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// $Id$
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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.BitSet;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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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.joda.time.DateTime;
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import org.joda.time.format.DateTimeFormat;
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import org.joda.time.format.DateTimeFormatter;
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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.berlinModel.BerlinModelTransformer;
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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.DbExtensionMapper;
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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.Annotation;
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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.Language;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.name.BacterialName;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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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.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.reference.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.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.profiler.ProfilerController;
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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.BacterialNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy;
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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.TaxonNameBase TaxonNames} except some data exported in the following phases.
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* <li>Phase 2: Export of additional data: ParenTaxonFk 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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* @author e.-m.lee
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* @date 23.02.2010
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*
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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 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 PreparedStatement parentTaxonFk_TreeIndex_KingdomFkStmt;
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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 NomenclaturalCode nomenclaturalCode;
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private Integer kingdomFk;
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private final HashMap<Rank, Rank> rank2endRankMap = new HashMap<Rank, Rank>();
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private final List<Rank> rankList = new ArrayList<Rank>();
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private static final UUID uuidTreeIndex = UUID.fromString("28f4e205-1d02-4d3a-8288-775ea8413009");
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private AnnotationType treeIndexAnnotationType;
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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 NonViralNameDefaultCacheStrategy<?> zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();
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public static NonViralNameDefaultCacheStrategy<?> botanicalNameStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
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public static NonViralNameDefaultCacheStrategy<?> nonViralNameStrategy = NonViralNameDefaultCacheStrategy.NewInstance();
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public static NonViralNameDefaultCacheStrategy<?> bacterialNameStrategy = BacterialNameDefaultCacheStrategy.NewInstance();
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private static int currentTaxonId;
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/**
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* @return the treeIndexAnnotationType
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*/
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protected AnnotationType getTreeIndexAnnotationType() {
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return treeIndexAnnotationType;
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}
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/**
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* @param treeIndexAnnotationType the treeIndexAnnotationType to set
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*/
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protected void setTreeIndexAnnotationType(AnnotationType treeIndexAnnotationType) {
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this.treeIndexAnnotationType = treeIndexAnnotationType;
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}
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter()
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
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*/
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@Override
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protected boolean doCheck(PesiExportState state) {
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boolean result = true;
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)
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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.lastActionUuid);
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lastActionDateExtensionType = (ExtensionType)getTermService().find(PesiTransformer.lastActionDateUuid);
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expertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.expertNameUuid);
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speciesExpertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.speciesExpertNameUuid);
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cacheCitationExtensionType = (ExtensionType)getTermService().find(PesiTransformer.cacheCitationUuid);
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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 &= doNames(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 4: 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.setUnsuccessfull();
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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.setUnsuccessfull();
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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) throws SQLException {
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int count = 0;
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int pastCount = 0;
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List<TaxonBase> list;
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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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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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int partitionCount = 0;
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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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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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TaxonNameBase<?,?> taxonName = taxon.getName();
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NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
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System.err.println(nvn.getTitleCache());
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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{
|
|
330
|
if (nvn.getRank().equals(Rank.KINGDOM())){
|
|
331
|
String treeIndex = ((Taxon)taxon).getTaxonNodes().iterator().next().treeIndex();
|
|
332
|
Integer kingdomId = PesiTransformer.pesiKingdomMap.get(nvn.getGenusOrUninomial());
|
|
333
|
state.getTreeIndexKingdomMap().put(treeIndex, kingdomId);
|
|
334
|
}}catch(NullPointerException e){
|
|
335
|
logger.error(nvn.getTitleCache() + "has no Rank!");
|
|
336
|
System.err.println(nvn.getTitleCache() + "has no Rank!");
|
|
337
|
}
|
|
338
|
//core mapping
|
|
339
|
success &= mapping.invoke(taxon);
|
|
340
|
//additional source
|
|
341
|
if (nvn.getNomenclaturalReference() != null || StringUtils.isNotBlank(nvn.getNomenclaturalMicroReference() )){
|
|
342
|
additionalSourceMapping.invoke(taxon);
|
|
343
|
}
|
|
344
|
|
|
345
|
validatePhaseOne(taxon, nvn);
|
|
346
|
taxon = null;
|
|
347
|
nvn = null;
|
|
348
|
taxonName = null;
|
|
349
|
|
|
350
|
|
|
351
|
|
|
352
|
}
|
|
353
|
|
|
354
|
|
|
355
|
// Commit transaction
|
|
356
|
commitTransaction(txStatus);
|
|
357
|
logger.debug("Committed transaction.");
|
|
358
|
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
|
|
359
|
pastCount = count;
|
|
360
|
/*logger.warn("Taking snapshot at the end of the loop of phase 1 of taxonExport");
|
|
361
|
//ProfilerController.memorySnapshot();
|
|
362
|
*/
|
|
363
|
// Start transaction
|
|
364
|
txStatus = startTransaction(true);
|
|
365
|
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
366
|
|
|
367
|
}
|
|
368
|
if (list == null ) {
|
|
369
|
logger.info("No " + pluralString + " left to fetch.");
|
|
370
|
}
|
|
371
|
|
|
372
|
|
|
373
|
|
|
374
|
// Commit transaction
|
|
375
|
commitTransaction(txStatus);
|
|
376
|
txStatus = null;
|
|
377
|
logger.debug("Committed transaction.");
|
|
378
|
list = null;
|
|
379
|
if (logger.isDebugEnabled()){
|
|
380
|
logger.debug("Taking snapshot at the end of phase 1 of taxonExport");
|
|
381
|
ProfilerController.memorySnapshot();
|
|
382
|
}
|
|
383
|
return success;
|
|
384
|
}
|
|
385
|
|
|
386
|
|
|
387
|
private void validatePhaseOne(TaxonBase<?> taxon, NonViralName taxonName) {
|
|
388
|
// Check whether some rules are violated
|
|
389
|
nomenclaturalCode = taxonName.getNomenclaturalCode();
|
|
390
|
String genusOrUninomial = taxonName.getGenusOrUninomial();
|
|
391
|
String specificEpithet = taxonName.getSpecificEpithet();
|
|
392
|
String infraSpecificEpithet = taxonName.getInfraSpecificEpithet();
|
|
393
|
String infraGenericEpithet = taxonName.getInfraGenericEpithet();
|
|
394
|
Integer rank = getRankFk(taxonName, nomenclaturalCode);
|
|
395
|
|
|
396
|
if (rank == null) {
|
|
397
|
logger.error("Rank was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
398
|
} else {
|
|
399
|
|
|
400
|
// Check whether infraGenericEpithet is set correctly
|
|
401
|
// 1. Childs of an accepted taxon of rank subgenus that are accepted taxa of rank species have to have an infraGenericEpithet
|
|
402
|
// 2. Grandchilds of an accepted taxon of rank subgenus that are accepted taxa of rank subspecies have to have an infraGenericEpithet
|
|
403
|
|
|
404
|
int ancestorLevel = 0;
|
|
405
|
if (taxonName.getRank().equals(Rank.SUBSPECIES())) {
|
|
406
|
// The accepted taxon two rank levels above should be of rank subgenus
|
|
407
|
ancestorLevel = 2;
|
|
408
|
}
|
|
409
|
if (taxonName.getRank().equals(Rank.SPECIES())) {
|
|
410
|
// The accepted taxon one rank level above should be of rank subgenus
|
|
411
|
ancestorLevel = 1;
|
|
412
|
}
|
|
413
|
if (ancestorLevel > 0) {
|
|
414
|
if (validateAncestorOfSpecificRank(taxon, ancestorLevel, Rank.SUBGENUS())) {
|
|
415
|
// The child (species or subspecies) of this parent (subgenus) has to have an infraGenericEpithet
|
|
416
|
if (infraGenericEpithet == null) {
|
|
417
|
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() + ")");
|
|
418
|
// maybe the taxon could be named here
|
|
419
|
}
|
|
420
|
}
|
|
421
|
}
|
|
422
|
|
|
423
|
if (infraGenericEpithet == null && rank.intValue() == 190) {
|
|
424
|
logger.warn("InfraGenericEpithet was not determined although it should exist for rank 190: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
425
|
}
|
|
426
|
if (specificEpithet != null && rank.intValue() < 216) {
|
|
427
|
logger.warn("SpecificEpithet was determined for rank " + rank + " although it should only exist for ranks higher or equal to 220: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
428
|
}
|
|
429
|
if (infraSpecificEpithet != null && rank.intValue() < 225) {
|
|
430
|
String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rank + " although it should only exist for ranks higher or equal to 230: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";
|
|
431
|
if (StringUtils.isNotBlank(infraSpecificEpithet)){
|
|
432
|
logger.warn(message);
|
|
433
|
}else{
|
|
434
|
logger.warn(message);
|
|
435
|
}
|
|
436
|
}
|
|
437
|
}
|
|
438
|
if (infraSpecificEpithet != null && specificEpithet == null) {
|
|
439
|
logger.warn("An infraSpecificEpithet was determined, but a specificEpithet was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
440
|
}
|
|
441
|
if (genusOrUninomial == null) {
|
|
442
|
logger.warn("GenusOrUninomial was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
443
|
}
|
|
444
|
}
|
|
445
|
|
|
446
|
|
|
447
|
|
|
448
|
/**
|
|
449
|
* 2nd Round: Add ParentTaxonFk to each taxon and add Biota if not exists
|
|
450
|
* @param state
|
|
451
|
* @return
|
|
452
|
*/
|
|
453
|
private boolean doPhase02(PesiExportState state) {
|
|
454
|
int count = 0;
|
|
455
|
int pastCount = 0;
|
|
456
|
boolean success = true;
|
|
457
|
if (! state.getConfig().isDoParentAndBiota()){
|
|
458
|
logger.info ("Ignore PHASE 2: Make ParentFk and Biota...");
|
|
459
|
return success;
|
|
460
|
}
|
|
461
|
|
|
462
|
List<Taxon> list;
|
|
463
|
|
|
464
|
// Get the limit for objects to save within a single transaction.
|
|
465
|
int limit = state.getConfig().getLimitSave();
|
|
466
|
|
|
467
|
insertBiota(state);
|
|
468
|
|
|
469
|
logger.info("PHASE 2: Make ParentFk and Biota ... limit is " + limit);
|
|
470
|
// Start transaction
|
|
471
|
TransactionStatus txStatus = startTransaction(true);
|
|
472
|
int partitionCount = 0;
|
|
473
|
|
|
474
|
// ProfilerController.memorySnapshot();
|
|
475
|
while ((list = getNextTaxonPartition(Taxon.class, limit, partitionCount++, null)) != null ) {
|
|
476
|
|
|
477
|
logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");
|
|
478
|
for (Taxon taxon : list) {
|
|
479
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
480
|
doCount(count++, modCount, pluralString);
|
|
481
|
TaxonNode parentNode = node.getParent();
|
|
482
|
if (parentNode != null && parentNode.getTaxon() != null){ //new root node handling requires has root taxon with taxon == null
|
|
483
|
int childId = state.getDbId( taxon);
|
|
484
|
int parentId = state.getDbId(parentNode.getTaxon());
|
|
485
|
success &= invokeParentTaxonFk(parentId, childId);
|
|
486
|
}
|
|
487
|
}
|
|
488
|
|
|
489
|
}
|
|
490
|
|
|
491
|
// Commit transaction
|
|
492
|
commitTransaction(txStatus);
|
|
493
|
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
|
|
494
|
pastCount = count;
|
|
495
|
// Start transaction
|
|
496
|
txStatus = startTransaction(true);
|
|
497
|
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
498
|
|
|
499
|
}
|
|
500
|
if (list == null ) {
|
|
501
|
logger.info("No " + pluralString + " left to fetch.");
|
|
502
|
}
|
|
503
|
list = null;
|
|
504
|
// Commit transaction
|
|
505
|
commitTransaction(txStatus);
|
|
506
|
|
|
507
|
return success;
|
|
508
|
|
|
509
|
}
|
|
510
|
|
|
511
|
/**
|
|
512
|
* Inserts the Biota Taxon if not yet exists.
|
|
513
|
* @param state
|
|
514
|
* @throws SQLException
|
|
515
|
*/
|
|
516
|
private void insertBiota(PesiExportState state) {
|
|
517
|
try {
|
|
518
|
ResultSet rs = state.getConfig().getDestination().getResultSet("SELECT * FROM Taxon WHERE GenusOrUninomial = 'Biota' ");
|
|
519
|
if (rs.next() == false){
|
|
520
|
int biotaId = state.getConfig().getNameIdStart() -1 ;
|
|
521
|
String sqlInsertBiota = "INSERT INTO Taxon (TaxonId, KingdomFk, RankFk, RankCache, GenusOrUninomial, WebSearchName, WebShowName, FullName, DisplayName, TaxonStatusFk, TaxonStatusCache) " +
|
|
522
|
" VALUES (" + biotaId + ", 0, 0, 'Superdomain', 'Biota', 'Biota', '<i>Biota</i>', 'Biota', '<i>Biota</i>', 1 , 'accepted')";
|
|
523
|
state.getConfig().getDestination().update(sqlInsertBiota);
|
|
524
|
}
|
|
525
|
rs = null;
|
|
526
|
} catch (SQLException e) {
|
|
527
|
logger.warn ("Biota could not be requested or inserted");
|
|
528
|
}
|
|
529
|
|
|
530
|
}
|
|
531
|
|
|
532
|
// 4th round: Add TreeIndex to each taxon
|
|
533
|
private boolean doPhase04(PesiExportState state) {
|
|
534
|
boolean success = true;
|
|
535
|
|
|
536
|
logger.info("PHASE 4: Make TreeIndex ... ");
|
|
537
|
|
|
538
|
//TODO test if possible to move to phase 02
|
|
539
|
String sql = " UPDATE Taxon SET ParentTaxonFk = (Select TaxonId from Taxon where RankFk = 0) " +
|
|
540
|
" WHERE (RankFk = 10) and TaxonStatusFk = 1 ";
|
|
541
|
state.getConfig().getDestination().update(sql);
|
|
542
|
|
|
543
|
state.getConfig().getDestination().update("EXEC dbo.recalculateallstoredpaths");
|
|
544
|
|
|
545
|
return success;
|
|
546
|
|
|
547
|
}
|
|
548
|
|
|
549
|
|
|
550
|
// 2nd Round: Add ParentTaxonFk, TreeIndex to each Taxon
|
|
551
|
private boolean doPhase02_OLD(PesiExportState state) {
|
|
552
|
boolean success = true;
|
|
553
|
if (! state.getConfig().isDoTreeIndex()){
|
|
554
|
logger.info ("Ignore PHASE 2: ParentTaxonFk and TreeIndex");
|
|
555
|
return success;
|
|
556
|
}
|
|
557
|
|
|
558
|
List<Classification> classificationList = null;
|
|
559
|
logger.info("PHASE 2: Add ParenTaxonFk and TreeIndex...");
|
|
560
|
|
|
561
|
// Specify starting ranks for tree traversing
|
|
562
|
rankList.add(Rank.KINGDOM());
|
|
563
|
rankList.add(Rank.GENUS());
|
|
564
|
|
|
565
|
// Specify where to stop traversing (value) when starting at a specific Rank (key)
|
|
566
|
rank2endRankMap.put(Rank.GENUS(), null); // Since NULL does not match an existing Rank, traverse all the way down to the leaves
|
|
567
|
rank2endRankMap.put(Rank.KINGDOM(), Rank.GENUS()); // excludes rank genus
|
|
568
|
|
|
569
|
StringBuffer treeIndex = new StringBuffer();
|
|
570
|
|
|
571
|
// Retrieve list of classifications
|
|
572
|
TransactionStatus txStatus = startTransaction(true);
|
|
573
|
logger.info("Started transaction for parentFk and treeIndex. Fetching all classifications...");
|
|
574
|
classificationList = getClassificationService().listClassifications(null, 0, null, null);
|
|
575
|
commitTransaction(txStatus);
|
|
576
|
logger.debug("Committed transaction.");
|
|
577
|
|
|
578
|
logger.info("Fetched " + classificationList.size() + " classification(s).");
|
|
579
|
|
|
580
|
setTreeIndexAnnotationType(getAnnotationType(uuidTreeIndex, "TreeIndex", "TreeIndex", "TI"));
|
|
581
|
List<TaxonNode> rankSpecificRootNodes;
|
|
582
|
for (Classification classification : classificationList) {
|
|
583
|
for (Rank rank : rankList) {
|
|
584
|
|
|
585
|
txStatus = startTransaction(true);
|
|
586
|
logger.info("Started transaction to fetch all rootNodes specific to Rank " + rank.getLabel() + " ...");
|
|
587
|
|
|
588
|
rankSpecificRootNodes = getClassificationService().listRankSpecificRootNodes(classification, rank, null, null, null);
|
|
589
|
logger.info("Fetched " + rankSpecificRootNodes.size() + " RootNodes for Rank " + rank.getLabel());
|
|
590
|
|
|
591
|
commitTransaction(txStatus);
|
|
592
|
logger.debug("Committed transaction.");
|
|
593
|
|
|
594
|
for (TaxonNode rootNode : rankSpecificRootNodes) {
|
|
595
|
txStatus = startTransaction(false);
|
|
596
|
Rank endRank = rank2endRankMap.get(rank);
|
|
597
|
if (endRank != null) {
|
|
598
|
logger.debug("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till Rank " + endRank.getLabel() + " ...");
|
|
599
|
} else {
|
|
600
|
logger.debug("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till leaves are reached ...");
|
|
601
|
}
|
|
602
|
|
|
603
|
TaxonNode newNode = getTaxonNodeService().load(rootNode.getUuid());
|
|
604
|
|
|
605
|
if (isPesiTaxon(newNode.getTaxon())){
|
|
606
|
TaxonNode parentNode = newNode.getParent();
|
|
607
|
if (rank.equals(Rank.KINGDOM())) {
|
|
608
|
treeIndex = new StringBuffer();
|
|
609
|
treeIndex.append("#");
|
|
610
|
} else {
|
|
611
|
// Get treeIndex from parentNode
|
|
612
|
if (parentNode != null) {
|
|
613
|
boolean annotationFound = false;
|
|
614
|
Set<Annotation> annotations = parentNode.getAnnotations();
|
|
615
|
for (Annotation annotation : annotations) {
|
|
616
|
AnnotationType annotationType = annotation.getAnnotationType();
|
|
617
|
if (annotationType != null && annotationType.equals(getTreeIndexAnnotationType())) {
|
|
618
|
treeIndex = new StringBuffer(CdmUtils.Nz(annotation.getText()));
|
|
619
|
annotationFound = true;
|
|
620
|
// logger.error("treeIndex: " + treeIndex);
|
|
621
|
break;
|
|
622
|
}
|
|
623
|
}
|
|
624
|
if (!annotationFound) {
|
|
625
|
// This should not happen because it means that the treeIndex was not set correctly as an annotation to parentNode
|
|
626
|
logger.error("TreeIndex could not be read from annotation of TaxonNode: " + parentNode.getUuid() + ", Taxon: " + parentNode.getTaxon().getUuid());
|
|
627
|
treeIndex = new StringBuffer();
|
|
628
|
treeIndex.append("#");
|
|
629
|
}
|
|
630
|
} else {
|
|
631
|
// TreeIndex could not be determined, but it's unclear how to proceed to generate a correct treeIndex if the parentNode is NULL
|
|
632
|
logger.error("ParentNode for RootNode is NULL. TreeIndex could not be determined: " + newNode.getUuid());
|
|
633
|
treeIndex = new StringBuffer(); // This just prevents growing of the treeIndex in a wrong manner
|
|
634
|
treeIndex.append("#");
|
|
635
|
}
|
|
636
|
}
|
|
637
|
nomenclaturalCode = newNode.getTaxon().getName().getNomenclaturalCode();
|
|
638
|
kingdomFk = PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);
|
|
639
|
traverseTree(newNode, parentNode, treeIndex, endRank, state);
|
|
640
|
parentNode =null;
|
|
641
|
}else{
|
|
642
|
logger.debug("Taxon is not a PESI taxon: " + newNode.getTaxon().getUuid());
|
|
643
|
}
|
|
644
|
|
|
645
|
newNode = null;
|
|
646
|
|
|
647
|
try {
|
|
648
|
commitTransaction(txStatus);
|
|
649
|
logger.debug("Committed transaction.");
|
|
650
|
} catch (Exception e) {
|
|
651
|
logger.error(e.getMessage());
|
|
652
|
e.printStackTrace();
|
|
653
|
}
|
|
654
|
|
|
655
|
}
|
|
656
|
rankSpecificRootNodes = null;
|
|
657
|
}
|
|
658
|
|
|
659
|
}
|
|
660
|
|
|
661
|
logger.warn("Taking snapshot at the end of phase 2 of taxonExport");
|
|
662
|
//ProfilerController.memorySnapshot();
|
|
663
|
return success;
|
|
664
|
}
|
|
665
|
|
|
666
|
//PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...
