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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.eflora.centralAfrica.ferns;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.api.service.ITaxonTreeService;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMethodMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectCreationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportTaxIncludedInMapper;
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import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.CentralAfricaChecklistImportState;
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.validation.CentralAfricaFernsTaxonImportValidator;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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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.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
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/**
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* @author a.mueller
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* @created 20.02.2010
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* @version 1.0
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*/
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@Component
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public class CentralAfricaFernsTaxonRelationImport extends CentralAfricaFernsImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaFernsImportState>{
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private static final Logger logger = Logger.getLogger(CentralAfricaFernsTaxonRelationImport.class);
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private DbImportMapping mapping;
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private int modCount = 10000;
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private static final String pluralString = "taxa";
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private static final String dbTableName = "[African pteridophytes]";
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private static final Class cdmTargetClass = TaxonBase.class;
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private Map<String, UUID> taxonMap = new HashMap<String, UUID>();
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public CentralAfricaFernsTaxonRelationImport(){
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super(pluralString, dbTableName, cdmTargetClass);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()
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*/
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@Override
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protected String getIdQuery() {
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String strQuery = " SELECT [Taxon number] FROM " + dbTableName;;
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
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*/
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protected DbImportMapping getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping();
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mapping.addMapper(DbImportMethodMapper.NewInstance(this, "createObject", ResultSet.class, CentralAfricaFernsImportState.class));
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// NewInstance(this, "Taxon number", TAXON_NAMESPACE)); //id + tu_status
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//funktioniert nicht wegen doppeltem Abfragen von Attributen
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// mapping.addMapper(DbImportSynonymMapper.NewInstance("Taxon number", "Current", TAXON_NAMESPACE, null));
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// mapping.addMapper(DbImportNameTypeDesignationMapper.NewInstance("id", "tu_typetaxon", NAME_NAMESPACE, "tu_typedesignationstatus"));
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}
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return mapping;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(CentralAfricaFernsImportConfigurator config) {
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String strSelect = " SELECT * ";
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String strFrom = " FROM [African pteridophytes] as ap";
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String strWhere = " WHERE ( ap.[taxon number] IN (" + ID_LIST_TOKEN + ") )";
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String strRecordQuery = strSelect + strFrom + strWhere;
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return strRecordQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#doInvoke(eu.etaxonomy.cdm.io.erms.ErmsImportState)
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*/
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@Override
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protected boolean doInvoke(CentralAfricaFernsImportState state) {
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//first path
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fillTaxonMap();
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boolean success = super.doInvoke(state);
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return success;
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}
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private void fillTaxonMap() {
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List<String> propPath = Arrays.asList(new String []{"name"});
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List<Taxon> taxonList = (List)getTaxonService().list(Taxon.class, null, null, null, propPath );
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for (Taxon taxon : taxonList){
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NonViralName nvn = CdmBase.deproxy(taxon.getName(), NonViralName.class);
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UUID uuid = taxon.getName().getUuid();
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String name = nvn.getNameCache();
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taxonMap.put(name, uuid);
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
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*/
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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String nameSpace;
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Class cdmClass;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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Set<String> taxonIdSet = new HashSet<String>();
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// Set<String> referenceIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "Current");
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handleForeignKey(rs, taxonIdSet, "Taxon number");
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// handleForeignKey(rs, referenceIdSet, "PTRefFk");
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}
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//reference map
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nameSpace = TAXON_NAMESPACE;
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cdmClass = TaxonBase.class;
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, taxonIdSet, nameSpace);
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result.put(nameSpace, taxonMap);
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//reference map
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// nameSpace = "Reference";
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// cdmClass = ReferenceBase.class;
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// Map<String, Person> referenceMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(Person.class, teamIdSet, nameSpace);
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// result.put(ReferenceBase.class, referenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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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.mapping.IMappingImport#createObject(java.sql.ResultSet)
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*/
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public TaxonBase createObject(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
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TaxonBase result = null;
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try {
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String status = rs.getString("Current/Synonym");
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if ("s".equalsIgnoreCase(status)){
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//synonym
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result = handleSynonym(rs, state);
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}else{
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//accepted Taxon
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result = handleTaxon(rs, state);
