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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 static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_ADDITIONAL_SOURCE;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_BASIS_OF_RECORD;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_EMENDATION;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_NEW_COMBINATION_REFERENCE;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_ORIGINAL_DESCRIPTION;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_REDESCRIPTION;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_SOURCE_OF_SYNONYMY;
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import static eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer.SOURCE_USE_STATUS_SOURCE;
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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.commons.lang.StringUtils;
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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.IImportConfigurator;
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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.mapping.DbImportMapping;
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import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsSourceUsesImportValidator;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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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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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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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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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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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 ErmsSourceUsesImport extends ErmsImportBase<CommonTaxonName> {
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private static final Logger logger = Logger.getLogger(ErmsSourceUsesImport.class);
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private DbImportMapping<ErmsImportState,ErmsImportConfigurator> mapping; //not needed
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private static final String pluralString = "source uses";
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private static final String dbTableName = "tu_sources";
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private static final Class<?> cdmTargetClass = null;
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public ErmsSourceUsesImport(){
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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#getIdQuery()
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*/
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@Override
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protected String getIdQuery() {
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String strQuery = " SELECT sourceuse_id, source_id, tu_id " + " " +
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" FROM tu_sources " +
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" ORDER BY sourceuse_id, source_id, tu_id ";
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return strQuery;
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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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@Override
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protected String getRecordQuery(ErmsImportConfigurator config) {
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String strRecordQuery =
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" SELECT * " +
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" FROM tu_sources INNER JOIN sourceuses ON tu_sources.sourceuse_id = sourceuses.sourceuse_id" +
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" WHERE ( tu_sources.sourceuse_id IN (" + ID_LIST_TOKEN + ") AND " +
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" tu_sources.source_id IN (" + ID_LIST_TOKEN + ") AND " +
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" tu_sources.tu_id IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery;
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}
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public boolean doPartition(ResultSetPartitioner partitioner, ErmsImportState state) {
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boolean success = true ;
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Set objectsToSave = new HashSet<IdentifiableEntity>();
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// DbImportMapping<?, ?> mapping = getMapping();
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// mapping.initialize(state, cdmTargetClass);
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ResultSet rs = partitioner.getResultSet();
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try{
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while (rs.next()){
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//success &= mapping.invoke(rs,referencesToSave);
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//read and normalize values
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int sourceUseId = rs.getInt("sourceuse_id");
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int sourceId = rs.getInt("source_id");
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String strSourceId = String.valueOf(sourceId);
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int taxonId = rs.getInt("tu_id");
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String strTaxonId = String.valueOf(taxonId);
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String strPageNr = rs.getString("pagenr");
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if (StringUtils.isBlank(strPageNr)){
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strPageNr = null;
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}
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Reference<?> ref = (Reference<?>)state.getRelatedObject(ErmsReferenceImport.REFERENCE_NAMESPACE, strSourceId);
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try {
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IdentifiableEntity<?> objectToSave = null;
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//invoke methods for each sourceUse type
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if (sourceUseId == SOURCE_USE_ORIGINAL_DESCRIPTION){
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objectToSave = makeOriginalDescription(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_BASIS_OF_RECORD){
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objectToSave = makeBasisOfRecord(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_ADDITIONAL_SOURCE){
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objectToSave = makeAdditionalSource(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_SOURCE_OF_SYNONYMY){
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objectToSave = makeSourceOfSynonymy(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_REDESCRIPTION){
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objectToSave = makeRedescription(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_NEW_COMBINATION_REFERENCE){
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objectToSave = makeCombinationReference(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_STATUS_SOURCE){
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objectToSave = makeStatusSource(partitioner, state, ref, strTaxonId, strPageNr);
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}else if (sourceUseId == SOURCE_USE_EMENDATION){
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objectToSave = makeEmendation(partitioner, state, ref, strTaxonId, strPageNr);
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}
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if(objectToSave != null){
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objectsToSave.add(objectToSave);
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}
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} catch (Exception e) {
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e.printStackTrace();
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success = false;
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}
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}
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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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partitioner.startDoSave();
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getCommonService().save(objectsToSave);
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return success;
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}
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/**
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* @param strTaxonId
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* @param ref
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* @param state
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* @param partitioner
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* @param strPageNr
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*
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*/
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private TaxonNameBase<?,?> makeOriginalDescription(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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TaxonNameBase<?,?> taxonName = (TaxonNameBase<?,?>)state.getRelatedObject(ErmsTaxonImport.NAME_NAMESPACE, strTaxonId);
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taxonName.setNomenclaturalReference(ref);
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taxonName.setNomenclaturalMicroReference(strPageNr);
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return taxonName;
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}
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/**
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* @param partitioner
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* @param state
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* @param ref
