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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 java.util.regex.Matcher;
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import java.util.regex.Pattern;
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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.hibernate.HibernateProxyHelper;
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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.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.RankClass;
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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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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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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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private static final boolean STRICT_TITLE_CHECK = false;
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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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long id = rs.getLong(RedListUtil.NAMNR);
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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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NonViralName<?> name = importName(state, rs, namesToSave);
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//--- AUTHORS ---
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importAuthors(state, rs, name);
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//---TAXON---
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TaxonBase<?> taxonBase = importTaxon(rs, name, state);
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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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//E, W, K, AW, AO, R, O, S
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cloneTaxon(taxonBase, relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxaToSave, id, state);
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cloneTaxon(taxonBase, relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxaToSave, id, state);
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//checklist
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TaxonBase<?> checklistTaxon = null;
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if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
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checklistTaxon = (TaxonBase<?>) taxonBase.clone();
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if(checklistTaxon.isInstanceOf(Taxon.class)){
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TaxonRelationship relation = HibernateProxyHelper.deproxy(checklistTaxon, Taxon.class).addTaxonRelation(HibernateProxyHelper.deproxy(taxonBase, Taxon.class), TaxonRelationshipType.CONGRUENT_TO(), null, null);
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relation.setDoubtful(true);
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}
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ImportHelper.setOriginalSource(checklistTaxon, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
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taxaToSave.add(checklistTaxon);
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}
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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 cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String relationString, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
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Taxon clonedTaxon = null;
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if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
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clonedTaxon = HibernateProxyHelper.deproxy(gesamtListeTaxon.clone(), Taxon.class);
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}
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else if(gesamtListeTaxon.isInstanceOf(Synonym.class)){
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clonedTaxon = Taxon.NewInstance(gesamtListeTaxon.getName(), gesamtListeTaxon.getSec());
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}
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else{
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RedListUtil.logMessage(id, "Taxon base "+gesamtListeTaxon+" is neither taxon nor synonym! Taxon could not be cloned", logger);
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return;
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}
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ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace);
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taxaToSave.add(clonedTaxon);
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}
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}
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private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name, RedListGefaesspflanzenImportState state) throws SQLException {
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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 epi1String = rs.getString(RedListUtil.EPI1);
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String gueltString = rs.getString(RedListUtil.GUELT);
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String trivialString = rs.getString(RedListUtil.TRIVIAL);
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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 florString = rs.getString(RedListUtil.FLOR);
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String atlasIdxString = rs.getString(RedListUtil.ATLAS_IDX);
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String kartString = rs.getString(RedListUtil.KART);
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String rl2015String = rs.getString(RedListUtil.RL2015);
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String ehrdString = rs.getString(RedListUtil.EHRD);
