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.eflora.centralAfrica.checklist;

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.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.api.service.IClassificationService;

import eu.etaxonomy.cdm.common.CdmUtils;

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.DbImportMarkerMapper;

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

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

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

import eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.validation.CentralAfricaChecklistTaxonImportValidator;

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.location.TdwgArea;

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.reference.ReferenceFactory;

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 20.02.2010

 * @version 1.0

 */

@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";

	private static final Class cdmTargetClass = TaxonBase.class;

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

	public CentralAfricaChecklistTaxonImport(){

		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.eflora.centralAfrica.checklist.CentralAfricaChecklistImportBase#getMapping()

	 */

	protected DbImportMapping 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;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getRecordQuery(CentralAfricaChecklistImportConfigurator 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, CentralAfricaChecklistImportState 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;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)

	 */

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

		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;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet)

	 */

	public TaxonBase createObject(ResultSet rs, CentralAfricaChecklistImportState 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;

	}

	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 = TdwgArea.getAreaByTdwgAbbreviation(label);

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

			description.addElement(distribution);

		}

	}

	private void saveHigherTaxon(CentralAfricaChecklistImportState state, Taxon higherTaxon, String family, String genus) {

		String higherName = normalizeHigherTaxonName(family, genus);

		UUID uuid = higherTaxon.getUuid();

		state.putHigherTaxon(higherName, uuid);

		higherTaxonMap.put(uuid, higherTaxon);

	}

	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);

			if (taxon == null){

				taxon = CdmBase.deproxy(getTaxonService().find(uuid), Taxon.class);

			}

		}

		return taxon;

	}

	/**

	 * @param family

	 * @param genus

	 */

	private String normalizeHigherTaxonName(String family, String genus) {

		return (CdmUtils.Nz(family) + "-" + CdmUtils.Nz(genus)).trim();

	}

//	private boolean makeTaxonomicallyIncluded(CentralAfricaChecklistImportState state, Taxon parent, Taxon child, Reference citation, String microCitation){

//		Reference sec = child.getSec();

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

//		Classification tree;

//		tree = state.getTree(sec);

//		

//		if (tree == null){

//			tree = makeTreeMemSave(state, sec);

//		}

//		TaxonNode childNode;

//		if (parent != null){

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

//		}else{

//			childNode = tree.addChildTaxon(child, citation, microCitation, null);

//		}

//		return (childNode != null);

//	}

	//TODO use Mapper

	private boolean makeTaxonomicallyIncluded(CentralAfricaChecklistImportState 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(CentralAfricaChecklistImportState 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(CentralAfricaChecklistImportState state){

		IOValidator<CentralAfricaChecklistImportState> validator = new CentralAfricaChecklistTaxonImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(CentralAfricaChecklistImportState state){

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

	}

}