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.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

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

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;

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

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

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

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

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

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

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

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;

import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;

/**

 * @author a.mueller

 * @created 27.02.2012

 */

@Component

public class IndexFungorumSpeciesImport  extends IndexFungorumImportBase {

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

	private static final String pluralString = "species";

	private static final String dbTableName = "[tblPESIfungi-IFdata]";

	private final Set<UUID> infraspecificTaxaUUIDs = new HashSet<UUID>();

	public IndexFungorumSpeciesImport(){

		super(pluralString, dbTableName, null);

	}

	@Override

	protected String getIdQuery() {

		String result = " SELECT PreferredNameIFnumber FROM " + getTableName() +

				" ORDER BY PreferredName ";

		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 distribution.PreferredNameFDCnumber, species.* , cl.[Phylum name]" +

				" FROM tblPESIfungi AS distribution RIGHT OUTER JOIN  dbo.[tblPESIfungi-IFdata] AS species ON distribution.PreferredNameIFnumber = species.PreferredNameIFnumber " +

					" LEFT OUTER JOIN [tblPESIfungi-Classification] cl ON species.PreferredName   = cl.PreferredName " +

				" WHERE ( species.PreferredNameIFnumber IN (" + ID_LIST_TOKEN + ") )" +

			"";

		return strRecordQuery;

	}

	@Override

    protected void doInvoke(IndexFungorumImportState state){

        System.out.println("start make " + getPluralString() + " ...");

        IndexFungorumImportConfigurator config = state.getConfig();

        Source source = config.getSource();

        super.doInvoke(state);

        Classification classification = getClassification(state);

        List<TaxonBase> infraspecificTaxa = new ArrayList<TaxonBase>();

        for (UUID uuid: infraspecificTaxaUUIDs){

            infraspecificTaxa.add(getTaxonService().load(uuid));

        }

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

        for (TaxonBase infraspecificTaxon: infraspecificTaxa){

            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);

            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.*");

            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);

        }

	}

	@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()){

				//DisplayName, NomRefCache -> don't use, created by Marc

				Integer id = (Integer)rs.getObject("PreferredNameIFnumber");

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

				String preferredName = rs.getString("PreferredName");

				if (StringUtils.isBlank(preferredName)){

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

				}

				//Rank rank = Rank.SPECIES();

				NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

				NonViralName<?> name = parser.parseSimpleName(preferredName, NomenclaturalCode.ICNAFP, null);

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

				//if name is infraspecific the parent should be the species not the genus

				Taxon parent;

				if (!name.isInfraSpecific()){

				    parent = getParentTaxon(state, rs);

				    if (parent == null){

	                    logger.warn("parent not found for name:" +preferredName);

	                }

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

				}

				//author + publication

				makeAuthorAndPublication(state, rs, name);

				//source

				makeSource(state, taxon, id, NAMESPACE_SPECIES );

				//fossil

				if (FOSSIL_FUNGI.equalsIgnoreCase(phylumName)){

					ExtensionType fossilExtType = getExtensionType(state, ErmsTransformer.uuidFossilStatus, "fossil status", "fossil status", "fos. stat.");

					Extension.NewInstance(taxon, PesiTransformer.STR_FOSSIL_ONLY, fossilExtType);

				}

				//save

				UUID uuidTaxon = getTaxonService().saveOrUpdate(taxon);

				getNameService().saveOrUpdate(name);

				if (name.isInfraSpecific()){

                    infraspecificTaxaUUIDs.add(uuidTaxon);

                }

			}

		} catch (Exception e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.setSuccess(false);

			success = false;

		}

		return success;

	}

	/**

     * @param taxon

     * @return

     */

    private String getParentNameInfraSpecific(TaxonNameBase taxonName){

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

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

       return parentName;

    }

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

		Integer genusId = rs.getInt("PreferredNameFDCnumber");

		Taxon taxon = state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);

		if (taxon == null){

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

		}

		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> taxonIdSet = new HashSet<String>();

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

 			while (rs.next()){

				handleForeignKey(rs, taxonIdSet,"PreferredNameFDCnumber" );

				handleForeignKey(rs, taxonSpeciesNames, "PreferredName");

			}

			//taxon map

			nameSpace = NAMESPACE_GENERA;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

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

			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();

	}

}