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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.erms;
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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 org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportNameTypeDesignationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportSynonymMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportTaxIncludedInMapper;
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import eu.etaxonomy.cdm.io.common.mapping.ICheckIgnoreMapper;
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import eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* @author a.mueller
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* @created 09.03.2010
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* @version 1.0
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*/
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@Component
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public class ErmsTaxonRelationImport extends ErmsImportBase<TaxonBase> implements ICheckIgnoreMapper{
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(ErmsTaxonRelationImport.class);
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private DbImportMapping mapping;
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private int modCount = 10000;
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private static final String pluralString = "taxon relations";
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private static final String dbTableName = "tu";
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private static final Class cdmTargetClass = TaxonBase.class;
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public ErmsTaxonRelationImport(){
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super(pluralString, dbTableName, cdmTargetClass);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
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*/
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protected DbImportMapping getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping();
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mapping.addMapper(DbImportTaxIncludedInMapper.NewInstance("id", TAXON_NAMESPACE, "parentId", TAXON_NAMESPACE, "accParentId", TAXON_NAMESPACE, null));//there is only one tree
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mapping.addMapper(DbImportSynonymMapper.NewInstance("id", "tu_acctaxon", TAXON_NAMESPACE, null));
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mapping.addMapper(DbImportNameTypeDesignationMapper.NewInstance("id", "tu_typetaxon", ErmsTaxonImport.NAME_NAMESPACE, "tu_typedesignationstatus"));
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// mapping.addMapper(DbNotYetImplementedMapper.NewInstance("tu_acctaxon"));
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}
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return mapping;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.erms.ErmsImportConfigurator)
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*/
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protected String getRecordQuery(ErmsImportConfigurator config) {
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//TODO get automatic by second path mappers
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String selectAttributes = " myTaxon.id, myTaxon.tu_parent, myTaxon.tu_typetaxon, myTaxon.tu_typedesignation, " +
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" myTaxon.tu_acctaxon, myTaxon.tu_status, parent.tu_status AS parentStatus, parent.id AS parentId, " +
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" accParent.tu_status AS accParentStatus, accParent.id AS accParentId ";
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String strRecordQuery =
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" SELECT " + selectAttributes +
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" FROM tu AS myTaxon LEFT OUTER JOIN " +
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" tu AS accTaxon ON myTaxon.tu_acctaxon = accTaxon.id LEFT OUTER JOIN " +
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" tu AS accParent RIGHT OUTER JOIN " +
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" tu AS parent ON accParent.id = parent.tu_acctaxon ON myTaxon.tu_parent = parent.id " +
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" WHERE ( myTaxon.id IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery;
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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> taxonIdSet = new HashSet<String>();
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Set<String> nameIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "parentId");
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handleForeignKey(rs, taxonIdSet, "accParentId");
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handleForeignKey(rs, taxonIdSet, "tu_acctaxon");
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handleForeignKey(rs, taxonIdSet, "id");
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handleForeignKey(rs, nameIdSet, "tu_typetaxon");
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handleForeignKey(rs, nameIdSet, "id");
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}
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//name map
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nameSpace = ErmsTaxonImport.NAME_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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//taxon map
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nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
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cdmClass = TaxonBase.class;
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idSet = taxonIdSet;
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, taxonMap);
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ICheckIgnoreMapper#checkIgnoreMapper(eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper, java.sql.ResultSet)
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*/
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public boolean checkIgnoreMapper(IDbImportMapper mapper, ResultSet rs) throws SQLException{
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boolean result = false;
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if (mapper instanceof DbImportTaxIncludedInMapper){
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int tu_status = rs.getInt("tu_status");
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if (tu_status != 1){
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result = true;
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}
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}else if (mapper instanceof DbImportSynonymMapper){
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int tu_status = rs.getInt("tu_status");
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if (tu_status == 1){
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result = true;
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}else{
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return false;
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}
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}else if (mapper instanceof DbImportNameTypeDesignationMapper){
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Object tu_typeTaxon = rs.getObject("tu_typetaxon");
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if (tu_typeTaxon == null){
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return true;
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}
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}
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
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*/
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public TaxonBase createObject(ResultSet rs, ErmsImportState state) throws SQLException {
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// not needed
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return null;
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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(ErmsImportState state){
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// IOValidator<ErmsImportState> validator = new ErmsTaxonImportValidator();
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// return validator.validate(state);
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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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protected boolean isIgnore(ErmsImportState state){
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return ! state.getConfig().isDoRelTaxa();
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}
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}
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