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.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

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

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

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

 * @since 27.02.2012

 */

@Component

public class IndexFungorumHigherClassificationImport  extends IndexFungorumImportBase {

    private static final long serialVersionUID = -6841466146506309309L;

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

	private static final String pluralString = "higher classifications";

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

	public IndexFungorumHigherClassificationImport(){

		super(pluralString, dbTableName, null);

	}

	@Override

	protected String getRecordQuery(IndexFungorumImportConfigurator config) {

		String strRecordQuery =

			" 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 " +

			" FROM [tblPESIfungi-Classification] c  LEFT OUTER JOIN " +

                      " tblGenera g ON c.PreferredNameFDCnumber = g.[RECORD NUMBER]" +

//			" WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";

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

		return strRecordQuery;

	}

	@Override

	protected void doInvoke(IndexFungorumImportState state) {

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

		String sql = getRecordQuery(state.getConfig());

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

		//only 1 partition here

		String lastKingdom = "";

		String lastPhylum = "";

		String lastSubphylum = "";

		String lastClassname = "";

		String lastSubclass = "";

		String lastOrder = "";

		String lastFamily = "";

//		String lastGenus = "";

//		String lastSpecies = "";

		Taxon taxonKingdom = null;

		Taxon taxonPhylum = null;

		Taxon taxonSubphylum = null;

		Taxon taxonClass = null;

		Taxon taxonSubclass = null;

		Taxon taxonOrder = null;

		Taxon taxonFamily = null;

//		Taxon taxonGenus = null;

//		Taxon taxonSpecies = null;

		Taxon higherTaxon = null;

		TransactionStatus tx = startTransaction();

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

		state.setRelatedObjects(getRelatedObjectsForPartition(rsRelatedObjects, state));

		Classification classification = getClassification(state);

		try {

			while (rs.next()){

				String kingdom = rs.getString("Kingdom name");

				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");

//				String genus = rs.getString("GenusName");

//				String species = rs.getString("SpeciesName");

//				if (isNewTaxon(species, lastSpecies)){

//					if (isNewTaxon(genus, lastGenus)){

				if (isNewTaxon(family, lastFamily)){

					if (isNewTaxon(order,lastOrder)){

						if (isNewTaxon(subclass,lastSubclass)){

							if (isNewTaxon(classname,lastClassname)){

								if (isNewTaxon(subphylum, lastSubphylum)){

									if (isNewTaxon(phylum,lastPhylum)){

										if (isNewTaxon(kingdom,lastKingdom)){

											taxonKingdom = makeTaxon(state, kingdom, Rank.KINGDOM());

											lastKingdom = kingdom;

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

											getTaxonService().saveOrUpdate(taxonKingdom);

										}else{

											higherTaxon = taxonKingdom;

										}

										higherTaxon = isIncertisSedis(kingdom) ? higherTaxon : taxonKingdom;

										Rank newRank = (lastKingdom.equals("Fungi") ? null : Rank.PHYLUM());

										taxonPhylum = makeTaxon(state, phylum, newRank);

										if (taxonPhylum != null){

											classification.addParentChild(higherTaxon, taxonPhylum, null, null);

										}

										higherTaxon = isIncertisSedis(phylum) ? higherTaxon : taxonPhylum;

										lastPhylum = phylum;

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

									}else{

										higherTaxon = taxonPhylum;

									}

									Rank newRank = (lastKingdom.equals("Fungi") ? null : Rank.SUBPHYLUM());

									taxonSubphylum = makeTaxon(state, subphylum, newRank);

									if (taxonSubphylum != null){

										getClassification(state).addParentChild(higherTaxon,taxonSubphylum, null, null);

									}

									higherTaxon = isIncertisSedis(subphylum) ? higherTaxon : taxonSubphylum;

									lastSubphylum = subphylum;

								}else{

									higherTaxon = taxonSubphylum;

								}

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

								if (taxonClass != null){

									getClassification(state).addParentChild(higherTaxon, taxonClass, null, null);

								}

								higherTaxon = isIncertisSedis(classname) ? higherTaxon : taxonClass;

								lastClassname = classname;

							}else{

								higherTaxon = taxonClass;

