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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.redlist.gefaesspflanzen;
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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.DbImportBase;
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import eu.etaxonomy.cdm.io.common.IPartitionedIO;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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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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/**
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*
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* @author pplitzner
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* @date Mar 1, 2016
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*
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*/
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@Component
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@SuppressWarnings("serial")
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public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
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private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportClassification.class);
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private static final String tableName = "Rote Liste Gefäßpflanzen";
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private static final String pluralString = "classifications";
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public RedListGefaesspflanzenImportClassification() {
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super(tableName, pluralString);
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}
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@Override
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protected String getIdQuery(RedListGefaesspflanzenImportState state) {
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return "SELECT NAMNR "
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+ "FROM V_TAXATLAS_D20_EXPORT t "
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+ " ORDER BY NAMNR";
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}
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@Override
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protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
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String result = " SELECT * "
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+ " FROM V_TAXATLAS_D20_EXPORT t "
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+ " WHERE t.NAMNR IN (@IDSET)";
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result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
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return result;
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}
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@Override
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protected void doInvoke(RedListGefaesspflanzenImportState state) {
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makeClassification(state);
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super.doInvoke(state);
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
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ResultSet rs = partitioner.getResultSet();
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Classification classification = getClassificationService().load(state.getConfig().getClassificationUuid());
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try {
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while (rs.next()){
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makeSingleTaxonNode(state, rs, classification);
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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logger.info("Update classification (1000 nodes)");
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getClassificationService().saveOrUpdate(classification);
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return true;
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}
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private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification classification)
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throws SQLException {
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String id = String.valueOf(rs.getLong(RedListUtil.NAMNR));
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String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
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String gueltString = rs.getString(RedListUtil.GUELT);
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TaxonBase taxonBase = state.getRelatedObject(RedListUtil.TAXON_NAMESPACE, id, TaxonBase.class);
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Taxon parent = (Taxon) state.getRelatedObject(RedListUtil.TAXON_NAMESPACE, parentId, TaxonBase.class);
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//taxon
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if(taxonBase.isInstanceOf(Taxon.class)){
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//misapplied name
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String appendedPhrase = taxonBase.getName().getAppendedPhrase();
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if(appendedPhrase!=null && appendedPhrase.contains(RedListUtil.AUCT)){
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parent.addMisappliedName((Taxon) taxonBase, null, null);
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}
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else{
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classification.addParentChild(parent, (Taxon)taxonBase, null, null);
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}
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}
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else if(taxonBase.isInstanceOf(Synonym.class)){
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//basionym
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if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
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parent.addHomotypicSynonym((Synonym) taxonBase, null, null);
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parent.getName().addBasionym(taxonBase.getName());
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}
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//regular synonym
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else{
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//TODO: how to correctly add a synonym?
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parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
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// parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.SYNONYM_OF(), null, null);
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}
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}
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
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RedListGefaesspflanzenImportState state) {
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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Set<String> idSet = new HashSet<String>();
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try {
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while (rs.next()){
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idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));
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idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));
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}
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} catch (SQLException e) {
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e.printStackTrace();
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}
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_NAMESPACE);
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result.put(RedListUtil.TAXON_NAMESPACE, taxonMap);
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return result;
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}
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private void makeClassification(RedListGefaesspflanzenImportState state) {
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Classification classification = Classification.NewInstance(state.getConfig().getClassificationName());
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classification.setUuid(state.getConfig().getClassificationUuid());
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getClassificationService().save(classification);
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}
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@Override
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protected boolean doCheck(RedListGefaesspflanzenImportState state) {
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return false;
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}
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@Override
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protected boolean isIgnore(RedListGefaesspflanzenImportState state) {
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return false;
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}
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}
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