1503
|
String result = getCacheStrategy(taxon.getName()).getNameCache(taxon.getName());
|
|
1504
|
result = result + " " + getMisappliedNameAuthorship(taxon);
|
|
1505
|
return result;
|
|
1506
|
}else{
|
|
1507
|
return getFullName(taxon.getName());
|
|
1508
|
}
|
|
1509
|
}
|
|
1510
|
|
|
1511
|
/**
|
|
1512
|
* Returns the <code>FullName</code> attribute.
|
|
1513
|
* @param taxonName The {@link NonViralName NonViralName}.
|
|
1514
|
* @return The <code>FullName</code> attribute.
|
|
1515
|
* @see MethodMapper
|
|
1516
|
*/
|
|
1517
|
//used by mapper
|
|
1518
|
private static String getFullName(TaxonName taxonName) {
|
|
1519
|
//TODO extensions?
|
|
1520
|
String result = getCacheStrategy(taxonName).getTitleCache(taxonName);
|
|
1521
|
//misapplied names are now handled differently in getFullName(TaxonBase)
|
|
1522
|
// Iterator<Taxon> taxa = taxonName.getTaxa().iterator();
|
|
1523
|
// if (taxonName.getTaxa().size() >0){
|
|
1524
|
// if (taxonName.getTaxa().size() == 1){
|
|
1525
|
// Taxon taxon = taxa.next();
|
|
1526
|
// if (isMisappliedName(taxon)){
|
|
1527
|
// result = result + " " + getAuthorString(taxon);
|
|
1528
|
// }
|
|
1529
|
// }
|
|
1530
|
// }
|
|
1531
|
return result;
|
|
1532
|
}
|
|
1533
|
|
|
1534
|
@SuppressWarnings("unused")
|
|
1535
|
private static String getGUID(TaxonName taxonName) {
|
|
1536
|
UUID uuid = taxonName.getUuid();
|
|
1537
|
String result = "NameUUID:" + uuid.toString();
|
|
1538
|
return result;
|
|
1539
|
}
|
|
1540
|
|
|
1541
|
static boolean isFirstAbbrevTitle = true;
|
|
1542
|
/**
|
|
1543
|
* Returns the SourceNameCache for the AdditionalSource table
|
|
1544
|
*/
|
|
1545
|
@SuppressWarnings("unused")
|
|
1546
|
private static String getSourceNameCache(TaxonName taxonName) {
|
|
1547
|
if (taxonName != null){
|
|
1548
|
Reference nomRef = taxonName.getNomenclaturalReference();
|
|
1549
|
if (nomRef != null ){
|
|
1550
|
if (isFirstAbbrevTitle){
|
|
1551
|
//#5388 is definetely not the correct ticket number
|
|
1552
|
logger.warn("Semantics of getAbbrevTitleCache has changed. Please check if output is still correct. See #5388");
|
|
1553
|
isFirstAbbrevTitle = false;
|
|
1554
|
}
|
|
1555
|
return nomRef.getAbbrevTitleCache();
|
|
1556
|
}
|
|
1557
|
}
|
|
1558
|
return null;
|
|
1559
|
}
|
|
1560
|
|
|
1561
|
/**
|
|
1562
|
* Returns the nomenclatural reference which is the reference
|
|
1563
|
* including the detail (microreference).
|
|
1564
|
* @param taxonName The {@link TaxonName taxon name}.
|
|
1565
|
* @see MethodMapper
|
|
1566
|
*/
|
|
1567
|
@SuppressWarnings("unused")
|
|
1568
|
private static String getNomRefString(TaxonName taxonName) {
|
|
1569
|
INomenclaturalReference ref = taxonName.getNomenclaturalReference();
|
|
1570
|
if (ref == null){
|
|
1571
|
return null;
|
|
1572
|
}
|
|
1573
|
String result = null;
|
|
1574
|
EnumSet<PesiSource> sources = getSources(taxonName);
|
|
1575
|
if(sources.contains(PesiSource.EM)){
|
|
1576
|
if (! ref.isProtectedAbbrevTitleCache()){
|
|
1577
|
ref.setAbbrevTitleCache(null, false); //to remove a false cache
|
|
1578
|
}
|
|
1579
|
result = ref.getNomenclaturalCitation(taxonName.getNomenclaturalMicroReference());
|
|
1580
|
}else if(sources.contains(PesiSource.FE)||sources.contains(PesiSource.IF) ){
|
|
1581
|
//TODO still need to check if correct for FE + IF
|
|
1582
|
if (! ref.isProtectedAbbrevTitleCache()){
|
|
1583
|
ref.setAbbrevTitleCache(null, false); //to remove a false cache
|
|
1584
|
}
|
|
1585
|
result = ref.getNomenclaturalCitation(taxonName.getNomenclaturalMicroReference());
|
|
1586
|
return result; // according to SQL script
|
|
1587
|
}else if(sources.contains(PesiSource.ERMS)) {
|
|
1588
|
//result = null; //according to SQL script
|
|
1589
|
}else{
|
|
1590
|
logger.warn("Source not yet supported");
|
|
1591
|
}
|
|
1592
|
return result;
|
|
1593
|
}
|
|
1594
|
|
|
1595
|
/**
|
|
1596
|
* Returns the <code>NameStatusFk</code> attribute.
|
|
1597
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1598
|
* @return The <code>NameStatusFk</code> attribute.
|
|
1599
|
* @see MethodMapper
|
|
1600
|
*/
|
|
1601
|
@SuppressWarnings("unused")
|
|
1602
|
private static Integer getNameStatusFk(TaxonName taxonName) {
|
|
1603
|
Integer result = null;
|
|
1604
|
|
|
1605
|
NomenclaturalStatus status = getNameStatus(taxonName);
|
|
1606
|
if (status != null) {
|
|
1607
|
result = PesiTransformer.nomStatus2nomStatusFk(status.getType());
|
|
1608
|
}
|
|
1609
|
return result;
|
|
1610
|
}
|
|
1611
|
|
|
1612
|
/**
|
|
1613
|
* Returns the <code>NameStatusCache</code> attribute.
|
|
1614
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1615
|
* @return The <code>NameStatusCache</code> attribute.
