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.Map;

import java.util.Set;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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.common.MarkerType;

import eu.etaxonomy.cdm.model.description.Distribution;

import eu.etaxonomy.cdm.model.description.PresenceTerm;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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

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

/**

 * @author a.mueller

 * @created 27.02.2012

 */

@Component

public class IndexFungorumDistributionImport  extends IndexFungorumImportBase {

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

	private static final String pluralString = "distributions";

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

	public IndexFungorumDistributionImport(){

		super(pluralString, dbTableName, null);

	}

	@Override

	protected String getIdQuery() {

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

				" ORDER BY PreferredNameIFnumber ";

		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 distribution.* " +

				" FROM tblPESIfungi AS distribution  " +

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

			"";

		return strRecordQuery;

	}

	@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();

		try {

			//column names that do not hold distribution information

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

			excludedColumns.add("PreferredName");

			excludedColumns.add("PreferredNameIFnumber");

			excludedColumns.add("PreferredNameFDCnumber");

			PresenceTerm status = PresenceTerm.PRESENT();

			MarkerType noLastActionMarkerType = getNoLastActionMarkerType(state);

			while (rs.next()){

				//get taxon description

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

				Taxon taxon = state.getRelatedObject(NAMESPACE_SPECIES, String.valueOf(id), Taxon.class);

				Reference<?> ref = null;

				if (taxon == null){

					logger.debug("taxon is null for id " + id);

				} else{

					TaxonDescription description = getTaxonDescription(taxon, ref, false, true);

					//handle single distributions

					int count = rs.getMetaData().getColumnCount();

					for (int i=1; i <= count; i++ ){

						String colName = rs.getMetaData().getColumnName(i);

						//exclude non distribution columns

						if (! excludedColumns.contains(colName)){

							String distributionValue = rs.getString(i);

							if (StringUtils.isNotBlank(distributionValue)){

								//create distribution for existing occurrences

								if (! distributionValue.equals("X")){

									logger.warn("Unexpected distribution value '" + distributionValue + "' for area " + colName);

								}

								NamedArea area = state.getTransformer().getNamedAreaByKey(colName);

								Distribution distribution = Distribution.NewInstance(area, status);

								description.addElement(distribution);

								//no last action

								distribution.addMarker(Marker.NewInstance(noLastActionMarkerType, true));

							}

						}

					}

					getTaxonService().saveOrUpdate(taxon);

				}

				//save

			}

		} catch (Exception e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.setSuccess(false);

			success = false;

		}

		return success;

	}

	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>();

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "PreferredNameIFnumber" );

			}

			//taxon map

			nameSpace = NAMESPACE_SPECIES;

			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().isDoOccurrence();

	}

}