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 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 org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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.CdmBase;

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 20.03.2008

 */

@Component

public class BerlinModelOccurrenceSourceImport  extends BerlinModelImportBase {

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

	private static int modCount = 5000;

	private static final String pluralString = "occurrence sources";

	private static final String dbTableName = "emOccurrenceSource";  //??

	private Map<String, Integer> sourceNumberRefIdMap;

	private Set<String> unfoundReferences = new HashSet<String>();

	public BerlinModelOccurrenceSourceImport(){

		super(dbTableName, pluralString);

	}

	@Override

	protected String getIdQuery(BerlinModelImportState state) {

		String result = "SELECT occurrenceSourceId FROM " + getTableName();

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

			result += " WHERE " +  state.getConfig().getOccurrenceSourceFilter();

		}

		return result;

	}

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

			String strQuery =   //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution 

            " SELECT * " + 

                " FROM emOccurrenceSource " +  

            " WHERE (OccurrenceSourceId IN (" + ID_LIST_TOKEN + ")  )" +  

             "";

		return strQuery;

	}

	@Override

	protected void doInvoke(BerlinModelImportState state) {

		unfoundReferences = new HashSet<String>();

		try {

			sourceNumberRefIdMap = makeSourceNumberReferenceIdMap(state);

		} catch (SQLException e) {

			e.printStackTrace();

			throw new RuntimeException(e);

		}

		super.doInvoke(state);

		sourceNumberRefIdMap = null;

		if (unfoundReferences.size()>0){

			String unfound = "'" + CdmUtils.concat("','", unfoundReferences.toArray(new String[]{})) + "'"; 

			logger.warn("Not found references: " + unfound);

		}

		return;

	}

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {

		boolean success = true;

		ResultSet rs = partitioner.getResultSet();

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

		Set<DescriptionElementBase> objectsToSave = new HashSet<DescriptionElementBase>();

		try {

			int i = 0;

			//for each reference

            while (rs.next()){

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

                Integer occurrenceSourceId = rs.getInt("OccurrenceSourceId");

                Integer occurrenceFk =nullSafeInt(rs, "OccurrenceFk");

    			String sourceNumber = rs.getString("SourceNumber");

    			String oldName = rs.getString("OldName");

    			Integer oldNameFk = nullSafeInt(rs, "OldNameFk");

    			Distribution distribution = (Distribution)state.getRelatedObject(BerlinModelOccurrenceImport.NAMESPACE, String.valueOf(occurrenceFk));

    			if (distribution == null){

    				//distribution = duplicateMap.get(occurrenceFk);

    			}

    			if (distribution != null){

    				Integer refId = sourceNumberRefIdMap.get(sourceNumber);

    				Reference<?> ref = refMap.get(String.valueOf(refId));

    				if (ref != null){

    					DescriptionElementSource originalSource = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);

    					originalSource.setCitation(ref);

    					TaxonNameBase<?, ?> taxonName;

						taxonName = getName(state, oldName, oldNameFk);

						if (taxonName != null){

    						originalSource.setNameUsedInSource(taxonName);

    					}else if(isNotBlank(oldName)){

    						originalSource.setOriginalNameString(oldName);

    					}

    					distribution.addSource(originalSource);

    				}else{

    					logger.warn("reference for sourceNumber "+sourceNumber+" could not be found. OccurrenceSourceId: " + occurrenceSourceId );

    					unfoundReferences.add(sourceNumber);

    				}

    			}else{

    				logger.warn("distribution ("+occurrenceFk+") for occurrence source (" + occurrenceSourceId + ") could not be found." );

    			}

            }

			logger.info("Distributions to save: " + objectsToSave.size());

			getDescriptionService().saveDescriptionElement(objectsToSave);	

			return success;

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

	}

	@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> occurrenceIdSet = new HashSet<String>();