|
|
1616
|
* @throws UndefinedTransformerMethodException
|
|
1617
|
* @see MethodMapper
|
|
1618
|
*/
|
|
1619
|
@SuppressWarnings("unused")
|
|
1620
|
private static String getNameStatusCache(TaxonName taxonName, PesiExportState state) throws UndefinedTransformerMethodException {
|
|
1621
|
String result = null;
|
|
1622
|
NomenclaturalStatus status = getNameStatus(taxonName);
|
|
1623
|
if (status != null) {
|
|
1624
|
result = state.getTransformer().getCacheByNomStatus(status.getType());
|
|
1625
|
}
|
|
1626
|
return result;
|
|
1627
|
}
|
|
1628
|
|
|
1629
|
private static NomenclaturalStatus getNameStatus(TaxonName taxonName) {
|
|
1630
|
try {
|
|
1631
|
if (taxonName != null) {
|
|
1632
|
Set<NomenclaturalStatus> states = taxonName.getStatus();
|
|
1633
|
if (states.size() >= 1) {
|
|
1634
|
if (states.size() > 1) {
|
|
1635
|
String statusStr = null;
|
|
1636
|
for (NomenclaturalStatus status: states){
|
|
1637
|
statusStr = CdmUtils.concat(",", statusStr, status.getType()== null? null:status.getType().getTitleCache());
|
|
1638
|
}
|
|
1639
|
//a known case is ad43508a-8a10-480a-8519-2a76de2c0a0f (Labiatae Juss.) from E+M
|
|
1640
|
logger.warn("This TaxonName has more than one nomenclatural status. This may happen in very rare cases but is not handled by the PESI data warehouse. Taxon name: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")Status:" + statusStr);
|
|
1641
|
}
|
|
1642
|
NomenclaturalStatus status = states.iterator().next();
|
|
1643
|
return status;
|
|
1644
|
}
|
|
1645
|
}
|
|
1646
|
} catch (Exception e) {
|
|
1647
|
e.printStackTrace();
|
|
1648
|
}
|
|
1649
|
return null;
|
|
1650
|
}
|
|
1651
|
|
|
1652
|
/**
|
|
1653
|
* Returns the <code>TaxonStatusFk</code> attribute.
|
|
1654
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1655
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1656
|
* @return The <code>TaxonStatusFk</code> attribute.
|
|
1657
|
* @see MethodMapper
|
|
1658
|
*/
|
|
1659
|
private static Integer getTaxonStatusFk(TaxonBase<?> taxon, PesiExportState state) {
|
|
1660
|
try {
|
|
1661
|
return PesiTransformer.taxonBase2statusFk(taxon);
|
|
1662
|
} catch (Exception e) {
|
|
1663
|
e.printStackTrace();
|
|
1664
|
return null;
|
|
1665
|
}
|
|
1666
|
}
|
|
1667
|
|
|
1668
|
/**
|
|
1669
|
* Returns the <code>TaxonStatusCache</code> attribute.
|
|
1670
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1671
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1672
|
* @return The <code>TaxonStatusCache</code> attribute.
|
|
1673
|
* @throws UndefinedTransformerMethodException
|
|
1674
|
* @see MethodMapper
|
|
1675
|
*/
|
|
1676
|
@SuppressWarnings("unused")
|
|
1677
|
private static String getTaxonStatusCache(TaxonBase<?> taxon, PesiExportState state) throws UndefinedTransformerMethodException {
|
|
1678
|
return state.getTransformer().getTaxonStatusCacheByKey(getTaxonStatusFk(taxon, state));
|
|
1679
|
}
|
|
1680
|
|
|
1681
|
/**
|
|
1682
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.
|
|
1683
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
1684
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1685
|
* @return The <code>TaxonFk1</code> attribute.
|
|
1686
|
* @see MethodMapper
|
|
1687
|
*/
|
|
1688
|
@SuppressWarnings("unused")
|
|
1689
|
private static Integer getSynonym(Synonym synonym, PesiExportState state) {
|
|
1690
|
return state.getDbId(synonym);
|
|
1691
|
}
|
|
1692
|
|
|
1693
|
/**
|
|
1694
|
* Returns the <code>TypeNameFk</code> attribute.
|
|
1695
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1696
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1697
|
* @return The <code>TypeNameFk</code> attribute.
|
|
1698
|
* @see MethodMapper
|
|
1699
|
*/
|
|
1700
|
private static Integer getTypeNameFk(TaxonName taxonName, PesiExportState state) {
|
|
1701
|
Integer result = null;
|
|
1702
|
if (taxonName != null) {
|
|
1703
|
Set<NameTypeDesignation> nameTypeDesignations = taxonName.getNameTypeDesignations();
|
|
1704
|
if (nameTypeDesignations.size() == 1) {
|
|
1705
|
NameTypeDesignation nameTypeDesignation = nameTypeDesignations.iterator().next();
|
|
1706
|
if (nameTypeDesignation != null) {
|
|
1707
|
TaxonName typeName = nameTypeDesignation.getTypeName();
|
|
1708
|
if (typeName != null) {
|
|
1709
|
if (typeName.getTaxonBases().isEmpty()){
|
|
1710
|
logger.warn("Type name does not belong to a taxon and therefore is not expected to be a European taxon. Type name not added. Type name: " + typeName.getTitleCache() + ", typified name: " + taxonName.getTitleCache());
|
|
1711
|
}else{
|
|
1712
|
result = state.getDbId(typeName);
|
|
1713
|
}
|
|
1714
|
}
|
|
1715
|
}
|
|
1716
|
} else if (nameTypeDesignations.size() > 1) {
|
|
1717
|
logger.warn("This TaxonName has " + nameTypeDesignations.size() + " NameTypeDesignations: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1718
|
}
|
|
1719
|
}
|
|
1720
|
return result;
|
|
1721
|
}
|
|
1722
|
|
|
1723
|
/**
|
|
1724
|
* Returns the <code>TypeFullnameCache</code> attribute.
|
|
1725
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1726
|
* @return The <code>TypeFullnameCache</code> attribute.
