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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.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.IOValidator;
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import eu.etaxonomy.cdm.io.common.mapping.DbIgnoreMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportAnnotationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportDescriptionElementSourceCreationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportDistributionCreationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbNotYetImplementedMapper;
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import eu.etaxonomy.cdm.io.erms.validation.ErmsReferenceImportValidator;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceTerm;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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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 20.02.2010
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* @version 1.0
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*/
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@Component
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public class ErmsDrImport extends ErmsImportBase<Distribution> {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(ErmsDrImport.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 = "distributions";
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private static final String dbTableName = "dr";
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private static final Class cdmTargetClass = Distribution.class;
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public ErmsDrImport(){
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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.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(ErmsImportConfigurator config) {
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String strRecordQuery =
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" SELECT dr.*, tu.tu_acctaxon, tu.id " +
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" FROM dr INNER JOIN tu ON dr.tu_id = tu.id " +
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" WHERE ( dr.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.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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PresenceTerm status = PresenceTerm.PRESENT();
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DbImportDistributionCreationMapper<?> distributionMapper = DbImportDistributionCreationMapper.NewFixedStatusInstance("id", DR_NAMESPACE, "tu_acctaxon", ErmsTaxonImport.TAXON_NAMESPACE, status);
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distributionMapper.setSource("source_id", REFERENCE_NAMESPACE, null);
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mapping.addMapper(distributionMapper);
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mapping.addMapper(DbImportObjectMapper.NewInstance("gu_id", "area", ErmsAreaImport.AREA_NAMESPACE));
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mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL()));
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mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptsource_id"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptreason"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("valid_flag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("certain_flag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("map_flag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("endemic_flag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("exotic_flag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("typelocality_flag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("specimenflag"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("lat"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("long"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("depthshallow"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("depthdeep"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("beginyear"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("beginmonth"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("beginday"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("endyear"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("endmonth"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("endday"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("min_abundance"));
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mapping.addMapper(DbIgnoreMapper.NewInstance("max_abundance"));
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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.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> areaIdSet = new HashSet<String>();
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Set<String> sourceIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet,"tu_acctaxon" );
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handleForeignKey(rs, areaIdSet, "gu_id");
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handleForeignKey(rs, sourceIdSet, "source_id");
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}
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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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//areas
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nameSpace = ErmsAreaImport.AREA_NAMESPACE;
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cdmClass = NamedArea.class;
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idSet = areaIdSet;
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Map<String, NamedArea> areaMap = (Map<String, NamedArea>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, areaMap);
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//reference map
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nameSpace = ErmsReferenceImport.REFERENCE_NAMESPACE;
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cdmClass = ReferenceBase.class;
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idSet = sourceIdSet;
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Map<String, ReferenceBase> referenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, referenceMap);
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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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/**
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* @param distribution
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* @param source_id
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* @param state
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*/
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private void addSource(Distribution distribution, Integer source_id, ErmsImportState state) {
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ReferenceBase ref = (ReferenceBase)state.getRelatedObject(ErmsReferenceImport.REFERENCE_NAMESPACE, String.valueOf(source_id));
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distribution.addSource(null, null, ref, null);
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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 Distribution createObject(ResultSet rs, ErmsImportState state)
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throws SQLException {
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return null; //not needed
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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 ErmsReferenceImportValidator();
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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.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().isDoOccurrence();
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}
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}
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