|
|
667
|
private boolean doPhase03(PesiExportState state) {
|
|
668
|
int count = 0;
|
|
669
|
int pastCount = 0;
|
|
670
|
boolean success = true;
|
|
671
|
if (! state.getConfig().isDoTreeIndex()){
|
|
672
|
logger.info ("Ignore PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...");
|
|
673
|
return success;
|
|
674
|
}
|
|
675
|
// Get the limit for objects to save within a single transaction.
|
|
676
|
int limit = state.getConfig().getLimitSave();
|
|
677
|
|
|
678
|
List<TaxonBase> list;
|
|
679
|
logger.info("PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...");
|
|
680
|
// Be sure to add rank information, KingdomFk, TypeNameFk, expertFk and speciesExpertFk to every taxonName
|
|
681
|
|
|
682
|
// Start transaction
|
|
683
|
TransactionStatus txStatus = startTransaction(true);
|
|
684
|
logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
685
|
int partitionCount = 0;
|
|
686
|
while ((list = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, null)) != null) {
|
|
687
|
|
|
688
|
logger.debug("Fetched " + list.size() + " " + pluralString + ". Exporting...");
|
|
689
|
for (TaxonBase<?> taxon : list) {
|
|
690
|
TaxonNameBase<?,?> taxonName = taxon.getName();
|
|
691
|
// Determine expertFk
|
|
692
|
// Integer expertFk = makeExpertFk(state, taxonName);
|
|
693
|
//
|
|
694
|
// // Determine speciesExpertFk
|
|
695
|
// Integer speciesExpertFk = makeSpeciesExpertFk(state, taxonName);
|
|
696
|
|
|
697
|
doCount(count++, modCount, pluralString);
|
|
698
|
Integer typeNameFk = getTypeNameFk(taxonName, state);
|
|
699
|
kingdomFk = findKingdomIdFromTreeIndex(taxon, state);
|
|
700
|
// PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);
|
|
701
|
|
|
702
|
//TODO why are expertFks needed? (Andreas M.)
|
|
703
|
// if (expertFk != null || speciesExpertFk != null) {
|
|
704
|
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, nomenclaturalCode, state.getDbId(taxon),
|
|
705
|
typeNameFk, kingdomFk, state);
|
|
706
|
// }
|
|
707
|
|
|
708
|
taxon = null;
|
|
709
|
taxonName = null;
|
|
710
|
}
|
|
711
|
|
|
712
|
// Commit transaction
|
|
713
|
commitTransaction(txStatus);
|
|
714
|
logger.debug("Committed transaction.");
|
|
715
|
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
|
|
716
|
pastCount = count;
|
|
717
|
|
|
718
|
// Start transaction
|
|
719
|
txStatus = startTransaction(true);
|
|
720
|
logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
721
|
}
|
|
722
|
if (list == null) {
|
|
723
|
logger.info("No " + pluralString + " left to fetch.");
|
|
724
|
}
|
|
725
|
|
|
726
|
list = null;
|
|
727
|
|
|
728
|
// Commit transaction
|
|
729
|
commitTransaction(txStatus);
|
|
730
|
|
|
731
|
logger.debug("Committed transaction.");
|
|
732
|
logger.debug("Try to take snapshot at the end of phase 3 of taxonExport, number of partitions: " + partitionCount);
|
|
733
|
//ProfilerController.memorySnapshot();
|
|
734
|
return success;
|
|
735
|
}
|
|
736
|
|
|
737
|
/**
|
|
738
|
* @param taxon
|
|
739
|
* @return
|
|
740
|
*/
|
|
741
|
private Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxon,PesiExportState state) {
|
|
742
|
if (taxon instanceof Taxon){
|
|
743
|
Set<TaxonNode> nodes = ((Taxon)taxon).getTaxonNodes();
|
|
744
|
if (!nodes.isEmpty()){
|
|
745
|
String treeIndex = nodes.iterator().next().treeIndex();
|
|
746
|
|
|
747
|
Pattern pattern = Pattern.compile("#t[0-9]+#[0-9]+#[0-9]+#");
|
|
748
|
Matcher matcher = pattern.matcher(treeIndex);
|
|
749
|
Integer kingdomID = null;
|
|
750
|
if(matcher.find()) {
|
|
751
|
String treeIndexKingdom = matcher.group(0);
|
|
752
|
kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom);
|
|
753
|
}
|
|
754
|
return kingdomID;
|
|
755
|
} else {
|
|
756
|
logger.debug("The taxon has no nodes: " + taxon.getTitleCache() + " the kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));
|
|
757
|
return PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);
|
|
758
|
}} else{
|
|
759
|
return PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);
|
|
760
|
}
|
|
761
|
}
|
|
762
|
|
|
763
|
// "PHASE 5: Creating Inferred Synonyms..."
|
|
764
|
private boolean doPhase05(PesiExportState state, PesiExportMapping mapping, PesiExportMapping synRelMapping) throws SQLException {
|
|
765
|
int count;
|
|
766
|
int pastCount;
|
|
767
|
boolean success = true;
|
|
768
|
// Get the limit for objects to save within a single transaction.
|
|
769
|
if (! state.getConfig().isDoInferredSynonyms()){
|
|
770
|
logger.info ("Ignore PHASE 5: Creating Inferred Synonyms...");
|
|
771
|
return success;
|
|
772
|
}
|
|
773
|
|
|
774
|
int limit = state.getConfig().getLimitSave();
|
|
775
|
// Create inferred synonyms for accepted taxa
|
|
776
|
logger.info("PHASE 4: Creating Inferred Synonyms...");
|
|
777
|
|
|
778
|
// Determine the count of elements in datawarehouse database table Taxon
|
|
779
|
currentTaxonId = determineTaxonCount(state);
|
|
780
|
currentTaxonId++;
|
|
781
|
|
|
782
|
count = 0;
|
|
783
|
pastCount = 0;
|
|
784
|
int pageSize = limit/10;
|
|
785
|
int pageNumber = 1;
|
|
786
|
String inferredSynonymPluralString = "Inferred Synonyms";
|
|
787
|
|
|
788
|
// Start transaction
|
|
789
|
TransactionStatus txStatus = startTransaction(true);
|
|
790
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
791
|
List<TaxonBase> taxonList = null;
|
|
792
|
|
|
793
|
|
|
794
|
|
|
795
|
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", Rank.SPECIES(), pageSize, pageNumber)).size() > 0) {
|
|
796
|
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
|
|
797
|
|
|
798
|
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
799
|
inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,
|
|
800
|
synRelMapping, taxonList));
|
|
801
|
|
|
802
|
doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);
|
|
803
|
// Commit transaction
|
|
804
|
commitTransaction(txStatus);
|
|
805
|
logger.debug("Committed transaction.");
|
|
806
|
logger.info("Exported " + (taxonList.size()) + " " + inferredSynonymPluralString + ". Total: " + count);
|
|
807
|
//pastCount = count;
|
|
808
|
|
|
809
|
// Save Rank Data and KingdomFk for inferred synonyms
|
|
810
|
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
|
811
|
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomenclaturalCode, taxonFk, kingdomFk, state);
|
|
812
|
}
|
|
813
|
|
|
814
|
// Start transaction
|
|
815
|
txStatus = startTransaction(true);
|
|
816
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
817
|
|
|
818
|
// Increment pageNumber
|
|
819
|
pageNumber++;
|
|
820
|
}
|
|
821
|
taxonList = null;
|
|
822
|
while ((taxonList = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", Rank.SUBSPECIES(), pageSize, pageNumber)).size() > 0) {
|
|
823
|
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
|
|
824
|
|
|
825
|
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
826
|
inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,
|
|
827
|
synRelMapping, taxonList));
|
|
828
|
;
|
|
829
|
doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);
|
|
830
|
// Commit transaction
|
|
831
|
commitTransaction(txStatus);
|
|
832
|
logger.debug("Committed transaction.");
|
|
833
|
logger.info("Exported " + taxonList.size()+ " " + inferredSynonymPluralString + ". Total: " + count);
|
|
834
|
//pastCount = count;
|
|
835
|
|
|
836
|
// Save Rank Data and KingdomFk for inferred synonyms
|
|
837
|
for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {
|
|
838
|
invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomenclaturalCode, taxonFk, kingdomFk, state);
|
|
839
|
}
|
|
840
|
|
|
841
|
// Start transaction
|
|
842
|
txStatus = startTransaction(true);
|
|
843
|
logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
|
|
844
|
|
|
845
|
// Increment pageNumber
|
|
846
|
pageNumber++;
|
|
847
|
inferredSynonymsDataToBeSaved = null;
|
|
848
|
}
|
|
849
|
if (taxonList.size() == 0) {
|
|
850
|
logger.info("No " + parentPluralString + " left to fetch.");
|
|
851
|
}
|
|
852
|
|
|
853
|
taxonList = null;
|
|
854
|
// logger.warn("Taking snapshot at the end of phase 4 of taxonExport");
|
|
855
|
// ProfilerController.memorySnapshot();
|
|
856
|
|
|
857
|
// Commit transaction
|
|
858
|
commitTransaction(txStatus);
|
|
859
|
System.gc();
|
|
860
|
logger.debug("Taking snapshot at the end of phase 4 after gc() of taxonExport");
|
|
861
|
//ProfilerController.memorySnapshot();
|
|
862
|
logger.debug("Committed transaction.");
|
|
863
|
return success;
|
|
864
|
}
|
|
865
|
|
|
866
|
/**
|
|
867
|
* @param state
|
|
868
|
* @param mapping
|
|
869
|
* @param synRelMapping
|
|
870
|
* @param currentTaxonId
|
|
871
|
* @param taxonList
|
|
872
|
* @param inferredSynonymsDataToBeSaved
|
|
873
|
* @return
|
|
874
|
*/
|
|
875
|
private HashMap<Integer, TaxonNameBase<?, ?>> createInferredSynonymsForTaxonList(PesiExportState state,
|
|
876
|
PesiExportMapping mapping, PesiExportMapping synRelMapping, List<TaxonBase> taxonList) {
|
|
877
|
|
|
878
|
Taxon acceptedTaxon;
|
|
879
|
Classification classification = null;
|
|
880
|
List<Synonym> inferredSynonyms = null;
|
|
881
|
boolean localSuccess = true;
|
|
882
|
|
|
883
|
HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();
|
|
884
|
|
|
885
|
for (TaxonBase<?> taxonBase : taxonList) {
|
|
886
|
|
|
887
|
if (taxonBase.isInstanceOf(Taxon.class)) { // this should always be the case since we should have fetched accepted taxon only, but you never know...
|
|
888
|
acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
889
|
TaxonNameBase<?,?> taxonName = acceptedTaxon.getName();
|
|
890
|
|
|
891
|
if (taxonName.isInstanceOf(ZoologicalName.class)) {
|
|
892
|
nomenclaturalCode = taxonName.getNomenclaturalCode();
|
|
893
|
kingdomFk = PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);
|
|
894
|
|
|
895
|
Set<TaxonNode> taxonNodes = acceptedTaxon.getTaxonNodes();
|
|
896
|
TaxonNode singleNode = null;
|
|
897
|
|
|
898
|
if (taxonNodes.size() > 0) {
|
|
899
|
// Determine the classification of the current TaxonNode
|
|
900
|
|
|
901
|
singleNode = taxonNodes.iterator().next();
|
|
902
|
if (singleNode != null) {
|
|
903
|
classification = singleNode.getClassification();
|
|
904
|
} else {
|
|
905
|
logger.error("A TaxonNode belonging to this accepted Taxon is NULL: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache() +")");
|
|
906
|
}
|
|
907
|
} else {
|
|
908
|
// Classification could not be determined directly from this TaxonNode
|
|
909
|
// The stored classification from another TaxonNode is used. It's a simple, but not a failsafe fallback solution.