|
|
1727
|
* @see MethodMapper
|
|
1728
|
*/
|
|
1729
|
@SuppressWarnings("unused")
|
|
1730
|
private static String getTypeFullnameCache(TaxonName taxonName) {
|
|
1731
|
String result = null;
|
|
1732
|
|
|
1733
|
try {
|
|
1734
|
if (taxonName != null) {
|
|
1735
|
Set<NameTypeDesignation> nameTypeDesignations = taxonName.getNameTypeDesignations();
|
|
1736
|
if (nameTypeDesignations.size() == 1) {
|
|
1737
|
NameTypeDesignation nameTypeDesignation = nameTypeDesignations.iterator().next();
|
|
1738
|
if (nameTypeDesignation != null) {
|
|
1739
|
TaxonName typeName = nameTypeDesignation.getTypeName();
|
|
1740
|
if (typeName != null) {
|
|
1741
|
result = typeName.getTitleCache();
|
|
1742
|
}
|
|
1743
|
}
|
|
1744
|
} else if (nameTypeDesignations.size() > 1) {
|
|
1745
|
logger.warn("This TaxonName has " + nameTypeDesignations.size() + " NameTypeDesignations: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1746
|
}
|
|
1747
|
}
|
|
1748
|
} catch (Exception e) {
|
|
1749
|
e.printStackTrace();
|
|
1750
|
}
|
|
1751
|
return result;
|
|
1752
|
}
|
|
1753
|
|
|
1754
|
|
|
1755
|
/**
|
|
1756
|
* Returns the <code>QualityStatusFk</code> attribute.
|
|
1757
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1758
|
* @return The <code>QualityStatusFk</code> attribute.
|
|
1759
|
* @see MethodMapper
|
|
1760
|
*/
|
|
1761
|
private static Integer getQualityStatusFk(TaxonName taxonName) {
|
|
1762
|
EnumSet<PesiSource> sources = getSources(taxonName);
|
|
1763
|
return PesiTransformer.getQualityStatusKeyBySource(sources, taxonName);
|
|
1764
|
}
|
|
1765
|
|
|
1766
|
/**
|
|
1767
|
* Returns the <code>QualityStatusCache</code> attribute.
|
|
1768
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1769
|
* @return The <code>QualityStatusCache</code> attribute.
|
|
1770
|
* @throws UndefinedTransformerMethodException
|
|
1771
|
* @see MethodMapper
|
|
1772
|
*/
|
|
1773
|
@SuppressWarnings("unused")
|
|
1774
|
private static String getQualityStatusCache(TaxonName taxonName, PesiExportState state) throws UndefinedTransformerMethodException {
|
|
1775
|
return state.getTransformer().getQualityStatusCacheByKey(getQualityStatusFk(taxonName));
|
|
1776
|
}
|
|
1777
|
|
|
1778
|
|
|
1779
|
/**
|
|
1780
|
* Returns the <code>TypeDesignationStatusFk</code> attribute.
|
|
1781
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1782
|
* @return The <code>TypeDesignationStatusFk</code> attribute.
|
|
1783
|
* @see MethodMapper
|
|
1784
|
*/
|
|
1785
|
//TODO seems not to be used
|
|
1786
|
private static Integer getTypeDesignationStatusFk(TaxonName taxonName) {
|
|
1787
|
Integer result = null;
|
|
1788
|
|
|
1789
|
try {
|
|
1790
|
if (taxonName != null) {
|
|
1791
|
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations();
|
|
1792
|
if (typeDesignations.size() == 1) {
|
|
1793
|
Object obj = typeDesignations.iterator().next().getTypeStatus();
|
|
1794
|
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class);
|
|
1795
|
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusId(designationStatus);
|
|
1796
|
} else if (typeDesignations.size() > 1) {
|
|
1797
|
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1798
|
}
|
|
1799
|
}
|
|
1800
|
} catch (Exception e) {
|
|
1801
|
e.printStackTrace();
|
|
1802
|
}
|
|
1803
|
return result;
|
|
1804
|
}
|
|
1805
|
|
|
1806
|
/**
|
|
1807
|
* Returns the <code>TypeDesignationStatusCache</code> attribute.
|
|
1808
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1809
|
* @return The <code>TypeDesignationStatusCache</code> attribute.
|
|
1810
|
* @see MethodMapper
|
|
1811
|
*/
|
|
1812
|
//TODO seems not to be used
|
|
1813
|
private static String getTypeDesignationStatusCache(TaxonName taxonName) {
|
|
1814
|
String result = null;
|
|
1815
|
|
|
1816
|
try {
|
|
1817
|
if (taxonName != null) {
|
|
1818
|
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations();
|
|
1819
|
if (typeDesignations.size() == 1) {
|
|
1820
|
Object obj = typeDesignations.iterator().next().getTypeStatus();
|
|
1821
|
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class);
|
|
1822
|
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusCache(designationStatus);
|
|
1823
|
} else if (typeDesignations.size() > 1) {
|
|
1824
|
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1825
|
}
|
|
1826
|
}
|
|
1827
|
} catch (Exception e) {
|
|
1828
|
e.printStackTrace();
|
|
1829
|
}
|
|
1830
|
return result;
|
|
1831
|
}
|
|
1832
|
|
|
1833
|
/**
|
|
1834
|
* Returns the <code>FossilStatusFk</code> attribute.
|
|
1835
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1836
|
* @return The <code>FossilStatusFk</code> attribute.
|
|
1837
|
* @see MethodMapper
|
|
1838
|
*/
|
|
1839
|
@SuppressWarnings("unused")
|
|
1840
|
private static Integer getFossilStatusFk(IdentifiableEntity<?> identEntity, PesiExportState state) {
|
|
1841
|
Integer result = null;
|
|
1842
|
|
|
1843
|
Set<String> fossilStatuus = identEntity.getExtensions(ErmsTransformer.uuidExtFossilStatus);
|
|
1844
|
if (fossilStatuus.size() == 0){
|
|
1845
|
return null;
|
|
1846
|
}else if (fossilStatuus.size() > 1){
|
|
1847
|
logger.warn("More than 1 fossil status given for " + identEntity.getTitleCache() + " " + identEntity.getUuid());
|
|
1848
|
}
|
|
1849
|
String fossilStatus = fossilStatuus.iterator().next();
|
|
1850
|
|
|
1851
|
int statusFk = state.getTransformer().fossilStatusCache2FossilStatusFk(fossilStatus);
|
|
1852
|
return statusFk;
|
|
1853
|
}
|
|
1854
|
|
|
1855
|
/**
|
|
1856
|
* Returns the <code>FossilStatusCache</code> attribute.
|
|
1857
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1858
|
* @return The <code>FossilStatusCache</code> attribute.
|
|
1859
|
* @see MethodMapper
|
|
1860
|
*/
|
|
1861
|
@SuppressWarnings("unused")
|
|
1862
|
private static String getFossilStatusCache(IdentifiableEntity<?> identEntity, PesiExportState state) {
|
|
1863
|
String result = null;
|
|
1864
|
Set<String> fossilStatuus = identEntity.getExtensions(ErmsTransformer.uuidExtFossilStatus);
|
|
1865
|
if (fossilStatuus.size() == 0){
|
|
1866
|
return null;
|
|
1867
|
}
|
|
1868
|
for (String strFossilStatus : fossilStatuus){
|
|
1869
|
result = CdmUtils.concat(";", result, strFossilStatus);
|
|
1870
|
}
|
|
1871
|
return result;
|
|
1872
|
}
|
|
1873
|
|
|
1874
|
/**
|
|
1875
|
* Returns the <code>sourceFk</code> attribute which is
|
|
1876
|
* a link to a reference.
