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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.berlinModel.in;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.database.update.DatabaseTypeNotSupportedException;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonNameImportValidator;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.ICultivarPlantName;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.IZoologicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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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.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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@Component
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public class BerlinModelTaxonNameImport extends BerlinModelImportBase {
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private static final long serialVersionUID = -8860800694286602016L;
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private static final boolean BLANK_TO_NULL = true;
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameImport.class);
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public static final String NAMESPACE = "TaxonName";
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public static final UUID SOURCE_ACC_UUID = UUID.fromString("c3959b4f-d876-4b7a-a739-9260f4cafd1c");
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private static int modCount = 5000;
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private static final String pluralString = "TaxonNames";
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private static final String dbTableName = "Name";
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public BerlinModelTaxonNameImport(){
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super(dbTableName, pluralString);
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}
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@Override
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protected String getIdQuery(BerlinModelImportState state) {
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if (state.getConfig().getNameIdTable()==null ){
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return super.getIdQuery(state);
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}else{
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return "SELECT nameId FROM " + state.getConfig().getNameIdTable() + "";
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}
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}
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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Source source = config.getSource();
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String facultativCols = "";
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String strFacTable = "RefDetail";
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String strFacColumn = "IdInSource";
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String strColAlias = null;
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if (checkSqlServerColumnExists(source, strFacTable, strFacColumn)){
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facultativCols += ", " + strFacTable + "." + strFacColumn ;
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if (! CdmUtils.Nz(strColAlias).equals("") ){
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facultativCols += " AS " + strColAlias;
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}
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}
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String strRecordQuery =
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"SELECT Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +
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" RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +
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" RefDetail.SecondarySources, Rank.RankAbbrev, Rank.Rank " +
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facultativCols +
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" FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND " +
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" Name.NomRefFk = RefDetail.RefFk " +
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" LEFT OUTER JOIN Rank ON Name.RankFk = Rank.rankID " +
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" WHERE name.nameId IN ("+ID_LIST_TOKEN+") ";
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//strQuery += " AND RefDetail.PreliminaryFlag = 1 ";
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//strQuery += " AND Name.Created_When > '03.03.2004' ";
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return strRecordQuery + "";
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}
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@Override
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protected void doInvoke(BerlinModelImportState state) {
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//update rank labels if necessary
