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.erms;

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

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

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

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

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

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

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

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

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.IImportConfigurator;

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

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

import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;

import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsSourceUsesImportValidator;

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

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

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

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

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

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

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.name.TaxonName;

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

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

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

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

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

/**

 * @author a.mueller

 * @since 20.02.2010

 */

@Component

public class ErmsSourceUsesImport  extends ErmsImportBase<CommonTaxonName> {

    private static final long serialVersionUID = -5139234838768878653L;

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

//	private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping; //not needed

	private static final String pluralString = "source uses";

	private static final String dbTableName = "tu_sources";

	private static final Class<?> cdmTargetClass = null;

	public ErmsSourceUsesImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	@Override

	protected String getIdQuery() {

		String strQuery = " SELECT sourceuse_id, source_id, tu_id " + " " +

						" FROM tu_sources " +

						" ORDER BY sourceuse_id, source_id, tu_id  ";

		return strQuery;

	}

	@Override

	protected String getRecordQuery(ErmsImportConfigurator config) {

		String strRecordQuery =

			" SELECT * " +

			" FROM tu_sources INNER JOIN sourceuses ON tu_sources.sourceuse_id = sourceuses.sourceuse_id" +

			" WHERE ( tu_sources.sourceuse_id IN (" + ID_LIST_TOKEN + ") AND " +

			" 		tu_sources.source_id IN (" + ID_LIST_TOKEN + ") AND " +

			"		tu_sources.tu_id IN (" + ID_LIST_TOKEN + ")  )";

		return strRecordQuery;

	}

	@Override

    public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, ErmsImportState state) {

		boolean success = true ;

		Set objectsToSave = new HashSet<>();

// 		DbImportMapping<?, ?> mapping = getMapping();

//		mapping.initialize(state, cdmTargetClass);

		ResultSet rs = partitioner.getResultSet();

		try{

			while (rs.next()){

				//success &= mapping.invoke(rs,referencesToSave);

				//read and normalize values

				int sourceUseId = rs.getInt("sourceuse_id");

				int sourceId = rs.getInt("source_id");

				String strSourceId = String.valueOf(sourceId);

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

				String strTaxonId = String.valueOf(taxonId);

				String strPageNr = rs.getString("pagenr");

				if (StringUtils.isBlank(strPageNr)){

					strPageNr = null;

				}

				Reference ref = (Reference)state.getRelatedObject(ErmsImportBase.REFERENCE_NAMESPACE, strSourceId);

				try {

				IdentifiableEntity<?> objectToSave = null;

				//invoke methods for each sourceUse type

				if (sourceUseId == SOURCE_USE_ORIGINAL_DESCRIPTION){

					objectToSave = makeOriginalDescription(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_BASIS_OF_RECORD){

					objectToSave = makeBasisOfRecord(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_ADDITIONAL_SOURCE){

					objectToSave = makeAdditionalSource(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_SOURCE_OF_SYNONYMY){

					objectToSave = makeSourceOfSynonymy(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_REDESCRIPTION){

					objectToSave = makeRedescription(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_NEW_COMBINATION_REFERENCE){

					objectToSave = makeCombinationReference(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_STATUS_SOURCE){

					objectToSave = makeStatusSource(partitioner, state, ref, strTaxonId, strPageNr);

				}else if (sourceUseId == SOURCE_USE_EMENDATION){

					objectToSave = makeEmendation(partitioner, state, ref, strTaxonId, strPageNr);

				}

				if(objectToSave != null){

					objectsToSave.add(objectToSave);

				}

				} catch (Exception e) {

					e.printStackTrace();

					success = false;

			}

			}

		} catch (SQLException e) {

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

			return false;

		}

		partitioner.startDoSave();

		getCommonService().save(objectsToSave);

		return success;

	}

	/**

	 * @param strTaxonId

	 * @param ref

	 * @param state

	 * @param partitioner

	 * @param strPageNr

	 *

	 */

	private TaxonName makeOriginalDescription(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

	    TaxonName taxonName = (TaxonName)state.getRelatedObject(ErmsImportBase.NAME_NAMESPACE, strTaxonId);

		taxonName.setNomenclaturalReference(ref);

		taxonName.setNomenclaturalMicroReference(strPageNr);

		return taxonName;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private boolean isFirstBasisOfRecord = true;

	@SuppressWarnings("unused")

    private IdentifiableEntity<?> makeBasisOfRecord(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		if (isFirstBasisOfRecord){

			logger.warn("Basis of record not yet implemented");

			isFirstBasisOfRecord = false;

		}

		return null;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private IdentifiableEntity<?> makeAdditionalSource(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		Feature citationFeature = Feature.CITATION();

		DescriptionElementBase element = TextData.NewInstance(citationFeature);

		DescriptionElementSource source = element.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, strPageNr);

		if (source == null){

			logger.warn("Source is null");

			return null;

		}

		TaxonBase<?> taxonBase = (TaxonBase<?>)state.getRelatedObject(ErmsImportBase.TAXON_NAMESPACE, strTaxonId);

		Taxon taxon;

		//if taxon base is a synonym, add the description to the accepted taxon

		if (taxonBase.isInstanceOf(Synonym.class)){

			Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);

			taxon = synonym.getAcceptedTaxon();

			if (taxon == null){

				String warning = "Synonym "+ strTaxonId + " has no accepted taxon";

				logger.warn(warning);

				return null;