|
|
910
|
if (taxonNodes.size() == 0) {
|
|
911
|
//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");
|
|
912
|
|
|
913
|
}
|
|
914
|
}
|
|
915
|
|
|
916
|
if (classification != null) {
|
|
917
|
try{
|
|
918
|
TaxonNameBase name = acceptedTaxon.getName();
|
|
919
|
//if (name.isSpecies() || name.isInfraSpecific()){
|
|
920
|
inferredSynonyms = getTaxonService().createAllInferredSynonyms(acceptedTaxon, classification, true);
|
|
921
|
//}
|
|
922
|
// inferredSynonyms = getTaxonService().createInferredSynonyms(classification, acceptedTaxon, SynonymRelationshipType.INFERRED_GENUS_OF());
|
|
923
|
if (inferredSynonyms != null) {
|
|
924
|
for (Synonym synonym : inferredSynonyms) {
|
|
925
|
// TaxonNameBase<?,?> synonymName = synonym.getName();
|
|
926
|
MarkerType markerType =getUuidMarkerType(PesiTransformer.uuidMarkerGuidIsMissing, state);
|
|
927
|
synonym.addMarker(Marker.NewInstance(markerType, true));
|
|
928
|
// Both Synonym and its TaxonName have no valid Id yet
|
|
929
|
synonym.setId(currentTaxonId++);
|
|
930
|
|
|
931
|
|
|
932
|
localSuccess &= mapping.invoke(synonym);
|
|
933
|
//get SynonymRelationship and export
|
|
934
|
if (synonym.getSynonymRelations().isEmpty() ){
|
|
935
|
SynonymRelationship synRel;
|
|
936
|
IdentifiableSource source = synonym.getSources().iterator().next();
|
|
937
|
if (source.getIdNamespace().contains("Potential combination")){
|
|
938
|
synRel = acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.POTENTIAL_COMBINATION_OF());
|
|
939
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to potential combination");
|
|
940
|
} else if (source.getIdNamespace().contains("Inferred Genus")){
|
|
941
|
synRel = acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.INFERRED_GENUS_OF());
|
|
942
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to inferred genus");
|
|
943
|
} else if (source.getIdNamespace().contains("Inferred Epithet")){
|
|
944
|
synRel = acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.INFERRED_EPITHET_OF());
|
|
945
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to inferred epithet");
|
|
946
|
} else{
|
|
947
|
synRel = acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.INFERRED_SYNONYM_OF());
|
|
948
|
logger.error(synonym.getTitleCache() + " has no synonym relationship to " + acceptedTaxon.getTitleCache() + " type is set to inferred synonym");
|
|
949
|
}
|
|
950
|
|
|
951
|
localSuccess &= synRelMapping.invoke(synRel);
|
|
952
|
if (!localSuccess) {
|
|
953
|
logger.error("Synonym relationship export failed " + synonym.getTitleCache() + " accepted taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
954
|
}
|
|
955
|
synRel = null;
|
|
956
|
} else {
|
|
957
|
for (SynonymRelationship synRel: synonym.getSynonymRelations()){
|
|
958
|
localSuccess &= synRelMapping.invoke(synRel);
|
|
959
|
if (!localSuccess) {
|
|
960
|
logger.error("Synonym relationship export failed " + synonym.getTitleCache() + " accepted taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
961
|
} else {
|
|
962
|
logger.info("Synonym relationship successfully exported: " + synonym.getTitleCache() + " " +acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache()+")");
|
|
963
|
}
|
|
964
|
synRel = null;
|
|
965
|
}
|
|
966
|
}
|
|
967
|
|
|
968
|
inferredSynonymsDataToBeSaved.put(synonym.getId(), synonym.getName());
|
|
969
|
}
|
|
970
|
}
|
|
971
|
}catch(Exception e){
|
|
972
|
logger.error(e.getMessage());
|
|
973
|
e.printStackTrace();
|
|
974
|
}
|
|
975
|
} else {
|
|
976
|
logger.error("Classification is NULL. Inferred Synonyms could not be created for this Taxon: " + acceptedTaxon.getUuid() + " (" + acceptedTaxon.getTitleCache() + ")");
|
|
977
|
}
|
|
978
|
} else {
|
|
979
|
// logger.error("TaxonName is not a ZoologicalName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
980
|
}
|
|
981
|
} else {
|
|
982
|
logger.error("This TaxonBase is not a Taxon even though it should be: " + taxonBase.getUuid() + " (" + taxonBase.getTitleCache() + ")");
|
|
983
|
}
|
|
984
|
}
|
|
985
|
taxonList = null;
|
|
986
|
return inferredSynonymsDataToBeSaved;
|
|
987
|
}
|
|
988
|
|
|
989
|
|
|
990
|
/**
|
|
991
|
* Handles names that do not appear in taxa
|
|
992
|
* @param state
|
|
993
|
* @param mapping
|
|
994
|
* @return
|
|
995
|
*/
|
|
996
|
private boolean doNames(PesiExportState state, PesiExportMapping additionalSourceMapping) throws SQLException {
|
|
997
|
|
|
998
|
boolean success = true;
|
|
999
|
if (! state.getConfig().isDoPureNames()){
|
|
1000
|
logger.info ("Ignore PHASE 1b: PureNames");
|
|
1001
|
return success;
|
|
1002
|
}
|
|
1003
|
|
|
1004
|
try {
|
|
1005
|
PesiExportMapping mapping = getPureNameMapping(state);
|
|
1006
|
mapping.initialize(state);
|
|
1007
|
int count = 0;
|
|
1008
|
int pastCount = 0;
|
|
1009
|
List<NonViralName<?>> list;
|
|
1010
|
success = true;
|
|
1011
|
// Get the limit for objects to save within a single transaction.
|
|
1012
|
int limit = state.getConfig().getLimitSave();
|
|
1013
|
|
|
1014
|
|
|
1015
|
logger.info("PHASE 1b: Export Pure Names ...");
|
|
1016
|
// Start transaction
|
|
1017
|
TransactionStatus txStatus = startTransaction(true);
|
|
1018
|
logger.info("Started new transaction for Pure Names. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
1019
|
|
|
1020
|
int partitionCount = 0;
|
|
1021
|
while ((list = getNextPureNamePartition(null, limit, partitionCount++)) != null ) {
|
|
1022
|
|
|
1023
|
logger.info("Fetched " + list.size() + " names without taxa. Exporting...");
|
|
1024
|
for (TaxonNameBase<?,?> taxonName : list) {
|
|
1025
|
doCount(count++, modCount, pluralString);
|
|
1026
|
success &= mapping.invoke(taxonName);
|
|
1027
|
//additional source
|
|
1028
|
if (taxonName.getNomenclaturalReference() != null || StringUtils.isNotBlank(taxonName.getNomenclaturalMicroReference() )){
|
|
1029
|
additionalSourceMapping.invoke(taxonName);
|
|
1030
|
}
|
|
1031
|
}
|
|
1032
|
|
|
1033
|
// Commit transaction
|
|
1034
|
commitTransaction(txStatus);
|
|
1035
|
logger.debug("Committed transaction.");
|
|
1036
|
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
|
|
1037
|
pastCount = count;
|
|
1038
|
|
|
1039
|
// Start transaction
|
|
1040
|
txStatus = startTransaction(true);
|
|
1041
|
logger.info("Started new transaction for PureNames. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
1042
|
}
|
|
1043
|
if (list == null) {
|
|
1044
|
logger.info("No " + pluralString + " left to fetch.");
|
|
1045
|
}
|
|
1046
|
list = null;
|
|
1047
|
// Commit transaction
|
|
1048
|
commitTransaction(txStatus);
|
|
1049
|
logger.debug("Committed transaction.");
|
|
1050
|
} catch (Exception e) {
|
|
1051
|
logger.error("Error occurred in pure name export");
|
|
1052
|
e.printStackTrace();
|
|
1053
|
success = false;
|
|
1054
|
}
|
|
1055
|
return success;
|
|
1056
|
}
|
|
1057
|
|
|
1058
|
/**
|
|
1059
|
* Determines the current number of entries in the DataWarehouse database table <code>Taxon</code>.
|
|
1060
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1061
|
* @return The count.
|
|
1062
|
*/
|
|
1063
|
private Integer determineTaxonCount(PesiExportState state) {
|
|
1064
|
Integer result = null;
|
|
1065
|
PesiExportConfigurator pesiConfig = state.getConfig();
|
|
1066
|
|
|
1067
|
String sql;
|
|
1068
|
Source destination = pesiConfig.getDestination();
|
|
1069
|
sql = "SELECT max(taxonId) FROM Taxon";
|
|
1070
|
destination.setQuery(sql);
|
|
1071
|
ResultSet resultSet = destination.getResultSet();
|
|
1072
|
try {
|
|
1073
|
resultSet.next();
|
|
1074
|
result = resultSet.getInt(1);
|
|
1075
|
} catch (SQLException e) {
|
|
1076
|
logger.error("TaxonCount could not be determined: " + e.getMessage());
|
|
1077
|
e.printStackTrace();
|
|
1078
|
}
|
|
1079
|
resultSet = null;
|
|
1080
|
return result;
|
|
1081
|
}
|
|
1082
|
|
|
1083
|
/**
|
|
1084
|
* Checks whether a parent at specific level has a specific Rank.
|
|
1085
|
* @param taxonName A {@link TaxonNameBase TaxonName}.
|
|
1086
|
* @param level The ancestor level.
|
|
1087
|
* @param ancestorRank The ancestor rank.
|
|
1088
|
* @return Whether a parent at a specific level has a specific Rank.
|
|
1089
|
*/
|
|
1090
|
private boolean validateAncestorOfSpecificRank(TaxonBase<?> taxonBase, int level, Rank ancestorRank) {
|
|
1091
|
boolean result = false;
|
|
1092
|
TaxonNode parentNode = null;
|
|
1093
|
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
1094
|
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
1095
|
// Get ancestor Taxon via TaxonNode
|
|
1096
|
Set<TaxonNode> taxonNodes = taxon.getTaxonNodes();
|
|
1097
|
if (taxonNodes.size() == 1) {
|
|
1098
|
TaxonNode taxonNode = taxonNodes.iterator().next();
|
|
1099
|
if (taxonNode != null) {
|
|
1100
|
for (int i = 0; i < level; i++) {
|
|
1101
|
if (taxonNode != null) {
|
|
1102
|
taxonNode = taxonNode.getParent();
|
|
1103
|
}
|
|
1104
|
}
|
|
1105
|
parentNode = taxonNode;
|
|
1106
|
}
|
|
1107
|
} else if (taxonNodes.size() > 1) {
|
|
1108
|
logger.error("This taxon has " + taxonNodes.size() + " taxonNodes: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
1109
|
}
|
|
1110
|
}
|
|
1111
|
//compare
|
|
1112
|
if (parentNode != null) {
|
|
1113
|
TaxonNode node = CdmBase.deproxy(parentNode, TaxonNode.class);
|
|
1114
|
Taxon parentTaxon = node.getTaxon();
|
|
1115
|
if (parentTaxon != null) {
|
|
1116
|
TaxonNameBase<?,?> parentTaxonName = parentTaxon.getName();
|
|
1117
|
if (parentTaxonName != null && parentTaxonName.getRank().equals(ancestorRank)) {
|
|
1118
|
result = true;
|
|
1119
|
}
|
|
1120
|
} else if (parentNode.treeIndex().matches("#t\\d+#\\d+#")) {
|
|
1121
|
//do nothing (is root node)
|
|
1122
|
} else {
|
|
1123
|
logger.error("This TaxonNode has no Taxon: " + node.getUuid());
|
|
1124
|
}
|
|
1125
|
}
|
|
1126
|
return result;
|
|
1127
|
}
|
|
1128
|
|
|
1129
|
/**
|
|
1130
|
* Returns the AnnotationType for a given UUID.
|
|
1131
|
* @param uuid The Annotation UUID.
|
|
1132
|
* @param label The Annotation label.
|
|
1133
|
* @param text The Annotation text.
|
|
1134
|
* @param labelAbbrev The Annotation label abbreviation.
|
|
1135
|
* @return The AnnotationType.
|
|
1136
|
*/
|
|
1137
|
protected AnnotationType getAnnotationType(UUID uuid, String label, String text, String labelAbbrev){
|
|
1138
|
AnnotationType annotationType = (AnnotationType)getTermService().find(uuid);
|
|
1139
|
if (annotationType == null) {
|
|
1140
|
annotationType = AnnotationType.NewInstance(label, text, labelAbbrev);
|
|
1141
|
annotationType.setUuid(uuid);
|
|
1142
|
// annotationType.setVocabulary(AnnotationType.EDITORIAL().getVocabulary());
|
|
1143
|
getTermService().save(annotationType);
|
|
1144
|
}
|
|
1145
|
return annotationType;
|
|
1146
|
}
|
|
1147
|
|
|
1148
|
/**
|
|
1149
|
* Traverses the classification recursively and stores determined values for every Taxon.
|
|
1150
|
* @param childNode The {@link TaxonNode TaxonNode} to process.
|
|
1151
|
* @param parentNode The parent {@link TaxonNode TaxonNode} of the childNode.
|
|
1152
|
* @param treeIndex The TreeIndex at the current level.
|
|
1153
|
* @param fetchLevel Rank to stop fetching at.
|
|
1154
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1155
|
*/
|
|
1156
|
private void traverseTree(TaxonNode childNode, TaxonNode parentNode, StringBuffer treeIndex, Rank fetchLevel, PesiExportState state) {
|
|
1157
|
// Traverse all branches from this childNode until specified fetchLevel is reached.
|
|
1158
|
StringBuffer localTreeIndex = new StringBuffer(treeIndex);
|
|
1159
|
Taxon childTaxon = childNode.getTaxon();
|
|
1160
|
if (childTaxon != null) {
|
|
1161
|
if (isPesiTaxon(childTaxon)){
|
|
1162
|
Integer taxonId = state.getDbId(childTaxon);
|
|
1163
|
TaxonNameBase<?,?> childName = childTaxon.getName();
|
|
1164
|
if (taxonId != null) {
|
|
1165
|
Rank childRank = childName.getRank();
|
|
1166
|
if (childRank != null) {
|
|
1167
|
if (! childRank.equals(fetchLevel)) {
|
|
1168
|
|
|
1169
|
localTreeIndex.append(taxonId + "#");
|
|
1170
|
|
|
1171
|
saveData(childNode, parentNode, localTreeIndex, state, taxonId);
|
|
1172
|
|
|
1173
|
// Store treeIndex as annotation for further use
|
|
1174
|
Annotation annotation = Annotation.NewInstance(localTreeIndex.toString(), getTreeIndexAnnotationType(), Language.DEFAULT());
|
|
1175
|
childNode.addAnnotation(annotation);
|
|
1176
|
|
|
1177
|
for (TaxonNode newNode : childNode.getChildNodes()) {
|
|
1178
|
if (newNode.getTaxon() != null && isPesiTaxon(newNode.getTaxon())){
|
|
1179
|
traverseTree(newNode, childNode, localTreeIndex, fetchLevel, state);
|
|
1180
|
}
|
|
1181
|
}
|
|
1182
|
|
|
1183
|
} else {
|
|
1184
|
// logger.debug("Target Rank " + fetchLevel.getLabel() + " reached");
|
|
1185
|
return;
|
|
1186
|
}
|
|
1187
|
} else {
|
|
1188
|
logger.error("Rank is NULL. FetchLevel can not be checked: " + childName.getUuid() + " (" + childName.getTitleCache() + ")");
|
|
1189
|
}
|
|
1190
|
} else {
|
|
1191
|
logger.error("Taxon can not be found in state: " + childTaxon.getUuid() + " (" + childTaxon.getTitleCache() + ")");
|
|
1192
|
}
|
|
1193
|
}else{
|
|
1194
|
if (logger.isDebugEnabled()){
|
|
1195
|
logger.debug("Taxon is not a PESI taxon: " + childTaxon.getUuid());
|
|
1196
|
}
|
|
1197
|
}
|
|
1198
|
|
|
1199
|
} else {
|
|
1200
|
logger.error("Taxon is NULL for TaxonNode: " + childNode.getUuid());
|
|
1201
|
}
|
|
1202
|
}
|
|
1203
|
|
|
1204
|
/**
|
|
1205
|
* Stores values in database for every recursive round.
|
|
1206
|
* @param childNode The {@link TaxonNode TaxonNode} to process.
|
|
1207
|
* @param parentNode The parent {@link TaxonNode TaxonNode} of the childNode.
|
|
1208
|
* @param treeIndex The TreeIndex at the current level.
|
|
1209
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1210
|
* @param currentTaxonFk The TaxonFk to store the values for.
|
|
1211
|
*/
|
|
1212
|
private void saveData(TaxonNode childNode, TaxonNode parentNode, StringBuffer treeIndex, PesiExportState state, Integer currentTaxonFk) {
|
|
1213
|
// We are differentiating kingdoms by the nomenclatural code for now.
|
|
1214
|
// This needs to be handled in a better way as soon as we know how to differentiate between more kingdoms.
