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.pesi.indexFungorum;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;

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

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

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

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;

/**

 * @author a.mueller

 * @created 27.02.2012

 */

@Component

public class IndexFungorumGeneraImport  extends IndexFungorumImportBase {

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

	private static final String pluralString = "genera";

	private static final String dbTableName = "tblGenera";

	public IndexFungorumGeneraImport(){

		super(pluralString, dbTableName, null);

	}

	@Override

	protected String getIdQuery() {

		String result = " SELECT [RECORD NUMBER] FROM " + getTableName() +

				" ORDER BY [NAME OF FUNGUS] ";

		return result;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getRecordQuery(IndexFungorumImportConfigurator config) {

		String strRecordQuery =

				" SELECT DISTINCT c.[Family name], c.[Order name], c.[Subclass name], c.[Class name], c.[Subphylum name], c.[Phylum name], c.[Kingdom name], g.* " +

                " FROM tblGenera AS g LEFT OUTER JOIN  dbo.[tblPESIfungi-Classification] AS c ON g.[RECORD NUMBER] = c.PreferredNameFDCnumber " +

			" WHERE ( g.[RECORD NUMBER] IN (" + ID_LIST_TOKEN + ") )" +

			"";

		return strRecordQuery;

	}

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, IndexFungorumImportState state) {

		boolean success =true;

		Reference sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);

		ResultSet rs = partitioner.getResultSet();

		Classification classification = getClassification(state);

		try {

			while (rs.next()){

				//TODO

				//DisplayName, NomRefCache

				Double id = (Double)rs.getObject("RECORD NUMBER");

				String preferredName = rs.getString("NAME OF FUNGUS");

				if (StringUtils.isBlank(preferredName)){

					logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD NUMBER" + id);

				}

				Rank rank = Rank.GENUS();

				NonViralName<?> name = BotanicalName.NewInstance(rank);

				name.setGenusOrUninomial(preferredName);

				Taxon taxon = Taxon.NewInstance(name, sourceReference);

				Taxon parent = getParentTaxon(state, rs);

				classification.addParentChild(parent, taxon, null, null);

				//author + publication

				makeAuthorAndPublication(state, rs, name);

				//source

				//makeSource(state, taxon, id, NAMESPACE_GENERA );

				if (id != null){

					makeSource(state, taxon, id.intValue(), NAMESPACE_GENERA );

				} else{

					makeSource(state, taxon, null,NAMESPACE_GENERA);

				}

				getTaxonService().saveOrUpdate(taxon);

			}

		} catch (Exception e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.setSuccess(false);

			success = false;

		}

		return success;

	}

	private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {

		String parentName = getParentNameString(rs);

		if (parentName == null){

			logger.warn("Parent name not found for: " + rs.getString("NAME OF FUNGUS"));

		}

		Taxon taxon = state.getRelatedObject(NAMESPACE_SUPRAGENERIC_NAMES, parentName, Taxon.class);

		if (taxon == null){

			logger.warn("Taxon not found for " + parentName + " name of fungus: " +rs.getString("NAME OF FUNGUS") );

		}

		return taxon;

	}

	private String getParentNameString(ResultSet rs) throws SQLException {

		String parentName = rs.getString("Family name");

		if (parentName == null){

			logger.warn(rs.getObject("NAME OF FUNGUS") + " has no family name. ");

			return null;

		}

		if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){

			parentName = rs.getString("Order name");

			if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){

				parentName = rs.getString("Subclass name");

				if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){

					parentName = rs.getString("Class name");

					if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){

						parentName = rs.getString("Subphylum name");

						if (parentName.equalsIgnoreCase(INCERTAE_SEDIS)){

							parentName = rs.getString("Phylum name");

							if (parentName.equalsIgnoreCase(INCERTAE_SEDIS) || parentName.equalsIgnoreCase(FOSSIL_FUNGI) ){

								parentName = rs.getString("Kingdom name");

							}

						}

					}

				}

			}

		}

		return parentName;

	}

	@Override

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

		String nameSpace;

		Class<?> cdmClass;

		Set<String> idSet;

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

		try{

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

			while (rs.next()){

//				handleForeignKey(rs, taxonIdSet,"tu_acctaxon" );

			}

			//taxon map

			nameSpace = NAMESPACE_SUPRAGENERIC_NAMES ;

			cdmClass = TaxonBase.class;

//			idSet = taxonNameSet;

			Map<String, TaxonBase<?>> taxonMap = new HashMap<String, TaxonBase<?>>();

			List<TaxonBase> list = getTaxonService().listTaxaByName(Taxon.class, "*", null, null, null, null, 1000000, null);

			for (TaxonBase<?> taxon : list){

				taxonMap.put(CdmBase.deproxy(taxon.getName(), NonViralName.class).getGenusOrUninomial(), taxon);

			}

			result.put(nameSpace, taxonMap);

			//sourceReference

			Reference sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);

			Map<String, Reference> referenceMap = new HashMap<String, Reference>();

			referenceMap.put(SOURCE_REFERENCE, sourceReference);

			result.put(NAMESPACE_REFERENCE, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	@Override

	protected boolean doCheck(IndexFungorumImportState state){

		return true;

	}

	@Override

	protected boolean isIgnore(IndexFungorumImportState state){

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

	}

}