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.api.service.IClassificationService;

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

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

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

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

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

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.description.Distribution;

import eu.etaxonomy.cdm.model.description.PresenceTerm;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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

import eu.etaxonomy.cdm.model.reference.Reference;

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

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

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

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

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

/**

 * @author a.mueller

 * @created 27.08.2012

 */

@Component

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

	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);

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getIdQuery() {

		String strQuery = " SELECT pk FROM " + dbTableName +

						strOrderBy;

		return strQuery;

	}

	/* (non-Javadoc)

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

	 */

	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;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)

	 */

	@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) {

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

//		Reference genevaReference = getReferenceService().find(state.getConfig().getUuidGenevaReference());

//		if (genevaReference == null){

//			genevaReference = makeGenevaReference(state);

//			getReferenceService().save(genevaReference);

//		}

//		state.setGenevaReference(genevaReference);

		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 = BotanicalName.NewInstance(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 = BotanicalName.NewInstance(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 = BotanicalName.NewInstance(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);

//		

//		

//		//geneva id

//		Reference genevaReference = state.getGenevaReference();

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

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

//		

//		//distribution

//		handleDistribution(rs, speciesTaxon);

//		

//		return speciesTaxon;

		return null;

	}

	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");

		addDistribution(description, isCongo, "ZAI");

		addDistribution(description, isBurundi, "BUR");

		addDistribution(description, isRwanda, "RWA");

	}

	/**

	 * @param description

	 * @param isCongo

	 */

	private void addDistribution(TaxonDescription description, Boolean exists, String label) {

		if (exists == true){

			NamedArea namedArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(label);

			Distribution distribution = Distribution.NewInstance(namedArea, PresenceTerm.PRESENT());

			description.addElement(distribution);

		}

	}

	//TODO use Mapper

	private boolean makeTaxonomicallyIncluded(RoteListeDbImportState state, Integer treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){

		String treeKey;

		UUID treeUuid;

		if (treeRefFk == null){

			treeKey = "1";  // there is only one tree and it gets the map key '1'

			treeUuid = state.getConfig().getClassificationUuid();

		}else{

			treeKey =String.valueOf(treeRefFk);

			treeUuid = state.getTreeUuidByTreeKey(treeKey);

		}

		Classification tree = (Classification)state.getRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey);

		if (tree == null){

			IClassificationService service = state.getCurrentIO().getClassificationService();

			tree = service.find(treeUuid);

			if (tree == null){

				String treeName = state.getConfig().getClassificationName();

				tree = Classification.NewInstance(treeName);

				tree.setUuid(treeUuid);

				//FIXME tree reference

				//tree.setReference(ref);

				service.save(tree);

			}

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

		}

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

		return (childNode != null);

	}

//	private Reference makeGenevaReference(RoteListeDbImportState state) {

//		Reference result = ReferenceFactory.newDatabase();

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

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

//		return result;

//	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	@Override

	protected boolean doCheck(RoteListeDbImportState state){

		IOValidator<RoteListeDbImportState> validator = new RoteListeDbTaxonImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	protected boolean isIgnore(RoteListeDbImportState state){

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

	}

}