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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.redlist.gefaesspflanzen;
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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 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.io.common.DbImportBase;
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import eu.etaxonomy.cdm.io.common.IPartitionedIO;
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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.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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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.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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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.taxon.Synonym;
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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.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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/**
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*
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* @author pplitzner
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* @date Mar 1, 2016
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*
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*/
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@Component
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@SuppressWarnings("serial")
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public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
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private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
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private static final String tableName = "Rote Liste Gefäßpflanzen";
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private static final String pluralString = "names";
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public RedListGefaesspflanzenImportNames() {
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super(tableName, pluralString);
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}
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@Override
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protected String getIdQuery(RedListGefaesspflanzenImportState state) {
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return "SELECT NAMNR "
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+ "FROM V_TAXATLAS_D20_EXPORT t "
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+ " ORDER BY NAMNR";
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}
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@Override
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protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
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String result = " SELECT * "
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+ " FROM V_TAXATLAS_D20_EXPORT t "
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+ " WHERE t.NAMNR IN (@IDSET)";
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result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
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return result;
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}
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@Override
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protected void doInvoke(RedListGefaesspflanzenImportState state) {
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super.doInvoke(state);
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
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ResultSet rs = partitioner.getResultSet();
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Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
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Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
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try {
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while (rs.next()){
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makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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getNameService().saveOrUpdate(namesToSave);
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getTaxonService().saveOrUpdate(taxaToSave);
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return true;
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}
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private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
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throws SQLException {
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//cell values
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long id = rs.getLong(RedListUtil.NAMNR);
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String taxNameString = rs.getString(RedListUtil.TAXNAME);
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String gueltString = rs.getString(RedListUtil.GUELT);
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String rangString = rs.getString(RedListUtil.RANG);
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String ep1String = rs.getString(RedListUtil.EPI1);
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String ep2String = rs.getString(RedListUtil.EPI2);
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String ep3String = rs.getString(RedListUtil.EPI3);
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String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
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String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
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String zusatzString = rs.getString(RedListUtil.ZUSATZ);
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String nonString = rs.getString(RedListUtil.NON);
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String sensuString = rs.getString(RedListUtil.SENSU);
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String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
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String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
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String hybString = rs.getString(RedListUtil.HYB);
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String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
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String relationE = rs.getString(RedListUtil.E);
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String relationW = rs.getString(RedListUtil.W);
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String relationK = rs.getString(RedListUtil.K);
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String relationAW = rs.getString(RedListUtil.AW);
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String relationAO = rs.getString(RedListUtil.AO);