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}
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return result;
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} catch (Exception e) {
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e.printStackTrace();
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return result;
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}
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}
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private Synonym handleSynonym(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
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String accTaxonId = rs.getString("Current");
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String synonymId = rs.getString("Taxon number");
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Synonym synonym = (Synonym)state.getRelatedObject(TAXON_NAMESPACE, synonymId);
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if (synonym == null){
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logger.warn ("Synonym ("+synonymId+")not found.");
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return null;
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}
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TaxonBase taxonBase = CdmBase.deproxy(state.getRelatedObject(TAXON_NAMESPACE, accTaxonId), TaxonBase.class);
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if (taxonBase != null){
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if (taxonBase.isInstanceOf(Taxon.class)){
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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taxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF());
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}else{
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logger.warn("Accepted taxon (" + accTaxonId + ") for synonym (" + synonymId +") is not of type 'Current'");
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}
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}else{
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logger.warn("Taxon (" + accTaxonId + ") not found for synonym (" + synonymId +")");
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}
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return synonym;
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}
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private Taxon handleTaxon(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException {
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String taxonNumber = rs.getString("Taxon number");
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Taxon child = (Taxon)state.getRelatedObject(TAXON_NAMESPACE, taxonNumber);
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if (child == null){
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logger.warn("Taxon does not exist: " + taxonNumber);
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return null;
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}
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String orderName = rs.getString("Order name");
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String subOrderName = rs.getString("Suborder name");
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String familyName = rs.getString("Family name");
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String subFamilyName = rs.getString("Subfamily name");
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String tribusName = rs.getString("Tribus name");
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String subTribusName = rs.getString("Subtribus name");
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String sectionName = rs.getString("Section name");
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String subsectionName = rs.getString("Subsection name");
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String genusName = rs.getString("Genus name");
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String subGenusName = rs.getString("Subgenus name");
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String seriesName = rs.getString("Series name");
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String specificEpihet = rs.getString("Specific epihet");
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String subspeciesName = rs.getString("Subspecies name");
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String varietyName = rs.getString("Variety name");
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String subVariety = rs.getString("Subvariery");
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String formaName = rs.getString("Forma name");
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String subFormaName = rs.getString("Subforma");
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makeNextHigherTaxon(state, child, orderName, subOrderName, familyName, subFamilyName, tribusName, subTribusName, sectionName,
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subsectionName, genusName, subGenusName, seriesName, specificEpihet, subspeciesName, varietyName, subVariety, formaName, subFormaName);
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return child;
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}
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/**
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* @param state
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* @param child
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* @param orderName
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* @param subOrderName
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* @param familyName
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* @param subFamilyName
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* @param tribusName
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* @param subTribusName
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* @param sectionName
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* @param subsectionName
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* @param genusName
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* @param subGenusName
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* @param seriesName
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* @param specificEpihet
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* @param subspeciesName
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* @param varietyName
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* @param subVariety
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* @param formaName
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* @param subFormaName
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*/
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private void makeNextHigherTaxon(CentralAfricaFernsImportState state, Taxon child, String orderName, String subOrderName,
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String familyName, String subFamilyName, String tribusName, String subTribusName, String sectionName, String subsectionName,
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String genusName, String subGenusName, String seriesName, String specificEpihet, String subspeciesName, String varietyName,
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String subVariety, String formaName, String subFormaName) {
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Taxon higherTaxon = getNextHigherTaxon(state, child, orderName, subOrderName, familyName, subFamilyName, tribusName, subTribusName, sectionName, subsectionName, genusName, subGenusName, seriesName, specificEpihet, subspeciesName, varietyName, subVariety, formaName, subFormaName);
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ReferenceBase citation = null;
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if (higherTaxon != null){
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if (! includedRelationshipExists(child, higherTaxon)){
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makeTaxonomicallyIncluded(state, null, child, higherTaxon, citation, null);
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}else{
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logger.info("Included exists");
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}
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makeNextHigherTaxon(state, higherTaxon, orderName, subOrderName, familyName, subFamilyName, tribusName, subTribusName, sectionName, subsectionName, genusName, subGenusName, seriesName, specificEpihet, subspeciesName, varietyName, subVariety, formaName, subFormaName);
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}
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}
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/**
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* Tests if this the child taxon already is a child of the higher taxon.
