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.berlinModel.in;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_HETEROTYPIC_SYNONYM_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_HOMOTYPIC_SYNONYM_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_INCLUDED_IN;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_MISAPPLIED_NAME_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PARTIAL_SYN_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_PROPARTE_SYN_OF;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.TAX_REL_IS_SYNONYM_OF;

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 org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.common.ResultWrapper;

import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;

import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonRelationImportValidator;

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

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

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

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

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

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

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

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

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

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

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

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.model.taxon.TaxonRelationship;

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

import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;

/**

 * @author a.mueller

 * @created 20.03.2008

 */

@Component

public class BerlinModelTaxonRelationImport  extends BerlinModelImportBase  {

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

	public static final String TREE_NAMESPACE = "PTRefFk";

	private static int modCount = 30000;

	private static final String pluralString = "taxon relations";

	private static final String dbTableName = "RelPTaxon";

	public BerlinModelTaxonRelationImport(){

		super(dbTableName, pluralString);

	}

	/**

	 * Creates a classification for each PTaxon reference which belongs to a taxon that is included at least in one

	 * <i>taxonomically included</i> relationship

	 * @param state

	 * @return

	 * @throws SQLException

	 */

	private void makeClassifications(BerlinModelImportState state) throws SQLException{

		logger.info("start make classification ...");

		Set<String> idSet = getTreeReferenceIdSet(state);

		//reference map

		String nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;

		Class<?> cdmClass = Reference.class;

		Map<String, Reference> refMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

		String treeName = "Classification - No Name";

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

		int i = 0;

		//for each reference

		try {

			//TODO handle case useSingleClassification = true && sourceSecId = null, which returns no record

			while (rs.next()){

				try {

					if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}

					Integer ptRefFkInt = nullSafeInt(rs,"PTRefFk");

					String ptRefFk= String.valueOf(ptRefFkInt);

					Reference<?> ref = refMap.get(ptRefFk);

					String refCache = rs.getString("RefCache");

					if (StringUtils.isNotBlank(refCache)){

						treeName = refCache;

					}

					if (ref != null && StringUtils.isNotBlank(ref.getTitleCache())){

						treeName = ref.getTitleCache();

					}

					Classification tree = Classification.NewInstance(treeName);

					tree.setReference(ref);

					if (i == 1 && state.getConfig().getClassificationUuid() != null){

						tree.setUuid(state.getConfig().getClassificationUuid());

					}

					IdentifiableSource identifiableSource = IdentifiableSource.NewDataImportInstance(ptRefFk, TREE_NAMESPACE);

					tree.addSource(identifiableSource);

					getClassificationService().save(tree);

					state.putClassificationUuidInt(ptRefFkInt, tree);

				} catch (Exception e) {

					logger.error("Error in BerlinModleTaxonRelationImport.makeClassifications: " + e.getMessage());

					e.printStackTrace();

				}

			}

		} catch (SQLException e) {

			logger.error("Error in BerlinModleTaxonRelationImport.makeClassifications: " + e.getMessage());

			throw e;

		}

		logger.info("end make classification ...");

		return;

	}

	/**

	 * @return

	 * @throws SQLException 

	 */

	private Set<String> getTreeReferenceIdSet(BerlinModelImportState state) throws SQLException {

		Source source = state.getConfig().getSource();

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

		ResultSet rs = source.getResultSet(getClassificationQuery(state)) ;

		while (rs.next()){

			Object id = rs.getObject("PTRefFk");

			result.add(String.valueOf(id));

		}

		return result;

	}

	/**

	 * @return

	 */

	private String getClassificationQuery(BerlinModelImportState state) {

		boolean includeAllClassifications = state.getConfig().isIncludeAllNonMisappliedRelatedClassifications();

		String strQuerySelect = "SELECT PTaxon.PTRefFk, r.RefCache ";  

		String strQueryFrom = " FROM RelPTaxon " + 

							" INNER JOIN PTaxon AS PTaxon ON RelPTaxon.PTNameFk2 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon.PTRefFk " +

							" INNER JOIN Reference r ON PTaxon.PTRefFk = r.RefId "; 

		String strQueryWhere = " WHERE (RelPTaxon.RelQualifierFk = 1) "; 

		if (includeAllClassifications){

			strQueryWhere = " WHERE (RelPTaxon.RelQualifierFk <> 3) ";

		}else{

			if (state.getConfig().isUseSingleClassification()){

				if (state.getConfig().getSourceSecId()!= null){

					strQueryWhere += " AND PTaxon.PTRefFk = " + state.getConfig().getSourceSecId() +  " ";

				}else{

					strQueryWhere += " AND (1=0) ";