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String strAbbrev = state.getConfig().getInfrGenericRankAbbrev();
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Rank rank = Rank.INFRAGENERICTAXON();
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testRankAbbrev(strAbbrev, rank);
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strAbbrev = state.getConfig().getInfrSpecificRankAbbrev();
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rank = Rank.INFRASPECIFICTAXON();
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testRankAbbrev(strAbbrev, rank);
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super.doInvoke(state);
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}
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private void testRankAbbrev(String strAbbrev, Rank rank) {
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if (strAbbrev != null){
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Representation rep = rank.getRepresentation(Language.ENGLISH());
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rep.setAbbreviatedLabel(strAbbrev);
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getTermService().saveOrUpdate(rank);
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}
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
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String dbAttrName;
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String cdmAttrName;
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boolean success = true ;
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BerlinModelImportConfigurator config = state.getConfig();
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Set<TaxonName> namesToSave = new HashSet<>();
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@SuppressWarnings("unchecked")
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Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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try {
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int i = 0;
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//for each reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i != 1 ){ logger.info("Names handled: " + (i-1));}
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//create TaxonName element
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int nameId = rs.getInt("nameId");
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Integer authorFk = nullSafeInt(rs, "AuthorTeamFk");
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Integer exAuthorFk = nullSafeInt(rs, "ExAuthorTeamFk");
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Integer basAuthorFk = nullSafeInt(rs, "BasAuthorTeamFk");
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Integer exBasAuthorFk = nullSafeInt(rs, "ExBasAuthorTeamFk");
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String strCultivarGroupName = rs.getString("CultivarGroupName");
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String strCultivarName = rs.getString("CultivarName");
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String nameCache = rs.getString("NameCache");
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String fullNameCache = rs.getString("FullNameCache");
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String uuid = null;
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if (resultSetHasColumn(rs,"UUID")){
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uuid = rs.getString("UUID");
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}
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try {
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//define rank
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boolean useUnknownRank = true;
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Rank rank = BerlinModelTransformer.rankId2Rank(rs, useUnknownRank, config.isSwitchSpeciesGroup());
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boolean allowInfraSpecTaxonRank = state.getConfig().isAllowInfraSpecTaxonRank() ;
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if (rank == null || rank.equals(Rank.UNKNOWN_RANK()) || (rank.equals(Rank.INFRASPECIFICTAXON()) && ! allowInfraSpecTaxonRank)){
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rank = handleProlesAndRaceSublusus(state, rs, rank);
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}
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if (rank.getId() == 0){
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getTermService().save(rank);
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logger.warn("Rank did not yet exist: " + rank.getTitleCache());
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}
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//create TaxonName
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TaxonName taxonName;
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if (config.getNomenclaturalCode() != null){
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taxonName = config.getNomenclaturalCode().getNewTaxonNameInstance(rank);
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//check cultivar