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String wisskString = rs.getString(RedListUtil.WISSK);
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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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//common name
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if(taxonBase.isInstanceOf(Taxon.class) && trivialString!=null){
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Taxon taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
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TaxonDescription description = TaxonDescription.NewInstance(taxon);
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description.addElement(CommonTaxonName.NewInstance(trivialString, Language.GERMAN()));
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}
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//add annotations
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addAnnotation(RedListUtil.FLOR+": "+florString, taxonBase);
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addAnnotation(RedListUtil.ATLAS_IDX+": "+atlasIdxString, taxonBase);
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addAnnotation(RedListUtil.KART+": "+kartString, taxonBase);
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addAnnotation(RedListUtil.RL2015+": "+rl2015String, taxonBase);
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addAnnotation(RedListUtil.EHRD+": "+ehrdString, taxonBase);
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addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase);
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//check taxon name consistency
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checkTaxonConsistency(id, taxNameString, hybString, epi1String, taxonBase, state);
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return taxonBase;
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}
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private void addAnnotation(String string, AnnotatableEntity entity) {
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if(CdmUtils.isNotBlank(string)){
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entity.addAnnotation(Annotation.NewInstance(string, AnnotationType.TECHNICAL(), Language.GERMAN()));
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}
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}
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private void importAuthors(RedListGefaesspflanzenImportState state, ResultSet rs, NonViralName<?> name) throws SQLException {
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long id = rs.getLong(RedListUtil.NAMNR);
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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 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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//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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}
|
|
312
|
}
|
|
313
|
}
|
|
314
|
}
|
|
315
|
else if(CdmUtils.isNotBlank(authorBasiString)){
|
|
316
|
//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
|
|
317
|
TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
|
|
318
|
if(CdmUtils.isBlank(authorKombString)){
|
|
319
|
name.setCombinationAuthorship(authorBasi);
|
|
320
|
}
|
|
321
|
else{
|
|
322
|
name.setBasionymAuthorship(authorBasi);
|
|
323
|
}
|
|
324
|
}
|
|
325
|
|
|
326
|
//check authorship consistency
|
|
327
|
String authorString = rs.getString(RedListUtil.AUTOR);
|
|
328
|
checkNameConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, hybString, name);
|
|
329
|
}
|
|
330
|
|
|
331
|
private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
|
|
332
|
|
|
333
|
long id = rs.getLong(RedListUtil.NAMNR);
|
|
334
|
String taxNameString = rs.getString(RedListUtil.TAXNAME);
|
|
335
|
String rangString = rs.getString(RedListUtil.RANG);
|
|
336
|
String ep1String = rs.getString(RedListUtil.EPI1);
|
|
337
|
String ep2String = rs.getString(RedListUtil.EPI2);
|
|
338
|
String ep3String = rs.getString(RedListUtil.EPI3);
|
|
339
|
String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
|
|
340
|
String hybString = rs.getString(RedListUtil.HYB);
|
|
341
|
String formelString = rs.getString(RedListUtil.FORMEL);
|
|
342
|
|
|
343
|
if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
|
|
344
|
RedListUtil.logMessage(id, "No name found!", logger);
|
|
345
|
}
|
|
346
|
|
|
347
|
NonViralName<?> name = null;
|
|
348
|
Rank rank = makeRank(id, state, rangString, ep3String!=null);
|
|
349
|
//cultivar
|
|
350
|
if(rank!= null && rank.equals(Rank.CULTIVAR())){
|
|
351
|
CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank);
|
|
352
|
cultivar.setGenusOrUninomial(ep1String);
|
|
353
|
cultivar.setSpecificEpithet(ep2String);
|
|
354
|
cultivar.setCultivarName(ep3String);
|
|
355
|
name = cultivar;
|
|
356
|
}
|
|
357
|
//botanical names
|
|
358
|
else{
|
|
359
|
name = BotanicalName.NewInstance(rank);
|
|
360
|
|
|
361
|
//ep1 should always be present
|
|
362
|
if(CdmUtils.isBlank(ep1String)){
|
|
363
|
RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
|
|
364
|
}
|
|
365
|
name.setGenusOrUninomial(ep1String);
|
|
366
|
if(CdmUtils.isNotBlank(ep2String)){
|
|
367
|
if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
|
|
368
|
name.setInfraGenericEpithet(ep2String);
|
|
369
|
}
|
|
370
|
else{
|
|
371
|
name.setSpecificEpithet(ep2String);
|
|
372
|
}
|
|
373
|
}
|
|
374
|
if(CdmUtils.isNotBlank(ep3String)){
|
|
375
|
name.setInfraSpecificEpithet(ep3String);
|
|
376
|
}
|
|
377
|
|
|
378
|
|
|
379
|
//nomenclatural status
|
|
380
|
if(CdmUtils.isNotBlank(nomZusatzString)){
|
|
381
|
NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
|
|
382
|
if(statusType!=null){
|
|
383
|
NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType);
|
|
384
|
//special case for invalid names where the DB entry contains
|
|
385
|
//additional information in brackets e.g. "nom. inval. (sine basion.)"