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String relationR = rs.getString(RedListUtil.R);
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String relationO = rs.getString(RedListUtil.O);
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String relationS = rs.getString(RedListUtil.S);
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//---NAME---
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BotanicalName name = importName(state, id, taxNameString, rangString, ep1String, ep2String, ep3String,
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nomZusatzString, hybString, namesToSave);
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//--- AUTHORS ---
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importAuthors(state, rs, id, nomZusatzString, taxZusatzString, zusatzString, authorKombString,
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authorBasiString, name);
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//---TAXON---
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TaxonBase taxonBase = importTaxon(id, taxNameString, gueltString, authorBasiString, hybString, name);
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if(taxonBase==null){
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RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
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return;
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}
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//---CONCEPT RELATIONSHIPS---
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/*check if taxon/synonym also exists in other classification
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* 1. create new taxon with the same name (in that classification)
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* 2. create concept relationship between both
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*/
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//checklist
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if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
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cloneTaxon(taxonBase, name, TaxonRelationshipType.CONGRUENT_TO(), taxaToSave, id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE, false, true, state);
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}
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//E, W, K, AW, AO, R, O, S
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addConceptRelation(relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxonBase, name, taxaToSave, id, state);
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//NOTE: the source has to be added after cloning or otherwise the clone would also get the source
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ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
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taxaToSave.add(taxonBase);
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}
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private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase taxonBase, TaxonNameBase name, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
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String substring = relationString.substring(relationString.length()-1, relationString.length());
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TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(substring);
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if(taxonRelationshipTypeByKey==null){
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RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+taxonBase.generateTitle(), logger);
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}
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//there is no type "included in" so we have to reverse the direction
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if(substring.equals("<")){
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cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, true, false, state);
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}
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else{
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cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, false, false, state);
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}
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}
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}
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/**
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* <b>NOTE:</b> the {@link TaxonRelationshipType} passed as parameter is
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* directed <b>from the clone</b> to the taxon.<br>
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* This can be changed with parameter <i>reverseRelation</i>
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*/
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private void cloneTaxon(TaxonBase taxonBase, TaxonNameBase name, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
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TaxonBase clone = (TaxonBase) taxonBase.clone();
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clone.setName(name);
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if(taxonBase.isInstanceOf(Taxon.class)){
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TaxonRelationship taxonRelation;
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if(reverseRelation){
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taxonRelation = ((Taxon) taxonBase).addTaxonRelation((Taxon) clone, relationFromCloneToTaxon, null, null);
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}
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else {
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taxonRelation = ((Taxon) clone).addTaxonRelation((Taxon) taxonBase, relationFromCloneToTaxon, null, null);
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}
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taxonRelation.setDoubtful(doubtful);
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}
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ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, sourceNameSpace);
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taxaToSave.add(clone);
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}
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private TaxonBase importTaxon(long id, String taxNameString, String gueltString, String authorBasiString,
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String hybString, BotanicalName name) {
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TaxonBase taxonBase = null;
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if(authorBasiString.trim().contains(RedListUtil.AUCT)){
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taxonBase = Taxon.NewInstance(name, null);