|
|
1215
|
Taxon childTaxon = childNode.getTaxon();
|
|
1216
|
if (isPesiTaxon(childTaxon)) {
|
|
1217
|
TaxonBase<?> parentTaxon = null;
|
|
1218
|
if (parentNode != null) {
|
|
1219
|
parentTaxon = parentNode.getTaxon();
|
|
1220
|
|
|
1221
|
}
|
|
1222
|
|
|
1223
|
invokeParentTaxonFkAndTreeIndex(state.getDbId(parentTaxon), currentTaxonFk, treeIndex);
|
|
1224
|
}
|
|
1225
|
|
|
1226
|
}
|
|
1227
|
|
|
1228
|
/**
|
|
1229
|
* Inserts values into the Taxon database table.
|
|
1230
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1231
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1232
|
* @param stmt The prepared statement.
|
|
1233
|
* @return Whether save was successful or not.
|
|
1234
|
*/
|
|
1235
|
protected boolean invokeParentTaxonFkAndTreeIndex(Integer parentTaxonFk, Integer currentTaxonFk, StringBuffer treeIndex) {
|
|
1236
|
try {
|
|
1237
|
if (parentTaxonFk != null) {
|
|
1238
|
parentTaxonFk_TreeIndex_KingdomFkStmt.setInt(1, parentTaxonFk);
|
|
1239
|
} else {
|
|
1240
|
parentTaxonFk_TreeIndex_KingdomFkStmt.setObject(1, null);
|
|
1241
|
}
|
|
1242
|
|
|
1243
|
if (treeIndex != null) {
|
|
1244
|
parentTaxonFk_TreeIndex_KingdomFkStmt.setString(2, treeIndex.toString());
|
|
1245
|
} else {
|
|
1246
|
parentTaxonFk_TreeIndex_KingdomFkStmt.setObject(2, null);
|
|
1247
|
}
|
|
1248
|
|
|
1249
|
if (currentTaxonFk != null) {
|
|
1250
|
parentTaxonFk_TreeIndex_KingdomFkStmt.setInt(3, currentTaxonFk);
|
|
1251
|
} else {
|
|
1252
|
parentTaxonFk_TreeIndex_KingdomFkStmt.setObject(3, null);
|
|
1253
|
}
|
|
1254
|
|
|
1255
|
parentTaxonFk_TreeIndex_KingdomFkStmt.executeUpdate();
|
|
1256
|
return true;
|
|
1257
|
} catch (SQLException e) {
|
|
1258
|
logger.error("ParentTaxonFk (" + parentTaxonFk ==null? "-":parentTaxonFk + ") and TreeIndex could not be inserted into database for taxon "+ (currentTaxonFk == null? "-" :currentTaxonFk) + ": " + e.getMessage());
|
|
1259
|
e.printStackTrace();
|
|
1260
|
return false;
|
|
1261
|
}
|
|
1262
|
}
|
|
1263
|
|
|
1264
|
protected boolean invokeParentTaxonFk(Integer parentId, Integer childId) {
|
|
1265
|
try {
|
|
1266
|
parentTaxonFkStmt.setInt(1, parentId);
|
|
1267
|
parentTaxonFkStmt.setInt(2, childId);
|
|
1268
|
parentTaxonFkStmt.executeUpdate();
|
|
1269
|
return true;
|
|
1270
|
} catch (SQLException e) {
|
|
1271
|
logger.warn("ParentTaxonFk (" + parentId ==null? "-":parentId + ") could not be inserted into database for taxon "+ (childId == null? "-" :childId) + ": " + e.getMessage());
|
|
1272
|
e.printStackTrace();
|
|
1273
|
return false;
|
|
1274
|
}
|
|
1275
|
}
|
|
1276
|
|
|
1277
|
|
|
1278
|
/**
|
|
1279
|
* Inserts Rank data and KingdomFk into the Taxon database table.
|
|
1280
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1281
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1282
|
* @param taxonFk The TaxonFk to store the values for.
|
|
1283
|
* @param state
|
|
1284
|
* @param kindomFk The KingdomFk.
|
|
1285
|
* @return Whether save was successful or not.
|
|
1286
|
*/
|
|
1287
|
private boolean invokeRankDataAndKingdomFk(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode, Integer taxonFk, Integer kingdomFk, PesiExportState state) {
|
|
1288
|
try {
|
|
1289
|
Integer rankFk = getRankFk(taxonName, nomenclaturalCode);
|
|
1290
|
if (rankFk != null) {
|
|
1291
|
rankUpdateStmt.setInt(1, rankFk);
|
|
1292
|
} else {
|
|
1293
|
rankUpdateStmt.setObject(1, null);
|
|
1294
|
}
|
|
1295
|
|
|
1296
|
String rankCache = getRankCache(taxonName, nomenclaturalCode, state);
|
|
1297
|
if (rankCache != null) {
|
|
1298
|
rankUpdateStmt.setString(2, rankCache);
|
|
1299
|
} else {
|
|
1300
|
rankUpdateStmt.setObject(2, null);
|
|
1301
|
}
|
|
1302
|
|
|
1303
|
if (kingdomFk != null) {
|
|
1304
|
|
|
1305
|
rankUpdateStmt.setInt(3, kingdomFk);
|
|
1306
|
} else {
|
|
1307
|
rankUpdateStmt.setObject(3, null);
|
|
1308
|
}
|
|
1309
|
|
|
1310
|
if (taxonFk != null) {
|
|
1311
|
rankUpdateStmt.setInt(4, taxonFk);
|
|
1312
|
} else {
|
|
1313
|
rankUpdateStmt.setObject(4, null);
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
rankUpdateStmt.executeUpdate();
|
|
1317
|
return true;
|
|
1318
|
} catch (SQLException e) {
|
|
1319
|
logger.error("Data (RankFk, RankCache, KingdomFk) could not be inserted into database: " + e.getMessage());
|
|
1320
|
e.printStackTrace();
|
|
1321
|
return false;
|
|
1322
|
}
|
|
1323
|
}
|
|
1324
|
|
|
1325
|
/**
|
|
1326
|
* Inserts Rank data, TypeNameFk, KingdomFk, expertFk and speciesExpertFk into the Taxon database table.
|
|
1327
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1328
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1329
|
* @param taxonFk The TaxonFk to store the values for.
|
|
1330
|
* @param typeNameFk The TypeNameFk.
|
|
1331
|
* @param state
|
|
1332
|
* @param kindomFk The KingdomFk.
|
|
1333
|
* @param expertFk The ExpertFk.
|
|
1334
|
* @param speciesExpertFk The SpeciesExpertFk.
|
|
1335
|
* @return Whether save was successful or not.
|
|
1336
|
*/
|
|
1337
|
private boolean invokeRankDataAndTypeNameFkAndKingdomFk(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode,
|
|
1338
|
Integer taxonFk, Integer typeNameFk, Integer kingdomFkk, PesiExportState state) {
|
|
1339
|
try {
|
|
1340
|
int index = 1;
|
|
1341
|
Integer rankFk = getRankFk(taxonName, nomenclaturalCode);
|
|
1342
|
if (rankFk != null) {
|
|
1343
|
rankTypeExpertsUpdateStmt.setInt(index++, rankFk);
|
|
1344
|
} else {
|
|
1345
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1346
|
}
|
|
1347
|
|
|
1348
|
String rankCache = getRankCache(taxonName, nomenclaturalCode, state);
|
|
1349
|
if (rankCache != null) {
|
|
1350
|
rankTypeExpertsUpdateStmt.setString(index++, rankCache);
|
|
1351
|
} else {
|
|
1352
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1353
|
}
|
|
1354
|
|
|
1355
|
if (typeNameFk != null) {
|
|
1356
|
rankTypeExpertsUpdateStmt.setInt(index++, typeNameFk);
|
|
1357
|
} else {
|
|
1358
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1359
|
}
|
|
1360
|
|
|
1361
|
if (kingdomFkk != null) {
|
|
1362
|
rankTypeExpertsUpdateStmt.setInt(index++, kingdomFkk);
|
|
1363
|
} else {
|
|
1364
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1365
|
}
|
|
1366
|
|
|
1367
|
// if (expertFk != null) {
|
|
1368
|
// rankTypeExpertsUpdateStmt.setInt(5, expertFk);
|
|
1369
|
// } else {
|
|
1370
|
// rankTypeExpertsUpdateStmt.setObject(5, null);
|
|
1371
|
// }
|
|
1372
|
//
|
|
1373
|
// //TODO handle experts GUIDS
|
|
1374
|
// if (speciesExpertFk != null) {
|
|
1375
|
// rankTypeExpertsUpdateStmt.setInt(6, speciesExpertFk);
|
|
1376
|
// } else {
|
|
1377
|
// rankTypeExpertsUpdateStmt.setObject(6, null);
|
|
1378
|
// }
|
|
1379
|
//
|
|
1380
|
if (taxonFk != null) {
|
|
1381
|
rankTypeExpertsUpdateStmt.setInt(index++, taxonFk);
|
|
1382
|
} else {
|
|
1383
|
rankTypeExpertsUpdateStmt.setObject(index++, null);
|
|
1384
|
}
|
|
1385
|
|
|
1386
|
rankTypeExpertsUpdateStmt.executeUpdate();
|
|
1387
|
return true;
|
|
1388
|
} catch (SQLException e) {
|
|
1389
|
logger.error("Data could not be inserted into database: " + e.getMessage());
|
|
1390
|
e.printStackTrace();
|
|
1391
|
return false;
|
|
1392
|
} catch (Exception e) {
|
|
1393
|
logger.error("Some exception occurred: " + e.getMessage());
|
|
1394
|
e.printStackTrace();
|
|
1395
|
return false;
|
|
1396
|
}
|
|
1397
|
}
|
|
1398
|
|
|
1399
|
/**
|
|
1400
|
* Deletes all entries of database tables related to <code>Taxon</code>.
|
|
1401
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1402
|
* @return Whether the delete operation was successful or not.
|
|
1403
|
*/
|
|
1404
|
protected boolean doDelete(PesiExportState state) {
|
|
1405
|
PesiExportConfigurator pesiConfig = state.getConfig();
|
|
1406
|
|
|
1407
|
String sql;
|
|
1408
|
Source destination = pesiConfig.getDestination();
|
|
1409
|
|
|
1410
|
// Clear Taxon
|
|
1411
|
sql = "DELETE FROM " + dbTableName;
|
|
1412
|
destination.setQuery(sql);
|
|
1413
|
destination.update(sql);
|
|
1414
|
return true;
|
|
1415
|
}
|
|
1416
|
|
|
1417
|
/* (non-Javadoc)
|
|
1418
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
1419
|
*/
|
|
1420
|
@Override
|
|
1421
|
protected boolean isIgnore(PesiExportState state) {
|
|
1422
|
return ! state.getConfig().isDoTaxa();
|
|
1423
|
}
|
|
1424
|
|
|
1425
|
|
|
1426
|
/**
|
|
1427
|
* Creates the kingdom fk.
|
|
1428
|
* @param taxonName
|
|
1429
|
* @return
|
|
1430
|
*/
|
|
1431
|
@SuppressWarnings("unused") //used by mapper
|
|
1432
|
private static Integer getKingdomFk(TaxonNameBase taxonName){
|
|
1433
|
return PesiTransformer.nomenClaturalCode2Kingdom(taxonName.getNomenclaturalCode());
|
|
1434
|
}
|
|
1435
|
|
|
1436
|
/**
|
|
1437
|
* Creates the parent fk.
|
|
1438
|
* @param taxonName
|
|
1439
|
* @return
|
|
1440
|
*/
|
|
1441
|
@SuppressWarnings("unused") //used by mapper
|
|
1442
|
private static Integer getParentTaxonFk(TaxonBase<?> taxonBase, PesiExportState state){
|
|
1443
|
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
1444
|
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
1445
|
if (! isMisappliedName(taxon)){
|
|
1446
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
1447
|
if (nodes.size() == 0){
|
|
1448
|
if (taxon.getName().getRank().isLower(Rank.KINGDOM())){
|
|
1449
|
logger.warn("Accepted taxon has no parent. " + taxon.getTitleCache() + ", " + taxon.getUuid());
|
|
1450
|
}
|
|
1451
|
}else if (nodes.size() > 1){
|
|
1452
|
logger.warn("Taxon has more than 1 node attached. This is not supported by PESI export." + taxon.getTitleCache() + ", " + taxon.getUuid());
|
|
1453
|
}else{
|
|
1454
|
Taxon parent =nodes.iterator().next().getParent().getTaxon();
|
|
1455
|
return state.getDbId(parent);
|
|
1456
|
}
|
|
1457
|
}
|
|
1458
|
}
|
|
1459
|
return null;
|
|
1460
|
}
|
|
1461
|
|
|
1462
|
/**
|
|
1463
|
* Returns the rankFk for the taxon name based on the names nomenclatural code.
|
|
1464
|
* You may not use this method for kingdoms other then Animalia, Plantae and Bacteria.
|
|
1465
|
* @param taxonName
|
|
1466
|
* @return
|
|
1467
|
*/
|
|
1468
|
@SuppressWarnings("unused") //used by mapper
|
|
1469
|
private static Integer getRankFk(TaxonNameBase<?,?> taxonName) {
|
|
1470
|
return getRankFk(taxonName, taxonName.getNomenclaturalCode());
|
|
1471
|
}
|
|
1472
|
|
|
1473
|
|
|
1474
|
/**
|
|
1475
|
* Returns the <code>RankFk</code> attribute.
|
|
1476
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1477
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1478
|
* @return The <code>RankFk</code> attribute.
|
|
1479
|
* @see MethodMapper
|
|
1480
|
*/
|
|
1481
|
private static Integer getRankFk(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode) {
|
|
1482
|
Integer result = null;
|
|
1483
|
try {
|
|
1484
|
if (nomenclaturalCode != null) {
|
|
1485
|
if (taxonName != null) {
|
|
1486
|
if (taxonName.getRank() == null) {
|
|
1487
|
logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1488
|
} else {
|
|
1489
|
result = PesiTransformer.rank2RankId(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));
|
|
1490
|
}
|
|
1491
|
if (result == null) {
|
|
1492
|
logger.warn("Rank could not be determined for PESI-Kingdom-Id " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode) + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1493
|
}
|
|
1494
|
}
|
|
1495
|
}
|
|
1496
|
} catch (Exception e) {
|
|
1497
|
e.printStackTrace();
|
|
1498
|
}
|
|
1499
|
return result;
|
|
1500
|
}
|
|
1501
|
|
|
1502
|
/**
|
|
1503
|
* Returns the rank cache for the taxon name based on the names nomenclatural code.
|
|
1504
|
* You may not use this method for kingdoms other then Animalia, Plantae and Bacteria.
|
|
1505
|
* @param taxonName
|
|
1506
|
* @return
|
|
1507
|
*/
|
|
1508
|
@SuppressWarnings("unused") //used by mapper
|
|
1509
|
private static String getRankCache(TaxonNameBase<?,?> taxonName, PesiExportState state) {
|
|
1510
|
return getRankCache(taxonName, taxonName.getNomenclaturalCode(), state);
|
|
1511
|
}
|
|
1512
|
|
|
1513
|
|
|
1514
|
/**
|
|
1515
|
* Returns the <code>RankCache</code> attribute.
|
|
1516
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1517
|
* @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.
|
|
1518
|
* @param state
|
|
1519
|
* @return The <code>RankCache</code> attribute.
|
|
1520
|
* @see MethodMapper
|
|
1521
|
*/
|
|
1522
|
private static String getRankCache(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode, PesiExportState state) {
|
|
1523
|
if (nomenclaturalCode != null) {
|
|
1524
|
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));
|
|
1525
|
}else{
|
|
1526
|
logger.warn("No nomenclatural code defined for name " + taxonName.getUuid());
|
|
1527
|
return null;
|
|
1528
|
}
|
|
1529
|
|
|
1530
|
}
|
|
1531
|
|
|
1532
|
|
|
1533
|
/**
|
|
1534
|
* Returns the <code>DisplayName</code> attribute.
|
|
1535
|
* @param taxon The {@link TaxonBase Taxon}.
|
|
1536
|
* @return The <code>DisplayName</code> attribute.
|
|
1537
|
* @see MethodMapper
|
|
1538
|
*/
|
|
1539
|
@SuppressWarnings("unused") //used by Mapper
|
|
1540
|
private static String getDisplayName(TaxonBase<?> taxon) {
|
|
1541
|
TaxonNameBase<?,?> taxonName = taxon.getName();
|
|
1542
|
String result = getDisplayName(taxonName);
|
|
1543
|
if (isMisappliedName(taxon)){
|
|
1544
|
result = result + " " + getAuthorString(taxon);
|
|
1545
|
}
|
|
1546
|
return result;
|
|
1547
|
}
|
|
1548
|
|
|
1549
|
/**
|
|
1550
|
* Returns the <code>AuthorString</code> attribute.