				}

			}

		}

		String strQueryGroupBy = " GROUP BY PTaxon.PTRefFk, r.RefCache ";

		String strQuery = strQuerySelect + " " + strQueryFrom + " " + strQueryWhere + " " + strQueryGroupBy;

		if (includeAllClassifications){

			//add otherdirection

			strQuerySelect = "SELECT PTaxon.PTRefFk, r.RefCache ";  

			strQueryFrom = " FROM RelPTaxon rel " + 

								" INNER JOIN PTaxon AS PTaxon ON rel.PTNameFk1 = PTaxon.PTNameFk AND rel.PTRefFk1 = PTaxon.PTRefFk " +

								" INNER JOIN Reference r ON PTaxon.PTRefFk = r.RefId "; 

			strQueryWhere =" WHERE (rel.RelQualifierFk <> 3) ";

			String strAllQuery =  strQuerySelect + " " + strQueryFrom + " " + strQueryWhere + " " + strQueryGroupBy;

			strQuery = strQuery + " UNION " + strAllQuery;

		}

		boolean includeFlatClassifications = state.getConfig().isIncludeFlatClassifications();

		//concepts with 

		if (includeFlatClassifications){

			String strFlatQuery = 

					" SELECT pt.PTRefFk AS secRefFk, r.RefCache AS secRef " +

					" FROM PTaxon AS pt LEFT OUTER JOIN " + 

					          " Reference r ON pt.PTRefFk = r.RefId LEFT OUTER JOIN " +

					          " RelPTaxon rel1 ON pt.PTNameFk = rel1.PTNameFk2 AND pt.PTRefFk = rel1.PTRefFk2 LEFT OUTER JOIN " +

					          " RelPTaxon AS rel2 ON pt.PTNameFk = rel2.PTNameFk1 AND pt.PTRefFk = rel2.PTRefFk1 " + 

					" WHERE (rel2.RelQualifierFk IS NULL) AND (rel1.RelQualifierFk IS NULL) " + 

					" GROUP BY pt.PTRefFk, r.RefCache "

					;

			strQuery = strQuery + " UNION " + strFlatQuery;

		}

		if (state.getConfig().getClassificationQuery() != null){

			strQuery = state.getConfig().getClassificationQuery();

		}

		return strQuery;

	}

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

		String strQuery = 

			" SELECT RelPTaxon.*, FromTaxon.RIdentifier as taxon1Id, ToTaxon.RIdentifier as taxon2Id, ToTaxon.PTRefFk as treeRefFk, FromTaxon.PTRefFk as fromRefFk, q.is_concept_relation " + 

			" FROM PTaxon as FromTaxon " +

              	" INNER JOIN RelPTaxon ON FromTaxon.PTNameFk = RelPTaxon.PTNameFk1 AND FromTaxon.PTRefFk = RelPTaxon.PTRefFk1 " +

              	" INNER JOIN PTaxon AS ToTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk " +

              	" INNER JOIN RelPTQualifier q ON q.RelPTQualifierId = RelPTaxon.RelQualifierFk " + 

            " WHERE RelPTaxon.RelPTaxonId IN ("+ID_LIST_TOKEN+") ORDER BY RelPTaxon.RelPTaxonId ";

		return strQuery;

	}

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {

		boolean success = true ;

		BerlinModelImportConfigurator config = state.getConfig();

		Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();

		Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);

		Map<Integer, Classification> classificationMap = new HashMap<Integer, Classification>();

		Map<String, Reference> refMap = (Map<String, Reference>)partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);

		ResultSet rs = partitioner.getResultSet();

		try{

			int i = 0;

			//for each reference

			while (rs.next()){

				if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}

				int relPTaxonId = rs.getInt("RelPTaxonId");

				Integer taxon1Id = nullSafeInt(rs, "taxon1Id");

				Integer taxon2Id = nullSafeInt(rs, "taxon2Id");

				try {

					Integer relRefFk = nullSafeInt(rs,"relRefFk");

					int treeRefFk = rs.getInt("treeRefFk");

					int fromRefFk = rs.getInt("fromRefFk");

					int relQualifierFk = rs.getInt("relQualifierFk");

					String notes = rs.getString("notes");

					boolean isConceptRelationship = rs.getBoolean("is_concept_relation");

					TaxonBase<?> taxon1 = taxonMap.get(String.valueOf(taxon1Id));

					TaxonBase<?> taxon2 = taxonMap.get(String.valueOf(taxon2Id));

					String refFk = String.valueOf(relRefFk);

					Reference<?> citation = refMap.get(refFk);