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taxonBase.setAppendedPhrase(RedListUtil.AUCT);
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}
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else if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON)){
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taxonBase = Taxon.NewInstance(name, null);
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}
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else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
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taxonBase = Synonym.NewInstance(name, null);
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}
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else{
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return null;
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}
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//check taxon name consistency
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checkTaxonNameConsistency(id, taxNameString, hybString, taxonBase);
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return taxonBase;
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}
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private void importAuthors(RedListGefaesspflanzenImportState state, ResultSet rs, long id, String nomZusatzString,
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String taxZusatzString, String zusatzString, String authorKombString, String authorBasiString,
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BotanicalName name) throws SQLException {
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//combination author
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if(authorKombString.contains(RedListUtil.EX)){
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//TODO: what happens with multiple ex authors??
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String[] kombSplit = authorKombString.split(RedListUtil.EX);
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if(kombSplit.length!=2){
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RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);
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}
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for (int i = 0; i < kombSplit.length; i++) {
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if(i==0){
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//first author is ex author
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TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
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name.setExCombinationAuthorship(authorKomb);
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}
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else{
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TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
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name.setCombinationAuthorship(authorKomb);
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}
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}
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}
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else if(authorKombString.trim().contains(RedListUtil.AUCT)){
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RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
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}
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else if(CdmUtils.isNotBlank(authorKombString)){
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TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
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name.setCombinationAuthorship(authorKomb);
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}
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//basionym author
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if(authorBasiString.contains(RedListUtil.EX)){
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String[] basiSplit = authorBasiString.split(RedListUtil.EX);
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for (int i = 0; i < basiSplit.length; i++) {
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if(basiSplit.length!=2){
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RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);
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}
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if(i==0){
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TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
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if(CdmUtils.isBlank(authorKombString)){
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name.setExCombinationAuthorship(authorBasi);
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}
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else{
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name.setExBasionymAuthorship(authorBasi);
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}
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}
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else{
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TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
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if(CdmUtils.isBlank(authorKombString)){
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name.setCombinationAuthorship(authorBasi);
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}
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else{
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name.setBasionymAuthorship(authorBasi);
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}
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}
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}
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}
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else if(CdmUtils.isNotBlank(authorBasiString)){
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//this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used
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TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
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if(CdmUtils.isBlank(authorKombString)){
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name.setCombinationAuthorship(authorBasi);
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}
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else{
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name.setBasionymAuthorship(authorBasi);
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}
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}
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//check authorship consistency
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String authorString = rs.getString(RedListUtil.AUTOR);
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String authorshipCache = name.getAuthorshipCache();