|
|
1551
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1552
|
* @return The <code>AuthorString</code> attribute.
|
|
1553
|
* @see MethodMapper
|
|
1554
|
*/
|
|
1555
|
@SuppressWarnings("unused") //used by mapper
|
|
1556
|
protected static String getAuthorString(TaxonBase<?> taxon) {
|
|
1557
|
try {
|
|
1558
|
String result = null;
|
|
1559
|
boolean isNonViralName = false;
|
|
1560
|
String authorshipCache = null;
|
|
1561
|
TaxonNameBase<?,?> taxonName = taxon.getName();
|
|
1562
|
if (taxonName != null && taxonName.isInstanceOf(NonViralName.class)){
|
|
1563
|
authorshipCache = CdmBase.deproxy(taxonName, NonViralName.class).getAuthorshipCache();
|
|
1564
|
isNonViralName = true;
|
|
1565
|
}
|
|
1566
|
result = authorshipCache;
|
|
1567
|
|
|
1568
|
// For a misapplied names there are special rules
|
|
1569
|
if (isMisappliedName(taxon)){
|
|
1570
|
if (taxon.getSec() != null){
|
|
1571
|
String secTitle = taxon.getSec().getTitleCache();
|
|
1572
|
if (! secTitle.startsWith("auct")){
|
|
1573
|
secTitle = "sensu " + secTitle;
|
|
1574
|
}else if (secTitle.equals("auct")){ //may be removed once the title cache is generated correctly for references with title auct. #
|
|
1575
|
secTitle = "auct.";
|
|
1576
|
}
|
|
1577
|
return secTitle;
|
|
1578
|
}else if (StringUtils.isBlank(authorshipCache)) {
|
|
1579
|
// Set authorshipCache to "auct."
|
|
1580
|
result = PesiTransformer.AUCT_STRING;
|
|
1581
|
}else{
|
|
1582
|
result = PesiTransformer.AUCT_STRING;
|
|
1583
|
// result = authorshipCache;
|
|
1584
|
}
|
|
1585
|
}
|
|
1586
|
|
|
1587
|
if (taxonName == null){
|
|
1588
|
logger.warn("TaxonName does not exist for taxon: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
|
1589
|
}else if (! isNonViralName){
|
|
1590
|
logger.warn("TaxonName is not of instance NonViralName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1591
|
}
|
|
1592
|
|
|
1593
|
if (StringUtils.isBlank(result)) {
|
|
1594
|
return null;
|
|
1595
|
} else {
|
|
1596
|
return result;
|
|
1597
|
}
|
|
1598
|
} catch (Exception e) {
|
|
1599
|
e.printStackTrace();
|
|
1600
|
return null;
|
|
1601
|
}
|
|
1602
|
|
|
1603
|
}
|
|
1604
|
|
|
1605
|
|
|
1606
|
/**
|
|
1607
|
* Returns the <code>DisplayName</code> attribute.
|
|
1608
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1609
|
* @return The <code>DisplayName</code> attribute.
|
|
1610
|
* @see MethodMapper
|
|
1611
|
*/
|
|
1612
|
@SuppressWarnings("unused") //used by Mapper
|
|
1613
|
private static String getDisplayName(TaxonNameBase<?,?> taxonName) {
|
|
1614
|
// TODO: extension?
|
|
1615
|
if (taxonName == null) {
|
|
1616
|
return null;
|
|
1617
|
}else{
|
|
1618
|
INonViralNameCacheStrategy<NonViralName<?>> cacheStrategy = getCacheStrategy(taxonName);
|
|
1619
|
HTMLTagRules tagRules = new HTMLTagRules().
|
|
1620
|
addRule(TagEnum.name, "i").
|
|
1621
|
addRule(TagEnum.nomStatus, "@status@");
|
|
1622
|
|
|
1623
|
NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1624
|
String result = cacheStrategy.getFullTitleCache(nvn, tagRules);
|
|
1625
|
cacheStrategy = null;
|
|
1626
|
nvn = null;
|
|
1627
|
return result.replaceAll(",?\\<@status@\\>.*\\</@status@\\>", "");
|
|
1628
|
}
|
|
1629
|
}
|
|
1630
|
|
|
1631
|
@SuppressWarnings("unused")
|
|
1632
|
private static String getGUID(TaxonNameBase<?,?> taxonName) {
|
|
1633
|
UUID uuid = taxonName.getUuid();
|
|
1634
|
String result = "NameUUID:" + uuid.toString();
|
|
1635
|
return result;
|
|
1636
|
}
|
|
1637
|
|
|
1638
|
|
|
1639
|
/**
|
|
1640
|
* Returns the <code>WebShowName</code> attribute for a taxon.
|
|
1641
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1642
|
* @return The <code>WebShowName</code> attribute.
|
|
1643
|
* @see MethodMapper
|
|
1644
|
*/
|
|
1645
|
@SuppressWarnings("unused")
|
|
1646
|
private static String getWebShowName(TaxonBase<?> taxon) {
|
|
1647
|
TaxonNameBase<?,?> taxonName = taxon.getName();
|
|
1648
|
String result = getWebShowName(taxonName);
|
|
1649
|
if (isMisappliedName(taxon)){
|
|
1650
|
result = result + " " + getAuthorString(taxon);
|
|
1651
|
}
|
|
1652
|
return result;
|
|
1653
|
}
|
|
1654
|
|
|
1655
|
/**
|
|
1656
|
* Returns the <code>WebShowName</code> attribute.
|
|
1657
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1658
|
* @return The <code>WebShowName</code> attribute.
|
|
1659
|
* @see MethodMapper
|
|
1660
|
*/
|
|
1661
|
private static String getWebShowName(TaxonNameBase<?,?> taxonName) {
|
|
1662
|
//TODO extensions?
|
|
1663
|
if (taxonName == null) {
|
|
1664
|
return null;
|
|
1665
|
}else{
|
|
1666
|
INonViralNameCacheStrategy<NonViralName<?>> cacheStrategy = getCacheStrategy(taxonName);
|
|
1667
|
|
|
1668
|
HTMLTagRules tagRules = new HTMLTagRules().addRule(TagEnum.name, "i");
|
|
1669
|
NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1670
|
String result = cacheStrategy.getTitleCache(nvn, tagRules);
|
|
1671
|
cacheStrategy = null;
|
|
1672
|
nvn = null;
|
|
1673
|
return result;
|
|
1674
|
}
|
|
1675
|
}
|
|
1676
|
|
|
1677
|
|
|
1678
|
/**
|
|
1679
|
* Returns the <code>WebSearchName</code> attribute.
|
|
1680
|
* @param taxonName The {@link NonViralName NonViralName}.
|
|
1681
|
* @return The <code>WebSearchName</code> attribute.
|
|
1682
|
* @see MethodMapper
|
|
1683
|
*/
|
|
1684
|
@SuppressWarnings("unused")
|
|
1685
|
private static String getWebSearchName(TaxonNameBase<?,?> taxonName) {
|
|
1686
|
//TODO extensions?
|
|
1687
|
NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1688
|
NonViralNameDefaultCacheStrategy<NonViralName<?>> strategy = getCacheStrategy(nvn);
|
|
1689
|
String result = strategy.getNameCache(nvn);
|
|
1690
|
strategy = null;
|
|
1691
|
nvn = null;
|
|
1692
|
return result;
|
|
1693
|
}
|
|
1694
|
|
|
1695
|
|
|
1696
|
/**
|
|
1697
|
* Returns the <code>FullName</code> attribute.
|
|
1698
|
* @param taxonName The {@link NonViralName NonViralName}.
|
|
1699
|
* @return The <code>FullName</code> attribute.
|
|
1700
|
* @see MethodMapper
|
|
1701
|
*/
|
|
1702
|
@SuppressWarnings("unused")
|
|
1703
|
private static String getFullName(TaxonNameBase taxonName) {
|
|
1704
|
//TODO extensions?
|
|
1705
|
NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1706
|
String result = getCacheStrategy(nvn).getTitleCache(nvn);
|
|
1707
|
Iterator<TaxonBase> taxa = taxonName.getTaxa().iterator();
|
|
1708
|
if (taxonName.getTaxa().size() >0){
|
|
1709
|
if (taxonName.getTaxa().size() == 1){
|
|
1710
|
TaxonBase taxon = taxa.next();
|
|
1711
|
if (isMisappliedName(taxon)){
|
|
1712
|
result = result + " " + getAuthorString(taxon);
|
|
1713
|
}
|
|
1714
|
taxon = null;
|
|
1715
|
}
|
|
1716
|
}
|
|
1717
|
taxa = null;
|
|
1718
|
nvn = null;
|
|
1719
|
return result;
|
|
1720
|
}
|
|
1721
|
|
|
1722
|
/**
|
|
1723
|
* Returns the SourceNameCache for the AdditionalSource table
|
|
1724
|
* @param taxonName
|
|
1725
|
* @return
|
|
1726
|
*/
|
|
1727
|
@SuppressWarnings("unused")
|
|
1728
|
private static String getSourceNameCache(TaxonNameBase taxonName) {
|
|
1729
|
NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1730
|
if (nvn != null){
|
|
1731
|
Reference<?> nomRef = (Reference)nvn.getNomenclaturalReference();
|
|
1732
|
if (nomRef != null){
|
|
1733
|
return nomRef.getAbbrevTitleCache();
|
|
1734
|
}
|
|
1735
|
|
|
1736
|
}
|
|
1737
|
return null;
|
|
1738
|
}
|
|
1739
|
|
|
1740
|
|
|
1741
|
|
|
1742
|
/**
|
|
1743
|
* Returns the <code>FullName</code> attribute.
|
|
1744
|
* @param taxon The {@link TaxonBase taxon}.
|
|
1745
|
* @return The <code>FullName</code> attribute.
|
|
1746
|
* @see MethodMapper
|
|
1747
|
*/
|
|
1748
|
/*@SuppressWarnings("unused")
|
|
1749
|
private static String getFullName(TaxonBase taxon) {
|
|
1750
|
//TODO extensions?
|
|
1751
|
TaxonNameBase name = taxon.getName();
|
|
1752
|
String result = getFullName(name);
|
|
1753
|
if (isMisappliedName(taxon)){
|
|
1754
|
result = result + " " + getAuthorString(taxon);
|
|
1755
|
}
|
|
1756
|
|
|
1757
|
return result;
|
|
1758
|
}
|
|
1759
|
*/
|
|
1760
|
|
|
1761
|
/**
|
|
1762
|
* Returns the nomenclatural reference which is the reference
|
|
1763
|
* including the detail (microreference).
|
|
1764
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1765
|
* @return The <code>AuthorString</code> attribute.
|
|
1766
|
* @see MethodMapper
|
|
1767
|
*/
|
|
1768
|
@SuppressWarnings("unused")
|
|
1769
|
private static String getNomRefString(TaxonNameBase<?,?> taxonName) {
|
|
1770
|
INomenclaturalReference ref = taxonName.getNomenclaturalReference();
|
|
1771
|
if (ref == null){
|
|
1772
|
return null;
|
|
1773
|
}
|
|
1774
|
if (! ref.isProtectedAbbrevTitleCache()){
|
|
1775
|
ref.setAbbrevTitleCache(null, false); //to remove a false cache
|
|
1776
|
}
|
|
1777
|
return ref.getNomenclaturalCitation(taxonName.getNomenclaturalMicroReference());
|
|
1778
|
}
|
|
1779
|
|
|
1780
|
|
|
1781
|
/**
|
|
1782
|
* Returns the <code>NameStatusFk</code> attribute.
|
|
1783
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1784
|
* @return The <code>NameStatusFk</code> attribute.
|
|
1785
|
* @see MethodMapper
|
|
1786
|
*/
|
|
1787
|
@SuppressWarnings("unused")
|
|
1788
|
private static Integer getNameStatusFk(TaxonNameBase<?,?> taxonName) {
|
|
1789
|
Integer result = null;
|
|
1790
|
|
|
1791
|
NomenclaturalStatus state = getNameStatus(taxonName);
|
|
1792
|
if (state != null) {
|
|
1793
|
result = PesiTransformer.nomStatus2nomStatusFk(state.getType());
|
|
1794
|
}
|
|
1795
|
return result;
|
|
1796
|
}
|
|
1797
|
|
|
1798
|
/**
|
|
1799
|
* Returns the <code>NameStatusCache</code> attribute.
|
|
1800
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1801
|
* @return The <code>NameStatusCache</code> attribute.
|
|
1802
|
* @throws UndefinedTransformerMethodException
|
|
1803
|
* @see MethodMapper
|
|
1804
|
*/
|
|
1805
|
@SuppressWarnings("unused")
|
|
1806
|
private static String getNameStatusCache(TaxonNameBase taxonName, PesiExportState state) throws UndefinedTransformerMethodException {
|
|
1807
|
String result = null;
|
|
1808
|
NomenclaturalStatus status = getNameStatus(taxonName);
|
|
1809
|
if (status != null) {
|
|
1810
|
result = state.getTransformer().getCacheByNomStatus(status.getType());
|
|
1811
|
}
|
|
1812
|
return result;
|
|
1813
|
}
|
|
1814
|
|
|
1815
|
|
|
1816
|
private static NomenclaturalStatus getNameStatus(TaxonNameBase<?,?> taxonName) {
|
|
1817
|
try {
|
|
1818
|
if (taxonName != null && (taxonName.isInstanceOf(NonViralName.class))) {
|
|
1819
|
NonViralName<?> nonViralName = CdmBase.deproxy(taxonName, NonViralName.class);
|
|
1820
|
Set<NomenclaturalStatus> states = nonViralName.getStatus();
|
|
1821
|
if (states.size() == 1) {
|
|
1822
|
NomenclaturalStatus status = states.iterator().next();
|
|
1823
|
return status;
|
|
1824
|
} else if (states.size() > 1) {
|
|
1825
|
logger.error("This TaxonName has more than one Nomenclatural Status: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1826
|
}
|
|
1827
|
}
|
|
1828
|
|
|
1829
|
} catch (Exception e) {
|
|
1830
|
e.printStackTrace();
|
|
1831
|
}
|
|
1832
|
return null;
|
|
1833
|
}
|
|
1834
|
/**
|
|
1835
|
* Returns the <code>TaxonStatusFk</code> attribute.
|
|
1836
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1837
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1838
|
* @return The <code>TaxonStatusFk</code> attribute.
|
|
1839
|
* @see MethodMapper
|
|
1840
|
*/
|
|
1841
|
private static Integer getTaxonStatusFk(TaxonBase<?> taxon, PesiExportState state) {
|
|
1842
|
Integer result = null;
|
|
1843
|
|
|
1844
|
try {
|
|
1845
|
if (isMisappliedName(taxon)) {
|
|
1846
|
Synonym synonym = Synonym.NewInstance(null, null);
|
|
1847
|
|
|
1848
|
// This works as long as only the instance is important to differentiate between TaxonStatus.
|
|
1849
|
result = PesiTransformer.taxonBase2statusFk(synonym); // Auct References are treated as Synonyms in Datawarehouse now.
|
|
1850
|
} else {
|
|
1851
|
result = PesiTransformer.taxonBase2statusFk(taxon);
|
|
1852
|
}
|
|
1853
|
|
|
1854
|
} catch (Exception e) {
|
|
1855
|
e.printStackTrace();
|
|
1856
|
}
|
|
1857
|
return result;
|
|
1858
|
}
|
|
1859
|
|
|
1860
|
/**
|
|
1861
|
* Returns the <code>TaxonStatusCache</code> attribute.
|
|
1862
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1863
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1864
|
* @return The <code>TaxonStatusCache</code> attribute.
|
|
1865
|
* @throws UndefinedTransformerMethodException
|
|
1866
|
* @see MethodMapper
|
|
1867
|
*/
|
|
1868
|
@SuppressWarnings("unused")
|
|
1869
|
private static String getTaxonStatusCache(TaxonBase<?> taxon, PesiExportState state) throws UndefinedTransformerMethodException {
|
|
1870
|
return state.getTransformer().getTaxonStatusCacheByKey(getTaxonStatusFk(taxon, state));
|
|
1871
|
}
|
|
1872
|
|
|
1873
|
/**
|
|
1874
|
* Returns the <code>TypeNameFk</code> attribute.