|
|
1877
|
* @see #8796
|
|
1878
|
* @return The <code>sourceFk</code> attribute.
|
|
1879
|
* @see MethodMapper
|
|
1880
|
*/
|
|
1881
|
@SuppressWarnings("unused") //used by methodmapper
|
|
1882
|
private static Integer getSourceFk(TaxonBase<?> taxonBase, PesiExportState state) {
|
|
1883
|
if (taxonBase.getSec() != null){
|
|
1884
|
return state.getDbId(taxonBase.getSec());
|
|
1885
|
}else{
|
|
1886
|
Set<IdentifiableSource> sources = getPesiSources(taxonBase);
|
|
1887
|
for (IdentifiableSource source : sources){
|
|
1888
|
Reference ref = source.getCitation();
|
|
1889
|
if (ref != null){
|
|
1890
|
return state.getDbId(ref);
|
|
1891
|
}
|
|
1892
|
}
|
|
1893
|
}
|
|
1894
|
logger.warn("No source found for " + taxonBase.getTitleCache());
|
|
1895
|
return null;
|
|
1896
|
}
|
|
1897
|
|
|
1898
|
/**
|
|
1899
|
* Returns the <code>sourceFk</code> attribute which is
|
|
1900
|
* a link to a reference.
|
|
1901
|
*
|
|
1902
|
* @return The <code>sourceFk</code> attribute.
|
|
1903
|
* @see MethodMapper
|
|
1904
|
* @see #8796
|
|
1905
|
*/
|
|
1906
|
@SuppressWarnings("unused") //used by methodmapper
|
|
1907
|
private static Integer getSourceFk(TaxonName taxonName, PesiExportState state) {
|
|
1908
|
//for now pure names (only coming from E+M) have no source
|
|
1909
|
//according to SQL scripts (#8796)
|
|
1910
|
return null;
|
|
1911
|
}
|
|
1912
|
|
|
1913
|
/**
|
|
1914
|
* Returns the <code>IdInSource</code> attribute.
|
|
1915
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1916
|
* @return The <code>IdInSource</code> attribute.
|
|
1917
|
* @see MethodMapper
|
|
1918
|
*/
|
|
1919
|
@SuppressWarnings("unused")
|
|
1920
|
private static String getIdInSource(IdentifiableEntity<?> taxonName) {
|
|
1921
|
String result = null;
|
|
1922
|
|
|
1923
|
try {
|
|
1924
|
Set<IdentifiableSource> sources = getPesiSources(taxonName);
|
|
1925
|
if (sources.size() > 1){
|
|
1926
|
logger.warn("There is > 1 Pesi source. This is not yet handled.");
|
|
1927
|
}
|
|
1928
|
if (sources.size() == 0){
|
|
1929
|
logger.warn("There is no Pesi source!" +taxonName.getUuid() + " (" + taxonName.getTitleCache() +")");
|
|
1930
|
}
|
|
1931
|
for (IdentifiableSource source : sources) {
|
|
1932
|
Reference ref = source.getCitation();
|
|
1933
|
UUID refUuid = ref.getUuid();
|
|
1934
|
String idInSource = source.getIdInSource();
|
|
1935
|
if (refUuid.equals(PesiTransformer.uuidSourceRefEuroMed)){
|
|
1936
|
result = idInSource != null ? ("NameId: " + source.getIdInSource()) : null;
|
|
1937
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)){
|
|
1938
|
result = idInSource != null ? ("TAX_ID: " + source.getIdInSource()) : null;
|
|
1939
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefErms)){
|
|
1940
|
result = idInSource != null ? ("tu_id: " + source.getIdInSource()) : null;
|
|
1941
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum)){ //Index Fungorum
|
|
1942
|
result = idInSource != null ? ("if_id: " + source.getIdInSource()) : null;
|
|
1943
|
}else{
|
|
1944
|
if (logger.isDebugEnabled()){logger.debug("Not a PESI source");}
|
|
1945
|
}
|
|
1946
|
|
|
1947
|
String sourceIdNameSpace = source.getIdNamespace();
|
|
1948
|
if (sourceIdNameSpace != null) {
|
|
1949
|
if (sourceIdNameSpace.equals(PesiTransformer.STR_NAMESPACE_NOMINAL_TAXON)) {
|
|
1950
|
result = idInSource != null ? ("Nominal Taxon from TAX_ID: " + source.getIdInSource()):null;
|
|
1951
|
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.INFERRED_EPITHET_NAMESPACE)) {
|
|
1952
|
result = idInSource != null ? ("Inferred epithet from TAX_ID: " + source.getIdInSource()) : null;
|
|
1953
|
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.INFERRED_GENUS_NAMESPACE)) {
|
|
1954
|
result = idInSource != null ? ("Inferred genus from TAX_ID: " + source.getIdInSource()):null;
|
|
1955
|
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.POTENTIAL_COMBINATION_NAMESPACE)) {
|
|
1956
|
result = idInSource != null ? ("Potential combination from TAX_ID: " + source.getIdInSource()):null;
|
|
1957
|
}
|
|
1958
|
}
|
|
1959
|
if (result == null) {
|
|
1960
|
logger.warn("IdInSource is NULL for this taxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() +", sourceIdNameSpace: " + source.getIdNamespace()+")");
|
|
1961
|
}
|
|
1962
|
}
|
|
1963
|
} catch (Exception e) {
|
|
1964
|
e.printStackTrace();
|
|
1965
|
logger.error("An error occurs while creating idInSource..." + taxonName.getUuid() + " (" + taxonName.getTitleCache()+ e.getMessage());
|
|
1966
|
}
|
|
1967
|
|
|
1968
|
if (result == null) {
|
|
1969
|
logger.warn("IdInSource is NULL for this taxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() +")");
|
|
1970
|
}
|
|
1971
|
return result;
|
|
1972
|
}
|
|
1973
|
|
|
1974
|
/**
|
|
1975
|
* Returns the idInSource for a given TaxonName only.
|
|
1976
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1977
|
* @return The idInSource.