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if (taxonName.isBotanical()){
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if (isNotBlank(strCultivarGroupName) && isNotBlank(strCultivarName)){
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taxonName = TaxonNameFactory.NewCultivarInstance(rank);
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}
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}
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}else{
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taxonName = TaxonNameFactory.NewNonViralInstance(rank);
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}
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if (uuid != null){
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taxonName.setUuid(UUID.fromString(uuid));
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}
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if (rank == null){
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//TODO rank should never be null or a more sophisticated algorithm has to be implemented for genus/supraGenericName
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logger.warn("Rank is null. Genus epithet was imported. May be wrong");
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success = false;
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}
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//epithets
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if (rank.isSupraGeneric()){
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dbAttrName = "supraGenericName";
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}else{
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dbAttrName = "genus";
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}
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cdmAttrName = "genusOrUninomial";
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success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);
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dbAttrName = "genusSubdivisionEpi";
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cdmAttrName = "infraGenericEpithet";
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success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);
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dbAttrName = "speciesEpi";
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cdmAttrName = "specificEpithet";
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success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);
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dbAttrName = "infraSpeciesEpi";
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cdmAttrName = "infraSpecificEpithet";
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success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);
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dbAttrName = "unnamedNamePhrase";
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cdmAttrName = "appendedPhrase";
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success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);
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//Details
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dbAttrName = "details";
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cdmAttrName = "nomenclaturalMicroReference";
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success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);
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//nomRef
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success &= makeNomenclaturalReference(config, taxonName, nameId, rs, partitioner);
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//Source_Acc
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boolean colExists = true;
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try {
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colExists = state.getConfig().getSource().checkColumnExists("Name", "Source_Acc");
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} catch (DatabaseTypeNotSupportedException e) {
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logger.debug("Source does not support 'checkColumnExists'");
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}
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if (colExists){
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String sourceAcc = rs.getString("Source_Acc");
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if (isNotBlank(sourceAcc)){
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ExtensionType sourceAccExtensionType = getExtensionType(state, SOURCE_ACC_UUID, "Source_Acc","Source_Acc","Source_Acc");
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Extension.NewInstance(taxonName, sourceAcc, sourceAccExtensionType);
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}
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}
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//created, notes
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boolean excludeUpdated = true;