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* @param strTaxonId
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* @param strPageNr
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*/
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private boolean isFirstBasisOfRecord = true;
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private IdentifiableEntity<?> makeBasisOfRecord(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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if (isFirstBasisOfRecord){
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logger.warn("Basis of record not yet implemented");
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isFirstBasisOfRecord = false;
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}
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return null;
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}
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/**
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* @param partitioner
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* @param state
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* @param ref
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* @param strTaxonId
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* @param strPageNr
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*/
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private IdentifiableEntity<?> makeAdditionalSource(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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Feature citationFeature = Feature.CITATION();
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DescriptionElementBase element = TextData.NewInstance(citationFeature);
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DescriptionElementSource source = element.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, strPageNr);
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if (source == null){
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logger.warn("Source is null");
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return null;
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}
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TaxonBase<?> taxonBase = (TaxonBase<?>)state.getRelatedObject(ErmsTaxonImport.TAXON_NAMESPACE, strTaxonId);
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Taxon taxon;
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//if taxon base is a synonym, add the description to the accepted taxon
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if (taxonBase.isInstanceOf(Synonym.class)){
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Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
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Set<Taxon> taxa = synonym.getAcceptedTaxa();
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if (taxa.size() < 1){
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String warning = "Synonym "+ strTaxonId + " has no accepted taxon";
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logger.warn(warning);
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return null;
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//throw new IllegalStateException(warning);
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}else if (taxa.size() > 1){
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String warning = "Synonym "+ strTaxonId + " has more than 1 accepted taxon";
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logger.warn(warning);
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return null;
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//throw new IllegalStateException(warning);
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}
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taxon = taxa.iterator().next();
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//add synonym name as name used in source
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source.setNameUsedInSource(synonym.getName());
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}else{
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taxon = (Taxon)taxonBase;
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}
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//get or create description and add the element
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TaxonDescription description;
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if (taxon.getDescriptions().size() > 0){
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description = taxon.getDescriptions().iterator().next();
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}else{
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description = TaxonDescription.NewInstance(taxon);
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}
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description.addElement(element);
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return taxon;
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}
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/**
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* @param partitioner
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* @param state
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* @param ref
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* @param strTaxonId
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* @param strPageNr
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*/
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private IdentifiableEntity<?> makeSourceOfSynonymy(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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TaxonBase<?> taxonBase = (TaxonBase<?>)state.getRelatedObject(ErmsTaxonImport.TAXON_NAMESPACE, strTaxonId);
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if (taxonBase == null){
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String warning = "taxonBase (id = " + strTaxonId + ") could not be found ";
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logger.warn(warning);
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return null;
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}else if (! taxonBase.isInstanceOf(Synonym.class)){
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String message = "TaxonBase is not of class Synonym but " + taxonBase.getClass().getSimpleName();
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logger.info(message);
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Taxon taxon =CdmBase.deproxy(taxonBase, Taxon.class);
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Set<TaxonRelationship> synRels = taxon.getTaxonRelations();
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if (synRels.size() != 1){
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logger.warn("TaxonSynonym (" + strTaxonId + ") has not 1 but " + synRels.size() + " relations!");
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}else{
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TaxonRelationship synRel = synRels.iterator().next();
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synRel.setCitation(ref);
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synRel.setCitationMicroReference(strPageNr);
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}
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}else{
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Synonym synonym =CdmBase.deproxy(taxonBase, Synonym.class);
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Set<SynonymRelationship> synRels = synonym.getSynonymRelations();
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if (synRels.size() != 1){
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logger.warn("Synonym (" + strTaxonId + ") has not 1 but " + synRels.size() + " relations!");
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}else{
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SynonymRelationship synRel = synRels.iterator().next();
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synRel.setCitation(ref);
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synRel.setCitationMicroReference(strPageNr);
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}
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}
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return taxonBase;
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}
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/**
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* @param partitioner
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* @param state
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* @param ref
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* @param strTaxonId
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* @param strPageNr
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*/
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private boolean isFirstRediscription = true;
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private IdentifiableEntity<?> makeRedescription(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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if (isFirstRediscription){
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logger.warn("Rediscription not yet implemented");
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isFirstRediscription = false;
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}
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return null;
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}
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/**
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* @param partitioner
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* @param state
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* @param ref
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* @param strTaxonId
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* @param strPageNr
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*/
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private IdentifiableEntity<?> makeCombinationReference(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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// Kopie von Orig. Comb.