					String microcitation = null; //does not exist in RelPTaxon

					if (taxon2 != null && taxon1 != null){

						if (!(taxon2 instanceof Taxon)){

							logger.error("ToTaxon (ID = " + taxon2.getId()+ ", RIdentifier = " + taxon2Id + ") can't be casted to Taxon. RelPTaxon: " + relPTaxonId );

							success = false;

							continue;

						}

						AnnotatableEntity taxonRelationship = null;

						Taxon toTaxon = (Taxon)taxon2;

						if (isTaxonRelationship(relQualifierFk)){

							if (!(taxon1 instanceof Taxon)){

								logger.error("TaxonBase (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") for TaxonRelation ("+relPTaxonId+") can't be casted to Taxon");

								success = false;

								continue;

							}

							Taxon fromTaxon = (Taxon)taxon1;

							if (relQualifierFk == TAX_REL_IS_INCLUDED_IN){

								taxonRelationship = makeTaxonomicallyIncluded(state, classificationMap, treeRefFk, fromTaxon, toTaxon, citation, microcitation);

							}else if (relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){

								 taxonRelationship = toTaxon.addMisappliedName(fromTaxon, citation, microcitation);

							}else{

								handleAllRelatedTaxa(state, fromTaxon, classificationMap, fromRefFk);

								handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);

								logger.warn("Unhandled taxon relationship: RelId:" + relPTaxonId + "; QualifierId: " + relQualifierFk);

							}

						}else if (isSynonymRelationship(relQualifierFk)){

							if (!(taxon1 instanceof Synonym)){

								logger.warn("Validated: Taxon (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Synonym");

								success = false;

								continue;

							}

							handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);

							Synonym synonym = (Synonym)taxon1;

							SynonymRelationship synRel = getSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation);

							taxonRelationship = synRel;

							if (relQualifierFk == TAX_REL_IS_SYNONYM_OF || 

									relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||

									relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF){

								addProParteAndPartial(synRel, synonym, config);

							}else if (relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||

									relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||

									relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ){

									synRel.setProParte(true);

							}else if(relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF || 

									relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||

									relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF ){

									synRel.setPartial(true);

							}else{

								success = false;

								logger.warn("Proparte/Partial not yet implemented for TaxonRelationShipType " + relQualifierFk);

							}

						}else if (isConceptRelationship){

							ResultWrapper<Boolean> isInverse = ResultWrapper.NewInstance(false);

							ResultWrapper<Boolean> isDoubtful = ResultWrapper.NewInstance(false);

							try {

								TaxonRelationshipType relType = BerlinModelTransformer.taxonRelId2TaxonRelType(relQualifierFk, isInverse, isDoubtful);	

								if (! (taxon1 instanceof Taxon)){

									success = false;

									logger.error("TaxonBase (ID = " + taxon1.getId()+ ", RIdentifier = " + taxon1Id + ") can't be casted to Taxon");

								}else{

									Taxon fromTaxon = (Taxon)taxon1;

									if (isInverse.getValue() == true){

										Taxon tmp = fromTaxon;

										fromTaxon = toTaxon;

										toTaxon = tmp;

									}

									taxonRelationship = fromTaxon.addTaxonRelation(toTaxon, relType, citation, microcitation);

									handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);

									handleAllRelatedTaxa(state, fromTaxon, classificationMap, fromRefFk);

									if (isDoubtful.getValue() == true){

										((TaxonRelationship)taxonRelationship).setDoubtful(true);

									}	

								}

							} catch (UnknownCdmTypeException e) {

								//TODO other relationships

								logger.warn("TaxonRelationShipType " + relQualifierFk + " (conceptRelationship) not yet implemented");

								success = false;

							}

						}else {

							//TODO

							logger.warn("TaxonRelationShipType " + relQualifierFk + " not yet implemented: RelPTaxonId = " + relPTaxonId );

							success = false;

						}

						doNotes(taxonRelationship, notes);

						taxaToSave.add(taxon2);

						//TODO

						//etc.