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boolean excludeNotes = true;
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success &= doIdCreatedUpdatedNotes(state, taxonName, rs, nameId, NAMESPACE, excludeUpdated, excludeNotes);
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handleNameNotes(state, taxonName, rs, nameId);
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//NonViralName
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if (taxonName.isNonViral()){
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INonViralName nonViralName = taxonName;
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//authorTeams
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if (teamMap != null ){
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nonViralName.setCombinationAuthorship(getAuthorTeam(teamMap, authorFk, nameId, config));
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nonViralName.setExCombinationAuthorship(getAuthorTeam(teamMap, exAuthorFk, nameId, config));
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nonViralName.setBasionymAuthorship(getAuthorTeam(teamMap, basAuthorFk, nameId, config));
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nonViralName.setExBasionymAuthorship(getAuthorTeam(teamMap, exBasAuthorFk, nameId, config));
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}else{
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logger.warn("TeamMap is null");
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success = false;
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}
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}//nonviralName
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285
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286
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287
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//zoologicalName
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if (taxonName.isZoological()){
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IZoologicalName zooName = taxonName;
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makeZoologialName(rs, zooName, nameId);
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}
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//botanicalName
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else if (taxonName.isBotanical()){
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IBotanicalName botName = taxonName;
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success &= makeBotanicalNamePart(rs, botName) ;
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297
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}
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299
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300
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// dbAttrName = "preliminaryFlag";
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Boolean preliminaryFlag = rs.getBoolean("PreliminaryFlag");
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Boolean hybridFormulaFlag = rs.getBoolean("HybridFormulaFlag"); //hybrid flag does not lead to cache update in Berlin Model
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if (preliminaryFlag == true || hybridFormulaFlag == true){
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//Computes all caches and sets
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taxonName.setTitleCache(fullNameCache, true);
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taxonName.setFullTitleCache(taxonName.getFullTitleCache(), true);
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taxonName.setNameCache(nameCache, true);
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taxonName.setAuthorshipCache(taxonName.getAuthorshipCache(), true);
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}
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namesToSave.add(taxonName);
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311
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}
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catch (UnknownCdmTypeException e) {
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logger.warn("Name with id " + nameId + " has unknown rankId " + " and could not be saved.");
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success = false;
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}
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317
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318
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} //while rs.hasNext()
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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322
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}
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323
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324
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// logger.info( i + " names handled");
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getNameService().save(namesToSave);
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return success;
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328
