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;

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

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

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

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.Collection;

import java.util.HashSet;

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.common.ICdmIO;

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 20.03.2008

 * @version 1.0

 */

@Component

public class BerlinModelFactsImport  extends BerlinModelImportBase {

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

	private int modCount = 10000;

	public BerlinModelFactsImport(){

		super();

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	@Override

	protected boolean doCheck(IImportConfigurator config){

		boolean result = true;

		logger.warn("Checking for Facts not yet implemented");

		//result &= checkArticlesWithoutJournal(bmiConfig);

		//result &= checkPartOfJournal(bmiConfig);

		return result;

	}

	private TermVocabulary<Feature> getFeatureVocabulary(){

		try {

			//TODO work around until service method works

			TermVocabulary<Feature> featureVocabulary =  BerlinModelTransformer.factCategory2Feature(1).getVocabulary();

			//TermVocabulary<Feature> vocabulary = getTermService().getVocabulary(vocabularyUuid);

			return featureVocabulary;

		} catch (UnknownCdmTypeException e) {

			logger.error("Feature vocabulary not available. New vocabulary created");

			return new TermVocabulary<Feature>() ;

		}

	}

	private MapWrapper<Feature> invokeFactCategories(BerlinModelImportConfigurator bmiConfig){

//		Map<Integer, Feature> featureMap = new HashMap<Integer, Feature>();

		MapWrapper<Feature> result = bmiConfig.getFeatureMap();

		Source source = bmiConfig.getSource();

		try {

			//get data from database

			String strQuery = 

					" SELECT FactCategory.* " + 

					" FROM FactCategory "+

                    " WHERE (1=1)";

			ResultSet rs = source.getResultSet(strQuery) ;

			TermVocabulary<Feature> featureVocabulary = getFeatureVocabulary();

			int i = 0;

			//for each reference

			while (rs.next()){

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

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

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

				Feature feature;

				try {

					feature = BerlinModelTransformer.factCategory2Feature(factCategoryId);

				} catch (UnknownCdmTypeException e) {

					logger.warn("New Feature (FactCategoryId: " + factCategoryId + ")");

					feature = Feature.NewInstance(factCategory, factCategory, null);

					feature.setVocabulary(featureVocabulary);

					feature.setSupportsTextData(true);

					//TODO

//					MaxFactNumber	int	Checked

//					ExtensionTableName	varchar(100)	Checked

//					Description	nvarchar(1000)	Checked

//					locExtensionFormName	nvarchar(80)	Checked

//					RankRestrictionFk	int	Checked

				}

			//	featureMap.put(factCategoryId, feature);

				result.put(factCategoryId, feature);

			}

			Collection<Feature> col = result.getAllValues();

			getTermService().saveTermsAll(col);

			return result;

		} catch (SQLException e) {

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

			return null;

		}

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)

	 */

	@Override

	protected boolean doInvoke(IImportConfigurator config,

			Map<String, MapWrapper<? extends CdmBase>> stores){

		boolean result = true;

		MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);

		MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);

		MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_STORE);

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

		BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;

		Source source = bmiConfig.getSource();

		logger.info("start makeFacts ...");

		MapWrapper<Feature> featureMap = invokeFactCategories(bmiConfig);

		//for testing only

		//TaxonBase taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(null), null);

		try {

			//get data from database

			String strQuery = 

					" SELECT Fact.*, PTaxon.RIdentifier as taxonId, RefDetail.Details " + 

					" FROM Fact " +

                      	" INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk " +

                      	" LEFT OUTER JOIN RefDetail ON Fact.FactRefDetailFk = RefDetail.RefDetailId AND Fact.FactRefFk = RefDetail.RefFk " +

                      	" WHERE (1=1)";

			ResultSet rs = source.getResultSet(strQuery) ;

			int i = 0;

			//for each reference

			while (rs.next()){

				try{

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

					//Map<String, Object> valueMap = getValueMap(rs);