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checkAuthorShipConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, authorshipCache);
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}
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private BotanicalName importName(RedListGefaesspflanzenImportState state, long id, String taxNameString,
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String rangString, String ep1String, String ep2String, String ep3String, String nomZusatzString,
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String hybString, Set<TaxonNameBase> namesToSave) {
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if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
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310
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RedListUtil.logMessage(id, "No name found!", logger);
|
|
311
|
}
|
|
312
|
|
|
313
|
Rank rank = makeRank(id, state, rangString);
|
|
314
|
BotanicalName name = BotanicalName.NewInstance(rank);
|
|
315
|
|
|
316
|
//ep1 should always be present
|
|
317
|
if(CdmUtils.isBlank(ep1String)){
|
|
318
|
RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
|
|
319
|
}
|
|
320
|
name.setGenusOrUninomial(ep1String);
|
|
321
|
if(CdmUtils.isNotBlank(ep2String)){
|
|
322
|
name.setSpecificEpithet(ep2String);
|
|
323
|
}
|
|
324
|
if(CdmUtils.isNotBlank(ep3String)){
|
|
325
|
if(rank==Rank.SUBSPECIES() ||
|
|
326
|
rank==Rank.VARIETY()){
|
|
327
|
name.setInfraSpecificEpithet(ep3String);
|
|
328
|
}
|
|
329
|
}
|
|
330
|
//nomenclatural status
|
|
331
|
if(CdmUtils.isNotBlank(nomZusatzString)){
|
|
332
|
NomenclaturalStatusType status = makeNomenclaturalStatus(id, state, nomZusatzString);
|
|
333
|
if(status!=null){
|
|
334
|
name.addStatus(NomenclaturalStatus.NewInstance(status));
|
|
335
|
}
|
|
336
|
}
|
|
337
|
//hybrid
|
|
338
|
if(hybString.equals(RedListUtil.HYB_X)){
|
|
339
|
name.setBinomHybrid(true);
|
|
340
|
}
|
|
341
|
else if(hybString.equals(RedListUtil.HYB_XF)){
|
|
342
|
name.setTrinomHybrid(true);
|
|
343
|
}
|
|
344
|
//add source
|
|
345
|
ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
|
|
346
|
|
|
347
|
namesToSave.add(name);
|
|
348
|
return name;
|
|
349
|
}
|
|
350
|
|
|
351
|
private void checkAuthorShipConsistency(long id, String nomZusatzString, String taxZusatzString,
|
|
352
|
String zusatzString, String authorString, String authorshipCache) {
|
|
353
|
if(CdmUtils.isNotBlank(zusatzString)){
|
|
354
|
authorString = authorString.replace(", "+zusatzString, "");
|
|
355
|
}
|
|
356
|
if(CdmUtils.isNotBlank(nomZusatzString)){
|
|
357
|
authorString = authorString.replace(", "+nomZusatzString, "");
|
|
358
|
}
|
|
359
|
if(CdmUtils.isNotBlank(taxZusatzString)){
|
|
360
|
authorString = authorString.replace(", "+taxZusatzString, "");
|
|
361
|
}
|
|
362
|
if(authorString.equals(RedListUtil.AUCT)){
|
|
363
|
authorString = "";
|
|
364
|
}
|
|
365
|
if(!authorString.equals(authorshipCache)){
|
|
366
|
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
|
|
367
|
}
|
|
368
|
}
|
|
369
|
|
|
370
|
private void checkTaxonNameConsistency(long id, String taxNameString, String hybString, TaxonBase taxonBase) {
|
|
371
|
String nameCache = ((BotanicalName)taxonBase.getName()).getNameCache().trim();
|
|
372
|
|
|
373
|
if(taxNameString.endsWith("agg.")){
|
|
374
|
taxNameString = taxNameString.replace("agg.", "aggr.");
|
|
375
|
}
|
|
376
|
if(hybString.equalsIgnoreCase(RedListUtil.HYB_X)){
|
|
377
|
taxNameString = taxNameString.replace("× ", "×");//hybrid sign has no space after it in titleCache for binomial hybrids
|
|
378
|
}
|
|
379
|
if(taxNameString.endsWith(Rank.SPECIESGROUP().toString())){
|
|
380
|
taxNameString.replaceAll(Rank.SPECIESGROUP().toString(), "- Gruppe");
|
|
381
|
if(!taxNameString.trim().equals(nameCache)){
|
|
382
|
taxNameString.replaceAll(Rank.SPECIESGROUP().toString(), "- group");
|
|
383
|
}
|
|
384
|
}
|
|
385
|
if(!taxNameString.trim().equals(nameCache)){
|
|
386
|
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
387
|
}
|
|
388
|
}
|
|
389
|
|
|
390
|
private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr) {
|
|
391
|
Rank rank = null;
|
|
392
|
try {
|
|
393
|
rank = state.getTransformer().getRankByKey(rankStr);
|
|
394
|
} catch (UndefinedTransformerMethodException e) {
|
|
395
|
e.printStackTrace();
|
|
396
|
}
|
|
397
|
if(rank==null){
|
|
398
|
RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
|
|
399
|
}
|
|
400
|
return rank;
|
|
401
|
}
|
|
402
|
|
|
403
|
private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
|
|
404
|
NomenclaturalStatusType status = null;
|
|
405
|
try {
|
|
406
|
status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
|
|
407
|
} catch (UndefinedTransformerMethodException e) {
|
|
408
|
e.printStackTrace();
|
|
409
|
}
|
|
410
|
if(status==null){
|
|
411
|
RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
|
|
412
|
}
|
|
413
|
return status;
|
|
414
|
}
|
|
415
|
|
|
416
|
|
|
417
|
|
|
418
|
@Override
|
|
419
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
|
|
420
|
RedListGefaesspflanzenImportState state) {
|
|
421
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
422
|
Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
|
|
423
|
|
|
424
|
try {
|
|
425
|
while (rs.next()){
|
|
426
|
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
|
|
427
|
|
|
428
|
if(authorKombString.contains(RedListUtil.EX)){
|
|
429
|
String[] kombSplit = authorKombString.split(RedListUtil.EX);
|
|
430
|
for (int i = 0; i < kombSplit.length; i++) {
|
|
431
|
if(!authorMap.containsKey(kombSplit[i])){
|
|
432
|
authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
|
|
433
|
}
|
|
434
|
}
|
|
435
|
}
|
|
436
|
else if(CdmUtils.isNotBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
|
|
437
|
authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
|
|
438
|
}
|
|
439
|
|
|
440
|
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
|
|
441
|
//basionym author
|
|
442
|
if(authorBasiString.contains(RedListUtil.EX)){
|
|
443
|
String[] basiSplit = authorBasiString.split(RedListUtil.EX);
|
|
444
|
for (int i = 0; i < basiSplit.length; i++) {
|
|
445
|
if(!authorMap.containsKey(basiSplit[i])){
|
|
446
|
authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
|
|
447
|
}
|
|
448
|
}
|
|
449
|
}
|
|
450
|
else if(CdmUtils.isNotBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
|
|
451
|
authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
|
|
452
|
}
|
|
453
|
}
|
|
454
|
} catch (SQLException e) {
|
|
455
|
e.printStackTrace();
|
|
456
|
}
|
|
457
|
result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
|
|
458
|
|
|
459
|
return result;
|
|
460
|
}
|
|
461
|
|
|
462
|
@Override
|
|
463
|
protected boolean doCheck(RedListGefaesspflanzenImportState state) {
|
|
464
|
return false;
|
|
465
|
}
|
|
466
|
|
|
467
|
@Override
|
|
468
|
protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
|
|
469
|
return false;
|
|
470
|
}
|
|
471
|
|
|
472
|
}
|