EDIT

/**

* Copyright (C) 2007 EDIT

* 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 org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

/**

 * @author a.mueller

@Component

    private static final long serialVersionUID = -6841466146506309309L;

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

	private static final String dbTableName = "tblPESIfungi-Classification";

	public IndexFungorumHigherClassificationImport(){

	@Override

	protected String getRecordQuery(IndexFungorumImportConfigurator config) {

			" SELECT DISTINCT [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name], [Family name], g.[NAME OF FUNGUS] as GenusName, c.PreferredName as SpeciesName " +

			" ORDER BY [Kingdom name], [Phylum name], [Subphylum name], [Class name], [Subclass name], [Order name],  [Family name], GenusName, SpeciesName ";

	}

	@Override

	protected void doInvoke(IndexFungorumImportState state) {

	    logger.info("Start higher classification ...");

		ResultSet rs = state.getConfig().getSource().getResultSet(sql);

		String lastPhylum = "";

		String lastSubphylum = "";

		String lastClassname = "";

		String lastSubclass = "";

		String lastOrder = "";

		String lastFamily = "";

		Taxon taxonPhylum = null;

		Taxon taxonSubphylum = null;

		Taxon taxonClass = null;

		Taxon taxonSubclass = null;

		Taxon taxonOrder = null;

		Taxon taxonFamily = null;

		ResultSet rsRelatedObjects = state.getConfig().getSource().getResultSet(sql);

			while (rs.next()){

				String phylum = rs.getString("Phylum name");

				String subphylum = rs.getString("Subphylum name");

				String classname = rs.getString("Class name");

				String subclass = rs.getString("Subclass name");

				String order = rs.getString("Order name");

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

					if (isNewTaxon(order,lastOrder)){

						if (isNewTaxon(subclass,lastSubclass)){

							if (isNewTaxon(classname,lastClassname)){

								if (isNewTaxon(subphylum, lastSubphylum)){

									if (isNewTaxon(phylum,lastPhylum)){

										if (isNewTaxon(kingdom,lastKingdom)){

											logger.info("Import kingdom " +  kingdom);

											getTaxonService().saveOrUpdate(taxonKingdom);

										}else{

											higherTaxon = taxonKingdom;

										taxonPhylum = makeTaxon(state, phylum, newRank);

										higherTaxon = isIncertisSedis(phylum) ? higherTaxon : taxonPhylum;

										lastPhylum = phylum;

										logger.info("Import Phylum " +  phylum);

									}else{

										higherTaxon = taxonPhylum;

									taxonSubphylum = makeTaxon(state, subphylum, newRank);

									higherTaxon = isIncertisSedis(subphylum) ? higherTaxon : taxonSubphylum;

									lastSubphylum = subphylum;

								}else{

									higherTaxon = taxonSubphylum;

								taxonClass = makeTaxon(state, classname, Rank.CLASS());

								higherTaxon = isIncertisSedis(classname) ? higherTaxon : taxonClass;

								lastClassname = classname;

							}else{

								higherTaxon = taxonClass;

							taxonSubclass = makeTaxon(state, subclass, Rank.SUBCLASS());

							higherTaxon = isIncertisSedis(subclass) ? higherTaxon : taxonSubclass;

							lastSubclass = subclass;

						}else{

							higherTaxon = taxonSubclass;

						taxonOrder = makeTaxon(state, order, Rank.ORDER());

						higherTaxon = isIncertisSedis(order) ? higherTaxon : taxonOrder;

						lastOrder = order;

					}else{

						higherTaxon = taxonOrder;

					taxonFamily = makeTaxon(state, family, Rank.FAMILY());

							if (e.getMessage().startsWith("The child taxon is already part of the tree")){

								logger.warn(e.getMessage() + taxonFamily.getTitleCache() + " " + higherTaxon.getTitleCache());

					higherTaxon = isIncertisSedis(family) ? higherTaxon : taxonFamily;

					lastFamily = family;

					getTaxonService().saveOrUpdate(higherTaxon);

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.setSuccess(false);

	}

		boolean result =  !uninomial.equalsIgnoreCase(lastUninomial);

		result |= lastUninomial.equalsIgnoreCase(INCERTAE_SEDIS);

	}

		}

		}else if (newRank != null){

			taxon.getName().setRank(newRank);

		return taxon;

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

			//taxon map

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

            List<Taxon> list = getCommonService().getHqlResult("SELECT t FROM Taxon t JOIN t.sources s WHERE s.citation.uuid = ?0", new Object[]{ PesiTransformer.uuidSourceRefIndexFungorum});

				TaxonBase<?> existing = taxonMap.put(uninomial, taxon);

				if (existing != null){

				    logger.warn("There seem to be duplicate taxa for uninomial: " + uninomial);

				}

			result.put(NAMESPACE_REFERENCE, referenceMap);

		}

		return result;

	}

	protected boolean doCheck(IndexFungorumImportState state){

		return true;

	}

}