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}
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329
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330
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331
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/**
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* @param state
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333
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* @param taxonName
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334
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* @param rs
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335
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* @param nameId
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336
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* @throws SQLException
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*/
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338
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private void handleNameNotes(BerlinModelImportState state, TaxonName taxonName, ResultSet rs, int nameId) throws SQLException {
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339
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String notesOrig = rs.getString("notes");
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340
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String notes = filterNotes(notesOrig, nameId);
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boolean isParentalSpecies = state.getConfig().isEuroMed() && isPostulatedParentalSpeciesNote(notes);
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342
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if (isNotBlank(notes) && taxonName != null && !isParentalSpecies ){
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343
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String notesString = String.valueOf(notes);
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344
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if (notesString.length() > 65530 ){
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345
|
notesString = notesString.substring(0, 65530) + "...";
|
|
346
|
logger.warn("Notes string is longer than 65530 and was truncated: " + taxonName);
|
|
347
|
}
|
|
348
|
Annotation notesAnnotation = Annotation.NewInstance(notesString, Language.DEFAULT());
|
|
349
|
//notesAnnotation.setAnnotationType(AnnotationType.EDITORIAL());
|
|
350
|
//notes.setCommentator(bmiConfig.getCommentator());
|
|
351
|
taxonName.addAnnotation(notesAnnotation);
|
|
352
|
}
|
|
353
|
|
|
354
|
}
|
|
355
|
|
|
356
|
private static final String MCL = "MCL\\s?[0-9]{1,3}(\\-[0-9]{1,4}(\\-[0-9]{1,4}(\\-[0-9]{1,4}(\\-[0-9]{1,3})?)?)?)?";
|
|
357
|
/**
|
|
358
|
* @param notes
|
|
359
|
*/
|
|
360
|
protected static String filterNotes(String notes, int nameId) {
|
|
361
|
String result;
|
|
362
|
if (isBlank(notes)){
|
|
363
|
result = null;
|
|
364
|
}else if (notes.matches("Acc:.*")){
|
|
365
|
if (notes.matches("Acc: .*\\$$") || (notes.matches("Acc: .*"+MCL))){
|
|
366
|
result = null;
|
|
367
|
}else if (notes.matches("Acc: .*(\\$|"+MCL+")\\s*\\{.*\\}")){
|
|
368
|
notes = notes.substring(notes.indexOf("{")+1, notes.length()-1);
|
|
369
|
result = notes;
|
|
370
|
}else if (notes.matches("Acc: .*(\\$|"+MCL+")\\s*\\[.*\\]")){
|
|
371
|
notes = notes.substring(notes.indexOf("[")+1, notes.length()-1);
|
|
372
|
result = notes;
|
|
373
|
}else{
|
|
374
|
logger.warn("Name id: " + nameId + ". Namenote: " + notes);
|
|
375
|
result = notes;
|
|
376
|
}
|
|
377
|
}else if (notes.matches("Syn:.*")){
|
|
378
|
if (notes.matches("Syn: .*\\$$") || (notes.matches("Syn: .*"+MCL))){
|
|
379
|
result = null;
|
|
380
|
}else if (notes.matches("Syn: .*(\\$|"+MCL+")\\s*\\{.*\\}")){
|
|
381
|
notes = notes.substring(notes.indexOf("{")+1, notes.length()-1);
|
|
382
|
result = notes;
|
|
383
|
}else if (notes.matches("Syn: .*(\\$|"+MCL+")\\s*\\[.*\\]")){
|
|
384
|
notes = notes.substring(notes.indexOf("[")+1, notes.length()-1);
|
|
385
|
result = notes;
|
|
386
|
}else{
|
|
387
|
logger.warn("Name id: " + nameId + ". Namenote: " + notes);
|
|
388
|
result = notes;
|
|
389
|
}
|
|
390
|
}else{
|
|
391
|
result = notes;
|
|
392
|
}
|
|
393
|
return result;
|
|
394
|
}
|
|
395
|
|
|
396
|
|
|
397
|
/**
|
|
398
|
* @param nameNotes
|
|
399
|
* @return
|
|
400
|
*/
|
|
401
|
protected static boolean isPostulatedParentalSpeciesNote(String nameNotes) {
|
|
402
|
if (nameNotes == null){
|
|
403
|
return false;
|
|
404
|
}else{
|
|
405
|
return nameNotes.matches(".*<>.*");
|
|
406
|
}
|
|
407
|
}
|
|
408
|
|
|
409
|
|
|
410
|
private Rank handleProlesAndRaceSublusus(BerlinModelImportState state, ResultSet rs, Rank rank) throws SQLException {
|
|
411
|
Rank result;
|
|
412
|
String rankAbbrev = rs.getString("RankAbbrev");
|
|
413
|
// String rankStr = rs.getString("Rank");
|
|
414
|
if (CdmUtils.nullSafeEqual(rankAbbrev, "prol.") ){
|
|
415
|
result = Rank.PROLES();
|
|
416
|
}else if(CdmUtils.nullSafeEqual(rankAbbrev, "race")){
|
|
417
|
result = Rank.RACE();
|
|
418
|