|
|
386
|
if(statusType.equals(NomenclaturalStatusType.INVALID()) || statusType.equals(NomenclaturalStatusType.REJECTED()) ){
|
|
387
|
Pattern pattern = Pattern.compile("\\((.*?)\\)");
|
|
388
|
Matcher matcher = pattern.matcher(nomZusatzString);
|
|
389
|
if (matcher.find()){
|
|
390
|
status.setRuleConsidered(matcher.group(1));
|
|
391
|
}
|
|
392
|
}
|
|
393
|
name.addStatus(status);
|
|
394
|
}
|
|
395
|
}
|
|
396
|
//hybrid
|
|
397
|
if(CdmUtils.isNotBlank(hybString)){
|
|
398
|
//save hybrid formula
|
|
399
|
if(CdmUtils.isNotBlank(formelString)){
|
|
400
|
Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
|
|
401
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
|
402
|
name.addAnnotation(annotation);
|
|
403
|
}
|
|
404
|
//more than two hybrids not yet handled by name parser
|
|
405
|
//TODO: use parser when implemented to fully support hybrids
|
|
406
|
if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
|
|
407
|
name = BotanicalName.NewInstance(rank);
|
|
408
|
name.setTitleCache(taxNameString, true);
|
|
409
|
}
|
|
410
|
else if(hybString.equals(RedListUtil.HYB_X)){
|
|
411
|
name.setBinomHybrid(true);
|
|
412
|
}
|
|
413
|
else if(hybString.equals(RedListUtil.HYB_G)){
|
|
414
|
name.setMonomHybrid(true);
|
|
415
|
}
|
|
416
|
else if(hybString.equals(RedListUtil.HYB_XF) || hybString.equals(RedListUtil.HYB_XU)){
|
|
417
|
name.setHybridFormula(true);
|
|
418
|
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
|
419
|
name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String, NomenclaturalCode.ICNAFP, rank);
|
|
420
|
}
|
|
421
|
else if(ep2String.contains(RedListUtil.HYB_SIGN)){
|
|
422
|
String[] split = ep2String.split(RedListUtil.HYB_SIGN);
|
|
423
|
String hybridFormula1 = ep1String+" "+split[0].trim();
|
|
424
|
String hybridFormula2 = ep1String+" "+split[1].trim();
|
|
425
|
//check if the genus is mentioned in EP2 or not
|
|
426
|
String[] secondHybrid = split[1].trim().split(" ");
|
|
427
|
//check if the genus is abbreviated like e.g. Centaurea jacea × C. decipiens
|
|
428
|
if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
|
|
429
|
hybridFormula2 = ep1String+" "+split[1].trim().substring(2);
|
|
430
|
}
|
|
431
|
else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
|
|
432
|
hybridFormula2 = split[1];
|
|
433
|
}
|
|
434
|
if(CdmUtils.isNotBlank(ep3String)){
|
|
435
|
hybridFormula1 += " "+ep3String;
|
|
436
|
hybridFormula2 += " "+ep3String;
|
|
437
|
}
|
|
438
|
String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
|
|
439
|
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
|
|
440
|
}
|
|
441
|
else if(ep3String.contains(RedListUtil.HYB_SIGN)){
|
|
442
|
String[] split = ep3String.split(RedListUtil.HYB_SIGN);
|
|
443
|
String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
|
|
444
|
String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
|
|
445
|
//check if the genus is mentioned in EP3 or not
|
|
446
|
String[] secondHybrid = split[1].trim().split(" ");
|
|
447
|
//check if the genus is abbreviated like e.g. Centaurea jacea jacea × C. jacea subsp. decipiens
|
|
448
|
if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
|
|
449
|
hybridFormula2 = ep1String+" "+split[1].trim().substring(2);
|
|
450
|
}
|
|
451
|
else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
|
|
452
|
hybridFormula2 = split[1];
|
|
453
|
}
|
|
454
|
String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