|
|
1875
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1876
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
1877
|
* @return The <code>TypeNameFk</code> attribute.
|
|
1878
|
* @see MethodMapper
|
|
1879
|
*/
|
|
1880
|
private static Integer getTypeNameFk(TaxonNameBase<?,?> taxonNameBase, PesiExportState state) {
|
|
1881
|
Integer result = null;
|
|
1882
|
if (taxonNameBase != null) {
|
|
1883
|
Set<NameTypeDesignation> nameTypeDesignations = taxonNameBase.getNameTypeDesignations();
|
|
1884
|
if (nameTypeDesignations.size() == 1) {
|
|
1885
|
NameTypeDesignation nameTypeDesignation = nameTypeDesignations.iterator().next();
|
|
1886
|
if (nameTypeDesignation != null) {
|
|
1887
|
TaxonNameBase<?,?> typeName = nameTypeDesignation.getTypeName();
|
|
1888
|
if (typeName != null) {
|
|
1889
|
result = state.getDbId(typeName);
|
|
1890
|
}
|
|
1891
|
}
|
|
1892
|
} else if (nameTypeDesignations.size() > 1) {
|
|
1893
|
logger.warn("This TaxonName has " + nameTypeDesignations.size() + " NameTypeDesignations: " + taxonNameBase.getUuid() + " (" + taxonNameBase.getTitleCache() + ")");
|
|
1894
|
}
|
|
1895
|
}
|
|
1896
|
return result;
|
|
1897
|
}
|
|
1898
|
|
|
1899
|
/**
|
|
1900
|
* Returns the <code>TypeFullnameCache</code> attribute.
|
|
1901
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1902
|
* @return The <code>TypeFullnameCache</code> attribute.
|
|
1903
|
* @see MethodMapper
|
|
1904
|
*/
|
|
1905
|
@SuppressWarnings("unused")
|
|
1906
|
private static String getTypeFullnameCache(TaxonNameBase<?,?> taxonName) {
|
|
1907
|
String result = null;
|
|
1908
|
|
|
1909
|
try {
|
|
1910
|
if (taxonName != null) {
|
|
1911
|
Set<NameTypeDesignation> nameTypeDesignations = taxonName.getNameTypeDesignations();
|
|
1912
|
if (nameTypeDesignations.size() == 1) {
|
|
1913
|
NameTypeDesignation nameTypeDesignation = nameTypeDesignations.iterator().next();
|
|
1914
|
if (nameTypeDesignation != null) {
|
|
1915
|
TaxonNameBase<?,?> typeName = nameTypeDesignation.getTypeName();
|
|
1916
|
if (typeName != null) {
|
|
1917
|
result = typeName.getTitleCache();
|
|
1918
|
}
|
|
1919
|
}
|
|
1920
|
} else if (nameTypeDesignations.size() > 1) {
|
|
1921
|
logger.warn("This TaxonName has " + nameTypeDesignations.size() + " NameTypeDesignations: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1922
|
}
|
|
1923
|
}
|
|
1924
|
|
|
1925
|
} catch (Exception e) {
|
|
1926
|
e.printStackTrace();
|
|
1927
|
}
|
|
1928
|
return result;
|
|
1929
|
}
|
|
1930
|
|
|
1931
|
|
|
1932
|
/**
|
|
1933
|
* Returns the <code>QualityStatusFk</code> attribute.
|
|
1934
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1935
|
* @return The <code>QualityStatusFk</code> attribute.
|
|
1936
|
* @see MethodMapper
|
|
1937
|
*/
|
|
1938
|
private static Integer getQualityStatusFk(TaxonNameBase taxonName) {
|
|
1939
|
BitSet sources = getSources(taxonName);
|
|
1940
|
return PesiTransformer.getQualityStatusKeyBySource(sources, taxonName);
|
|
1941
|
}
|
|
1942
|
|
|
1943
|
|
|
1944
|
/**
|
|
1945
|
* Returns the <code>QualityStatusCache</code> attribute.
|
|
1946
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1947
|
* @return The <code>QualityStatusCache</code> attribute.
|
|
1948
|
* @throws UndefinedTransformerMethodException
|
|
1949
|
* @see MethodMapper
|
|
1950
|
*/
|
|
1951
|
@SuppressWarnings("unused")
|
|
1952
|
private static String getQualityStatusCache(TaxonNameBase taxonName, PesiExportState state) throws UndefinedTransformerMethodException {
|
|
1953
|
return state.getTransformer().getQualityStatusCacheByKey(getQualityStatusFk(taxonName));
|
|
1954
|
}
|
|
1955
|
|
|
1956
|
|
|
1957
|
/**
|
|
1958
|
* Returns the <code>TypeDesignationStatusFk</code> attribute.
|
|
1959
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1960
|
* @return The <code>TypeDesignationStatusFk</code> attribute.
|
|
1961
|
* @see MethodMapper
|
|
1962
|
*/
|
|
1963
|
@SuppressWarnings("unused")
|
|
1964
|
private static Integer getTypeDesignationStatusFk(TaxonNameBase<?,?> taxonName) {
|
|
1965
|
Integer result = null;
|
|
1966
|
|
|
1967
|
try {
|
|
1968
|
if (taxonName != null) {
|
|
1969
|
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations();
|
|
1970
|
if (typeDesignations.size() == 1) {
|
|
1971
|
Object obj = typeDesignations.iterator().next().getTypeStatus();
|
|
1972
|
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class);
|
|
1973
|
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusId(designationStatus);
|
|
1974
|
} else if (typeDesignations.size() > 1) {
|
|
1975
|
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
1976
|
}
|
|
1977
|
}
|
|
1978
|
|
|
1979
|
} catch (Exception e) {
|
|
1980
|
e.printStackTrace();
|
|
1981
|
}
|
|
1982
|
return result;
|
|
1983
|
}
|
|
1984
|
|
|
1985
|
/**
|
|
1986
|
* Returns the <code>TypeDesignationStatusCache</code> attribute.
|
|
1987
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
1988
|
* @return The <code>TypeDesignationStatusCache</code> attribute.
|
|
1989
|
* @see MethodMapper
|
|
1990
|
*/
|
|
1991
|
@SuppressWarnings("unused")
|
|
1992
|
private static String getTypeDesignationStatusCache(TaxonNameBase<?,?> taxonName) {
|
|
1993
|
String result = null;
|
|
1994
|
|
|
1995
|
try {
|
|
1996
|
if (taxonName != null) {
|
|
1997
|
Set<NameTypeDesignation> typeDesignations = taxonName.getNameTypeDesignations();
|
|
1998
|
if (typeDesignations.size() == 1) {
|
|
1999
|
Object obj = typeDesignations.iterator().next().getTypeStatus();
|
|
2000
|
NameTypeDesignationStatus designationStatus = CdmBase.deproxy(obj, NameTypeDesignationStatus.class);
|
|
2001
|
result = PesiTransformer.nameTypeDesignationStatus2TypeDesignationStatusCache(designationStatus);
|
|
2002
|
} else if (typeDesignations.size() > 1) {
|
|
2003
|
logger.error("Found a TaxonName with more than one NameTypeDesignation: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2004
|
}
|
|
2005
|
}
|
|
2006
|
|
|
2007
|
} catch (Exception e) {
|
|
2008
|
e.printStackTrace();
|
|
2009
|
}
|
|
2010
|
return result;
|
|
2011
|
}
|
|
2012
|
|
|
2013
|
/**
|
|
2014
|
* Returns the <code>FossilStatusFk</code> attribute.
|
|
2015
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2016
|
* @return The <code>FossilStatusFk</code> attribute.
|
|
2017
|
* @see MethodMapper
|
|
2018
|
*/
|
|
2019
|
@SuppressWarnings("unused")
|
|
2020
|
private static Integer getFossilStatusFk(IdentifiableEntity<?> identEntity, PesiExportState state) {
|
|
2021
|
Integer result = null;
|
|
2022
|
|
|
2023
|
Set<String> fossilStatuus = identEntity.getExtensions(ErmsTransformer.uuidFossilStatus);
|
|
2024
|
if (fossilStatuus.size() == 0){
|
|
2025
|
return null;
|
|
2026
|
}else if (fossilStatuus.size() > 1){
|
|
2027
|
logger.warn("More than 1 fossil status given for " + identEntity.getTitleCache() + " " + identEntity.getUuid());
|
|
2028
|
}
|
|
2029
|
String fossilStatus = fossilStatuus.iterator().next();
|
|
2030
|
|
|
2031
|
int statusFk = state.getTransformer().FossilStatusCache2FossilStatusFk(fossilStatus);
|
|
2032
|
return statusFk;
|
|
2033
|
}
|
|
2034
|
|
|
2035
|
/**
|
|
2036
|
* Returns the <code>FossilStatusCache</code> attribute.
|
|
2037
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2038
|
* @return The <code>FossilStatusCache</code> attribute.
|
|
2039
|
* @see MethodMapper
|
|
2040
|
*/
|
|
2041
|
@SuppressWarnings("unused")
|
|
2042
|
private static String getFossilStatusCache(IdentifiableEntity<?> identEntity, PesiExportState state) {
|
|
2043
|
String result = null;
|
|
2044
|
Set<String> fossilStatuus = identEntity.getExtensions(ErmsTransformer.uuidFossilStatus);
|
|
2045
|
if (fossilStatuus.size() == 0){
|
|
2046
|
return null;
|
|
2047
|
}
|
|
2048
|
for (String strFossilStatus : fossilStatuus){
|
|
2049
|
result = CdmUtils.concat(";", result, strFossilStatus);
|
|
2050
|
}
|
|
2051
|
return result;
|
|
2052
|
}
|
|
2053
|
|
|
2054
|
/**
|
|
2055
|
* Returns the <code>IdInSource</code> attribute.
|
|
2056
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2057
|
* @return The <code>IdInSource</code> attribute.
|
|
2058
|
* @see MethodMapper
|
|
2059
|
*/
|
|
2060
|
@SuppressWarnings("unused")
|
|
2061
|
private static String getIdInSource(IdentifiableEntity taxonName) {
|
|
2062
|
String result = null;
|
|
2063
|
|
|
2064
|
try {
|
|
2065
|
Set<IdentifiableSource> sources = getPesiSources(taxonName);
|
|
2066
|
if (sources.size() > 1){
|
|
2067
|
logger.warn("There is > 1 Pesi source. This is not yet handled.");
|
|
2068
|
}
|
|
2069
|
if (sources.size() == 0){
|
|
2070
|
logger.warn("There is no Pesi source!" +taxonName.getUuid() + " (" + taxonName.getTitleCache() +")");
|
|
2071
|
}
|
|
2072
|
for (IdentifiableSource source : sources) {
|
|
2073
|
Reference<?> ref = source.getCitation();
|
|
2074
|
UUID refUuid = ref.getUuid();
|
|
2075
|
String idInSource = source.getIdInSource();
|
|
2076
|
if (refUuid.equals(BerlinModelTransformer.uuidSourceRefEuroMed)){
|
|
2077
|
result = idInSource != null ? ("NameId: " + source.getIdInSource()) : null;
|
|
2078
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)){
|
|
2079
|
result = idInSource != null ? ("TAX_ID: " + source.getIdInSource()) : null;
|
|
2080
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefErms)){
|
|
2081
|
result = idInSource != null ? ("tu_id: " + source.getIdInSource()) : null;
|
|
2082
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum)){ //Index Fungorum
|
|
2083
|
result = idInSource != null ? ("if_id: " + source.getIdInSource()) : null;
|
|
2084
|
}else{
|
|
2085
|
if (logger.isDebugEnabled()){logger.debug("Not a PESI source");};
|
|
2086
|
}
|
|
2087
|
|
|
2088
|
String sourceIdNameSpace = source.getIdNamespace();
|
|
2089
|
if (sourceIdNameSpace != null) {
|
|
2090
|
if (sourceIdNameSpace.equals(PesiTransformer.STR_NAMESPACE_NOMINAL_TAXON)) {
|
|
2091
|
result = idInSource != null ? ("Nominal Taxon from TAX_ID: " + source.getIdInSource()):null;
|
|
2092
|
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.INFERRED_EPITHET_NAMESPACE)) {
|
|
2093
|
result = idInSource != null ? ("Inferred epithet from TAX_ID: " + source.getIdInSource()) : null;
|
|
2094
|
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.INFERRED_GENUS_NAMESPACE)) {
|
|
2095
|
result = idInSource != null ? ("Inferred genus from TAX_ID: " + source.getIdInSource()):null;
|
|
2096
|
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.POTENTIAL_COMBINATION_NAMESPACE)) {
|
|
2097
|
result = idInSource != null ? ("Potential combination from TAX_ID: " + source.getIdInSource()):null;
|
|
2098
|
}
|
|
2099
|
}
|
|
2100
|
if (result == null) {
|
|
2101
|
logger.warn("IdInSource is NULL for this taxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() +", sourceIdNameSpace: " + source.getIdNamespace()+")");
|
|
2102
|
}
|
|
2103
|
}
|
|
2104
|
} catch (Exception e) {
|
|
2105
|
e.printStackTrace();
|
|
2106
|
logger.error("An error occurs while creating idInSource..." + taxonName.getUuid() + " (" + taxonName.getTitleCache()+ e.getMessage());
|
|
2107
|
}
|
|
2108
|
|
|
2109
|
if (result == null) {
|
|
2110
|
logger.warn("IdInSource is NULL for this taxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() +")");
|
|
2111
|
}
|
|
2112
|
return result;
|
|
2113
|
}
|
|
2114
|
|
|
2115
|
/**
|
|
2116
|
* Returns the idInSource for a given TaxonName only.
|
|
2117
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2118
|
* @return The idInSource.
|
|
2119
|
*/
|
|
2120
|
private static String getIdInSourceOnly(IdentifiableEntity identEntity) {
|
|
2121
|
String result = null;
|
|
2122
|
|
|
2123
|
// Get the sources first
|
|
2124
|
Set<IdentifiableSource> sources = getPesiSources(identEntity);
|
|
2125
|
|
|
2126
|
// Determine the idInSource
|
|
2127
|
if (sources.size() == 1) {
|
|
2128
|
IdentifiableSource source = sources.iterator().next();
|
|
2129
|
if (source != null) {
|
|
2130
|
result = source.getIdInSource();
|
|
2131
|
}
|
|
2132
|
} else if (sources.size() > 1) {
|
|
2133
|
int count = 1;
|
|
2134
|
result = "";
|
|
2135
|
for (IdentifiableSource source : sources) {
|
|
2136
|
result += source.getIdInSource();
|
|
2137
|
if (count < sources.size()) {
|
|
2138
|
result += "; ";
|
|
2139
|
}
|
|
2140
|
count++;
|
|
2141
|
}
|
|
2142
|
|
|
2143
|
}
|
|
2144
|
|
|
2145
|
return result;
|
|
2146
|
}
|
|
2147
|
|
|
2148
|
/**
|
|
2149
|
* Returns the Sources for a given TaxonName only.
|
|
2150
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2151
|
* @return The Sources.