					}else{

						if (taxon2 != null && taxon1 == null){

							logger.warn("First taxon ("+taxon1Id+") for RelPTaxon " + relPTaxonId + " does not exist in store. RelType: " + relQualifierFk);

						}else if (taxon2 == null && taxon1 != null){

							logger.warn("Second taxon ("+taxon2Id +") for RelPTaxon " + relPTaxonId + " does not exist in store. RelType: " + relQualifierFk);

						}else{

							logger.warn("Both taxa ("+taxon1Id+","+taxon2Id +") for RelPTaxon " + relPTaxonId + " do not exist in store. RelType: " + relQualifierFk);

						}

						success = false;

					}

				} catch (Exception e) {

					logger.error("Exception occurred when trying to handle taxon relationship " + relPTaxonId + " (" + taxon1Id + ","+ taxon2Id + "): " + e.getMessage());

//					e.printStackTrace();

				}

			}

		}catch(SQLException e){

			throw new RuntimeException(e);

		}

		logger.info("Taxa to save: " + taxaToSave.size());

		partitioner.startDoSave();

		getTaxonService().saveOrUpdate(taxaToSave);

		classificationMap = null;

		taxaToSave = null;

		return success;

	}

	private void handleAllRelatedTaxa(BerlinModelImportState state, Taxon taxon, Map<Integer, Classification> classificationMap, Integer secRefFk) {

		if (taxon.getTaxonNodes().size() > 0){

			return;

		}else{

			Classification classification = getClassificationTree(state, classificationMap, secRefFk);

			classification.addChildTaxon(taxon, null, null);

		}

	}

	@Override

	protected void doInvoke(BerlinModelImportState state){				

		try {

			makeClassifications(state);

			super.doInvoke(state);

			makeFlatClassificationTaxa(state);

			return;

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

	}

	private void makeFlatClassificationTaxa(BerlinModelImportState state) {

		//Note: this part still does not use partitions

		logger.info("Flat classifications start");

		TransactionStatus txStatus = startTransaction();

		if (! state.getConfig().isIncludeFlatClassifications()){

			return;

		}

		String sql = " SELECT pt.PTRefFk AS secRefFk, pt.RIdentifier " +

						" FROM PTaxon AS pt " +

							" LEFT OUTER JOIN RelPTaxon ON pt.PTNameFk = RelPTaxon.PTNameFk2 AND pt.PTRefFk = RelPTaxon.PTRefFk2 " +

							"  LEFT OUTER JOIN RelPTaxon AS RelPTaxon_1 ON pt.PTNameFk = RelPTaxon_1.PTNameFk1 AND pt.PTRefFk = RelPTaxon_1.PTRefFk1 " +

						" WHERE (RelPTaxon_1.RelQualifierFk IS NULL) AND (dbo.RelPTaxon.RelQualifierFk IS NULL) " +

						" ORDER BY pt.PTRefFk "	;

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

		Map<Object, Map<String, ? extends CdmBase>> maps = getRelatedObjectsForFlatPartition(rs);

		Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) maps.get(BerlinModelTaxonImport.NAMESPACE);

		Map<Integer, Classification> classificationMap = new HashMap<Integer, Classification>();

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

		try {

			while (rs.next()){

				Integer treeRefFk = rs.getInt("secRefFk");

				String taxonId = rs.getString("RIdentifier");

				Classification classification = getClassificationTree(state, classificationMap, treeRefFk);

				TaxonBase<?> taxon = taxonMap.get(taxonId);

				if (taxon == null){

					String message = "TaxonBase for taxon id (%s) not found in taxonMap";

					logger.warn(String.format(message, taxonId, taxonId));

				}else if (taxon.isInstanceOf(Taxon.class)){

					classification.addChildTaxon(CdmBase.deproxy(taxon, Taxon.class), null, null);

				}else{

					String message = "TaxonBase for taxon is not of class Taxon but %s (RIdentifier %s)";

					logger.warn(String.format(message, taxon.getClass(), taxonId));

				}

			}

		} catch (SQLException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		commitTransaction(txStatus);

		logger.info("Flat classifications end");

	}

	@Override

	protected String getIdQuery(BerlinModelImportState state) {

		if (state.getConfig().getRelTaxaIdQuery() != null){

			return state.getConfig().getRelTaxaIdQuery();

		}else{

			return super.getIdQuery(state);

		}

	}

	@Override

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition( ResultSet rs, BerlinModelImportState 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> taxonIdSet = new HashSet<String>();

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

//			Set<String> classificationIdSet = new HashSet<String>();

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "taxon1Id");

				handleForeignKey(rs, taxonIdSet, "taxon2Id");

//				handleForeignKey(rs, classificationIdSet, "treeRefFk");

				handleForeignKey(rs, referenceIdSet, "RelRefFk");

	}

			//taxon map

			nameSpace = BerlinModelTaxonImport.NAMESPACE;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

			Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, taxonMap);

//			//tree map

//			nameSpace = "Classification";

//			cdmClass = Classification.class;

//			idSet = classificationIdSet;

//			Map<String, Classification> treeMap = (Map<String, Classification>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

//			result.put(cdmClass, treeMap);

//			Set<UUID> treeUuidSet = state

//			getClassificationService().find(uuidSet);