|
|
455
|
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
|
|
456
|
}
|
|
457
|
}
|
|
458
|
else if(hybString.equals(RedListUtil.HYB_N)){
|
|
459
|
name = NonViralNameParserImpl.NewInstance().parseFullName(taxNameString, NomenclaturalCode.ICNAFP, rank);
|
|
460
|
}
|
|
461
|
else if(hybString.equals(RedListUtil.HYB_GF)){
|
|
462
|
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
|
463
|
name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String, NomenclaturalCode.ICNAFP, rank);
|
|
464
|
}
|
|
465
|
else{
|
|
466
|
RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
|
|
467
|
}
|
|
468
|
}
|
|
469
|
else if(hybString.equals(RedListUtil.HYB_XS)){
|
|
470
|
//nothing to do
|
|
471
|
}
|
|
472
|
else{
|
|
473
|
logger.error("HYB value "+hybString+" not yet handled");
|
|
474
|
}
|
|
475
|
}
|
|
476
|
}
|
|
477
|
|
|
478
|
//add source
|
|
479
|
ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
|
|
480
|
|
|
481
|
namesToSave.add(name);
|
|
482
|
return name;
|
|
483
|
}
|
|
484
|
|
|
485
|
private void checkNameConsistency(long id, String nomZusatzString, String taxZusatzString,
|
|
486
|
String zusatzString, String authorString, String hybString, NonViralName<?> name) {
|
|
487
|
String authorshipCache = name.getAuthorshipCache();
|
|
488
|
//FIXME: remove split length check when name parser can parse multiple hybrid parents
|
|
489
|
if(hybString.equals(RedListUtil.HYB_XF) && name.getTitleCache().split(RedListUtil.HYB_SIGN).length==2){
|
|
490
|
if(name.getHybridChildRelations().isEmpty()){
|
|
491
|
RedListUtil.logMessage(id, "Hybrid formula but no hybrid child relations: "+name.getTitleCache(), logger);
|
|
492
|
return;
|
|
493
|
}
|
|
494
|
return;
|
|
495
|
}
|
|
496
|
|
|
497
|
if(CdmUtils.isNotBlank(zusatzString)){
|
|
498
|
authorString = authorString.replace(", "+zusatzString, "");
|
|
499
|
}
|
|
500
|
if(CdmUtils.isNotBlank(nomZusatzString)){
|
|
501
|
authorString = authorString.replace(", "+nomZusatzString, "");
|
|
502
|
}
|
|
503
|
if(CdmUtils.isNotBlank(taxZusatzString)){
|
|
504
|
authorString = authorString.replace(", "+taxZusatzString, "");
|
|
505
|
}
|
|
506
|
if(authorString.equals(RedListUtil.AUCT)){
|
|
507
|
authorString = "";
|
|
508
|
}
|
|
509
|
if(STRICT_TITLE_CHECK){
|
|
510
|
if(!authorString.equals(authorshipCache)){
|
|
511
|
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
|
|
512
|
}
|
|
513
|
}
|
|
514
|
else{
|
|
515
|
if(CdmUtils.isNotBlank(authorString) && !authorString.startsWith(authorshipCache)){
|
|
516
|
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
|
|
517
|
}
|
|
518
|
}
|
|
519
|
}
|
|
520
|
|
|
521
|
private void checkTaxonConsistency(long id, String taxNameString, String hybString, String epi1String, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {
|
|
522
|
if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
|
|
523
|
RedListUtil.logInfoMessage(id, "multiple hybrid signs. No name check for "+taxNameString, logger);
|
|
524
|
return;
|
|
525
|
}
|
|
526
|
|
|
527
|
String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim();
|
|
528
|
taxNameString = taxNameString.trim();
|
|
529
|
taxNameString = taxNameString.replaceAll(" +", " ");
|
|
530
|
|
|
531
|
|
|
532
|
if(hybString.equals(RedListUtil.HYB_X) || hybString.equals(RedListUtil.HYB_N)){
|
|
533
|
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);//hybrid sign has no space after it in titleCache for binomial hybrids
