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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.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.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.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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 ErmsSourceUsesImport extends ErmsImportBase<CommonTaxonName> {
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private static final long serialVersionUID = -5139234838768878653L;
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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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@Override
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protected String getIdQuery() {
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String strQuery = " SELECT tu_id, source_id, sourceuse_id " +
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" FROM tu_sources " +
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" ORDER BY tu_id, source_id, sourceuse_id ";
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return strQuery;
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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.tu_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.sourceuse_id IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery;
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, ErmsImportState state) {
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boolean success = true ;
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Set<CdmBase> objectsToSave = new HashSet<>();
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int i = 0;
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ResultSet rs = partitioner.getResultSet();
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try{
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while (rs.next()){
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i++;
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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 strSourceUse = rs.getString("sourceuse_name");
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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(ErmsImportBase.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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String srcUseStr = normalizeSourceUse(strSourceUse);
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objectToSave = makeSourceUse(state, srcUseStr, ref, strTaxonId, strPageNr, strSourceId);
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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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logger.debug("real partition size: " + i);
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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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private String normalizeSourceUse(String sourceUse) {
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return sourceUse;
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}
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private IdentifiableEntity<?> makeSourceUse(ErmsImportState state, String srcUseString,
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Reference ref, String strTaxonId, String strPageNr, String strSourceId) {
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TaxonBase<?> taxonBase = (TaxonBase<?>)state.getRelatedObject(ErmsImportBase.TAXON_NAMESPACE, strTaxonId);
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if (taxonBase == null){
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logger.warn("TaxonBase " + strTaxonId + " could not be found for source ID " + strSourceId + " and source use " + srcUseString);
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}else{
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taxonBase.addSource(OriginalSourceType.Other, ref, strPageNr, srcUseString);
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}
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return taxonBase;
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}
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// private TaxonName makeOriginalDescription(ResultSetPartitioner<?> partitioner,
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// ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {
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// TaxonName taxonName = (TaxonName)state.getRelatedObject(ErmsImportBase.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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// private IdentifiableEntity<?> makeAdditionalSource(ResultSetPartitioner<?> partitioner,
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// ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {
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//
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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(ErmsImportBase.TAXON_NAMESPACE, strTaxonId);
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// Taxon taxon;
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//
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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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// taxon = synonym.getAcceptedTaxon();
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// if (taxon == null){
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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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// }
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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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//
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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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// private IdentifiableEntity<?> makeSourceOfSynonymy(@SuppressWarnings("unused") ResultSetPartitioner<?> partitioner,
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// ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {
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//
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// TaxonBase<?> taxonBase = (TaxonBase<?>)state.getRelatedObject(ErmsImportBase.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(Taxon.class)){
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// Taxon taxon =CdmBase.deproxy(taxonBase, Taxon.class);
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// Feature sourceOfSynonymyFeature = getFeature(state, ErmsTransformer.uuidSourceOfSynonymy, "Source of synonymy", "Source of synonymy", null, null);
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// TextData element = TextData.NewInstance(sourceOfSynonymyFeature);
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// getTaxonDescription(taxon, false, true).addElement(element);
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// element.addPrimaryTaxonomicSource(ref, strPageNr);
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// }else if (taxonBase.isInstanceOf(Synonym.class)){
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// Synonym synonym =CdmBase.deproxy(taxonBase, Synonym.class);
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// if (synonym.getSec()!= null){
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// logger.warn("Synonym has sec reference already. Source of synonym can not be set: " + strTaxonId);
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// }else{
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// synonym.setSec(ref);
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// }
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// if (synonym.getSecMicroReference()!= null){
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// logger.warn("Synonym has sec micro reference already. Source of synonym detail can not be set: " + strTaxonId);
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// }else{
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// synonym.setSecMicroReference(strPageNr);
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// }
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// }else{
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// throw new RuntimeException("Unsupported taxonbase class");
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// }
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//
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// return taxonBase;
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// }
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// private boolean isFirstRediscription = true;
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// @SuppressWarnings("unused")
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// private IdentifiableEntity<?> makeRedescription(ResultSetPartitioner<?> partitioner, ErmsImportState state,
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// 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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// private IdentifiableEntity<?> makeCombinationReference(ResultSetPartitioner<?> partitioner,
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// 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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// TaxonName taxonName = (TaxonName)state.getRelatedObject(ErmsImportBase.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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// private boolean isFirstStatusSource = true;
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// @SuppressWarnings("unused")
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// private IdentifiableEntity<?> makeStatusSource(ResultSetPartitioner<?> partitioner,
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// 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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// private boolean isFirstEmendation = true;
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// @SuppressWarnings("unused")
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// private IdentifiableEntity<?> makeEmendation(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {
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// if (isFirstEmendation){
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// logger.warn("Emmendation not yet implemented");
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// isFirstEmendation = false;
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// }
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// return null;
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// }
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@SuppressWarnings("unused")
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public CommonTaxonName 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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//************************************ RELATED OBJECTS *************************************************/
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
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ErmsImportState state) {
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String nameSpace;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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try{
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Set<String> taxonIdSet = new HashSet<>();
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Set<String> nameIdSet = new HashSet<>();
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Set<String> referenceIdSet = new HashSet<>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "tu_id");
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handleForeignKey(rs, nameIdSet, "tu_id");
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handleForeignKey(rs, referenceIdSet, "source_id");
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}
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//name map
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nameSpace = ErmsImportBase.NAME_NAMESPACE;
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idSet = nameIdSet;
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Map<String, TaxonName> nameMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
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result.put(nameSpace, nameMap);
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//taxon map
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nameSpace = ErmsImportBase.TAXON_NAMESPACE;
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idSet = taxonIdSet;
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@SuppressWarnings("rawtypes")
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Map<String, TaxonBase> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace);
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result.put(nameSpace, taxonMap);
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//reference map
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nameSpace = ErmsImportBase.REFERENCE_NAMESPACE;
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idSet = referenceIdSet;
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Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, 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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@Override
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protected DbImportMapping<?, ?> getMapping() {
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logger.info("getMapping not implemented for EmrsSourceUsesImport");
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return null; // not needed because Mapping is not implemented in this class yet
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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 ErmsSourceUsesImportValidator();
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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().isDoSourceUse();
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}
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}
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