|
|
1978
|
*/
|
|
1979
|
private static String getIdInSourceOnly(IdentifiableEntity<?> identEntity) {
|
|
1980
|
String result = null;
|
|
1981
|
|
|
1982
|
// Get the sources first
|
|
1983
|
Set<IdentifiableSource> sources = getPesiSources(identEntity);
|
|
1984
|
|
|
1985
|
// Determine the idInSource
|
|
1986
|
if (sources.size() == 1) {
|
|
1987
|
IdentifiableSource source = sources.iterator().next();
|
|
1988
|
if (source != null) {
|
|
1989
|
result = source.getIdInSource();
|
|
1990
|
}
|
|
1991
|
} else if (sources.size() > 1) {
|
|
1992
|
int count = 1;
|
|
1993
|
result = "";
|
|
1994
|
for (IdentifiableSource source : sources) {
|
|
1995
|
result += source.getIdInSource();
|
|
1996
|
if (count < sources.size()) {
|
|
1997
|
result += "; ";
|
|
1998
|
}
|
|
1999
|
count++;
|
|
2000
|
}
|
|
2001
|
|
|
2002
|
}
|
|
2003
|
|
|
2004
|
return result;
|
|
2005
|
}
|
|
2006
|
|
|
2007
|
/**
|
|
2008
|
* Returns the <code>GUID</code> attribute.
|
|
2009
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2010
|
* @return The <code>GUID</code> attribute.
|
|
2011
|
* @see MethodMapper
|
|
2012
|
*/
|
|
2013
|
private static String getGUID(TaxonBase<?> taxon) {
|
|
2014
|
if (taxon.getLsid() != null ){
|
|
2015
|
return taxon.getLsid().getLsid();
|
|
2016
|
}else if (taxon.hasMarker(PesiTransformer.uuidMarkerGuidIsMissing, true)){
|
|
2017
|
return null;
|
|
2018
|
}else{
|
|
2019
|
return taxon.getUuid().toString();
|
|
2020
|
}
|
|
2021
|
}
|
|
2022
|
|
|
2023
|
/**
|
|
2024
|
* Returns the <code>DerivedFromGuid</code> attribute.
|
|
2025
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2026
|
* @return The <code>DerivedFromGuid</code> attribute.
|
|
2027
|
* @see MethodMapper
|
|
2028
|
*/
|
|
2029
|
@SuppressWarnings("unused")
|
|
2030
|
private static String getDerivedFromGuid(TaxonBase<?> taxon) {
|
|
2031
|
String result = null;
|
|
2032
|
try {
|
|
2033
|
// The same as GUID for now
|
|
2034
|
result = getGUID(taxon);
|
|
2035
|
} catch (Exception e) {
|
|
2036
|
e.printStackTrace();
|
|
2037
|
}
|
|
2038
|
return result;
|
|
2039
|
}
|
|
2040
|
|
|
2041
|
/**
|
|
2042
|
* Returns the <code>CacheCitation</code> attribute.
|
|
2043
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2044
|
* @return The CacheCitation.
|
|
2045
|
* @see MethodMapper
|
|
2046
|
*/
|
|
2047
|
@SuppressWarnings("unused")
|
|
2048
|
private static String getCacheCitation(TaxonBase<?> taxon) {
|
|
2049
|
// !!! See also doPhaseUpdates
|
|
2050
|
|
|
2051
|
TaxonName taxonName = taxon.getName();
|
|
2052
|
String result = "";
|
|
2053
|
//TODO implement anew for taxa
|
|
2054
|
try {
|
|
2055
|
EnumSet<PesiSource> sources = getSources(taxon);
|
|
2056
|
//TODO what if 2 sources? In PESI 2014 they were pipe separated
|
|
2057
|
//TODO why does ERMS use accessed through eu-nomen, while E+M uses accessed through E+M
|
|
2058
|
if (sources.isEmpty()) {
|
|
2059
|
// logger.error("OriginalDB is NULL for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2060
|
} else if (sources.contains(PesiSource.ERMS)) {
|
|
2061
|
//TODO check if correct, compare with PESI 2014
|
|
2062
|
Set<Extension> extensions = taxon.getExtensions();
|
|
2063
|
for (Extension extension : extensions) {
|
|
2064
|
if (extension.getType().equals(cacheCitationExtensionType)) {
|
|
2065
|
result = extension.getValue();
|
|
2066
|
}
|
|
2067
|
}
|
|
2068
|
} else if (sources.contains(PesiSource.EM)) {
|
|
2069
|
//TODO
|
|
2070
|
boolean isMisapplied = isMisappliedName(taxon);
|
|
2071
|
boolean isProParteSyn = isProParteOrPartialSynonym(taxon);
|
|
2072
|
Reference sec = null;
|
|
2073
|
if(!isMisapplied && !isProParteSyn){
|
|
2074
|
sec = taxon.getSec();
|
|
2075
|
}else if (isMisapplied){
|
|
2076
|
sec = getAcceptedTaxonForMisappliedName(taxon).getSec();
|
|
2077
|
}else if (isProParteSyn){
|
|
2078
|
sec = getAcceptedTaxonForProParteSynonym(taxon).getSec();
|
|
2079
|
}
|
|
2080
|
if (sec == null){
|
|
2081
|
logger.warn("Sec could not be defined for taxon " + taxon.getTitleCache()+ "; " + taxon.getUuid());
|
|
2082
|
}
|
|
2083
|
String author = sec == null? "" : sec.getTitleCache();
|
|
2084
|
String webShowName = isMisapplied? getDisplayName(taxon):getWebShowName(taxonName); //for misapplied we need also the sensu and non author part, for ordinary names name + author is enough
|
|
2085
|
String accessed = ". Accessed through: Euro+Med PlantBase at https://www.europlusmed.org/cdm_dataportal/taxon/";
|
|
2086
|
result = CdmUtils.removeTrailingDot(author)
|
|
2087
|
+ ". " + CdmUtils.removeTrailingDot(webShowName)
|
|
2088
|
+ accessed + taxon.getUuid();
|
|
2089
|
} else {
|
|
2090
|
//TODO check for IF + FE
|
|
2091
|
|
|
2092
|
String expertName = getExpertName(taxon);
|
|
2093
|
String webShowName = getWebShowName(taxonName);
|
|
2094
|
|
|
2095
|
// idInSource only
|
|
2096
|
String idInSource = getIdInSourceOnly(taxonName);
|
|
2097
|
|
|
2098
|
// build the cacheCitation
|
|
2099
|
if (expertName != null) {
|
|
2100
|
result += expertName + ". ";
|
|
2101
|
} else {
|
|
2102
|
if (logger.isDebugEnabled()){logger.debug("ExpertName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");}
|
|
2103
|
}
|
|
2104
|
if (webShowName != null) {
|
|
2105
|
result += webShowName + ". ";
|
|
2106
|
} else {
|
|
2107
|
logger.warn("WebShowName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2108
|
}
|
|
2109
|
|
|
2110
|
if (getOriginalDB(taxonName).equals("FaEu")) {
|
|
2111
|
result += "Accessed through: Fauna Europaea at http://faunaeur.org/full_results.php?id=";
|
|
2112
|
} else if (getOriginalDB(taxonName).equals("EM")) {
|
|
2113
|
result += "Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=";
|
|
2114
|
}
|
|
2115
|
|
|
2116
|
if (idInSource != null) {
|
|
2117
|
result += idInSource;
|
|
2118
|
} else {
|
|
2119
|
logger.warn("IdInSource could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2120
|
}
|
|
2121
|
}
|
|
2122
|
} catch (Exception e) {
|
|
2123
|
e.printStackTrace();
|
|
2124
|
}
|
|
2125
|
|
|
2126
|
if (StringUtils.isBlank(result)) {
|
|
2127
|
return null;
|
|
2128
|
} else {
|
|
2129
|
return result;
|
|
2130
|
}
|
|
2131
|
}
|
|
2132
|
|
|
2133
|
/**
|
|
2134
|
* Returns the <code>OriginalDB</code> attribute.