//			

			//reference map

			nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;

			cdmClass = Reference.class;

			idSet = referenceIdSet;

			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	private Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForFlatPartition( ResultSet rs) {

		String nameSpace;

		Class cdmClass;

		Set<String> idSet;

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

		try{

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

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

//			Set<String> classificationIdSet = new HashSet<String>();

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "RIdentifier");

//				handleForeignKey(rs, classificationIdSet, "treeRefFk");

	}

			//taxon map

			nameSpace = BerlinModelTaxonImport.NAMESPACE;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

			Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, taxonMap);

//			//tree map

//			nameSpace = "Classification";

//			cdmClass = Classification.class;

//			idSet = classificationIdSet;

//			Map<String, Classification> treeMap = (Map<String, Classification>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

//			result.put(cdmClass, treeMap);

//			Set<UUID> treeUuidSet = state

//			getClassificationService().find(uuidSet);

//			

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	private SynonymRelationship getSynRel (int relQualifierFk, Taxon toTaxon, Synonym synonym, Reference citation, String microcitation){

		SynonymRelationship result;

		if (relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||

				relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||

				relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF){

			result = toTaxon.addHomotypicSynonym(synonym, citation, microcitation);

		}else if (relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF ||

				relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||

				relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF){

			result = toTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), citation, microcitation);

		}else if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||

				relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF ||

				relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF){

			result = toTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF(), citation, microcitation);

		}else{

			logger.warn("SynonymyRelationShipType could not be defined for relQualifierFk " + relQualifierFk + ". 'Unknown'-Type taken instead.");

			result = toTaxon.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF(), citation, microcitation);

		}

		return result;

	}

	private  boolean isSynonymRelationship(int relQualifierFk){

		if (relQualifierFk == TAX_REL_IS_SYNONYM_OF || 

			relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF || 

			relQualifierFk == TAX_REL_IS_HETEROTYPIC_SYNONYM_OF ||

			relQualifierFk == TAX_REL_IS_PROPARTE_SYN_OF || 

			relQualifierFk == TAX_REL_IS_PARTIAL_SYN_OF ||

			relQualifierFk == TAX_REL_IS_PROPARTE_HOMOTYPIC_SYNONYM_OF ||

			relQualifierFk == TAX_REL_IS_PROPARTE_HETEROTYPIC_SYNONYM_OF ||

			relQualifierFk == TAX_REL_IS_PARTIAL_HOMOTYPIC_SYNONYM_OF ||

			relQualifierFk == TAX_REL_IS_PARTIAL_HETEROTYPIC_SYNONYM_OF

		){

			return true;

		}else{

			return false;

		}

	}

	private  boolean isTaxonRelationship(int relQualifierFk){

		if (relQualifierFk == TAX_REL_IS_INCLUDED_IN || 

				relQualifierFk == TAX_REL_IS_MISAPPLIED_NAME_OF){

			return true;

		}else{

			return false;

		}

	}

	private void addProParteAndPartial(SynonymRelationship synRel, Synonym synonym, BerlinModelImportConfigurator bmiConfig){

		if (bmiConfig.isPartialSynonym(synonym)){

			synRel.setPartial(true);

		}

		if (bmiConfig.isProParteSynonym(synonym)){

			synRel.setProParte(true);

		}

	}

	private TaxonNode makeTaxonomicallyIncluded(BerlinModelImportState state, Map<Integer, Classification> classificationMap, int treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){

		Classification tree = getClassificationTree(state, classificationMap, treeRefFk);

		return tree.addParentChild(parent, child, citation, microCitation);

	}

	private Classification getClassificationTree(BerlinModelImportState state, Map<Integer, Classification> classificationMap, int treeRefFk) {

		if (state.getConfig().isUseSingleClassification()){

			if (state.getConfig().getSourceSecId() != null){

				treeRefFk = (Integer)state.getConfig().getSourceSecId();	

			}else{

				treeRefFk = 1;

			}

		}

		Classification tree = classificationMap.get(treeRefFk);

		if (tree == null){

			UUID treeUuid = state.getTreeUuidByIntTreeKey(treeRefFk);

			tree = getClassificationService().find(treeUuid);

			classificationMap.put(treeRefFk, tree);

		}

		if (tree == null){

			throw new IllegalStateException("Tree for ToTaxon reference " + treeRefFk + " does not exist.");

		}

		return tree;

	}

	@Override

	protected boolean doCheck(BerlinModelImportState state){

		IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonRelationImportValidator();

		return validator.validate(state);

	}

	@Override

	protected boolean isIgnore(BerlinModelImportState state){

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

	}

}