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* @param child
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* @param higherTaxon
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* @return
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*/
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private boolean includedRelationshipExists(Taxon child, Taxon higherTaxon) {
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int countNodes = higherTaxon.getTaxonNodes().size();
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if (countNodes < 1){
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return false;
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}else if (countNodes > 1){
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throw new IllegalStateException("Multiple nodes exist for higher taxon. This is an invalid state.");
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}else{
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TaxonNode higherNode = higherTaxon.getTaxonNodes().iterator().next();
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return childExists(child, higherNode);
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}
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}
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private boolean childExists(Taxon child, TaxonNode higherNode) {
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for (TaxonNode childNode : higherNode.getChildNodes()){
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String existingChildTitle = childNode.getTaxon().getName().getTitleCache();
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String newChildTitle = child.getName().getTitleCache();
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if (existingChildTitle.equals(newChildTitle)){
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return true;
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}
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}
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return false;
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}
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// private boolean makeTaxonomicallyIncluded(CentralAfricaFernsImportState state, Taxon parent, Taxon child, ReferenceBase citation, String microCitation){
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// ReferenceBase sec = child.getSec();
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// TaxonomicTree tree = state.getTree(sec);
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// if (tree == null){
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// tree = makeTreeMemSave(state, sec);
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// }
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// TaxonNode childNode;
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// if (parent != null){
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// childNode = tree.addParentChild(parent, child, citation, microCitation);
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// }else{
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// childNode = tree.addChildTaxon(child, citation, microCitation, null);
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// }
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// return (childNode != null);
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// }
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//TODO use Mapper
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private boolean makeTaxonomicallyIncluded(CentralAfricaFernsImportState state, Integer treeRefFk, Taxon child, Taxon parent, ReferenceBase citation, String microCitation){
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String treeKey;
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UUID treeUuid;
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if (treeRefFk == null){
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treeKey = "1"; // there is only one tree and it gets the map key '1'
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treeUuid = state.getConfig().getTaxonomicTreeUuid();
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}else{
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treeKey =String.valueOf(treeRefFk);
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treeUuid = state.getTreeUuidByTreeKey(treeKey);
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}
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TaxonomicTree tree = (TaxonomicTree)state.getRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey);