|
|
2135
|
* @param identifiableEntity
|
|
2136
|
* @return The <code>OriginalDB</code> attribute.
|
|
2137
|
* @see MethodMapper
|
|
2138
|
*/
|
|
2139
|
// @SuppressWarnings("unused")
|
|
2140
|
private static String getOriginalDB(IdentifiableEntity<?> identifiableEntity) {
|
|
2141
|
EnumSet<PesiSource> sources = getSources(identifiableEntity);
|
|
2142
|
return PesiTransformer.getOriginalDbBySources(sources);
|
|
2143
|
}
|
|
2144
|
|
|
2145
|
/**
|
|
2146
|
* Returns the <code>ExpertName</code> attribute.
|
|
2147
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2148
|
* @return The <code>ExpertName</code> attribute.
|
|
2149
|
* @see MethodMapper
|
|
2150
|
*/
|
|
2151
|
@SuppressWarnings("unused") //for some reason it is also called by getCacheCitation
|
|
2152
|
private static String getExpertName(TaxonBase<?> taxon) {
|
|
2153
|
try {
|
|
2154
|
String result = null;
|
|
2155
|
if(expertNameExtensionType!=null){ //some databases do not have this extension type
|
|
2156
|
Set<Extension> extensions = taxon.getExtensions();
|
|
2157
|
for (Extension extension : extensions) {
|
|
2158
|
if (extension.getType().equals(expertNameExtensionType)) {
|
|
2159
|
result = extension.getValue();
|
|
2160
|
}
|
|
2161
|
}
|
|
2162
|
}
|
|
2163
|
if (getPesiSources(taxon).contains(PesiSource.EM)){
|
|
2164
|
return taxon.getSec().getTitleCache();
|
|
2165
|
}
|
|
2166
|
return null;
|
|
2167
|
} catch (Exception e) {
|
|
2168
|
e.printStackTrace();
|
|
2169
|
return null;
|
|
2170
|
}
|
|
2171
|
}
|
|
2172
|
|
|
2173
|
//TODO change to ExpertGUID
|
|
2174
|
private static Integer getExpertFk(Reference reference, PesiExportState state) {
|
|
2175
|
Integer result = state.getDbId(reference);
|
|
2176
|
return result;
|
|
2177
|
}
|
|
2178
|
|
|
2179
|
/**
|
|
2180
|
* Returns the <code>SpeciesExpertName</code> attribute.
|
|
2181
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2182
|
* @return The <code>SpeciesExpertName</code> attribute.
|
|
2183
|
* @see MethodMapper
|
|
2184
|
*/
|
|
2185
|
@SuppressWarnings("unused")
|
|
2186
|
private static String getSpeciesExpertName(TaxonBase<?> taxon) {
|
|
2187
|
try {
|
|
2188
|
Set<Extension> extensions = taxon.getExtensions();
|
|
2189
|
if(speciesExpertNameExtensionType != null){ //some databases do not have this extension type
|
|
2190
|
for (Extension extension : extensions) {
|
|
2191
|
if (extension.getType().equals(speciesExpertNameExtensionType)) {
|
|
2192
|
return extension.getValue();
|
|
2193
|
}
|
|
2194
|
}
|
|
2195
|
}
|
|
2196
|
if (getPesiSources(taxon).contains(PesiSource.EM)){
|
|
2197
|
return taxon.getSec().getTitleCache();
|
|
2198
|
}
|
|
2199
|
return null;
|
|
2200
|
} catch (Exception e) {
|
|
2201
|
e.printStackTrace();
|
|
2202
|
return null;
|
|
2203
|
}
|
|
2204
|
}
|
|
2205
|
|
|
2206
|
/**
|
|
2207
|
* Returns the <code>SpeciesExpertFk</code> attribute.
|
|
2208
|
* @param reference The {@link Reference Reference}.
|
|
2209
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
2210
|
* @return The <code>SpeciesExpertFk</code> attribute.
|
|
2211
|
* @see MethodMapper
|
|
2212
|
*/
|
|
2213
|
//TODO should be changed to SpeciesExpertGUID
|
|
2214
|
private static Integer getSpeciesExpertFk(Reference reference, PesiExportState state) {
|
|
2215
|
Integer result = state.getDbId(reference);
|
|
2216
|
return result;
|
|
2217
|
}
|
|
2218
|
|
|
2219
|
protected static TaxonNameDefaultCacheStrategy getCacheStrategy(TaxonName taxonName) {
|
|
2220
|
taxonName = CdmBase.deproxy(taxonName);
|
|
2221
|
TaxonNameDefaultCacheStrategy cacheStrategy;
|
|
2222
|
if (taxonName.isZoological()){
|
|
2223
|
cacheStrategy = zooNameStrategy;
|
|
2224
|
}else if (taxonName.isBotanical()) {
|
|
2225
|
cacheStrategy = nonViralNameStrategy;
|
|
2226
|
}else if (taxonName.isNonViral()) {
|
|
2227
|
cacheStrategy = nonViralNameStrategy;
|
|
2228
|
}else if (taxonName.isBacterial()) {
|
|
2229
|
cacheStrategy = nonViralNameStrategy;
|
|
2230
|
}else{
|
|
2231
|
logger.error("Unhandled taxon name type. Can't define strategy class");
|
|
2232
|
cacheStrategy = nonViralNameStrategy;
|
|
2233
|
}
|
|
2234
|
return cacheStrategy;
|
|
2235
|
}
|
|
2236
|
|
|
2237
|
/**
|
|
2238
|
* Returns the <code>RelTaxonQualifierFk</code> attribute.