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

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

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

			while (rs.next()){

				handleForeignKey(rs, occurrenceIdSet, "occurrenceFk");

				handleForeignKey(rs, nameIdSet, "oldNameFk");

				sourceNumberSet.add(CdmUtils.NzTrim(rs.getString("SourceNumber")));

			}

			sourceNumberSet.remove("");

			referenceIdSet = handleSourceNumber(rs, sourceNumberSet, result);

			//occurrence map

			nameSpace = BerlinModelOccurrenceImport.NAMESPACE;

			cdmClass = Distribution.class;

			idSet = occurrenceIdSet;

			Map<String, Distribution> occurrenceMap = (Map<String, Distribution>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, occurrenceMap);

			//name map

			nameSpace = BerlinModelTaxonNameImport.NAMESPACE;

			cdmClass = TaxonNameBase.class;

			idSet =nameIdSet;

			Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, nameMap);

			//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 Set<String> handleSourceNumber(ResultSet rs, Set<String> sourceNumberSet, Map<Object, Map<String, ? extends CdmBase>> result) {

		Map<String, Integer> sourceNumberReferenceIdMap = this.sourceNumberRefIdMap;

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

		for(String sourceNumber : sourceNumberSet){

			Integer refId = sourceNumberReferenceIdMap.get(sourceNumber);

			referenceIdSet.add(String.valueOf(refId));		

		}

		return referenceIdSet;

	}

	/**

	 * @param state

	 * @param oldName

	 * @param oldNameFk

	 * @return

	 */

	boolean isFirstTimeNoNameByService = true;

	private TaxonNameBase<?, ?> getName(BerlinModelImportState state, String oldName, Integer oldNameFk) {

		TaxonNameBase<?,?> taxonName = (TaxonNameBase)state.getRelatedObject(BerlinModelTaxonNameImport.NAMESPACE, String.valueOf(oldNameFk));

		if (taxonName == null && oldName != null){

			if (isFirstTimeNoNameByService){

				logger.warn("oldName not checked against names in BerlinModel. Just take it as a string");

				isFirstTimeNoNameByService = false;

			}

			List<NonViralName> names = new ArrayList<NonViralName>();

//			names = getNameService().getNamesByNameCache(oldName);

			if (names.size() == 1){

				return names.get(0);

			}else {

				if (names.size()> 2){

					logger.info("There is more than one name matching oldName: " + oldName + ".");

				}

				return null;

				//taxonName = nameParser.parseSimpleName(oldName);

			}

		}

		return taxonName;

	}

	/**

	 * Creates a map which maps source numbers on references

	 * @param state

	 * @return

     * @throws SQLException 

	 */

	private Map<String, Integer> makeSourceNumberReferenceIdMap(BerlinModelImportState state) throws SQLException {

		Map<String, Integer> result = new HashMap<String, Integer>();

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

		String strQuery = " SELECT RefId, IdInSource " +  

						  " FROM Reference " + 

						  " WHERE     (IdInSource IS NOT NULL) AND (IdInSource NOT LIKE '') ";

		ResultSet rs = source.getResultSet(strQuery) ;

		while (rs.next()){

			int refId = rs.getInt("RefId");

			String idInSource = rs.getString("IdInSource");

			if (idInSource != null){

				String[] singleSources = idInSource.split("\\|");

				for (String singleSource : singleSources){

					singleSource = singleSource.trim();

					result.put(singleSource, refId);

				}

			}

		}

		return result;

	}

	@Override

	protected boolean doCheck(BerlinModelImportState state){

		IOValidator<BerlinModelImportState> validator = new BerlinModelOccurrenceSourceImportValidator();

		return validator.validate(state);

	}

	@Override

	protected boolean isIgnore(BerlinModelImportState state){

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

			return true;

		}else{

			if (!this.checkSqlServerColumnExists(state.getConfig().getSource(), "emOccurrenceSource", "OccurrenceSourceId")){

				logger.error("emOccurrenceSource table or emOccurrenceSourceId does not exist. Must ignore occurrence import");

				return true;

			}else{

				return false;

			}

		}

	}

}