|
|
534
|
taxNameString = taxNameString.replace(" x ", " "+RedListUtil.HYB_SIGN);//in some cases a standard 'x' is used
|
|
535
|
}
|
|
536
|
else if(hybString.equals(RedListUtil.HYB_G)){
|
|
537
|
taxNameString = taxNameString.replace("X ", RedListUtil.HYB_SIGN);
|
|
538
|
}
|
|
539
|
else if(hybString.equals(RedListUtil.HYB_GF)){
|
|
540
|
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);
|
|
541
|
}
|
|
542
|
else if(hybString.equals(RedListUtil.HYB_XF)){
|
|
543
|
nameCache = taxonBase.getName().getTitleCache();
|
|
544
|
if(nameCache.contains("sec")){
|
|
545
|
nameCache = nameCache.substring(0, nameCache.indexOf("sec"));
|
|
546
|
}
|
|
547
|
if(taxNameString.matches((".*[A-Z]\\..*"))){
|
|
548
|
taxNameString = taxNameString.replaceAll("[A-Z]\\.", epi1String);
|
|
549
|
}
|
|
550
|
if(taxNameString.matches((".*"+RedListUtil.HYB_SIGN+"\\s[a-z].*"))){
|
|
551
|
taxNameString = taxNameString.replaceAll(RedListUtil.HYB_SIGN+" ", RedListUtil.HYB_SIGN+" "+epi1String+" ");
|
|
552
|
}
|
|
553
|
}
|
|
554
|
|
|
555
|
if(taxNameString.endsWith("- Gruppe")){
|
|
556
|
taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
|
|
557
|
}
|
|
558
|
if(taxNameString.endsWith("- group")){
|
|
559
|
taxNameString = taxNameString.replaceAll("- group", "species group");
|
|
560
|
}
|
|
561
|
|
|
562
|
taxNameString = taxNameString.replace("agg.", "aggr.");
|
|
563
|
taxNameString = taxNameString.replace("[ranglos]", "[unranked]");
|
|
564
|
|
|
565
|
if(taxonBase.getName().getRank()!=null){
|
|
566
|
if(taxonBase.getName().getRank().equals(Rank.PROLES())){
|
|
567
|
taxNameString = taxNameString.replace("proles", "prol.");
|
|
568
|
}
|
|
569
|
else if(taxonBase.getName().getRank().equals(state.getRank(RedListUtil.uuidRankCollectionSpecies))){
|
|
570
|
taxNameString = taxNameString.replace("\"Sammelart\"", "\"Coll. Species\"");
|
|
571
|
}
|
|
572
|
}
|
|
573
|
if(STRICT_TITLE_CHECK){
|
|
574
|
if(!taxNameString.trim().equals(nameCache)){
|
|
575
|
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
576
|
}
|
|
577
|
}
|
|
578
|
else{
|
|
579
|
if(!taxNameString.startsWith(nameCache)){
|
|
580
|
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
581
|
}
|
|
582
|
}
|
|
583
|
}
|
|
584
|
|
|
585
|
private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr, boolean hasSpecificEpithet) {
|
|
586
|
Rank rank = null;
|
|
587
|
try {
|
|
588
|
if(rankStr.equals("ORA")){
|
|
589
|
//special handling for ORA because of two possibilities
|
|
590
|
if(hasSpecificEpithet){
|
|
591
|
return Rank.UNRANKED_INFRASPECIFIC();
|
|
592
|
}
|
|
593
|
else{
|
|
594
|
return Rank.UNRANKED_INFRAGENERIC();
|
|
595
|
}
|
|
596
|
}
|
|
597
|
else if(rankStr.equals("SAM")){
|
|
598
|
return getRank(state, RedListUtil.uuidRankCollectionSpecies, "Collective Species", "Collective Species", "\"Coll. Species\"", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.SpeciesGroup);
|
|
599
|
}
|
|
600
|
else if(rankStr.equals("SPR")){
|
|
601
|
return getRank(state, RedListUtil.uuidRankSubproles, "Subproles", "Subproles", "subproles", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
|
|
602
|
}
|
|
603
|
else if(rankStr.equals("MOD")){
|
|
604
|
return getRank(state, RedListUtil.uuidRankModification, "Modification", "Modification", "modificatio", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
|
|
605
|
}
|
|
606
|
else if(rankStr.equals("LUS")){
|
|
607
|
