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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.in;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceSourceImportValidator;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author a.mueller
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* @created 20.03.2008
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* @version 1.0
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*/
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@Component
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public class BerlinModelOccurrenceSourceImport extends BerlinModelImportBase {
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private static final Logger logger = Logger.getLogger(BerlinModelOccurrenceSourceImport.class);
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private static int modCount = 5000;
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private static final String pluralString = "occurrence sources";
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private static final String dbTableName = "emOccurrenceSource"; //??
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private Map<String, Integer> sourceNumberRefIdMap;
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public BerlinModelOccurrenceSourceImport(){
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super();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
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*/
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@Override
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protected String getIdQuery() {
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return " SELECT occurrenceSourceId FROM " + getTableName();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery = //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution
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" SELECT * " +
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" FROM emOccurrenceSource " +
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" WHERE (OccurrenceSourceId IN (" + ID_LIST_TOKEN + ") )" +
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"";
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return strQuery;
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}
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@Override
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protected void doInvoke(BerlinModelImportState state) {
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try {
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sourceNumberRefIdMap = makeSourceNameReferenceIdMap(state);
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} catch (SQLException e) {
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e.printStackTrace();
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throw new RuntimeException(e);
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}
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super.doInvoke(state);
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sourceNumberRefIdMap = null;
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return;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
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*/
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
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boolean success = true;
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ResultSet rs = partitioner.getResultSet();
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Set<DescriptionElementBase> objectsToSave = new HashSet<DescriptionElementBase>();
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try {
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int i = 0;
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//for each reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("occurrence sources handled: " + (i-1));}
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Integer occurrenceFk = (Integer)rs.getObject("OccurrenceFk");
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String sourceNumber = rs.getString("SourceNumber");
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String oldName = rs.getString("OldName");
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Integer oldNameFk = (Integer)rs.getObject("OldNameFk");
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Distribution distribution = (Distribution)state.getRelatedObject(BerlinModelOccurrenceImport.NAMESPACE, String.valueOf(occurrenceFk));
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if (distribution == null){
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//distribution = duplicateMap.get(occurrenceFk);
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}
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if (distribution != null){
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Integer refId = sourceNumberRefIdMap.get(sourceNumber);
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Reference ref = getReference(refId, state);
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if (ref != null){
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DescriptionElementSource originalSource = DescriptionElementSource.NewInstance();
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originalSource.setCitation(ref);
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TaxonNameBase<?, ?> taxonName;
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taxonName = getName(state, oldName, oldNameFk);
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if (taxonName != null){
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originalSource.setNameUsedInSource(taxonName);
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}else if(CdmUtils.isNotEmpty(oldName)){
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originalSource.setOriginalNameString(oldName);
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}
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distribution.addSource(originalSource);
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}else{
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logger.warn("reference for sourceNumber "+sourceNumber+" could not be found." );
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}
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}else{
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logger.warn("distribution ("+occurrenceFk+") could not be found." );
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}
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}
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logger.info("Distributions to save: " + objectsToSave.size());
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getDescriptionService().saveDescriptionElement(objectsToSave);
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return success;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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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.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
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*/
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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String nameSpace;
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Class cdmClass;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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Set<String> occurrenceIdSet = new HashSet<String>();
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Set<String> referenceIdSet = new HashSet<String>();
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Set<String> nameIdSet = new HashSet<String>();
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Set<String> sourceNumberSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, occurrenceIdSet, "occurrenceFk");
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handleForeignKey(rs, nameIdSet, "oldNameFk");
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sourceNumberSet.add(CdmUtils.NzTrim(rs.getString("SourceNumber")));
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}
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sourceNumberSet.remove("");
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referenceIdSet = handleSourceNumber(rs, sourceNumberSet, result);
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//occurrence map
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nameSpace = BerlinModelOccurrenceImport.NAMESPACE;
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cdmClass = Distribution.class;
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idSet = occurrenceIdSet;
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Map<String, Distribution> occurrenceMap = (Map<String, Distribution>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, occurrenceMap);
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//name map
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nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
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cdmClass = TaxonNameBase.class;
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idSet =nameIdSet;
