EDIT

/**

* Copyright (C) 2007 EDIT

* 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.

*/

@Component

public class CentralAfricaChecklistTaxonImport  extends CentralAfricaChecklistImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaChecklistImportState>{

	private static final Logger logger = Logger.getLogger(CentralAfricaChecklistTaxonImport.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";

	public CentralAfricaChecklistTaxonImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.CentralAfricaChecklistImportBase#getMapping()

	 */

		if (mapping == null){

			mapping = new DbImportMapping();

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

			UUID uuidKew = CentralAfricaChecklistTransformer.uuidAcceptedKew;

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

			UUID uuidGeneva = CentralAfricaChecklistTransformer.uuidAcceptedGeneva;

			mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted geneva", uuidGeneva, "Accepted Geneva", "Accepted Geneva", "Geneva", null));

			UUID uuidItis = CentralAfricaChecklistTransformer.uuidAcceptedItis;

			mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted itis", uuidItis, "Accepted ITIS", "Accepted ITIS", "ITIS", null));

		}

		return mapping;

	}

		return strRecordQuery;

	}

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, CentralAfricaChecklistImportState state) {

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

		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");

		}

		return result;

	}

	@Override

	public TaxonBase<?> createObject(ResultSet rs, CentralAfricaChecklistImportState state) throws SQLException {

		BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES());

		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 = Taxon.NewInstance(familyName, sec);

				saveHigherTaxon(state, familyTaxon, familyString, null);

			}

		}

		//genus

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

		if (genusTaxon == null){

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

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

		speciesTaxon.addSource(OriginalSourceType.Import, sourceId, REFERENCE_NAMESPACE, sourceRef, null);

		//geneva id

		Object genevaId = rs.getObject("geneva_ID");

		speciesTaxon.addSource(OriginalSourceType.Import, String.valueOf(genevaId), null, genevaReference, null);

		//distribution

		handleDistribution(rs, speciesTaxon);

		return speciesTaxon;

	}

	private void handleDistribution(ResultSet rs, Taxon speciesTaxon) throws SQLException {

		TaxonDescription description = TaxonDescription.NewInstance(speciesTaxon);

		Boolean isCongo = rs.getBoolean("drc");

		Boolean isBurundi = rs.getBoolean("burundi");

		Boolean isRwanda = rs.getBoolean("rwanda");

	private Taxon getHigherTaxon(CentralAfricaChecklistImportState state, String family, String genus) {

		String higherName = normalizeHigherTaxonName(family, genus);

		UUID uuid = state.getHigherTaxon(higherName);

		Taxon taxon = null;

		if (uuid != null){

			taxon = higherTaxonMap.get(uuid);

//		UUID uuid = state.getTreeUuid(sec);

//		Classification tree;

//		tree = state.getTree(sec);

//		if (tree == null){

//			tree = makeTreeMemSave(state, sec);

//		}

//		}

//		return (childNode != null);

//	}

	//TODO use Mapper

		String treeKey;

		UUID treeUuid;

		if (treeRefFk == null){

			}

			state.addRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey, tree);

		}

		TaxonNode childNode = tree.addParentChild(parent, child, citation, microCitation);

		return (childNode != null);

	}

		result.setTitleCache(state.getConfig().getGenevaReferenceTitle(), true);

		result.setUuid(state.getConfig().getUuidGenevaReference());

		return result;

		IOValidator<CentralAfricaChecklistImportState> validator = new CentralAfricaChecklistTaxonImportValidator();

		return validator.validate(state);

	}

	@Override

	protected boolean isIgnore(CentralAfricaChecklistImportState state){

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