}else if(CdmUtils.nullSafeEqual(rankAbbrev, "sublusus")){
|
|
419
|
result = Rank.SUBLUSUS();
|
|
420
|
}else{
|
|
421
|
result = rank;
|
|
422
|
logger.warn("Unhandled rank: " + rankAbbrev);
|
|
423
|
}
|
|
424
|
return result;
|
|
425
|
}
|
|
426
|
|
|
427
|
@Override
|
|
428
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
|
429
|
String nameSpace;
|
|
430
|
Class<?> cdmClass;
|
|
431
|
Set<String> idSet;
|
|
432
|
|
|
433
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
434
|
|
|
435
|
try{
|
|
436
|
Set<String> teamIdSet = new HashSet<>();
|
|
437
|
Set<String> referenceIdSet = new HashSet<>();
|
|
438
|
Set<String> refDetailIdSet = new HashSet<>();
|
|
439
|
while (rs.next()){
|
|
440
|
handleForeignKey(rs, teamIdSet, "AuthorTeamFk");
|
|
441
|
handleForeignKey(rs, teamIdSet, "ExAuthorTeamFk");
|
|
442
|
handleForeignKey(rs, teamIdSet, "BasAuthorTeamFk");
|
|
443
|
handleForeignKey(rs, teamIdSet, "ExBasAuthorTeamFk");
|
|
444
|
handleForeignKey(rs, referenceIdSet, "nomRefFk");
|
|
445
|
handleForeignKey(rs, refDetailIdSet, "nomRefDetailFk");
|
|
446
|
}
|
|
447
|
|
|
448
|
//team map
|
|
449
|
nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;
|
|
450
|
cdmClass = TeamOrPersonBase.class;
|
|
451
|
idSet = teamIdSet;
|
|
452
|
@SuppressWarnings("unchecked")
|
|
453
|
Map<String, TeamOrPersonBase<?>> teamMap = (Map<String, TeamOrPersonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
454
|
result.put(nameSpace, teamMap);
|
|
455
|
|
|
456
|
//reference map
|
|
457
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
458
|
cdmClass = Reference.class;
|
|
459
|
idSet = referenceIdSet;
|
|
460
|
@SuppressWarnings("unchecked")
|
|
461
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
462
|
result.put(nameSpace, referenceMap);
|
|
463
|
|
|
464
|
//refDetail map
|
|
465
|
nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
|
|
466
|
cdmClass = Reference.class;
|
|
467
|
idSet = refDetailIdSet;
|
|
468
|
@SuppressWarnings("unchecked")
|
|
469
|
Map<String, Reference> refDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
470
|
result.put(nameSpace, refDetailMap);
|
|
471
|
|
|
472
|
} catch (SQLException e) {
|
|
473
|
throw new RuntimeException(e);
|
|
474
|
}
|
|
475
|
return result;
|
|
476
|
}
|
|
477
|
|
|
478
|
private boolean makeZoologialName(ResultSet rs, IZoologicalName zooName, int nameId)
|
|
479
|
throws SQLException{
|
|
480
|
boolean success = true;
|
|
481
|
//publicationYear
|
|
482
|
String authorTeamYear = rs.getString("authorTeamYear");
|
|
483
|
try {
|
|
484
|
if (! "".equals(CdmUtils.Nz(authorTeamYear).trim())){
|
|
485
|
Integer publicationYear = Integer.valueOf(authorTeamYear.trim());
|
|
486
|
zooName.setPublicationYear(publicationYear);
|
|
487
|
}
|
|
488
|
} catch (NumberFormatException e) {
|
|
489
|
logger.warn("authorTeamYear could not be parsed for taxonName: "+ nameId);
|
|
490
|
}
|
|
491
|
//original publication year
|
|
492
|
String basAuthorTeamYear = rs.getString("basAuthorTeamYear");
|
|
493
|
try {
|
|
494
|
if (! "".equals(CdmUtils.Nz(basAuthorTeamYear).trim())){
|
|
495
|
Integer OriginalPublicationYear = Integer.valueOf(basAuthorTeamYear.trim());
|
|
496
|
zooName.setOriginalPublicationYear(OriginalPublicationYear);
|
|
497
|
}
|
|
498
|
} catch (NumberFormatException e) {
|
|
499
|
logger.warn("basAuthorTeamYear could not be parsed for taxonName: "+ nameId);
|
|
500
|
}
|
|
501
|
return success;
|
|
502
|
}
|
|
503
|
|
|
504
|
private boolean makeBotanicalNamePart(ResultSet rs, IBotanicalName botanicalName)throws SQLException{
|
|
505
|
boolean success = true;
|
|
506
|
String dbAttrName;
|
|
507
|
String cdmAttrName;
|
|
508
|
|
|
509
|
dbAttrName = "HybridFormulaFlag";
|
|
510
|
cdmAttrName = "isHybridFormula";
|
|
511
|
success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
|
|
512
|
|
|
513
|
dbAttrName = "MonomHybFlag";
|
|
514
|
cdmAttrName = "isMonomHybrid";
|
|
515
|
success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
|
|
516
|
|
|
517
|
dbAttrName = "BinomHybFlag";
|
|
518
|
cdmAttrName = "isBinomHybrid";
|
|
519
|
success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
|
|
520
|
|
|
521
|
dbAttrName = "TrinomHybFlag";
|
|
522
|
cdmAttrName = "isTrinomHybrid";
|
|
523
|
success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
|
|
524
|
|
|
525
|
try {
|
|
526
|
String strCultivarGroupName = rs.getString("CultivarGroupName");
|
|
527
|
String strCultivarName = rs.getString("CultivarName");
|
|
528
|
if (botanicalName.isCultivar()){
|
|
529
|
ICultivarPlantName cultivarName = (ICultivarPlantName)botanicalName;
|
|
530
|
String concatCultivarName = CdmUtils.concat("-", strCultivarName, strCultivarGroupName);
|
|
531
|
if (isNotBlank(strCultivarGroupName) && isNotBlank(strCultivarName)){
|
|
532
|
logger.warn("CDM does not support cultivarGroupName and CultivarName together: " + concatCultivarName);
|
|
533
|
}
|
|
534
|
cultivarName.setCultivarName(strCultivarGroupName);
|
|
535
|
}
|
|
536
|
} catch (SQLException e) {
|
|
537
|
throw e;
|
|
538
|
}
|
|
539
|
return success;
|
|
540
|
}
|
|
541
|
|
|
542
|
|
|
543
|