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if (tree == null){
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ITaxonTreeService service = state.getCurrentIO().getTaxonTreeService();
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tree = service.getTaxonomicTreeByUuid(treeUuid);
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if (tree == null){
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String treeName = state.getConfig().getTaxonomicTreeName();
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tree = TaxonomicTree.NewInstance(treeName);
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tree.setUuid(treeUuid);
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//FIXME tree reference
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tree.setReference(citation);
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service.save(tree);
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}
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state.addRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey, tree);
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}
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TaxonNode childNode = tree.addParentChild(parent, child, citation, microCitation);
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return (childNode != null);
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}
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private Taxon getNextHigherTaxon(CentralAfricaFernsImportState state, Taxon childTaxon, String orderName, String subOrderName, String familyName, String subFamilyName,
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String tribusName, String subTribusName, String sectionName, String subsectionName, String genusName, String subGenusName, String seriesName, String speciesName, String subspeciesName, String varietyName, String subVariety, String formaName, String subFormaName) {
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Taxon result = null;
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BotanicalName childName = CdmBase.deproxy(childTaxon.getName(), BotanicalName.class);
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Rank childRank = childName.getRank();
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BotanicalName higherName;
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393
|
higherName = handleInfraSpecific(childRank, genusName, speciesName, subspeciesName, varietyName, subVariety, formaName, subFormaName);
|
394
|
if (higherName.getRank() == null){
|
395
|
handleSpecies(childRank, higherName, genusName, speciesName);
|
396
|
}
|
397
|
if (higherName.getRank() == null){
|
398
|
handleInfraGeneric(childRank, higherName, genusName, subGenusName, seriesName);
|
399
|
}
|
400
|
if (higherName.getRank() == null){
|
401
|
handleUninomial(childRank, higherName, orderName, subOrderName, familyName, subFamilyName, tribusName, subTribusName, sectionName, subsectionName, genusName);
|
402
|
}
|
403
|
//if higher taxon must exist, create it if it was not yet created
|
404
|
if (higherName.getRank() != null && getExistingTaxon(higherName, state) == null ){
|
405
|
result = Taxon.NewInstance(higherName, childTaxon.getSec());
|
406
|
UUID uuid = higherName.getUuid();
|
407
|
String name = higherName.getNameCache();
|
408
|
taxonMap.put(name, uuid);
|
409
|
state.addRelatedObject(HIGHER_TAXON_NAMESPACE, higherName.getNameCache(), result);
|
410
|
}
|
411
|
return result;
|
412
|
}
|
413
|
|
414
|
|
415
|
|
416
|
private Taxon getExistingTaxon(BotanicalName higherName, CentralAfricaFernsImportState state) {
|
417
|
String nameCache = higherName.getNameCache();
|
418
|
UUID uuid = taxonMap.get(nameCache);
|
419
|
|
420
|
Taxon taxon = null;
|
421
|
if (uuid != null){
|
422
|
taxon = CdmBase.deproxy(getTaxonService().find(uuid), Taxon.class);
|
423
|
Taxon taxon2 = state.getRelatedObject(HIGHER_TAXON_NAMESPACE, nameCache, Taxon.class);
|
424
|
if (taxon != taxon2){
|
425
|
logger.warn("Difference in related taxa: " + nameCache);
|
426
|
}
|
427
|
|
428
|
}
|
429
|
return taxon;
|
430
|
}
|
431
|
|
432
|
|
433
|
|
434
|
private BotanicalName handleInfraSpecific(Rank lowerTaxonRank, String genusName, String specificEpithet, String subspeciesName, String varietyName, String subVariety, String formaName, String subFormaName) {
|
435
|
|
436
|
BotanicalName taxonName = BotanicalName.NewInstance(null);
|
437
|
Rank newRank = null;
|
438
|
|
439
|
if (StringUtils.isNotBlank(subFormaName) && lowerTaxonRank.isLower(Rank.SUBFORM())){
|
440
|
