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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 java.util.UUID;
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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.DbImportAnnotationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportCommonNameCreationMapper;
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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.DbImportStringMapper;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsVernacularImportValidator;
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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.common.Language;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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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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* @since 20.02.2010
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*/
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@Component
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public class ErmsVernacularImport extends ErmsImportBase<CommonTaxonName> {
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private static final long serialVersionUID = -5928250782824234181L;
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private static final Logger logger = Logger.getLogger(ErmsVernacularImport.class);
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private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping;
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// private ErmsImportState state; //import instance is never used more than once for Erms ; dirty
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private static final String pluralString = "vernaculars";
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private static final String dbTableName = "vernaculars";
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private static final Class<?> cdmTargetClass = CommonTaxonName.class;
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public ErmsVernacularImport(){
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super(pluralString, dbTableName, cdmTargetClass);
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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 v.*, tu.tu_acctaxon, tu.id, l.* " +
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" FROM vernaculars v INNER JOIN tu ON v.tu_id = tu.id "
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+ " LEFT OUTER JOIN languages l ON l.LanID = v.lan_id " +
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" WHERE ( v.id IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery;
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}
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@Override
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protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping<ErmsImportState, ErmsImportConfigurator>();
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mapping.addMapper(DbImportCommonNameCreationMapper.NewInstance("id", VERNACULAR_NAMESPACE, "tu_id", ErmsImportBase.TAXON_NAMESPACE));
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mapping.addMapper(DbImportObjectMapper.NewInstance("lan_id", "language", LANGUAGE_NAMESPACE));
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mapping.addMapper(DbImportStringMapper.NewInstance("vername", "name"));
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mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL(), Language.DEFAULT()));
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}
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return mapping;
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}
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@Override
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protected void doInvoke(ErmsImportState state) {
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super.doInvoke(state);
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, ErmsImportState state) {
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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<>();
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Map<String, Language> languageMap = new HashMap<>();
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try{
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Set<String> taxonIdSet = new HashSet<>();
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// Set<String> languageIdSet = new HashSet<>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "tu_id");
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addLanguage(rs, languageMap, state);
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}
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//taxon map
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nameSpace = ErmsImportBase.TAXON_NAMESPACE;
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cdmClass = TaxonBase.class;
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idSet = taxonIdSet;
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@SuppressWarnings("unchecked")
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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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//language map
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nameSpace = LANGUAGE_NAMESPACE;
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result.put(nameSpace, languageMap);
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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 rs
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* @param languageMap
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* @param state
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* @throws SQLException
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*/
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private void addLanguage(ResultSet rs, Map<String, Language> languageMap, ErmsImportState state) throws SQLException {
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IInputTransformer transformer = state.getTransformer();
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String id639_1 = rs.getString("639_1");
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String id639_2 = rs.getString("639_2");
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String id639_3 = rs.getString("639_3");
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String lanId = rs.getString("LanID");
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if (id639_1 != null && Language.getLanguageByIsoCode(id639_1)!= null){
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languageMap.put(lanId, Language.getLanguageByIsoCode(id639_1));
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}else if (id639_2 != null && Language.getLanguageByIsoCode(id639_2)!= null){
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languageMap.put(lanId, Language.getLanguageByIsoCode(id639_2));
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}else{
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Language language = null;
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try {
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language = transformer.getLanguageByKey(lanId);
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if (language == null || language.equals(Language.UNDETERMINED())){
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UUID uuidLang = transformer.getLanguageUuid(lanId);
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if (uuidLang != null){
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language = getLanguage(state, uuidLang, rs.getString("LanName"), "LanName", "639_3");
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}
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if (language == null || language.equals(Language.UNDETERMINED() )){
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logger.warn("Langauge undefined: " + lanId);
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}
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}
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} catch (IllegalArgumentException e) {
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e.printStackTrace();
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace();
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}
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}
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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 ErmsVernacularImportValidator();
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return validator.validate(state);
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}
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@Override
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protected boolean isIgnore(ErmsImportState state){
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return ! state.getConfig().isDoVernaculars();
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}
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}
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