EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.redlist;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.io.common.IOValidator;

import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;

import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;

import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;

import eu.etaxonomy.cdm.io.redlist.validation.RoteListeDbTaxonImportValidator;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.name.BotanicalName;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.cdm.model.name.TaxonNameFactory;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;

/**

 * TODO do we still need this class?

 * @author a.mueller

 * @created 27.08.2012

 */

@Component

public class RoteListeDbTaxonImport  extends RoteListeDbImportBase<TaxonBase> implements IMappingImport<TaxonBase, RoteListeDbImportState>{

	@SuppressWarnings("unused")

	private static final Logger logger = Logger.getLogger(RoteListeDbTaxonImport.class);

	private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

	private Map<UUID, Taxon> higherTaxonMap;

	private Integer TREE_ID = null;

	private DbImportMapping mapping;

	private int modCount = 10000;

	private static final String pluralString = "taxa";

	private static final String dbTableName = "checklist";

	private static final Class cdmTargetClass = TaxonBase.class;

	private static final String strOrderBy = " ORDER BY family, genus, species ";

	public RoteListeDbTaxonImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	@Override

	protected String getIdQuery() {

		String strQuery = " SELECT pk FROM " + dbTableName +

						strOrderBy;

		return strQuery;

	}

	@Override

	protected DbImportMapping getMapping() {

		if (mapping == null){

			mapping = new DbImportMapping();

// 			mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "pk", TAXON_NAMESPACE)); //id + tu_status

//

//			UUID uuidKew = RoteListeDbTransformer.uuidAcceptedKew;

//			mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted kew", uuidKew, "Accepted Kew", "Accepted Kew", "Kew", null));

		}

		return mapping;

	}

	@Override

	protected String getRecordQuery(RoteListeDbImportConfigurator config) {

		String strSelect = " SELECT * ";

		String strFrom = " FROM checklist";

		String strWhere = " WHERE ( pk IN (" + ID_LIST_TOKEN + ") )";

		String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy;

		return strRecordQuery;

	}

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, RoteListeDbImportState state) {

		boolean success = super.doPartition(partitioner, state);

//		higherTaxonMap = new HashMap<UUID, Taxon>();

//		state.setGenevaReference(null);

		return success;

	}

	@Override

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, RoteListeDbImportState state) {

		String nameSpace;

		Class<?> cdmClass;

		Set<String> idSet;

		Set<String> referenceIdSet = new HashSet<String>();

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();

		try{

			while (rs.next()){

				handleForeignKey(rs, referenceIdSet, "source");

			}

//			//reference map

//			nameSpace = REFERENCE_NAMESPACE;

//			cdmClass = Reference.class;

//			idSet = referenceIdSet;

//			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, referenceIdSet, nameSpace);

//			result.put(REFERENCE_NAMESPACE, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	@Override

	public TaxonBase createObject(ResultSet rs, RoteListeDbImportState state) throws SQLException {

		BotanicalName speciesName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());

//		Reference sec = state.getConfig().getSourceReference();

//		getReferenceService().saveOrUpdate(sec);

//

//		String familyString = rs.getString("family");

//		String genusString = rs.getString("genus");

//		String speciesString = rs.getString("species");

//		String authorityString = rs.getString("authority");

//

//		if (logger.isDebugEnabled()){

//			System.out.println(familyString + " " + genusString + " " + speciesString);

//		}

//

//		Taxon speciesTaxon = Taxon.NewInstance(speciesName, sec);;

//		speciesName.setGenusOrUninomial(genusString);

//		speciesName.setSpecificEpithet(speciesString);

//		parser.handleAuthors(speciesName, CdmUtils.concat(" ", new String[] {"", genusString, speciesString, authorityString}), authorityString);

//

//		//family

//		Taxon familyTaxon = null;

//		if (StringUtils.isNotBlank(familyString)){

//			familyTaxon = getHigherTaxon(state, familyString, null);

//			if (familyTaxon == null){

//				BotanicalName familyName = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());

//				familyName.setGenusOrUninomial(familyString);

//				familyTaxon = Taxon.NewInstance(familyName, sec);

//				saveHigherTaxon(state, familyTaxon, familyString, null);

//			}

//			getTaxonService().saveOrUpdate(familyTaxon);

//		}

//

//

//		//genus

//		Taxon genusTaxon = getHigherTaxon(state, familyString, genusString);

//		if (genusTaxon == null){

//			BotanicalName genusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());

//			genusName.setGenusOrUninomial(genusString);

//			genusTaxon = Taxon.NewInstance(genusName, sec);

//			saveHigherTaxon(state, genusTaxon, familyString, genusString);

//			if (familyTaxon != null){

//				makeTaxonomicallyIncluded(state, TREE_ID, genusTaxon, familyTaxon, null, null);

//			}

//		}

//		makeTaxonomicallyIncluded(state, TREE_ID, speciesTaxon, genusTaxon, null, null);

//		getTaxonService().saveOrUpdate(genusTaxon);

//

//		String sourceString = rs.getString("source");

//		String sourceId = rs.getString("source_id");

//

//		Reference sourceRef = state.getRelatedObject(REFERENCE_NAMESPACE, sourceString, Reference.class);

//		speciesTaxon.addSource(sourceId, REFERENCE_NAMESPACE, sourceRef, null);

//

//

//		//distribution

//		handleDistribution(rs, speciesTaxon);

//

//		return speciesTaxon;

		return null;

	}

	@Override

	protected boolean doCheck(RoteListeDbImportState state){

		IOValidator<RoteListeDbImportState> validator = new RoteListeDbTaxonImportValidator();

		return validator.validate(state);

	}

	@Override

	protected boolean isIgnore(RoteListeDbImportState state){

		return ! state.getConfig().isDoTaxa();

	}

}