taxonName.setInfraSpecificEpithet(subFormaName);
|
441
|
newRank = Rank.SUBFORM();
|
442
|
}else if (StringUtils.isNotBlank(formaName) && lowerTaxonRank.isLower(Rank.FORM())){
|
443
|
taxonName.setInfraSpecificEpithet(formaName);
|
444
|
newRank = Rank.FORM();
|
445
|
}else if (StringUtils.isNotBlank(subVariety) && lowerTaxonRank.isLower(Rank.SUBVARIETY())){
|
446
|
taxonName.setInfraSpecificEpithet(subVariety);
|
447
|
newRank = Rank.SUBVARIETY();
|
448
|
}else if (StringUtils.isNotBlank(varietyName) && lowerTaxonRank.isLower(Rank.VARIETY())){
|
449
|
taxonName.setInfraSpecificEpithet(varietyName);
|
450
|
newRank = Rank.VARIETY();
|
451
|
}else if (StringUtils.isNotBlank(subspeciesName) && lowerTaxonRank.isLower(Rank.SUBSPECIES())){
|
452
|
taxonName.setInfraSpecificEpithet(subspeciesName);
|
453
|
newRank = Rank.SUBSPECIES();
|
454
|
}
|
455
|
|
456
|
if (newRank != null){
|
457
|
taxonName.setSpecificEpithet(specificEpithet);
|
458
|
taxonName.setGenusOrUninomial(genusName);
|
459
|
taxonName.setRank(newRank);
|
460
|
}
|
461
|
|
462
|
return taxonName;
|
463
|
}
|
464
|
|
465
|
private BotanicalName handleSpecies(Rank lowerTaxonRank, BotanicalName taxonName, String genusName, String speciesEpithet) {
|
466
|
Rank newRank = null;
|
467
|
|
468
|
if (StringUtils.isNotBlank(speciesEpithet) && lowerTaxonRank.isLower(Rank.SPECIES())){
|
469
|
taxonName.setSpecificEpithet(speciesEpithet);
|
470
|
newRank = Rank.SPECIES();
|
471
|
}
|
472
|
if (newRank != null){
|
473
|
taxonName.setGenusOrUninomial(genusName);
|
474
|
taxonName.setRank(newRank);
|
475
|
}
|
476
|
return taxonName;
|
477
|
}
|
478
|
|
479
|
private BotanicalName handleInfraGeneric(Rank lowerTaxonRank, BotanicalName taxonName, String genusName, String subGenusName, String seriesName) {
|
480
|
Rank newRank = null;
|
481
|
|
482
|
if (StringUtils.isNotBlank(seriesName) && lowerTaxonRank.isLower(Rank.SERIES())){
|
483
|
taxonName.setInfraGenericEpithet(seriesName);
|
484
|
newRank = Rank.SERIES();
|
485
|
}else if (StringUtils.isNotBlank(subGenusName) && lowerTaxonRank.isLower(Rank.SUBGENUS())){
|
486
|
taxonName.setInfraGenericEpithet(subGenusName);
|
487
|
newRank = Rank.SUBGENUS();
|
488
|
}
|
489
|
if (newRank != null){
|
490
|
taxonName.setGenusOrUninomial(genusName);
|
491
|
taxonName.setRank(newRank);
|
492
|
}
|
493
|
return taxonName;
|
494
|
}
|
495
|
|
496
|
|
497
|
|
498
|
private BotanicalName handleUninomial(Rank lowerTaxonRank, BotanicalName taxonName, String orderName, String subOrderName, String familyName, String subFamilyName,
|
499
|
String tribusName, String subTribusName, String sectionName, String subsectionName, String genusName) {
|
500
|
|
501
|
Rank newRank = null;
|
502
|
if (StringUtils.isNotBlank(genusName) && lowerTaxonRank.isLower(Rank.GENUS())){
|
503
|
taxonName.setGenusOrUninomial(genusName);
|
504
|
newRank = Rank.GENUS();
|
505
|
}else if (StringUtils.isNotBlank(subsectionName) && lowerTaxonRank.isLower(Rank.SUBSECTION_BOTANY())){
|
506
|
taxonName.setGenusOrUninomial(subsectionName);
|
507
|
newRank = Rank.SUBSECTION_BOTANY();
|
508
|
}else if (StringUtils.isNotBlank(sectionName) && lowerTaxonRank.isLower(Rank.SECTION_BOTANY())){
|
509
|
taxonName.setGenusOrUninomial(sectionName);
|
510
|
newRank = Rank.SECTION_BOTANY();
|
511
|
}else if (StringUtils.isNotBlank(subTribusName) && lowerTaxonRank.isLower(Rank.SUBTRIBE())){
|
512
|
taxonName.setGenusOrUninomial(subTribusName);
|
513
|
newRank = Rank.SUBTRIBE();
|
514
|
}else if (StringUtils.isNotBlank(tribusName) && lowerTaxonRank.isLower(Rank.TRIBE())){
|
515
|
taxonName.setGenusOrUninomial(tribusName);
|
516
|
newRank = Rank.TRIBE();
|
517
|
}else if (StringUtils.isNotBlank(subFamilyName) && lowerTaxonRank.isLower(Rank.SUBFAMILY())){
|
518
|
taxonName.setGenusOrUninomial(subFamilyName);
|
519
|
newRank = Rank.SUBFAMILY();
|
520
|
}else if (StringUtils.isNotBlank(familyName) && lowerTaxonRank.isLower(Rank.FAMILY())){
|
521
|
taxonName.setGenusOrUninomial(familyName);
|
522
|
newRank = Rank.FAMILY();
|
523
|
}else if (StringUtils.isNotBlank(subOrderName) && lowerTaxonRank.isLower(Rank.SUBORDER())){
|
524
|
taxonName.setGenusOrUninomial(subOrderName);
|
525
|
newRank = Rank.SUBORDER();
|
526
|
}else if (StringUtils.isNotBlank(orderName) && lowerTaxonRank.isLower(Rank.ORDER())){
|
527
|
taxonName.setGenusOrUninomial(orderName);
|
528
|
newRank = Rank.ORDER();
|
529
|
}
|
530
|
taxonName.setRank(newRank);
|
531
|
return taxonName;
|
532
|
}
|
533
|
|
534
|
|
535
|
|
536
|
|
537
|
private void setAuthor(BotanicalName taxonName, ResultSet rs) throws SQLException {
|