|
|
2152
|
*/
|
|
2153
|
private static Set<IdentifiableSource> getPesiSources(IdentifiableEntity identEntity) {
|
|
2154
|
Set<IdentifiableSource> sources = new java.util.HashSet<IdentifiableSource>();
|
|
2155
|
|
|
2156
|
//Taxon Names
|
|
2157
|
if (identEntity.isInstanceOf(TaxonNameBase.class)){
|
|
2158
|
// Sources from TaxonName
|
|
2159
|
TaxonNameBase taxonName = CdmBase.deproxy(identEntity, TaxonNameBase.class);
|
|
2160
|
Set<IdentifiableSource> testSources = identEntity.getSources();
|
|
2161
|
sources = filterPesiSources(identEntity.getSources());
|
|
2162
|
|
|
2163
|
if (sources.size() == 0 && testSources.size()>0){
|
|
2164
|
IdentifiableSource source = testSources.iterator().next();
|
|
2165
|
logger.warn("There are sources, but they are no pesi sources!!!" + source.getIdInSource() + " - " + source.getIdNamespace() + " - " + source.getCitation().getTitleCache());
|
|
2166
|
}
|
|
2167
|
if (sources.size() > 1) {
|
|
2168
|
logger.warn("This TaxonName has more than one Source: " + identEntity.getUuid() + " (" + identEntity.getTitleCache() + ")");
|
|
2169
|
}
|
|
2170
|
|
|
2171
|
// name has no PESI source, take sources from TaxonBase
|
|
2172
|
if (sources == null || sources.isEmpty()) {
|
|
2173
|
Set<TaxonBase> taxa = taxonName.getTaxonBases();
|
|
2174
|
for (TaxonBase taxonBase: taxa){
|
|
2175
|
sources.addAll(filterPesiSources(taxonBase.getSources()));
|
|
2176
|
}
|
|
2177
|
}
|
|
2178
|
|
|
2179
|
//for TaxonBases
|
|
2180
|
}else if (identEntity.isInstanceOf(TaxonBase.class)){
|
|
2181
|
sources = filterPesiSources(identEntity.getSources());
|
|
2182
|
}
|
|
2183
|
|
|
2184
|
/*TODO: deleted only for testing the inferred synonyms
|
|
2185
|
if (sources == null || sources.isEmpty()) {
|
|
2186
|
logger.warn("This TaxonName has no PESI Sources: " + identEntity.getUuid() + " (" + identEntity.getTitleCache() +")");
|
|
2187
|
}else if (sources.size() > 1){
|
|
2188
|
logger.warn("This Taxon(Name) has more than 1 PESI source: " + identEntity.getUuid() + " (" + identEntity.getTitleCache() +")");
|
|
2189
|
}
|
|
2190
|
*/
|
|
2191
|
return sources;
|
|
2192
|
}
|
|
2193
|
|
|
2194
|
// return all sources with a PESI reference
|
|
2195
|
private static Set<IdentifiableSource> filterPesiSources(Set<? extends IdentifiableSource> sources) {
|
|
2196
|
Set<IdentifiableSource> result = new HashSet<IdentifiableSource>();
|
|
2197
|
for (IdentifiableSource source : sources){
|
|
2198
|
Reference ref = source.getCitation();
|
|
2199
|
UUID refUuid = ref.getUuid();
|
|
2200
|
if (refUuid.equals(BerlinModelTransformer.uuidSourceRefEuroMed) ||
|
|
2201
|
refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)||
|
|
2202
|
refUuid.equals(PesiTransformer.uuidSourceRefErms)||
|
|
2203
|
refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum) ||
|
|
2204
|
refUuid.equals(PesiTransformer.uuidSourceRefAuct)){
|
|
2205
|
result.add(source);
|
|
2206
|
}
|
|
2207
|
}
|
|
2208
|
return result;
|
|
2209
|
}
|
|
2210
|
|
|
2211
|
/**
|
|
2212
|
* Returns the <code>GUID</code> attribute.
|
|
2213
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2214
|
* @return The <code>GUID</code> attribute.
|
|
2215
|
* @see MethodMapper
|
|
2216
|
*/
|
|
2217
|
private static String getGUID(TaxonBase<?> taxon) {
|
|
2218
|
if (taxon.getLsid() != null ){
|
|
2219
|
return taxon.getLsid().getLsid();
|
|
2220
|
}else if (taxon.hasMarker(PesiTransformer.uuidMarkerGuidIsMissing, true)){
|
|
2221
|
return null;
|
|
2222
|
}else{
|
|
2223
|
return taxon.getUuid().toString();
|
|
2224
|
}
|
|
2225
|
}
|
|
2226
|
|
|
2227
|
|
|
2228
|
|
|
2229
|
|
|
2230
|
/**
|
|
2231
|
* Returns the <code>DerivedFromGuid</code> attribute.
|
|
2232
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2233
|
* @return The <code>DerivedFromGuid</code> attribute.
|
|
2234
|
* @see MethodMapper
|
|
2235
|
*/
|
|
2236
|
@SuppressWarnings("unused")
|
|
2237
|
private static String getDerivedFromGuid(TaxonBase<?> taxon) {
|
|
2238
|
String result = null;
|
|
2239
|
try {
|
|
2240
|
// The same as GUID for now
|
|
2241
|
result = getGUID(taxon);
|
|
2242
|
} catch (Exception e) {
|
|
2243
|
e.printStackTrace();
|
|
2244
|
}
|
|
2245
|
return result;
|
|
2246
|
}
|
|
2247
|
|
|
2248
|
/**
|
|
2249
|
* Returns the <code>CacheCitation</code> attribute.
|
|
2250
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2251
|
* @return The CacheCitation.
|
|
2252
|
* @see MethodMapper
|
|
2253
|
*/
|
|
2254
|
@SuppressWarnings("unused")
|
|
2255
|
private static String getCacheCitation(TaxonBase taxon) {
|
|
2256
|
// !!! See also doPhaseUpdates
|
|
2257
|
|
|
2258
|
TaxonNameBase<?,?> taxonName = taxon.getName();
|
|
2259
|
String result = "";
|
|
2260
|
//TODO implement anew for taxa
|
|
2261
|
try {
|
|
2262
|
BitSet sources = getSources(taxonName);
|
|
2263
|
if (sources.isEmpty()) {
|
|
2264
|
// logger.error("OriginalDB is NULL for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2265
|
} else if (sources.get(PesiTransformer.SOURCE_ERMS)) {
|
|
2266
|
// TODO: 19.08.2010: An import of CacheCitation does not exist in the ERMS import yet or it will be imported in a different way...
|
|
2267
|
// So the following code is some kind of harmless assumption.
|
|
2268
|
Set<Extension> extensions = taxonName.getExtensions();
|
|
2269
|
for (Extension extension : extensions) {
|
|
2270
|
if (extension.getType().equals(cacheCitationExtensionType)) {
|
|
2271
|
result = extension.getValue();
|
|
2272
|
}
|
|
2273
|
}
|
|
2274
|
} else {
|
|
2275
|
String expertName = getExpertName(taxon);
|
|
2276
|
String webShowName = getWebShowName(taxonName);
|
|
2277
|
|
|
2278
|
// idInSource only
|
|
2279
|
String idInSource = getIdInSourceOnly(taxonName);
|
|
2280
|
|
|
2281
|
// build the cacheCitation
|
|
2282
|
if (expertName != null) {
|
|
2283
|
result += expertName + ". ";
|
|
2284
|
} else {
|
|
2285
|
if (logger.isDebugEnabled()){logger.debug("ExpertName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");}
|
|
2286
|
}
|
|
2287
|
if (webShowName != null) {
|
|
2288
|
result += webShowName + ". ";
|
|
2289
|
} else {
|
|
2290
|
logger.warn("WebShowName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2291
|
}
|
|
2292
|
|
|
2293
|
if (getOriginalDB(taxonName).equals("FaEu")) {
|
|
2294
|
result += "Accessed through: Fauna Europaea at http://faunaeur.org/full_results.php?id=";
|
|
2295
|
} else if (getOriginalDB(taxonName).equals("EM")) {
|
|
2296
|
result += "Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=";
|
|
2297
|
}
|
|
2298
|
|
|
2299
|
if (idInSource != null) {
|
|
2300
|
result += idInSource;
|
|
2301
|
} else {
|
|
2302
|
logger.warn("IdInSource could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
2303
|
}
|
|
2304
|
}
|
|
2305
|
} catch (Exception e) {
|
|
2306
|
e.printStackTrace();
|
|
2307
|
}
|
|
2308
|
|
|
2309
|
if (StringUtils.isBlank(result)) {
|
|
2310
|
return null;
|
|
2311
|
} else {
|
|
2312
|
return result;
|
|
2313
|
}
|
|
2314
|
}
|
|
2315
|
|
|
2316
|
/**
|
|
2317
|
* Returns the <code>OriginalDB</code> attribute.
|
|
2318
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2319
|
* @return The <code>OriginalDB</code> attribute.
|
|
2320
|
* @see MethodMapper
|
|
2321
|
*/
|
|
2322
|
private static String getOriginalDB(IdentifiableEntity identEntity) {
|
|
2323
|
// Sources from TaxonName
|
|
2324
|
BitSet sources = getSources(identEntity);
|
|
2325
|
return PesiTransformer.getOriginalDbBySources(sources);
|
|
2326
|
}
|
|
2327
|
|
|
2328
|
/**
|
|
2329
|
* Returns the <code>LastAction</code> attribute.
|
|
2330
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2331
|
* @return The <code>LastAction</code> attribute.
|
|
2332
|
* @see MethodMapper
|
|
2333
|
*/
|
|
2334
|
@SuppressWarnings("unused")
|
|
2335
|
private static String getLastAction(IdentifiableEntity<?> identEntity) {
|
|
2336
|
String result = null;
|
|
2337
|
try {
|
|
2338
|
Set<Extension> extensions = identEntity.getExtensions();
|
|
2339
|
for (Extension extension : extensions) {
|
|
2340
|
if (extension.getType().equals(lastActionExtensionType)) {
|
|
2341
|
result = extension.getValue();
|
|
2342
|
}
|
|
2343
|
}
|
|
2344
|
} catch (Exception e) {
|
|
2345
|
e.printStackTrace();
|
|
2346
|
}
|
|
2347
|
return result;
|
|
2348
|
}
|
|
2349
|
|
|
2350
|
/**
|
|
2351
|
* Returns the <code>LastActionDate</code> attribute.
|
|
2352
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2353
|
* @return The <code>LastActionDate</code> attribute.
|
|
2354
|
* @see MethodMapper
|
|
2355
|
*/
|
|
2356
|
@SuppressWarnings({ "unused" })
|
|
2357
|
private static DateTime getLastActionDate(IdentifiableEntity identEntity) {
|
|
2358
|
DateTime result = null;
|
|
2359
|
try {
|
|
2360
|
Set<Extension> extensions = identEntity.getExtensions();
|
|
2361
|
for (Extension extension : extensions) {
|
|
2362
|
if (extension.getType().equals(lastActionDateExtensionType)) {
|
|
2363
|
String dateTime = extension.getValue();
|
|
2364
|
if (dateTime != null) {
|
|
2365
|
DateTimeFormatter formatter = DateTimeFormat.forPattern("yyyy-MM-dd HH:mm:ss.S");
|
|
2366
|
result = formatter.parseDateTime(dateTime);
|
|
2367
|
}
|
|
2368
|
}
|
|
2369
|
}
|
|
2370
|
} catch (Exception e) {
|
|
2371
|
e.printStackTrace();
|
|
2372
|
}
|
|
2373
|
return result;
|
|
2374
|
}
|
|
2375
|
|
|
2376
|
/**
|
|
2377
|
* Returns the <code>ExpertName</code> attribute.
|
|
2378
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2379
|
* @return The <code>ExpertName</code> attribute.
|
|
2380
|
* @see MethodMapper
|
|
2381
|
*/
|
|
2382
|
@SuppressWarnings("unused")
|
|
2383
|
private static String getExpertName(TaxonBase<?> taxonName) {
|
|
2384
|
String result = null;
|
|
2385
|
try {
|
|
2386
|
Set<Extension> extensions = taxonName.getExtensions();
|
|
2387
|
for (Extension extension : extensions) {
|
|
2388
|
if (extension.getType().equals(expertNameExtensionType)) {
|
|
2389
|
result = extension.getValue();
|
|
2390
|
}
|
|
2391
|
}
|
|
2392
|
} catch (Exception e) {
|
|
2393
|
e.printStackTrace();
|
|
2394
|
}
|
|
2395
|
return result;
|
|
2396
|
}
|
|
2397
|
|
|
2398
|
/**
|
|
2399
|
* Returns the <code>ExpertFk</code> attribute.
|
|
2400
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2401
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
2402
|
* @return The <code>ExpertFk</code> attribute.
|
|
2403
|
* @see MethodMapper
|
|
2404
|
*/
|
|
2405
|
private static Integer getExpertFk(Reference<?> reference, PesiExportState state) {
|
|
2406
|
Integer result = state.getDbId(reference);
|
|
2407
|
return result;
|
|
2408
|
}
|
|
2409
|
|
|
2410
|
/**
|
|
2411
|
* Returns the <code>SpeciesExpertName</code> attribute.
|
|
2412
|
* @param taxonName The {@link TaxonNameBase TaxonName}.
|
|
2413
|
* @return The <code>SpeciesExpertName</code> attribute.
|
|
2414
|
* @see MethodMapper
|
|
2415
|
*/
|
|
2416
|
@SuppressWarnings("unused")
|
|
2417
|
private static String getSpeciesExpertName(TaxonBase<?> taxonName) {
|
|
2418
|
String result = null;
|
|
2419
|
try {
|
|
2420
|
Set<Extension> extensions = taxonName.getExtensions();
|
|
2421
|
for (Extension extension : extensions) {
|
|
2422
|
if (extension.getType().equals(speciesExpertNameExtensionType)) {
|
|
2423
|
result = extension.getValue();
|
|
2424
|
}
|
|
2425
|
}
|
|
2426
|
} catch (Exception e) {
|
|
2427
|
e.printStackTrace();
|
|
2428
|
}
|
|
2429
|
return result;
|
|
2430
|
}
|
|
2431
|
|
|
2432
|
/**
|
|
2433
|
* Returns the <code>SpeciesExpertFk</code> attribute.
|
|
2434
|
* @param reference The {@link Reference Reference}.
|
|
2435
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
2436
|
* @return The <code>SpeciesExpertFk</code> attribute.
|
|
2437
|
* @see MethodMapper
|
|
2438
|
*/
|
|
2439
|
private static Integer getSpeciesExpertFk(Reference<?> reference, PesiExportState state) {
|
|
2440
|
Integer result = state.getDbId(reference);
|
|
2441
|
return result;
|
|
2442
|
}
|
|
2443
|
|
|
2444
|
|
|
2445
|
/**
|
|
2446
|
* Returns the source (E+M, Fauna Europaea, Index Fungorum, ERMS) of a given
|
|
2447
|
* Identifiable Entity as a BitSet
|
|
2448
|
* @param identEntity
|
|
2449
|
* @return
|
|
2450
|
*/
|
|
2451
|
private static BitSet getSources(IdentifiableEntity<?> identEntity){
|
|
2452
|
BitSet bitSet = new BitSet();
|
|
2453
|
Set<IdentifiableSource> sources = getPesiSources(identEntity);
|
|
2454
|
for (IdentifiableSource source : sources) {
|
|
2455
|
Reference<?> ref = source.getCitation();
|
|
2456
|
UUID refUuid = ref.getUuid();
|
|
2457
|
if (refUuid.equals(BerlinModelTransformer.uuidSourceRefEuroMed)){
|
|
2458
|
bitSet.set(PesiTransformer.SOURCE_EM);
|
|
2459
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)){
|
|
2460
|
bitSet.set(PesiTransformer.SOURCE_FE);
|
|
2461
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefErms)){
|
|
2462
|
bitSet.set(PesiTransformer.SOURCE_ERMS);
|
|
2463
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum)){
|
|
2464
|
bitSet.set(PesiTransformer.SOURCE_IF);
|
|
2465
|
}else{
|
|
2466
|
if (logger.isDebugEnabled()){logger.debug("Not a PESI source");};
|
|
2467
|
}
|
|
2468
|
}
|
|
2469
|
return bitSet;
|
|
2470
|
|
|
2471
|
}
|
|
2472
|
|
|
2473
|
protected static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {
|
|
2474
|
taxonName = CdmBase.deproxy(taxonName, TaxonNameBase.class);
|
|
2475
|
NonViralNameDefaultCacheStrategy<?> cacheStrategy;
|
|
2476
|
if (taxonName.isInstanceOf(ZoologicalName.class)){
|
|
2477
|
cacheStrategy = zooNameStrategy;
|
|
2478
|
}else if (taxonName.isInstanceOf(BotanicalName.class)) {
|
|
2479
|
cacheStrategy = botanicalNameStrategy;
|
|
2480
|
}else if (taxonName.getClass().equals(NonViralName.class)) {
|
|
2481
|
cacheStrategy = nonViralNameStrategy;
|
|
2482
|
}else if (taxonName.getClass().equals(BacterialName.class)) {
|
|
2483
|
cacheStrategy = bacterialNameStrategy;
|
|
2484
|
}else{
|
|
2485
|
logger.error("Unhandled taxon name type. Can't define strategy class");
|
|
2486
|
cacheStrategy = botanicalNameStrategy;
|
|
2487
|
}
|
|
2488
|
return cacheStrategy;
|
|
2489
|
}
|
|
2490
|
|
|
2491
|
/**
|
|
2492
|
* Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.
|
|
2493
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
2494
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
2495
|
* @return The <code>TaxonFk1</code> attribute.
|
|
2496
|
* @see MethodMapper
|
|
2497
|
*/
|
|
2498
|
private static Integer getTaxonFk1(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
|
2499
|
|
|
2500
|
return getObjectFk(relationship, state, true);
|
|
2501
|
}
|
|
2502
|
|
|
2503
|
/**
|
|
2504
|
* Returns the <code>TaxonFk2</code> attribute. It corresponds to a CDM <code>SynonymRelationship</code>.
