EDIT

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumSubSpeciesImport.java -text

package eu.etaxonomy.cdm.io.pesi.indexFungorum;

import java.sql.ResultSet;

import java.util.ArrayList;

import java.util.List;

import java.util.Map;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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

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

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

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

/**

 * @author k.luther

 * @created 19.08.2014

 */

@Component

public class IndexFungorumSubSpeciesImport extends IndexFungorumImportBase {

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

	private static final String pluralString = "subSpecies";

	public IndexFungorumSubSpeciesImport(){

		super(pluralString, null, null);

	}

	public IndexFungorumSubSpeciesImport(String pluralString,

			String dbTableName, Class cdmTargetClass) {

		super(pluralString, dbTableName, cdmTargetClass);

	}

	@Override

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(

			ResultSet rs, IndexFungorumImportState state) {

		// TODO Auto-generated method stub

		return null;

	}

	@Override

	protected String getRecordQuery(IndexFungorumImportConfigurator config) {

		// TODO Auto-generated method stub

		return null;

	}

	@Override

	protected boolean doCheck(IndexFungorumImportState state) {

		// TODO Auto-generated method stub

		return false;

	}

	@Override

	protected boolean isIgnore(IndexFungorumImportState state) {

		// TODO Auto-generated method stub

		return false;

	}

	@Override

    protected void doInvoke(IndexFungorumImportState state){

		System.out.println("create infraspecific - specific relationship: " + state.getInfraspecificTaxaUUIDs().size() + " taxa");

		 List<String> propertyPaths = new ArrayList<String>();

         propertyPaths.add("taxonNodes.*");

         propertyPaths.add("taxonNodes.classification");

         propertyPaths.add("taxonNodes.childNodes.*");

         propertyPaths.add("taxonNodes.childNodes.taxon.*");

         propertyPaths.add("taxonNodes.parent.*");

         propertyPaths.add("taxonNodes.parent.taxon.*");

         Classification classification = getClassification(state);

        for (UUID infraspecificTaxonUUID: state.getInfraspecificTaxaUUIDs()){

        	TransactionStatus txStatus = startTransaction();

        	Taxon infraspecificTaxon = (Taxon)getTaxonService().load(infraspecificTaxonUUID, propertyPaths);

            //HibernateProxyHelper.deproxy(infraspecificTaxon);

            TaxonNameBase name = infraspecificTaxon.getName();

            UUID uuid = getNameService().saveOrUpdate(name);

            String parentNameString = getParentNameInfraSpecific(name);

            System.out.println("Parent name string: " + parentNameString);

            MatchingTaxonConfigurator matchingConfig = new MatchingTaxonConfigurator();

            matchingConfig.setTaxonNameTitle(parentNameString);

            matchingConfig.setPropertyPath(propertyPaths);

            List<TaxonBase> potentialParents = getTaxonService().findTaxaByName(matchingConfig);

                    //Taxon.class, parentNameString + "sec. ", MatchMode.BEGINNING, , pageSize, pageNumber, orderHints, propertyPaths)

                    //.searchNames(String uninomial,String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,

            if (potentialParents.size()>1){

                for (TaxonBase potentialParent:potentialParents){

                    if (potentialParent.getTitleCache().equals(parentNameString + " sec*")){

                        classification.addParentChild((Taxon)potentialParent, (Taxon)infraspecificTaxon, null, null);

                    }

                }

            }else if (!potentialParents.isEmpty()){

                Taxon parent = HibernateProxyHelper.deproxy(potentialParents.get(0), Taxon.class);

                Taxon child = (Taxon)getTaxonService().load(infraspecificTaxon.getUuid(), propertyPaths);

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

            } else{

                System.out.println("No parent for: " + name.getTitleCache());

            }

            getTaxonService().saveOrUpdate(infraspecificTaxon);

            commitTransaction(txStatus);

        }

	}

	/**

     * @param taxon

     * @return

     */

    private String getParentNameInfraSpecific(TaxonNameBase taxonName){

       NonViralName<NonViralName> name =  HibernateProxyHelper.deproxy(taxonName, NonViralName.class);

       String parentName = name.getGenusOrUninomial() + " " + name.getSpecificEpithet();

       return parentName;

    }

}