private boolean makeNomenclaturalReference(BerlinModelImportConfigurator config, TaxonName taxonName,
|
|
544
|
int nameId, ResultSet rs, @SuppressWarnings("rawtypes") ResultSetPartitioner partitioner) throws SQLException{
|
|
545
|
|
|
546
|
@SuppressWarnings("unchecked")
|
|
547
|
Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
|
|
548
|
@SuppressWarnings("unchecked")
|
|
549
|
Map<String, Reference> refDetailMap = partitioner.getObjectMap(BerlinModelRefDetailImport.REFDETAIL_NAMESPACE);
|
|
550
|
|
|
551
|
Integer nomRefFkInt = nullSafeInt(rs, "NomRefFk");
|
|
552
|
Integer nomRefDetailFkInt = nullSafeInt(rs, "NomRefDetailFk");
|
|
553
|
boolean refDetailPrelim = rs.getBoolean("RefDetailPrelim");
|
|
554
|
|
|
555
|
boolean success = true;
|
|
556
|
//nomenclatural Reference
|
|
557
|
if (refMap != null){
|
|
558
|
if (nomRefFkInt != null){
|
|
559
|
String nomRefFk = String.valueOf(nomRefFkInt);
|
|
560
|
String nomRefDetailFk = String.valueOf(nomRefDetailFkInt);
|
|
561
|
//get nomRef
|
|
562
|
Reference nomReference =
|
|
563
|
getReferenceFromMaps(refDetailMap, refMap, nomRefDetailFk, nomRefFk);
|
|
564
|
|
|
565
|
if(config.isDoPreliminaryRefDetailsWithNames() && refDetailPrelim){
|
|
566
|
makePrelimRefDetailRef(config, rs, taxonName, nameId);
|
|
567
|
}
|
|
568
|
|
|
569
|
//setNomRef
|
|
570
|
if (nomReference == null ){
|
|
571
|
//TODO
|
|
572
|
if (! config.isIgnoreNull()){
|
|
573
|
logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFk + ") for TaxonName (nameId = " + nameId + ")"+
|
|
574
|
" was not found in reference store. Nomenclatural reference not set!!");
|
|
575
|
}
|
|
576
|
}else{
|
|
577
|
if (! INomenclaturalReference.class.isAssignableFrom(nomReference.getClass())){
|
|
578
|
logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFk + ") for TaxonName (nameId = " + nameId + ")"+
|
|
579
|
" is not assignable from INomenclaturalReference. (Class = " + nomReference.getClass()+ ")");
|
|
580
|
}
|
|
581
|
nomReference.setNomenclaturallyRelevant(true);
|
|
582
|
taxonName.setNomenclaturalReference(nomReference);
|
|
583
|
}
|
|
584
|
}
|
|
585
|
}
|
|
586
|
return success;
|
|
587
|
}
|
|
588
|
|
|
589
|
|
|
590
|
private INonViralNameParser<?> parser = NonViralNameParserImpl.NewInstance();
|
|
591
|
|
|
592
|
/**
|
|
593
|
* @param config
|
|
594
|
* @param rs
|
|
595
|
* @param taxonName
|
|
596
|
* @param nameId
|
|
597
|
* @throws SQLException
|
|
598
|
*/
|
|
599
|
private void makePrelimRefDetailRef(IImportConfigurator config, ResultSet rs, TaxonName taxonName, int nameId) throws SQLException {
|
|
600
|
String fullNomRefCache = rs.getString("FullNomRefCache");
|
|
601
|
if (fullNomRefCache == null){
|
|
602
|
logger.warn("fullNomRefCache is null for preliminary refDetail. NameId: " + nameId);
|
|
603
|
return;
|
|
604
|
}else if (fullNomRefCache.trim().startsWith(": ")){
|
|
605
|
logger.warn("fullNomRefCache starts with for preliminary refDetail. NameId: " + nameId);
|
|
606
|
return;
|
|
607
|
}else if (fullNomRefCache.trim().startsWith("in ")){
|
|
608
|
String fullStr = taxonName.getTitleCache()+ " " + fullNomRefCache;
|
|
609
|
INonViralName newName = parser.parseReferencedName(fullStr, config.getNomenclaturalCode(), taxonName.getRank());
|
|
610
|
if (newName.isProtectedFullTitleCache()){
|
|
611
|
Reference nomRef = ReferenceFactory.newGeneric();
|
|
612
|
nomRef.setAbbrevTitleCache(fullNomRefCache, true);
|
|
613
|
taxonName.setNomenclaturalReference(nomRef);
|
|
614
|
//check detail
|
|
615
|
}else{
|
|
616
|
Reference nomRef = newName.getNomenclaturalReference();
|
|
617
|
taxonName.setNomenclaturalReference(nomRef);
|
|
618
|
String detail = newName.getNomenclaturalMicroReference();
|
|
619
|
String oldDetail = taxonName.getNomenclaturalMicroReference();
|
|
620
|
if (isBlank(detail)){
|
|
621
|
if (isNotBlank(oldDetail)){
|
|
622
|
logger.warn("Detail could not be parsed but seems to exist. NameId: " + nameId);
|
|
623
|
}
|
|
624
|
}else{
|
|
625
|
if (isNotBlank(oldDetail) && !detail.equals(oldDetail)){
|
|
626
|
logger.warn("Details differ: " + detail + " <-> " + oldDetail + ". NameId: " + nameId);
|
|
627
|
}
|
|
628
|
taxonName.setNomenclaturalMicroReference(detail);
|
|
629
|
}
|
|
630
|
}
|
|
631
|
}else{
|
|
632
|
String fullStrComma = taxonName.getTitleCache()+ ", " + fullNomRefCache;
|
|
633
|
String fullStrIn = taxonName.getTitleCache()+ " in " + fullNomRefCache;
|
|
634
|
INonViralName newNameComma = parser.parseReferencedName(fullStrComma, config.getNomenclaturalCode(), taxonName.getRank());
|
|
635
|
INonViralName newNameIn = parser.parseReferencedName(fullStrIn, config.getNomenclaturalCode(), taxonName.getRank());
|
|
636
|
|
|
637
|
INonViralName newName;
|
|
638
|
boolean commaProtected = newNameComma.isProtectedFullTitleCache() || (newNameComma.getNomenclaturalReference() != null
|
|
639
|
&& newNameComma.getNomenclaturalReference().isProtectedTitleCache());
|
|
640
|
boolean inProtected = newNameIn.isProtectedFullTitleCache() || (newNameIn.getNomenclaturalReference() != null
|
|
641
|
&& newNameIn.getNomenclaturalReference().isProtectedTitleCache());
|
|
642
|
if (commaProtected && !inProtected){
|
|
643
|