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//TODO ist das wirklich der richtige Name, oder muss ein verknüpfter Name verwendet werden
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TaxonNameBase<?,?> taxonName = (TaxonNameBase<?,?>)state.getRelatedObject(ErmsTaxonImport.NAME_NAMESPACE, strTaxonId);
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taxonName.setNomenclaturalReference(ref);
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taxonName.setNomenclaturalMicroReference(strPageNr);
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return taxonName;
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}
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/**
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* @param partitioner
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* @param state
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* @param ref
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* @param strTaxonId
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* @param strPageNr
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*/
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private boolean isFirstStatusSource = true;
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private IdentifiableEntity<?> makeStatusSource(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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if (isFirstStatusSource){
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logger.warn("StatusSource not yet implemented");
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isFirstStatusSource = false;
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}
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return null;
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}
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335
|
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336
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/**
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337
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* @param partitioner
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338
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* @param state
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339
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* @param ref
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340
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* @param strTaxonId
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341
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* @param strPageNr
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342
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*/
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343
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private boolean isFirstEmendation = true;
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344
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private IdentifiableEntity<?> makeEmendation(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference<?> ref, String strTaxonId, String strPageNr) {
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345
|
if (isFirstEmendation){
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346
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logger.warn("Emmendation not yet implemented");
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347
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isFirstEmendation = false;
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|
348
|
}
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349
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return null;
|
|
350
|
}
|
|
351
|
|
|
352
|
|
|
353
|
|
|
354
|
/* (non-Javadoc)
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|
355
|
* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)
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356
|
*/
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|
357
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public CommonTaxonName createObject(ResultSet rs, ErmsImportState state)
|
|
358
|
throws SQLException {
|
|
359
|
return null; //not needed
|
|
360
|
}
|
|
361
|
|
|
362
|
|
|
363
|
//************************************ RELATED OBJECTS *************************************************/
|
|
364
|
|
|
365
|
/* (non-Javadoc)
|
|
366
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
|
|
367
|
*/
|
|
368
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
|
369
|
String nameSpace;
|
|
370
|
Class<?> cdmClass;
|
|
371
|
Set<String> idSet;
|
|
372
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
373
|
|
|
374
|
try{
|
|
375
|
Set<String> taxonIdSet = new HashSet<String>();
|
|
376
|
Set<String> nameIdSet = new HashSet<String>();
|
|
377
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
378
|
while (rs.next()){
|
|
379
|
handleForeignKey(rs, taxonIdSet, "tu_id");
|
|
380
|
handleForeignKey(rs, nameIdSet, "tu_id");
|
|
381
|
handleForeignKey(rs, referenceIdSet, "source_id");
|
|
382
|
}
|
|
383
|
|
|
384
|
//name map
|
|
385
|
nameSpace = ErmsTaxonImport.NAME_NAMESPACE;
|
|
386
|
cdmClass = TaxonNameBase.class;
|
|
387
|
idSet = nameIdSet;
|
|
388
|
Map<String, TaxonNameBase<?,?>> nameMap = (Map<String, TaxonNameBase<?,?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
389
|
result.put(nameSpace, nameMap);
|
|
390
|
|
|
391
|
//taxon map
|
|
392
|
nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;
|
|
393
|
cdmClass = TaxonBase.class;
|
|
394
|
idSet = taxonIdSet;
|
|
395
|
Map<String, TaxonBase<?>> taxonMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
396
|
result.put(nameSpace, taxonMap);
|
|
397
|
|
|
398
|
//reference map
|
|
399
|
nameSpace = ErmsReferenceImport.REFERENCE_NAMESPACE;
|
|
400
|
cdmClass = Reference.class;
|
|
401
|
idSet = referenceIdSet;
|
|
402
|
Map<String, Reference<?>> referenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(Reference.class, idSet, nameSpace);
|
|
403
|
result.put(nameSpace, referenceMap);
|
|
404
|
|
|
405
|
|
|
406
|
} catch (SQLException e) {
|
|
407
|
throw new RuntimeException(e);
|
|
408
|
}
|
|
409
|
return result;
|
|
410
|
|
|
411
|
}
|
|
412
|
|
|
413
|
/* (non-Javadoc)
|
|
414
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
415
|
*/
|
|
416
|
@Override
|
|
417
|
protected boolean doCheck(ErmsImportState state){
|
|
418
|
IOValidator<ErmsImportState> validator = new ErmsSourceUsesImportValidator();
|
|
419
|
return validator.validate(state);
|
|
420
|
}
|
|
421
|
|
|
422
|
/* (non-Javadoc)
|
|
423
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
424
|
*/
|
|
425
|
protected boolean isIgnore(ErmsImportState state){
|
|
426
|
boolean result = state.getConfig().getDoReferences() != IImportConfigurator.DO_REFERENCES.ALL;
|
|
427
|
result |= ! state.getConfig().isDoTaxa();
|
|
428
|
return result;
|
|
429
|
}
|
|
430
|
|
|
431
|
|
|
432
|
/* (non-Javadoc)
|
|
433
|
* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()
|
|
434
|
*/
|
|
435
|
@Override
|
|
436
|
protected DbImportMapping<?, ?> getMapping() {
|
|
437
|
logger.info("getMapping not implemented for EmrsSourceUsesImport");
|
|
438
|
return null; // not needed because Mapping is not implemented in this class yet
|
|
439
|
}
|
|
440
|
|
|
441
|
}
|