|
|
2239
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
2240
|
* @return The <code>RelTaxonQualifierFk</code> attribute.
|
|
2241
|
* @see MethodMapper
|
|
2242
|
*/
|
|
2243
|
@SuppressWarnings("unused")
|
|
2244
|
private static Integer getRelTaxonQualifierFk(RelationshipBase<?, ?, ?> relationship) {
|
|
2245
|
return PesiTransformer.taxonRelation2RelTaxonQualifierFk(relationship);
|
|
2246
|
}
|
|
2247
|
|
|
2248
|
//TODO still in use?
|
|
2249
|
private static String getSynonymTypeCache(Synonym synonym, PesiExportState state) {
|
|
2250
|
String result = null;
|
|
2251
|
NomenclaturalCode code = null;
|
|
2252
|
code = CdmBase.deproxy(synonym, Synonym.class).getAcceptedTaxon().getName().getNameType();
|
|
2253
|
|
|
2254
|
if (code != null) {
|
|
2255
|
result = state.getConfig().getTransformer().getCacheBySynonymType(synonym, code);
|
|
2256
|
} else {
|
|
2257
|
logger.error("NomenclaturalCode is NULL while creating the following synonym: " + synonym.getUuid());
|
|
2258
|
}
|
|
2259
|
return result;
|
|
2260
|
}
|
|
2261
|
|
|
2262
|
// ********************************** MAPPINGS ********************************/
|
|
2263
|
|
|
2264
|
/**
|
|
2265
|
* Returns the CDM to PESI specific export mappings.
|
|
2266
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
|
2267
|
*/
|
|
2268
|
private PesiExportMapping getMapping() {
|
|
2269
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
|
2270
|
|
|
2271
|
mapping.addMapper(IdMapper.NewInstance("TaxonId"));
|
|
2272
|
mapping.addMapper(MethodMapper.NewInstance("SourceFk", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));
|
|
2273
|
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusFk", this.getClass(), "getTaxonStatusFk", standardMethodParameter, PesiExportState.class));
|
|
2274
|
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusCache", this.getClass(), "getTaxonStatusCache", standardMethodParameter, PesiExportState.class));
|
|
2275
|
|
|
2276
|
mapping.addMapper(MethodMapper.NewInstance("GUID", this));
|
|
2277
|
|
|
2278
|
mapping.addMapper(MethodMapper.NewInstance("DerivedFromGuid", this));
|
|
2279
|
mapping.addMapper(MethodMapper.NewInstance("CacheCitation", this));
|
|
2280
|
mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because misapplied names are handled differently
|
|
2281
|
mapping.addMapper(MethodMapper.NewInstance("FullName", this)); //For Taxon because misapplied names are handled differently
|
|
2282
|
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this));
|
|
2283
|
|
|
2284
|
// DisplayName
|
|
2285
|
mapping.addMapper(MethodMapper.NewInstance("DisplayName", this));
|
|
2286
|
|
|
2287
|
// FossilStatus (Fk, Cache)
|
|
2288
|
mapping.addMapper(MethodMapper.NewInstance("FossilStatusCache", this, IdentifiableEntity.class, PesiExportState.class));
|
|
2289
|
mapping.addMapper(MethodMapper.NewInstance("FossilStatusFk", this, IdentifiableEntity.class, PesiExportState.class)); // PesiTransformer.FossilStatusCache2FossilStatusFk?
|
|
2290
|
|
|
2291
|
//handled by name mapping
|
|
2292
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastActionDate", false));
|
|
2293
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));
|
|
2294
|
|
|
2295
|
//experts
|
|
2296
|
// mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeSpeciesExpertName, "SpeciesExpertName"));
|
|
2297
|
mapping.addMapper(MethodMapper.NewInstance("SpeciesExpertName", this, TaxonBase.class));
|
|
2298
|
// ExtensionType extensionTypeExpertName = (ExtensionType)getTermService().find(PesiTransformer.uuidExtExpertName);
|
|
2299
|
// mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeExpertName, "ExpertName"));
|
|
2300
|
mapping.addMapper(MethodMapper.NewInstance("ExpertName", this, TaxonBase.class));
|
|
2301
|
|
|
2302
|
//ParentTaxonFk handled in Phase02 now
|
|
2303
|
mapping.addMapper(ObjectChangeMapper.NewInstance(TaxonBase.class, TaxonName.class, "Name"));
|
|
2304
|
|
|
2305
|
addNameMappers(mapping);
|
|
2306
|
|
|
2307
|
return mapping;
|
|
2308
|
}
|
|
2309
|
|
|
2310
|
/**
|
|
2311
|
* Returns the CDM to PESI specific export mappings.