newName = newNameIn;
|
|
644
|
}else if (!commaProtected && inProtected){
|
|
645
|
newName = newNameComma;
|
|
646
|
}else if (commaProtected && inProtected){
|
|
647
|
logger.warn("Can't parse preliminary refDetail: " + fullNomRefCache + " for name " + taxonName.getTitleCache() + "; nameId: " + nameId );
|
|
648
|
newName = newNameComma;
|
|
649
|
}else{
|
|
650
|
logger.warn("Can't decide ref type for preliminary refDetail: " + fullNomRefCache + " for name " + taxonName.getTitleCache() + "; nameId: " + nameId );
|
|
651
|
newName = newNameComma;
|
|
652
|
}
|
|
653
|
|
|
654
|
|
|
655
|
if (newName.isProtectedFullTitleCache()){
|
|
656
|
Reference nomRef = ReferenceFactory.newGeneric();
|
|
657
|
nomRef.setAbbrevTitleCache(fullNomRefCache, true);
|
|
658
|
taxonName.setNomenclaturalReference(nomRef);
|
|
659
|
//check detail
|
|
660
|
}else{
|
|
661
|
Reference nomRef = newName.getNomenclaturalReference();
|
|
662
|
taxonName.setNomenclaturalReference(nomRef);
|
|
663
|
String detail = newName.getNomenclaturalMicroReference();
|
|
664
|
String oldDetail = taxonName.getNomenclaturalMicroReference();
|
|
665
|
if (isBlank(detail)){
|
|
666
|
if (isNotBlank(oldDetail)){
|
|
667
|
logger.warn("Detail could not be parsed but seems to exist. NameId: " + nameId);
|
|
668
|
}
|
|
669
|
}else{
|
|
670
|
if (isNotBlank(oldDetail) && !detail.equals(oldDetail)){
|
|
671
|
logger.warn("Details differ: " + detail + " <-> " + oldDetail + ". NameId: " + nameId);
|
|
672
|
}
|
|
673
|
taxonName.setNomenclaturalMicroReference(detail);
|
|
674
|
}
|
|
675
|
}
|
|
676
|
}
|
|
677
|
}
|
|
678
|
|
|
679
|
|
|
680
|
private static TeamOrPersonBase<?> getAuthorTeam(Map<String, Team> teamMap, Integer teamIdInt, int nameId, BerlinModelImportConfigurator config){
|
|
681
|
if (teamIdInt == null){
|
|
682
|
return null;
|
|
683
|
}else {
|
|
684
|
String teamIdStr = String.valueOf(teamIdInt);
|
|
685
|
TeamOrPersonBase<?> author = teamMap.get(teamIdStr);
|
|
686
|
if (author == null){
|
|
687
|
//TODO
|
|
688
|
if (!config.isIgnoreNull() && ! (teamIdStr.equals(0) && config.isIgnore0AuthorTeam()) ){
|
|
689
|
logger.warn("AuthorTeam (teamId = " + teamIdStr + ") for TaxonName (nameId = " + nameId + ")"+
|
|
690
|
" was not found in authorTeam store. Relation was not set!");
|
|
691
|
}
|
|
692
|
return null;
|
|
693
|
}else{
|
|
694
|
return author;
|
|
695
|
}
|
|
696
|
}
|
|
697
|
}
|
|
698
|
|
|
699
|
@Override
|
|
700
|
protected boolean doCheck(BerlinModelImportState state){
|
|
701
|
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameImportValidator();
|
|
702
|
return validator.validate(state);
|
|
703
|
}
|
|
704
|
|
|
705
|
@Override
|
|
706
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
707
|
return ! state.getConfig().isDoTaxonNames();
|
|
708
|
}
|
|
709
|
|
|
710
|
|
|
711
|
|
|
712
|
|
|
713
|
|
|
714
|
|
|
715
|
//FOR FUTURE USE , DONT DELETE
|
|
716
|
// new CdmStringMapper("nameId", "nameId"),
|
|
717
|
// new CdmStringMapper("rankFk", "rankFk"),
|
|
718
|
// new CdmStringMapper("nameCache", "nameCache"),
|
|
719
|
// new CdmStringMapper("unnamedNamePhrase", "unnamedNamePhrase"),
|
|
720
|
// new CdmStringMapper("fullNameCache", "fullNameCache"),
|
|
721
|
// new CdmStringMapper("preliminaryFlag", "preliminaryFlag"),
|
|
722
|
// new CdmStringMapper("supragenericName", "supragenericName"),
|
|
723
|
// new CdmStringMapper("genus", "genus"),
|
|
724
|
// new CdmStringMapper("genusSubdivisionEpi", "genusSubdivisionEpi"),
|
|
725
|
// new CdmStringMapper("speciesEpi", "speciesEpi"),
|
|
726
|
// new CdmStringMapper("infraSpeciesEpi", "infraSpeciesEpi"),
|
|
727
|
// new CdmStringMapper("authorTeamFk", "authorTeamFk"),
|
|
728
|
// new CdmStringMapper("exAuthorTeamFk", "exAuthorTeamFk"),
|
|
729
|
// new CdmStringMapper("basAuthorTeamFk", "basAuthorTeamFk"),
|
|
730
|
// new CdmStringMapper("exBasAuthorTeamFk", "exBasAuthorTeamFk"),
|
|
731
|
// new CdmStringMapper("hybridFormulaFlag", "hybridFormulaFlag"),
|
|
732
|
// new CdmStringMapper("monomHybFlag", "monomHybFlag"),
|
|
733
|
// new CdmStringMapper("binomHybFlag", "binomHybFlag"),
|
|
734
|
// new CdmStringMapper("trinomHybFlag", "trinomHybFlag"),
|
|
735
|
// new CdmStringMapper("cultivarGroupName", "cultivarGroupName"),
|
|
736
|
// new CdmStringMapper("cultivarName", "cultivarName"),
|
|
737
|
// new CdmStringMapper("nomRefFk", "nomRefFk"),
|
|
738
|
// new CdmStringMapper("nomRefDetailFk", "nomRefDetailFk"),
|
|
739
|
// new CdmStringMapper("nameSourceRefFk", "nameSourceRefFk"),
|
|
740
|
// new CdmStringMapper("source_Acc", "source_Acc"),
|
|
741
|
// new CdmStringMapper("created_When", "created_When"),
|
|
742
|
// new CdmStringMapper("created_Who", "created_Who"),
|
|
743
|
// new CdmStringMapper("notes", "notes"),
|
|
744
|
// new CdmStringMapper("parsingComments", "parsingComments"),
|
|
745
|
// new CdmStringMapper("oldNomRefFk", "oldNomRefFk"),
|
|
746
|
// new CdmStringMapper("oldNomRefDetailFk", "oldNomRefDetailFk"),
|
|
747
|
// new CdmStringMapper("updated_Who", "updated_Who"),
|
|
748
|
// new CdmStringMapper("orthoProjection", "orthoProjection"),
|
|
749
|
|
|
750
|
|
|
751
|
}
|