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// $Id$
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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.faunaEuropaea;
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import java.util.Collection;
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import java.util.HashSet;
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import java.util.List;
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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 org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.ICdmImport;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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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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/**
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* This class creates heterotypic synonymy relationships to the accepted taxon for
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* basionym synonyms.
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*
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* @author a.babadshanjan
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* @created 22.09.2009
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* @version 1.0
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*/
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@Component
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public class FaunaEuropaeaHeterotypicSynonymImport extends CdmImportBase<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState>
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implements ICdmImport<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState> {
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private static final Logger logger = Logger
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.getLogger(FaunaEuropaeaHeterotypicSynonymImport.class);
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
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*/
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@Override
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protected boolean doCheck(FaunaEuropaeaImportState state) {
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logger.warn("Checking for heterotypic synonyms for basionyms not yet implemented");
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return false;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)
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*/
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@Override
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protected void doInvoke(FaunaEuropaeaImportState state) {
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TransactionStatus txStatus = null;
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List<Synonym> synonymList = null;
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Set<Taxon> taxonSet = null;
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int i = 0;
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int start = 0;
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int limit = state.getConfig().getLimitSave();
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int nbrOfSynonyms = getTaxonService().count(Synonym.class);
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if (logger.isInfoEnabled()) {
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logger.info("Number of synonyms = " + nbrOfSynonyms);
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}
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if(state.getConfig().isDoHeterotypicSynonyms()){
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while (i < nbrOfSynonyms) {
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try {
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if ((i++ % limit) == 0) {
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start = (i == 1) ? 0 : i;
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if (logger.isInfoEnabled()) {
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logger.info("Retrieving synonyms starting from: " + start);
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}
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txStatus = startTransaction();
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synonymList = getTaxonService().list(Synonym.class, limit, start, null, null);
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taxonSet = new HashSet<Taxon>(limit);
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}
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if (((i % limit) == 0 && i != 1 ) || i == nbrOfSynonyms) {
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HomotypicalGroup homotypicalGroup = null;
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Set<TaxonNameBase> basionyms = null;
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Set<NameRelationship> nameRelations = null;
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TaxonNameBase basionym = null;
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Set<TaxonBase> taxonBases = null;
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TaxonBase taxonBase = null;
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Taxon acceptedTaxon = null;
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TaxonNameBase synonymName = null;
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NameRelationship nameRelation = null;
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TaxonNameBase acceptedName = null;
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for (TaxonBase synonym : synonymList) {
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synonymName = synonym.getName();
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if (synonymName.isGroupsBasionym()) {
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nameRelations = synonymName.getNameRelations();
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if (nameRelations != null && nameRelations.iterator().hasNext()) {
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nameRelation = nameRelations.iterator().next();
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acceptedName = nameRelation.getToName();
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logger.debug("SynonymName: " + synonymName + " titleCache of synonym: "+synonym.getTitleCache() + " name of acceptedTaxon: " + acceptedName.getTitleCache());
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if (logger.isTraceEnabled()) {
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logger.trace("toName: " + acceptedName);
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logger.trace("fromName: " + nameRelation.getFromName());
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}
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taxonBases = acceptedName.getTaxa();
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if (taxonBases != null && taxonBases.iterator().hasNext()) {
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taxonBase = taxonBases.iterator().next();
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acceptedTaxon = taxonBase.deproxy(taxonBase, Taxon.class);
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Set <Synonym> synonyms = acceptedTaxon.getSynonyms();
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if (!synonyms.contains(synonym)){
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//TODO: Achtung!!!!! dies wird auch bei homotypischen Synonymen aufgerufen! Dadurch wird ein weiteres Synonym erzeugt
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acceptedTaxon.addHeterotypicSynonymName(synonymName);
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taxonSet.add(acceptedTaxon);
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}
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}
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}
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}
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}
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getTaxonService().save((Collection)taxonSet);
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taxonSet = null;
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synonymList = null;
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commitTransaction(txStatus);
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Transaction committed");
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}
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}
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} catch (Exception e) {
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logger.warn("An exception occurred when creating heterotypic synonym relationship # " + i );
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e.printStackTrace();
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}
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}
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}
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return;
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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.IoStateBase)
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*/
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@Override
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protected boolean isIgnore(FaunaEuropaeaImportState state) {
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return !(state.getConfig().isDoHeterotypicSynonymsForBasionyms());
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}
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}
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