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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.berlinModel.out;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonNameImport;
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import eu.etaxonomy.cdm.io.berlinModel.out.mapper.RefDetailMapper;
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import eu.etaxonomy.cdm.io.berlinModel.out.mapper.TeamOrPersonMapper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.mapping.out.CdmDbExportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.out.CollectionExportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.out.CreatedAndNotesMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbBooleanMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbExtensionMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbMarkerMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbStringMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;
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import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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/**
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* @author a.mueller
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* @created 20.03.2008
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*/
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@Component
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public class BerlinModelTaxonNameExport extends BerlinModelExportBase<TaxonName> {
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private static final long serialVersionUID = 4478799976310317219L;
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameExport.class);
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private static int modCount = 2500;
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private static final String dbTableName = "Name";
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private static final String pluralString = "TaxonNames";
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private static final Class<? extends CdmBase> standardMethodParameter = TaxonName.class;
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public BerlinModelTaxonNameExport(){
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super();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean doCheck(BerlinModelExportState state){
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boolean result = true;
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logger.warn("Checking for " + pluralString + " not yet fully implemented");
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List<TaxonName> list = getObjectList();
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checkRank(list);
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//result &= checkRank(config);
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return result;
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}
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private boolean checkRank(List<TaxonName> list){
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List<TaxonName> errorNames = new ArrayList<>();
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for (TaxonName<?,?> name : list){
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if (name.getRank() == null) {
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;
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}
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errorNames.add(name);
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}
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if (errorNames.size() >0){
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System.out.println("The following names have no Rank:\n=======================");
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for (TaxonName<?,?> name : errorNames){
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System.out.println(" " + name.toString());
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System.out.println(" " + name.getUuid());
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System.out.println(" " + name.getTitleCache());
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}
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return false;
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}else{
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return true;
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}
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}
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private CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer> getMapping(){
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String tableName = dbTableName;
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CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer> mapping = new CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer>(tableName);
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mapping.addMapper(IdMapper.NewInstance("NameId"));
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mapping.addMapper(MethodMapper.NewInstance("RankFk", this));
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mapping.addMapper(MethodMapper.NewInstance("SupraGenericName", this));
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mapping.addMapper(MethodMapper.NewInstance("Genus", this));
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mapping.addMapper(MethodMapper.NewInstance("NameCache", this));
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mapping.addMapper(MethodMapper.NewInstance("FullNameCache", this));
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mapping.addMapper(MethodMapper.NewInstance("PreliminaryFlag", this));
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mapping.addMapper(DbStringMapper.NewInstance("infraGenericEpithet", "GenusSubDivisionEpi"));
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mapping.addMapper(DbStringMapper.NewInstance("SpecificEpithet", "SpeciesEpi"));
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mapping.addMapper(DbStringMapper.NewInstance("infraSpecificEpithet", "InfraSpeciesEpi"));
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mapping.addMapper(DbStringMapper.NewInstance("appendedPhrase", "UnnamedNamePhrase"));
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mapping.addMapper(DbBooleanMapper.NewInstance("isHybridFormula", "HybridFormulaFlag", false, false));
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mapping.addMapper(DbBooleanMapper.NewInstance("isMonomHybrid", "MonomHybFlag", false, false));
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mapping.addMapper(DbBooleanMapper.NewInstance("isBinomHybrid", "BinomHybFlag", false, false));
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mapping.addMapper(DbBooleanMapper.NewInstance("isTrinomHybrid", "TrinomHybFlag", false, false));
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mapping.addMapper(DbStringMapper.NewFacultativeInstance("cultivarName", "CultivarName"));
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mapping.addMapper(TeamOrPersonMapper.NewInstance("combinationAuthorship", "AuthorTeamFk"));
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mapping.addMapper(TeamOrPersonMapper.NewInstance("exCombinationAuthorship", "ExAuthorTeamFk"));
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mapping.addMapper(TeamOrPersonMapper.NewInstance("basionymAuthorship", "BasAuthorTeamFk"));
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mapping.addMapper(TeamOrPersonMapper.NewInstance("exBasionymAuthorship", "ExBasAuthorTeamFk"));
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mapping.addMapper(DbObjectMapper.NewInstance("nomenclaturalReference", "NomRefFk"));
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mapping.addMapper(RefDetailMapper.NewInstance("nomenclaturalMicroReference","nomenclaturalReference", "NomRefDetailFk"));
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mapping.addMapper(CreatedAndNotesMapper.NewInstance(false));
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ExtensionType sourceAccExtensionType = (ExtensionType)getTermService().find(BerlinModelTaxonNameImport.SOURCE_ACC_UUID);
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if (sourceAccExtensionType != null){
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mapping.addMapper(DbExtensionMapper.NewInstance(sourceAccExtensionType, "Source_Acc"));
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}
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mapping.addCollectionMapping(getNomStatusMapping());
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//TODO
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//CultivarGroupName
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//NameSourceRefFk
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// ,[Source_ACC]
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//publicationYear
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//originalPublicationYear
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//breed
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// INonViralName n = null;
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//n.getNomenclaturalMicroReference()
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return mapping;
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}
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private CollectionExportMapping getNomStatusMapping(){
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String tableName = "NomStatusRel";
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String collectionAttribute = "status";
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IdMapper parentMapper = IdMapper.NewInstance("NameFk");
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CollectionExportMapping mapping = CollectionExportMapping.NewInstance(tableName, collectionAttribute, parentMapper);
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mapping.addMapper(MethodMapper.NewInstance("NomStatusFk", this.getClass(), "getNomStatusFk", NomenclaturalStatus.class));
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mapping.addMapper(DbObjectMapper.NewInstance("citation", "NomStatusRefFk"));
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mapping.addMapper(RefDetailMapper.NewInstance("citationMicroReference","citation", "NomStatusRefDetailFk"));
