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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.pesi.indexFungorum;
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import java.sql.ResultSet;
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import java.util.HashMap;
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import java.util.Map;
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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.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* @author a.mueller
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* @since 27.02.2012
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*/
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@Component
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public class IndexFungorumSupraGeneraImport extends IndexFungorumImportBase {
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private static final long serialVersionUID = -8504227175493151403L;
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private static final Logger logger = Logger.getLogger(IndexFungorumSupraGeneraImport.class);
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private static final String pluralString = "Supragenera";
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private static final String dbTableName = "tblSupragenericNames";
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private static final String SUPRAGENERIC_NAMES = "Suprageneric names";
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private static final String COL_RECORD_NUMBER = "RECORD NUMBER";
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public IndexFungorumSupraGeneraImport(){
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super(pluralString, dbTableName, null);
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}
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@Override
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protected String getRecordQuery(IndexFungorumImportConfigurator config) {
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String strRecordQuery =
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" SELECT * " +
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" FROM [tblSupragenericNames] " +
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// " WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";
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"";
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return strRecordQuery;
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}
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@Override
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protected void doInvoke(IndexFungorumImportState state) {
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logger.info("Start supra genera ...");
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//handle source reference first
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Reference sourceReference = state.getConfig().getSourceReference();
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getReferenceService().save(sourceReference);
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//query
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String sql = getRecordQuery(state.getConfig());
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ResultSet rs = state.getConfig().getSource().getResultSet(sql);
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//transaction and related objects
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TransactionStatus tx = startTransaction();
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state.setRelatedObjects(getRelatedObjectsForPartition(null, state));
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sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
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try {
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while (rs.next()){
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//Don't use (created by Marc): DisplayName, NomRefCache
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Integer id = ((Number)rs.getObject(COL_RECORD_NUMBER)).intValue();
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String supragenericNames = rs.getString(SUPRAGENERIC_NAMES);
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//String preferredName = rs.getString("PreferredName");
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Integer rankFk = rs.getInt("PESI_RankFk");
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//name
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Rank rank = state.getTransformer().getRankByKey(String.valueOf(rankFk));
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TaxonName name = TaxonNameFactory.NewBotanicalInstance(rank);
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name.setGenusOrUninomial(supragenericNames);
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/*if (preferredName != null && !preferredName.equals(supragenericNames)){
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logger.warn("Suprageneric names and preferredName is not equal. This case is not yet handled by IF import. I take SupragenericNames for import. RECORD NUMBER" +id);
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}*/
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//taxon
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Taxon taxon = Taxon.NewInstance(name, sourceReference);
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//author + nom.ref.
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makeAuthorAndPublication(state, rs, name);
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//source
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// if (id != null){
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makeSource(state, taxon, id.intValue(), NAMESPACE_SUPRAGENERIC_NAMES );
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// } else{
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// makeSource(state, taxon, null, NAMESPACE_SUPRAGENERIC_NAMES);
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// }
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getTaxonService().saveOrUpdate(taxon);
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}
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} catch (Exception e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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tx.setRollbackOnly();
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state.setSuccess(false);
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}
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commitTransaction(tx);
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logger.info("End supra genera ...");
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return;
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}
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private Taxon makeTaxon(IndexFungorumImportState state, String uninomial, Rank rank) {
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TaxonName name = TaxonNameFactory.NewBotanicalInstance(rank);
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name.setGenusOrUninomial(uninomial);
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return Taxon.NewInstance(name, state.getConfig().getSourceReference());
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
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HashMap<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); //not needed here
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//sourceReference
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Reference sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);
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Map<String, Reference> referenceMap = new HashMap<>();
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referenceMap.put(SOURCE_REFERENCE, sourceReference);
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result.put(NAMESPACE_REFERENCE, referenceMap);
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return result;
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}
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@Override
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protected boolean doCheck(IndexFungorumImportState state){
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return true;
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}
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@Override
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protected boolean isIgnore(IndexFungorumImportState state){
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return ! state.getConfig().isDoTaxa();
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}
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}
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