538
|
String orderAuthor = rs.getString("Order name author");
|
539
|
String subOrderAuthor = rs.getString("Suborder name author");
|
540
|
String familyAuthor = rs.getString("Family name author");
|
541
|
String subFamilyAuthor = rs.getString("Subfamily name author");
|
542
|
String tribusAuthor = rs.getString("Tribus author");
|
543
|
String subTribusAuthor = rs.getString("Subtribus author");
|
544
|
String sectionAuthor = rs.getString("Section name author");
|
545
|
String subsectionAuthor = rs.getString("Subsection author");
|
546
|
String genusAuthor = rs.getString("Genus name author");
|
547
|
String subGenusAuthor = rs.getString("Subgenus name author");
|
548
|
String seriesAuthor = rs.getString("Series name author");
|
549
|
String specificEpihetAuthor = rs.getString("Specific epithet author");
|
550
|
String subspeciesAuthor = rs.getString("Subspecies author");
|
551
|
String varietyAuthor = rs.getString("Variety name author");
|
552
|
String subVarietyAuthor = rs.getString("Subvariety author");
|
553
|
String formaAuthor = rs.getString("Forma name author");
|
554
|
String subFormaAuthor = rs.getString("Subforma author");
|
555
|
|
556
|
String authorsFull = rs.getString("Author/s - full");
|
557
|
String authorsAbbrev = rs.getString("Author/s - abbreviated");
|
558
|
|
559
|
|
560
|
Rank rank = taxonName.getRank();
|
561
|
String authorString;
|
562
|
if (rank != null){
|
563
|
if (rank.equals(Rank.ORDER())){
|
564
|
authorString = orderAuthor;
|
565
|
}else if (rank.equals(Rank.SUBORDER())){
|
566
|
authorString = subOrderAuthor;
|
567
|
}else if (rank.equals(Rank.FAMILY())){
|
568
|
authorString = familyAuthor;
|
569
|
}else if (rank.equals(Rank.SUBFAMILY())){
|
570
|
authorString = subFamilyAuthor;
|
571
|
}else if (rank.equals(Rank.TRIBE())){
|
572
|
authorString = tribusAuthor;
|
573
|
}else if (rank.equals(Rank.SUBTRIBE())){
|
574
|
authorString = subTribusAuthor;
|
575
|
}else if (rank.equals(Rank.SECTION_BOTANY())){
|
576
|
authorString = sectionAuthor;
|
577
|
}else if (rank.equals(Rank.SUBSECTION_BOTANY())){
|
578
|
authorString = subsectionAuthor;
|
579
|
}else if (rank.equals(Rank.GENUS())){
|
580
|
authorString = genusAuthor;
|
581
|
}else if (rank.equals(Rank.SUBGENUS())){
|
582
|
authorString = subGenusAuthor;
|
583
|
}else if (rank.equals(Rank.SERIES())){
|
584
|
authorString = seriesAuthor;
|
585
|
}else if (rank.equals(Rank.SPECIES())){
|
586
|
authorString = specificEpihetAuthor;
|
587
|
}else if (rank.equals(Rank.SUBSPECIES())){
|
588
|
authorString = subspeciesAuthor;
|
589
|
}else if (rank.equals(Rank.VARIETY())){
|
590
|
authorString = varietyAuthor;
|
591
|
}else if (rank.equals(Rank.SUBVARIETY())){
|
592
|
authorString = subVarietyAuthor;
|
593
|
}else if (rank.equals(Rank.FORM())){
|
594
|
authorString = formaAuthor;
|
595
|
}else if (rank.equals(Rank.SUBFORM())){
|
596
|
authorString = subFormaAuthor;
|
597
|
}else{
|
598
|
logger.warn("Author string could not be defined");
|
599
|
authorString = authorsAbbrev;
|
600
|
if (StringUtils.isBlank(authorString)){
|
601
|
logger.warn("Authors abbrev string could not be defined");
|
602
|
authorString = authorsFull;
|
603
|
}
|
604
|
}
|
605
|
}else{
|
606
|
logger.warn("Rank is null");
|
607
|
authorString = authorsAbbrev;
|
608
|
if (StringUtils.isBlank(authorString)){
|
609
|
logger.warn("Authors abbrev string could not be defined");
|
610
|
authorString = authorsFull;
|
611
|
}
|
612
|
}
|
613
|
if (StringUtils.isNotBlank(authorsAbbrev) && ! authorsAbbrev.equalsIgnoreCase(authorString)){
|
614
|
logger.warn("Rank author and abbrev author are not equal");
|
615
|
}
|
616
|
if (StringUtils.isNotBlank(authorsFull) && ! authorsFull.equalsIgnoreCase(authorString)){
|
617
|
logger.warn("Rank author and full author are not equal");
|
618
|
}
|
619
|
|
620
|
Team team = Team.NewTitledInstance(authorString, authorString);
|
621
|
taxonName.setCombinationAuthorTeam(team);
|
622
|
|
623
|
}
|
624
|
|
625
|
|
626
|
/* (non-Javadoc)
|
627
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
628
|
*/
|
629
|
@Override
|
630
|
protected boolean doCheck(CentralAfricaFernsImportState state){
|
631
|
IOValidator<CentralAfricaFernsImportState> validator = new CentralAfricaFernsTaxonImportValidator();
|
632
|
return validator.validate(state);
|
633
|
}
|
634
|
|
635
|
|
636
|
/* (non-Javadoc)
|
637
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
638
|
*/
|
639
|
protected boolean isIgnore(CentralAfricaFernsImportState state){
|
640
|
return ! state.getConfig().isDoTaxa();
|
641
|
}
|
642
|
|
643
|
|
644
|
|
645
|
|
646
|
|
647
|
}
|