|
|
2312
|
* @param state
|
|
2313
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
|
2314
|
* @throws UndefinedTransformerMethodException
|
|
2315
|
*/
|
|
2316
|
private PesiExportMapping getPureNameMapping(PesiExportState state) throws UndefinedTransformerMethodException {
|
|
2317
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
|
2318
|
|
|
2319
|
mapping.addMapper(IdMapper.NewInstance("TaxonId"));
|
|
2320
|
|
|
2321
|
mapping.addMapper(MethodMapper.NewInstance("SourceFk", this, TaxonName.class, PesiExportState.class)); //for now is only null
|
|
2322
|
mapping.addMapper(MethodMapper.NewInstance("KingdomFk", this, TaxonName.class));
|
|
2323
|
mapping.addMapper(MethodMapper.NewInstance("RankFk", this, TaxonName.class));
|
|
2324
|
mapping.addMapper(MethodMapper.NewInstance("RankCache", this, TaxonName.class, PesiExportState.class));
|
|
2325
|
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusFk", Types.INTEGER, PesiTransformer.T_STATUS_UNACCEPTED));
|
|
2326
|
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusCache", Types.VARCHAR, state.getTransformer().getTaxonStatusCacheByKey( PesiTransformer.T_STATUS_UNACCEPTED)));
|
|
2327
|
mapping.addMapper(DbStringMapper.NewInstance("AuthorshipCache", "AuthorString").setBlankToNull(true));
|
|
2328
|
mapping.addMapper(MethodMapper.NewInstance("FullName", this, TaxonName.class));
|
|
2329
|
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this, TaxonName.class));
|
|
2330
|
mapping.addMapper(MethodMapper.NewInstance("GUID", this, TaxonName.class));
|
|
2331
|
|
|
2332
|
// DisplayName
|
|
2333
|
mapping.addMapper(MethodMapper.NewInstance("DisplayName", this, TaxonName.class));
|
|
2334
|
|
|
2335
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastActionDate", false));
|
|
2336
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));
|
|
2337
|
|
|
2338
|
addNameMappers(mapping);
|
|
2339
|
return mapping;
|
|
2340
|
}
|
|
2341
|
|
|
2342
|
private void addNameMappers(PesiExportMapping mapping) {
|
|
2343
|
|
|
2344
|
//epithets
|
|
2345
|
mapping.addMapper(DbStringMapper.NewInstance("GenusOrUninomial", "GenusOrUninomial"));
|
|
2346
|
mapping.addMapper(DbStringMapper.NewInstance("InfraGenericEpithet", "InfraGenericEpithet"));
|
|
2347
|
mapping.addMapper(DbStringMapper.NewInstance("SpecificEpithet", "SpecificEpithet"));
|
|
2348
|
mapping.addMapper(DbStringMapper.NewInstance("InfraSpecificEpithet", "InfraSpecificEpithet"));
|
|
2349
|
|
|
2350
|
//full name
|
|
2351
|
// mapping.addMapper(DbStringMapper.NewInstance("NameCache", "WebSearchName")); //does not work as we need other cache strategy
|
|
2352
|
mapping.addMapper(MethodMapper.NewInstance("WebSearchName", this, TaxonName.class));
|
|
2353
|
|
|
2354
|
//nom ref
|
|
2355
|
mapping.addMapper(MethodMapper.NewInstance("NomRefString", this, TaxonName.class));
|
|
2356
|
|
|
2357
|
//status
|
|
2358
|
mapping.addMapper(MethodMapper.NewInstance("NameStatusFk", this, TaxonName.class));
|
|
2359
|
mapping.addMapper(MethodMapper.NewInstance("NameStatusCache", this, TaxonName.class, PesiExportState.class));
|
|
2360
|
mapping.addMapper(MethodMapper.NewInstance("QualityStatusFk", this, TaxonName.class));
|
|
2361
|
mapping.addMapper(MethodMapper.NewInstance("QualityStatusCache", this, TaxonName.class, PesiExportState.class));
|
|
2362
|
|
|
2363
|
//types
|
|
2364
|
mapping.addMapper(MethodMapper.NewInstance("TypeFullnameCache", this, TaxonName.class));
|
|
2365
|
//TypeNameFk handled in Phase3
|
|
2366
|
|
|
2367
|
//supplemental
|
|
2368
|
mapping.addMapper(MethodMapper.NewInstance("IdInSource", this, IdentifiableEntity.class));
|
|
2369
|
mapping.addMapper(MethodMapper.NewInstance("OriginalDB", this, IdentifiableEntity.class) );
|
|
2370
|
|
|
2371
|
//mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());
|
|
2372
|
|
|
2373
|
}
|
|
2374
|
|
|
2375
|
private PesiExportMapping getSynRelMapping() {
|
|
2376
|
PesiExportMapping mapping = new PesiExportMapping(dbTableNameSynRel);
|
|
2377
|
logger.warn("SynRelMapping currently not implemented. Needs to be checked");
|
|
2378
|
|
|
2379
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getSynonym", Synonym.class, PesiExportState.class));
|
|
2380
|
mapping.addMapper(DbObjectMapper.NewInstance("acceptedTaxon", "TaxonFk2"));
|
|
2381
|
mapping.addMapper(DbObjectMapper.NewInstance("type", "RelTaxonQualifierFk"));
|
|
2382
|
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this.getClass(), "getSynonymTypeCache", Synonym.class, PesiExportState.class));
|
|
2383
|
// TODO
|
|
2384
|
// mapping.addMapper(MethodMapper.NewInstance("Notes", this, RelationshipBase.class));
|
|
2385
|
|
|
2386
|
return mapping;
|
|
2387
|
}
|
|
2388
|
|
|
2389
|
private PesiExportMapping getAdditionalSourceMapping(PesiExportState state) {
|
|
2390
|
PesiExportMapping mapping = new PesiExportMapping(dbTableAdditionalSourceRel);
|
|
2391
|
|
|
2392
|
mapping.addMapper(IdMapper.NewInstance("TaxonFk"));
|
|
2393
|
mapping.addMapper(ObjectChangeMapper.NewInstance(TaxonBase.class, TaxonName.class, "Name"));
|
|
2394
|
|
|
2395
|
mapping.addMapper(DbObjectMapper.NewInstance("NomenclaturalReference", "SourceFk"));
|
|
2396
|
// mapping.addMapper(DbObjectMapper.NewInstance("NomenclaturalReference", "SourceNameCache", IS_CACHE));
|
|
2397
|
mapping.addMapper(MethodMapper.NewInstance("SourceNameCache", this, TaxonName.class));
|
|
2398
|
|
|
2399
|
//we have only nomenclatural references here
|
|
2400
|
mapping.addMapper(DbConstantMapper.NewInstance("SourceUseFk", Types.INTEGER , PesiTransformer.NOMENCLATURAL_REFERENCE));
|
|
2401
|
mapping.addMapper(DbConstantMapper.NewInstance("SourceUseCache", Types.VARCHAR, state.getTransformer().getSourceUseCacheByKey( PesiTransformer.NOMENCLATURAL_REFERENCE)));
|
|
2402
|
|
|
2403
|
mapping.addMapper(DbStringMapper.NewInstance("NomenclaturalMicroReference", "SourceDetail"));
|
|
2404
|
|
|
2405
|
return mapping;
|
|
2406
|
}
|
|
2407
|
|
|
2408
|
|
|
2409
|
@Override
|
|
2410
|
protected boolean doCheck(PesiExportState state) {
|
|
2411
|
return true;
|
|
2412
|
}
|
|
2413
|
|
|
2414
|
@Override
|
|
2415
|
protected boolean isIgnore(PesiExportState state) {
|
|
2416
|
return ! state.getConfig().isDoTaxa();
|
|
2417
|
}
|
|
2418
|
}
|