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Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, nameMap);
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//nom reference map
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nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
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cdmClass = Reference.class;
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idSet = referenceIdSet;
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Map<String, Reference> nomReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, nomReferenceMap);
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//biblio reference map
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nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
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cdmClass = Reference.class;
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idSet = referenceIdSet;
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Map<String, Reference> biblioReferenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, biblioReferenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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return result;
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}
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private Set<String> handleSourceNumber(ResultSet rs, Set<String> sourceNumberSet, Map<Object, Map<String, ? extends CdmBase>> result) {
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Map<String, Integer> sourceNumberReferenceIdMap = this.sourceNumberRefIdMap;
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Set<String> referenceIdSet = new HashSet<String>();
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for(String sourceNumber : sourceNumberSet){
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Integer refId = sourceNumberReferenceIdMap.get(sourceNumber);
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referenceIdSet.add(String.valueOf(refId));
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}
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return referenceIdSet;
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}
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/**
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* @param state
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* @param oldName
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* @param oldNameFk
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* @return
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*/
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boolean isFirstTimeNoNameByService = true;
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private TaxonNameBase<?, ?> getName(BerlinModelImportState state, String oldName, Integer oldNameFk) {
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TaxonNameBase<?,?> taxonName = (TaxonNameBase)state.getRelatedObject(BerlinModelTaxonNameImport.NAMESPACE, String.valueOf(oldNameFk));
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if (taxonName == null && oldName != null){
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if (isFirstTimeNoNameByService){
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logger.warn("oldName not checked against names in BerlinModel. Just take it as a string");
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isFirstTimeNoNameByService = false;
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}
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List<NonViralName> names = new ArrayList<NonViralName>();
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// names = getNameService().getNamesByNameCache(oldName);
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if (names.size() == 1){
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return names.get(0);
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}else {
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if (names.size()> 2){
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logger.info("There is more than one name matching oldName: " + oldName + ".");
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}
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return null;
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//taxonName = nameParser.parseSimpleName(oldName);
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}
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}
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return taxonName;
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}
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/**
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* Creates a map which maps source numbers on references
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* @param state
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* @return
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* @throws SQLException
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*/
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private Map<String, Integer> makeSourceNameReferenceIdMap(BerlinModelImportState state) throws SQLException {
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Map<String, Integer> result = new HashMap<String, Integer>();
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Source source = state.getConfig().getSource();
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String strQuery = " SELECT RefId, IdInSource " +
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" FROM Reference " +
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" WHERE (IdInSource IS NOT NULL) AND (IdInSource NOT LIKE '') ";
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ResultSet rs = source.getResultSet(strQuery) ;
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while (rs.next()){
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int refId = rs.getInt("RefId");
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String idInSource = rs.getString("IdInSource");
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if (idInSource != null){
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String[] singleSources = idInSource.split("\\|");
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for (String singleSource : singleSources){
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singleSource = singleSource.trim();
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result.put(singleSource, refId);
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}
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}
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}
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return result;
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}
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private Reference getReference(Integer refId, BerlinModelImportState state) {
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Reference<?> ref = (Reference)state.getRelatedObject(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE, String.valueOf(refId));
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if (ref == null){
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ref = (Reference)state.getRelatedObject(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE, String.valueOf(refId));;
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}
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return ref;
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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.IoStateBase)
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*/
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@Override
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protected boolean doCheck(BerlinModelImportState state){
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IOValidator<BerlinModelImportState> validator = new BerlinModelOccurrenceSourceImportValidator();
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return validator.validate(state);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
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*/
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@Override
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protected String getTableName() {
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return dbTableName;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
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*/
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@Override
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public String getPluralString() {
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return pluralString;
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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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protected boolean isIgnore(BerlinModelImportState state){
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return ! state.getConfig().isDoOccurrence();
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}
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}
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