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

					Object taxonIdObj = rs.getObject("taxonId");

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

					Object factRefFkObj = rs.getObject("factRefFk");

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

					Object categoryFkObj = rs.getObject("factCategoryFk");

					Integer categoryFk = rs.getInt("factCategoryFk");

					String details = rs.getString("Details");

	//				int ptDesignationRefFk = rs.getInt("PTDesignationRefFk");

	//				String ptDesignation details = rs.getInt("PTDesignationRefDetailFk");

					String fact = CdmUtils.Nz(rs.getString("Fact"));

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

					TaxonBase taxonBase;

					if (taxonIdObj != null){

						taxonBase = taxonMap.get(taxonId);

					}else{

						taxonBase = null;

					}

					Feature feature;

					if (categoryFkObj != null){

						feature = featureMap.get(categoryFk); 

					}else{

						feature = null;

					}

					if (taxonBase != null){

						Taxon taxon;

						if ( taxonBase instanceof Taxon ) {

							taxon = (Taxon) taxonBase;

						}else{

							logger.warn("TaxonBase " + (taxonIdObj==null?"(null)":taxonIdObj) + " for Fact " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());

							continue;

						}

						TaxonDescription taxonDescription;

						Set<TaxonDescription> descriptionSet= taxon.getDescriptions();

						if (descriptionSet.size() > 0) {

							taxonDescription = descriptionSet.iterator().next(); 

						}else{

							taxonDescription = TaxonDescription.NewInstance();

							taxon.addDescription(taxonDescription);

						}

						//textData

						TextData textData = TextData.NewInstance();

						//TODO textData.putText(fact, bmiConfig.getFactLanguage());  //doesn't work because  bmiConfig.getFactLanguage() is not not a persistent Language Object

						//throws  in thread "main" org.springframework.dao.InvalidDataAccessApiUsageException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language; nested exception is org.hibernate.TransientObjectException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language

						//for diptera database

						if (categoryFk == 99 && notes.contains("<OriginalName>")){

							notes = notes.replaceAll("<OriginalName>", "");

							notes = notes.replaceAll("</OriginalName>", "");

							fact = notes + ": " +  fact ;

						}

						textData.putText(fact, Language.DEFAULT());

						textData.setType(feature);

						//

						ReferenceBase citation;

						if (factRefFkObj != null){

							citation = referenceMap.get(factRefFk);	

							if (citation == null){

								citation = nomRefMap.get(factRefFk);

							}

							if (citation == null && (factRefFk != 0)){

								logger.warn("Citation not found in referenceMap: " + factRefFk);

							}

						}else{

							citation = null;

						}

						textData.setCitation(citation);

						textData.setCitationMicroReference(details);

						taxonDescription.addElement(textData);

//						if (categoryFkObj == FACT_DESCRIPTION){

//							//;

//						}else if (categoryFkObj == FACT_OBSERVATION){

//							//;

//						}else if (categoryFkObj == FACT_DISTRIBUTION_EM){

//							//

//						}else {

//							//TODO

//							//logger.warn("FactCategory " + categoryFk + " not yet implemented");

//						}

						//TODO

						//References

						//etc.

						//TODO created, notes

						//doIdCreatedUpdatedNotes(bmiConfig, textData, rs, factId);

						taxonStore.add(taxon);

					}else{

						//TODO

						logger.warn("Taxon for Fact " + factId + " does not exist in store");

					}

				} catch (RuntimeException re){

					logger.error("A runtime exception occurred during the facts import");

					result = false;

					throw re;

				}

				//put

			}

			logger.info("Facts handled: " + (i-1));

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

			getTaxonService().saveTaxonAll(taxonStore);	

			logger.info("end makeFacts ...");

			return result;

		} catch (SQLException e) {

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

			return false;

		}

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	protected boolean isIgnore(IImportConfigurator config){

		return ! config.isDoFacts();

	}

}