|
|
2505
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
2506
|
* @param state The {@link PesiExportState PesiExportState}.
|
|
2507
|
* @return The <code>TaxonFk2</code> attribute.
|
|
2508
|
* @see MethodMapper
|
|
2509
|
*/
|
|
2510
|
private static Integer getTaxonFk2(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
|
2511
|
return getObjectFk(relationship, state, false);
|
|
2512
|
}
|
|
2513
|
|
|
2514
|
/**
|
|
2515
|
* Returns the database key of an object in the given relationship.
|
|
2516
|
* @param relationship {@link RelationshipBase RelationshipBase}.
|
|
2517
|
* @param state {@link PesiExportState PesiExportState}.
|
|
2518
|
* @param isFrom A boolean value indicating whether the database key of the parent or child in this relationship is searched. <code>true</code> means the child is searched. <code>false</code> means the parent is searched.
|
|
2519
|
* @return The database key of an object in the given relationship.
|
|
2520
|
*/
|
|
2521
|
private static Integer getObjectFk(RelationshipBase<?, ?, ?> relationship, PesiExportState state, boolean isFrom) {
|
|
2522
|
TaxonBase<?> taxonBase = null;
|
|
2523
|
if (relationship.isInstanceOf(TaxonRelationship.class)) {
|
|
2524
|
TaxonRelationship tr = (TaxonRelationship)relationship;
|
|
2525
|
taxonBase = (isFrom) ? tr.getFromTaxon(): tr.getToTaxon();
|
|
2526
|
} else if (relationship.isInstanceOf(SynonymRelationship.class)) {
|
|
2527
|
SynonymRelationship sr = (SynonymRelationship)relationship;
|
|
2528
|
taxonBase = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon();
|
|
2529
|
} else if (relationship.isInstanceOf(NameRelationship.class) || relationship.isInstanceOf(HybridRelationship.class)) {
|
|
2530
|
if (isFrom){
|
|
2531
|
return state.getDbId(state.getCurrentFromObject());
|
|
2532
|
}else{
|
|
2533
|
return state.getDbId(state.getCurrentToObject());
|
|
2534
|
}
|
|
2535
|
}
|
|
2536
|
if (taxonBase != null) {
|
|
2537
|
if (! isPesiTaxon(taxonBase)){
|
|
2538
|
logger.warn("Related taxonBase is not a PESI taxon. Taxon: " + taxonBase.getId() + "/" + taxonBase.getUuid() + "; TaxonRel: " + relationship.getId() + "(" + relationship.getType().getTitleCache() + ")");
|
|
2539
|
return null;
|
|
2540
|
}else{
|
|
2541
|
return state.getDbId(taxonBase);
|
|
2542
|
}
|
|
2543
|
|
|
2544
|
}
|
|
2545
|
logger.warn("No taxon found in state for relationship: " + relationship.toString());
|
|
2546
|
return null;
|
|
2547
|
}
|
|
2548
|
|
|
2549
|
/**
|
|
2550
|
* Returns the <code>RelQualifierCache</code> attribute.
|
|
2551
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
2552
|
* @return The <code>RelQualifierCache</code> attribute.
|
|
2553
|
* @see MethodMapper
|
|
2554
|
*/
|
|
2555
|
@SuppressWarnings("unused")
|
|
2556
|
private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
|
|
2557
|
String result = null;
|
|
2558
|
NomenclaturalCode code = null;
|
|
2559
|
if (relationship.isInstanceOf(TaxonRelationship.class)){
|
|
2560
|
code = CdmBase.deproxy(relationship, TaxonRelationship.class).getToTaxon().getName().getNomenclaturalCode();
|
|
2561
|
}else if (relationship.isInstanceOf(SynonymRelationship.class)){
|
|
2562
|
code = CdmBase.deproxy(relationship, SynonymRelationship.class).getAcceptedTaxon().getName().getNomenclaturalCode();
|
|
2563
|
}else if (relationship.isInstanceOf(NameRelationship.class)){
|
|
2564
|
code = CdmBase.deproxy(relationship, NameRelationship.class).getFromName().getNomenclaturalCode();
|
|
2565
|
}else if (relationship.isInstanceOf(HybridRelationship.class)){
|
|
2566
|
code = CdmBase.deproxy(relationship, HybridRelationship.class).getParentName().getNomenclaturalCode();
|
|
2567
|
}
|
|
2568
|
if (code != null) {
|
|
2569
|
result = state.getConfig().getTransformer().getCacheByRelationshipType(relationship, code);
|
|
2570
|
} else {
|
|
2571
|
logger.error("NomenclaturalCode is NULL while creating the following relationship: " + relationship.getUuid());
|
|
2572
|
}
|
|
2573
|
return result;
|
|
2574
|
}
|
|
2575
|
|
|
2576
|
/**
|
|
2577
|
* Returns the <code>RelTaxonQualifierFk</code> attribute.
|
|
2578
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
2579
|
* @return The <code>RelTaxonQualifierFk</code> attribute.
|
|
2580
|
* @see MethodMapper
|
|
2581
|
*/
|
|
2582
|
@SuppressWarnings("unused")
|
|
2583
|
private static Integer getRelTaxonQualifierFk(RelationshipBase<?, ?, ?> relationship) {
|
|
2584
|
return PesiTransformer.taxonRelation2RelTaxonQualifierFk(relationship);
|
|
2585
|
}
|
|
2586
|
/**
|
|
2587
|
* Returns the <code>Notes</code> attribute.
|
|
2588
|
* @param relationship The {@link RelationshipBase Relationship}.
|
|
2589
|
* @return The <code>Notes</code> attribute.
|
|
2590
|
* @see MethodMapper
|
|
2591
|
*/
|
|
2592
|
@SuppressWarnings("unused")
|
|
2593
|
private static String getNotes(RelationshipBase<?, ?, ?> relationship) {
|
|
2594
|
// TODO
|
|
2595
|
return null;
|
|
2596
|
}
|
|
2597
|
|
|
2598
|
|
|
2599
|
/**
|
|
2600
|
* Returns the CDM to PESI specific export mappings.
|
|
2601
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
|
2602
|
*/
|
|
2603
|
private PesiExportMapping getMapping() {
|
|
2604
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
|
2605
|
|
|
2606
|
mapping.addMapper(IdMapper.NewInstance("TaxonId"));
|
|
2607
|
mapping.addMapper(DbObjectMapper.NewInstance("sec", "sourceFk")); //OLD:mapping.addMapper(MethodMapper.NewInstance("SourceFK", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));
|
|
2608
|
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusFk", this.getClass(), "getTaxonStatusFk", standardMethodParameter, PesiExportState.class));
|
|
2609
|
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusCache", this.getClass(), "getTaxonStatusCache", standardMethodParameter, PesiExportState.class));
|
|
2610
|
|
|
2611
|
mapping.addMapper(MethodMapper.NewInstance("GUID", this));
|
|
2612
|
|
|
2613
|
mapping.addMapper(MethodMapper.NewInstance("DerivedFromGuid", this));
|
|
2614
|
mapping.addMapper(MethodMapper.NewInstance("CacheCitation", this));
|
|
2615
|
mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because Misallied Names are handled differently
|
|
2616
|
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this));
|
|
2617
|
|
|
2618
|
// DisplayName
|
|
2619
|
mapping.addMapper(MethodMapper.NewInstance("DisplayName", this));
|
|
2620
|
|
|
2621
|
// FossilStatus (Fk, Cache)
|
|
2622
|
mapping.addMapper(MethodMapper.NewInstance("FossilStatusCache", this, IdentifiableEntity.class, PesiExportState.class));
|
|
2623
|
mapping.addMapper(MethodMapper.NewInstance("FossilStatusFk", this, IdentifiableEntity.class, PesiExportState.class)); // PesiTransformer.FossilStatusCache2FossilStatusFk?
|
|
2624
|
|
|
2625
|
//handled by name mapping
|
|
2626
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastActionDate", false));
|
|
2627
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));
|
|
2628
|
|
|
2629
|
//experts
|
|
2630
|
ExtensionType extensionTypeSpeciesExpertName = (ExtensionType)getTermService().find(PesiTransformer.speciesExpertNameUuid);
|
|
2631
|
mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeSpeciesExpertName, "SpeciesExpertName"));
|
|
2632
|
ExtensionType extensionTypeExpertName = (ExtensionType)getTermService().find(PesiTransformer.expertNameUuid);
|
|
2633
|
mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeExpertName, "ExpertName"));
|
|
2634
|
|
|
2635
|
// mapping.addMapper(MethodMapper.NewInstance("ParentTaxonFk", this, TaxonBase.class, PesiExportState.class)); //by AM, doesn't work, FK exception
|
|
2636
|
mapping.addMapper(ObjectChangeMapper.NewInstance(TaxonBase.class, TaxonNameBase.class, "Name"));
|
|
2637
|
|
|
2638
|
addNameMappers(mapping);
|
|
2639
|
|
|
2640
|
return mapping;
|
|
2641
|
}
|
|
2642
|
|
|
2643
|
/**
|
|
2644
|
* Returns the CDM to PESI specific export mappings.
|
|
2645
|
* @param state
|
|
2646
|
* @return The {@link PesiExportMapping PesiExportMapping}.
|
|
2647
|
* @throws UndefinedTransformerMethodException
|
|
2648
|
*/
|
|
2649
|
private PesiExportMapping getPureNameMapping(PesiExportState state) throws UndefinedTransformerMethodException {
|
|
2650
|
PesiExportMapping mapping = new PesiExportMapping(dbTableName);
|
|
2651
|
|
|
2652
|
mapping.addMapper(IdMapper.NewInstance("TaxonId"));
|
|
2653
|
|
|
2654
|
// mapping.addMapper(MethodMapper.NewInstance("TaxonStatusFk", this.getClass(), "getTaxonStatusFk", standardMethodParameter, PesiExportState.class));
|
|
2655
|
|
|
2656
|
mapping.addMapper(MethodMapper.NewInstance("KingdomFk", this, TaxonNameBase.class));
|
|
2657
|
mapping.addMapper(MethodMapper.NewInstance("RankFk", this, TaxonNameBase.class));
|
|
2658
|
mapping.addMapper(MethodMapper.NewInstance("RankCache", this, TaxonNameBase.class, PesiExportState.class));
|
|
2659
|
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusFk", Types.INTEGER , PesiTransformer.T_STATUS_UNACCEPTED));
|
|
2660
|
mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusCache", Types.VARCHAR , state.getTransformer().getTaxonStatusCacheByKey( PesiTransformer.T_STATUS_UNACCEPTED)));
|
|
2661
|
mapping.addMapper(DbStringMapper.NewInstance("AuthorshipCache", "AuthorString").setBlankToNull(true));
|
|
2662
|
mapping.addMapper(MethodMapper.NewInstance("WebShowName", this, TaxonNameBase.class));
|
|
2663
|
mapping.addMapper(MethodMapper.NewInstance("GUID", this, TaxonNameBase.class));
|
|
2664
|
|
|
2665
|
|
|
2666
|
|
|
2667
|
// DisplayName
|
|
2668
|
mapping.addMapper(MethodMapper.NewInstance("DisplayName", this, TaxonNameBase.class));
|
|
2669
|
|
|
2670
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastActionDate", false));
|
|
2671
|
mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));
|
|
2672
|
|
|
2673
|
addNameMappers(mapping);
|
|
2674
|
//TODO add author mapper, TypeNameFk
|
|
2675
|
|
|
2676
|
return mapping;
|
|
2677
|
}
|
|
2678
|
|
|
2679
|
private void addNameMappers(PesiExportMapping mapping) {
|
|
2680
|
mapping.addMapper(DbStringMapper.NewInstance("GenusOrUninomial", "GenusOrUninomial"));
|
|
2681
|
mapping.addMapper(DbStringMapper.NewInstance("InfraGenericEpithet", "InfraGenericEpithet"));
|
|
2682
|
mapping.addMapper(DbStringMapper.NewInstance("SpecificEpithet", "SpecificEpithet"));
|
|
2683
|
mapping.addMapper(DbStringMapper.NewInstance("InfraSpecificEpithet", "InfraSpecificEpithet"));
|
|
2684
|
|
|
2685
|
// mapping.addMapper(DbStringMapper.NewInstance("NameCache", "WebSearchName")); //does not work as we need other cache strategy
|
|
2686
|
mapping.addMapper(MethodMapper.NewInstance("WebSearchName", this, TaxonNameBase.class));
|
|
2687
|
|
|
2688
|
// mapping.addMapper(DbStringMapper.NewInstance("TitleCache", "FullName")); //does not work as we need other cache strategy
|
|
2689
|
mapping.addMapper(MethodMapper.NewInstance("FullName", this, TaxonNameBase.class));
|
|
2690
|
|
|
2691
|
|
|
2692
|
mapping.addMapper(MethodMapper.NewInstance("NomRefString", this, TaxonNameBase.class));
|
|
2693
|
|
|
2694
|
mapping.addMapper(MethodMapper.NewInstance("NameStatusFk", this, TaxonNameBase.class));
|
|
2695
|
mapping.addMapper(MethodMapper.NewInstance("NameStatusCache", this, TaxonNameBase.class, PesiExportState.class));
|
|
2696
|
mapping.addMapper(MethodMapper.NewInstance("TypeFullnameCache", this, TaxonNameBase.class));
|
|
2697
|
//TODO TypeNameFk
|
|
2698
|
|
|
2699
|
//quality status
|
|
2700
|
mapping.addMapper(MethodMapper.NewInstance("QualityStatusFk", this, TaxonNameBase.class));
|
|
2701
|
mapping.addMapper(MethodMapper.NewInstance("QualityStatusCache", this, TaxonNameBase.class, PesiExportState.class));
|
|
2702
|
|
|
2703
|
mapping.addMapper(MethodMapper.NewInstance("IdInSource", this, IdentifiableEntity.class));
|
|
2704
|
mapping.addMapper(MethodMapper.NewInstance("OriginalDB", this, IdentifiableEntity.class) );
|
|
2705
|
|
|
2706
|
//mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());
|
|
2707
|
|
|
2708
|
}
|
|
2709
|
|
|
2710
|
private PesiExportMapping getSynRelMapping() {
|
|
2711
|
PesiExportMapping mapping = new PesiExportMapping(dbTableNameSynRel);
|
|
2712
|
|
|
2713
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getTaxonFk1", RelationshipBase.class, PesiExportState.class));
|
|
2714
|
mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getTaxonFk2", RelationshipBase.class, PesiExportState.class));
|
|
2715
|
mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this, RelationshipBase.class));
|
|
2716
|
mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this, RelationshipBase.class, PesiExportState.class));
|
|
2717
|
mapping.addMapper(MethodMapper.NewInstance("Notes", this, RelationshipBase.class));
|
|
2718
|
|
|
2719
|
return mapping;
|
|
2720
|
}
|
|
2721
|
|
|
2722
|
private PesiExportMapping getAdditionalSourceMapping(PesiExportState state) throws UndefinedTransformerMethodException{
|
|
2723
|
PesiExportMapping mapping = new PesiExportMapping(dbTableAdditionalSourceRel);
|
|
2724
|
|
|
2725
|
mapping.addMapper(IdMapper.NewInstance("TaxonFk"));
|
|
2726
|
mapping.addMapper(ObjectChangeMapper.NewInstance(TaxonBase.class, TaxonNameBase.class, "Name"));
|
|
2727
|
|
|
2728
|
mapping.addMapper(DbObjectMapper.NewInstance("NomenclaturalReference", "SourceFk"));
|
|
2729
|
// mapping.addMapper(DbObjectMapper.NewInstance("NomenclaturalReference", "SourceNameCache", IS_CACHE));
|
|
2730
|
mapping.addMapper(MethodMapper.NewInstance("SourceNameCache", this, TaxonNameBase.class));
|
|
2731
|
|
|
2732
|
|
|
2733
|
//we have only nomenclatural references here
|
|
2734
|
mapping.addMapper(DbConstantMapper.NewInstance("SourceUseFk", Types.INTEGER , PesiTransformer.NOMENCLATURAL_REFERENCE));
|
|
2735
|
mapping.addMapper(DbConstantMapper.NewInstance("SourceUseCache", Types.VARCHAR, state.getTransformer().getSourceUseCacheByKey( PesiTransformer.NOMENCLATURAL_REFERENCE)));
|
|
2736
|
|
|
2737
|
mapping.addMapper(DbStringMapper.NewInstance("NomenclaturalMicroReference", "SourceDetail"));
|
|
2738
|
|
|
2739
|
return mapping;
|
|
2740
|
}
|
|
2741
|
|
|
2742
|
}
|