							}

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

							if (taxonSubclass != null){

								getClassification(state).addParentChild(higherTaxon, taxonSubclass,null, null);

							}

							higherTaxon = isIncertisSedis(subclass) ? higherTaxon : taxonSubclass;

							lastSubclass = subclass;

						}else{

							higherTaxon = taxonSubclass;

						}

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

						if (taxonOrder != null){

							getClassification(state).addParentChild(higherTaxon, taxonOrder, null, null);

						}

						higherTaxon = isIncertisSedis(order) ? higherTaxon : taxonOrder;

						lastOrder = order;

					}else{

						higherTaxon = taxonOrder;

					}

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

					if (taxonFamily != null){

						try{

							//if this shown a warning see single issue in #2826 about Glomerelllaceae (which has 2 different parents)

						    getClassification(state).addParentChild(higherTaxon, taxonFamily, null, null);

						}catch(IllegalStateException e){

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

								//TaxonNode node = getClassification(state).getNode(taxonFamily);

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

								}

						}

					}

					higherTaxon = isIncertisSedis(family) ? higherTaxon : taxonFamily;

					lastFamily = family;

					getTaxonService().saveOrUpdate(higherTaxon);

				}

//						else{

//							higherTaxon = taxonFamily;

//						}

//						taxonGenus = makeTaxon(state, genus, Rank.GENUS());

//						if (taxonGenus != null){

//							getClassification(state).addParentChild(higherTaxon, taxonGenus, null, null);

//						}

//						higherTaxon = isIncertisSedis(genus) ? higherTaxon : taxonGenus;

//						lastGenus = genus;

//					}else{

//						higherTaxon = taxonGenus;

//					}

//					taxonSpecies = makeTaxon(state, species, Rank.SPECIES());

//					if (taxonSpecies != null){

//						getClassification(state).addParentChild(higherTaxon, taxonSpecies, null, null);

//					}

//					higherTaxon = isIncertisSedis(species) ? higherTaxon : taxonSpecies;

//					lastSpecies = species;

//					getTaxonService().saveOrUpdate(higherTaxon);

//				}

				getTaxonService().saveOrUpdate(higherTaxon);

			}

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			tx.setRollbackOnly();

			state.setSuccess(false);

		}

		commitTransaction(tx);

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

		return;

	}

	private boolean isIncertisSedis(String uninomial) {

		return  uninomial.equalsIgnoreCase(INCERTAE_SEDIS) || uninomial.equalsIgnoreCase(FOSSIL_FUNGI);

	}

	private boolean isNewTaxon(String uninomial, String lastUninomial) {

		boolean result =  !uninomial.equalsIgnoreCase(lastUninomial);

		result |= lastUninomial.equalsIgnoreCase(INCERTAE_SEDIS);

		result |= lastUninomial.equalsIgnoreCase(FOSSIL_FUNGI);

		return result;

	}

	private Taxon makeTaxon(IndexFungorumImportState state, String uninomial, Rank newRank) {

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

			return null;

		}

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

		if (taxon == null){

			if (! newRank.equals(Rank.KINGDOM())){

				logger.warn("Taxon not found for uninomial " + uninomial);

			}

			TaxonName name = TaxonNameFactory.NewBotanicalInstance(newRank);

			name.setGenusOrUninomial(uninomial);

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

			taxon = Taxon.NewInstance(name, sourceReference);

			taxon.addMarker(Marker.NewInstance(getMissingGUIDMarkerType(state), true));

		}else if (newRank != null){

			taxon.getName().setRank(newRank);

		}

		return taxon;

	}

	@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_accfinal" );

//			}

			//taxon map

			nameSpace = IndexFungorumSupraGeneraImport.NAMESPACE_SUPRAGENERIC_NAMES ;

			cdmClass = TaxonBase.class;

//			idSet = taxonNameSet;

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

			List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null);

			for (Taxon taxon : list){

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

			}

			result.put(nameSpace, taxonMap);

			//source reference

			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 (Exception e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	@Override

	protected boolean doCheck(IndexFungorumImportState state){

		return true;

	}

	@Override

	protected boolean isIgnore(IndexFungorumImportState state){

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

	}

}