				//throw new IllegalStateException(warning);

			}

			//add synonym name as name used in source

			source.setNameUsedInSource(synonym.getName());

		}else{

			taxon = (Taxon)taxonBase;

		}

		//get or create description and add the element

		TaxonDescription description;

		if (taxon.getDescriptions().size() > 0){

			description = taxon.getDescriptions().iterator().next();

		}else{

			description = TaxonDescription.NewInstance(taxon);

		}

		description.addElement(element);

		return taxon;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private IdentifiableEntity<?> makeSourceOfSynonymy(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		TaxonBase<?> taxonBase = (TaxonBase<?>)state.getRelatedObject(ErmsImportBase.TAXON_NAMESPACE, strTaxonId);

		if (taxonBase == null){

			String warning = "taxonBase (id = " + strTaxonId + ") could not be found ";

			logger.warn(warning);

			return null;

		}else if (! taxonBase.isInstanceOf(Synonym.class)){

			String message = "TaxonBase is not of class Synonym but " + taxonBase.getClass().getSimpleName();

			logger.info(message);

			Taxon taxon =CdmBase.deproxy(taxonBase, Taxon.class);

			Set<TaxonRelationship> synRels = taxon.getTaxonRelations();

			if (synRels.size() != 1){

				logger.warn("TaxonSynonym (" + strTaxonId + ") has not 1 but " + synRels.size() + " relations!");

			}else{

				TaxonRelationship synRel = synRels.iterator().next();

				synRel.setCitation(ref);

				synRel.setCitationMicroReference(strPageNr);

			}

		}else{

			Synonym synonym =CdmBase.deproxy(taxonBase, Synonym.class);

			synonym.setSec(ref);

			synonym.setSecMicroReference(strPageNr);

		}

		return taxonBase;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private boolean isFirstRediscription = true;

	@SuppressWarnings("unused")

    private IdentifiableEntity<?> makeRedescription(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		if (isFirstRediscription){

			logger.warn("Rediscription not yet implemented");

			isFirstRediscription = false;

		}

		return null;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private IdentifiableEntity<?> makeCombinationReference(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		// Kopie von Orig. Comb.

		//TODO ist das wirklich der richtige Name, oder muss ein verknüpfter Name verwendet werden

	    TaxonName taxonName = (TaxonName)state.getRelatedObject(ErmsImportBase.NAME_NAMESPACE, strTaxonId);

		taxonName.setNomenclaturalReference(ref);

		taxonName.setNomenclaturalMicroReference(strPageNr);

		return taxonName;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private boolean isFirstStatusSource = true;

	@SuppressWarnings("unused")

    private IdentifiableEntity<?> makeStatusSource(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		if (isFirstStatusSource){

			logger.warn("StatusSource not yet implemented");

			isFirstStatusSource = false;

		}

		return null;

	}

	/**

	 * @param partitioner

	 * @param state

	 * @param ref

	 * @param strTaxonId

	 * @param strPageNr

	 */

	private boolean isFirstEmendation = true;

	@SuppressWarnings("unused")

    private IdentifiableEntity<?> makeEmendation(ResultSetPartitioner<?> partitioner, ErmsImportState state, Reference ref, String strTaxonId, String strPageNr) {

		if (isFirstEmendation){

			logger.warn("Emmendation not yet implemented");

			isFirstEmendation = false;

		}

		return null;

	}

	@SuppressWarnings("unused")

    public CommonTaxonName createObject(ResultSet rs, ErmsImportState state)

			throws SQLException {

		return null;  //not needed

	}

//************************************ RELATED OBJECTS *************************************************/

	@Override

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, ErmsImportState state) {

		String nameSpace;

		Class<?> cdmClass;

		Set<String> idSet;

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();

		try{

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

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

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

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "tu_id");

				handleForeignKey(rs, nameIdSet, "tu_id");

				handleForeignKey(rs, referenceIdSet, "source_id");

			}

			//name map

			nameSpace = ErmsImportBase.NAME_NAMESPACE;

			cdmClass = TaxonName.class;

			idSet = nameIdSet;

			@SuppressWarnings("unchecked")

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

			result.put(nameSpace, nameMap);

			//taxon map

			nameSpace = ErmsImportBase.TAXON_NAMESPACE;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

			@SuppressWarnings("unchecked")

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

			result.put(nameSpace, taxonMap);

			//reference map

			nameSpace = ErmsImportBase.REFERENCE_NAMESPACE;

			cdmClass = Reference.class;

			idSet = referenceIdSet;

			@SuppressWarnings("unchecked")

            Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(Reference.class, idSet, nameSpace);

			result.put(nameSpace, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	@Override

	protected boolean doCheck(ErmsImportState state){

		IOValidator<ErmsImportState> validator = new ErmsSourceUsesImportValidator();

		return validator.validate(state);

	}

	@Override

    protected boolean isIgnore(ErmsImportState state){

		boolean result = state.getConfig().getDoReferences() != IImportConfigurator.DO_REFERENCES.ALL;

		result |= ! state.getConfig().isDoTaxa();

		return result;

	}

	@Override

	protected DbImportMapping<?, ?> getMapping() {

		logger.info("getMapping not implemented for EmrsSourceUsesImport");

		return null;  // not needed because Mapping is not implemented in this class yet

	}

}