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mapping.addMapper(DbMarkerMapper.NewInstance(MarkerType.IS_DOUBTFUL(), "DoubtfulFlag", false));
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mapping.addMapper(CreatedAndNotesMapper.NewInstance());
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return mapping;
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}
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@Override
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protected void doInvoke(BerlinModelExportState state){
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try{
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logger.info("start make "+pluralString+" ...");
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boolean success = true ;
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doDelete(state);
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TransactionStatus txStatus = startTransaction(true);
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logger.info("load "+pluralString+" ...");
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List<TaxonName> names = getObjectList();
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CdmDbExportMapping<BerlinModelExportState, BerlinModelExportConfigurator, IExportTransformer> mapping = getMapping();
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mapping.initialize(state);
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logger.info("save "+pluralString+" ...");
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int count = 0;
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for (TaxonName<?,?> name : names){
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doCount(count++, modCount, pluralString);
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success &= mapping.invoke(name);
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//TODO rank = null or rank < genus and genusOrUninomial != null
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}
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commitTransaction(txStatus);
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logger.info("end make " + pluralString+ " ..." + getSuccessString(success));
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if (!success){
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String message = "An undefined error occurred during Taxonname export";
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state.getResult().addError(message);
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}
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return;
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}catch(SQLException e){
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e.printStackTrace();
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logger.error(e.getMessage());
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state.getResult().addException(e);
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return;
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}
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}
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protected List<TaxonName> getObjectList(){
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List<TaxonName> list = getNameService().list(null,100000000, null,null,null);
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return list;
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}
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protected boolean doDelete(BerlinModelExportState state){
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BerlinModelExportConfigurator bmeConfig = state.getConfig();
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String sql;
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Source destination = bmeConfig.getDestination();
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//RelPTaxon
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sql = "DELETE FROM RelPTaxon";
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destination.setQuery(sql);
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destination.update(sql);
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//Fact
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sql = "DELETE FROM Fact";
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destination.setQuery(sql);
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destination.update(sql);
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//PTaxon
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sql = "DELETE FROM PTaxon";
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destination.setQuery(sql);
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destination.update(sql);
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//NameHistory
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sql = "DELETE FROM NameHistory";
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destination.setQuery(sql);
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destination.update(sql);
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//RelName
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sql = "DELETE FROM RelName";
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destination.setQuery(sql);
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destination.update(sql);
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//NomStatusRel
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sql = "DELETE FROM NomStatusRel";
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destination.setQuery(sql);
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destination.update(sql);
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//Name
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sql = "DELETE FROM Name";
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destination.setQuery(sql);
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destination.update(sql);
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return true;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean isIgnore(BerlinModelExportState state){
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return ! state.getConfig().isDoTaxonNames();
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static Integer getRankFk(INonViralName name){
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Integer result = BerlinModelTransformer.rank2RankId(name.getRank());
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if (result == null){
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logger.warn ("Rank = null is not allowed in Berlin Model. Rank was changed to KINGDOM: " + name);
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result = 1;
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}
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return result;
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static Integer getNomStatusFk(NomenclaturalStatus status){
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return BerlinModelTransformer.nomStatus2nomStatusFk(status.getType());
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static String getSupraGenericName(INonViralName name){
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if (name.isSupraGeneric()){
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return name.getGenusOrUninomial();
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}else{
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return null;
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}
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static String getGenus(INonViralName name){
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if (! name.isSupraGeneric()){
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return name.getGenusOrUninomial();
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}else{
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return null;
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}
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static String getNameCache(INonViralName name){
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if (name.isProtectedNameCache()){
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return name.getNameCache();
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}else{
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return null;
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}
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static String getFullNameCache(INonViralName name){
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if (name.isProtectedTitleCache()){
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return name.getTitleCache();
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}else{
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return null;
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}
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}
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//called by MethodMapper
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@SuppressWarnings("unused")
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private static Boolean getPreliminaryFlag(INonViralName name){
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if (name.isProtectedTitleCache() || name.isProtectedNameCache()){
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if (name.isProtectedTitleCache() && name.isProtectedNameCache()){
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logger.warn("protectedTitleCache and protectedNameCache do not have the same value for name " + name.getTitleCache() + ". This can not be mapped appropriately to the Berlin Model ");
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}
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return true;
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}else{
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return false;
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.out.BerlinModelExportBase#getStandardMethodParameter()
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*/
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@Override
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public Class<? extends CdmBase> getStandardMethodParameter() {
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return standardMethodParameter;
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}
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}
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