return getRank(state, RedListUtil.uuidRankLusus, "Lusus", "Lusus", "lusus", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
|
|
608
|
}
|
|
609
|
else if(rankStr.equals("SPI")){
|
|
610
|
return getRank(state, RedListUtil.uuidRankSubspeciesPrincipes, "Subspecies principes", "Subspecies principes", "subsp. princ.", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
|
|
611
|
}
|
|
612
|
else if(rankStr.equals("KMB")){
|
|
613
|
return getRank(state, RedListUtil.uuidRankCombination, "Combination", "Combination", "", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
|
|
614
|
}
|
|
615
|
else{
|
|
616
|
rank = state.getTransformer().getRankByKey(rankStr);
|
|
617
|
}
|
|
618
|
} catch (UndefinedTransformerMethodException e) {
|
|
619
|
e.printStackTrace();
|
|
620
|
}
|
|
621
|
if(rank==null){
|
|
622
|
RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
|
|
623
|
}
|
|
624
|
return rank;
|
|
625
|
}
|
|
626
|
|
|
627
|
private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
|
|
628
|
NomenclaturalStatusType status = null;
|
|
629
|
try {
|
|
630
|
status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
|
|
631
|
} catch (UndefinedTransformerMethodException e) {
|
|
632
|
e.printStackTrace();
|
|
633
|
}
|
|
634
|
if(status==null){
|
|
635
|
RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
|
|
636
|
}
|
|
637
|
return status;
|
|
638
|
}
|
|
639
|
|
|
640
|
|
|
641
|
|
|
642
|
@Override
|
|
643
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
|
|
644
|
RedListGefaesspflanzenImportState state) {
|
|
645
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
646
|
Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
|
|
647
|
|
|
648
|
try {
|
|
649
|
while (rs.next()){
|
|
650
|
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
|
|
651
|
|
|
652
|
if(authorKombString.contains(RedListUtil.EX)){
|
|
653
|
String[] kombSplit = authorKombString.split(RedListUtil.EX);
|
|
654
|
for (int i = 0; i < kombSplit.length; i++) {
|
|
655
|
if(!authorMap.containsKey(kombSplit[i])){
|
|
656
|
authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
|
|
657
|
}
|
|
658
|
}
|
|
659
|
}
|
|
660
|
else if(CdmUtils.isNotBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
|
|
661
|
authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
|
|
662
|
}
|
|
663
|
|
|
664
|
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
|
|
665
|
//basionym author
|
|
666
|
if(authorBasiString.contains(RedListUtil.EX)){
|
|
667
|
String[] basiSplit = authorBasiString.split(RedListUtil.EX);
|
|
668
|
for (int i = 0; i < basiSplit.length; i++) {
|
|
669
|
if(!authorMap.containsKey(basiSplit[i])){
|
|
670
|
authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
|
|
671
|
}
|
|
672
|
}
|
|
673
|
}
|
|
674
|
else if(CdmUtils.isNotBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
|
|
675
|
authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
|
|
676
|
}
|
|
677
|
}
|
|
678
|
} catch (SQLException e) {
|
|
679
|
e.printStackTrace();
|
|
680
|
}
|
|
681
|
result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
|
|
682
|
|
|
683
|
return result;
|
|
684
|
}
|
|
685
|
|
|
686
|
@Override
|
|
687
|
protected boolean doCheck(RedListGefaesspflanzenImportState state) {
|
|
688
|
return false;
|
|
689
|
}
|
|
690
|
|
|
691
|
@Override
|
|
692
|
protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
|
|
693
|
return false;
|
|
694
|
}
|
|
695
|
|
|
696
|
}
|