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.common.mapping;

import java.sql.ResultSet;

import java.sql.SQLException;

import org.apache.log4j.Logger;

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

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

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

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

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

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

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

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

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

/**

 * TODO synonyms are no relationships anymore, maybe we need to change something here

 * @author a.mueller

 * @since 02.03.2010

 * @param <CDM_BASE>

 * @param <STATE>

 */

public class DbImportSynonymMapper<STATE extends DbImportStateBase<?,?>> extends DbImportMultiAttributeMapperBase<CdmBase, STATE> {

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

//******************************** FACTORY METHOD ***************************************************/

	/**

	 * Creates a new instance of SynonymMapper.

	 * @param dbFromAttribute

	 * @param dbToAttribute

	 * @param relatedObjectNamespace

	 * @param relTypeAttribute

	 * @param taxonRelationshipType this relationship type is taken for accepted taxa being synonyms (may be the case if data are dirty)

	 * @return

	 */

	public static DbImportSynonymMapper<?> NewInstance(String dbFromAttribute, String dbToAttribute, String relatedObjectNamespace, String relTypeAttribute, TaxonRelationshipType taxonRelationshipType){

		return new DbImportSynonymMapper(dbFromAttribute, dbToAttribute, taxonRelationshipType, relatedObjectNamespace, relTypeAttribute);

	}

//******************************* ATTRIBUTES ***************************************/

	private String fromAttribute;

	private String toAttribute;

	private TaxonRelationshipType relType;

	private String relatedObjectNamespace;

	private String citationAttribute;

	private String microCitationAttribute;

	private String relationshipTypeAttribute;

	private boolean useTaxonRelationship;

//********************************* CONSTRUCTOR ****************************************/

	/**

	 * @param relatedObjectNamespace

	 * @param mappingImport

	 */

	protected DbImportSynonymMapper(String fromAttribute, String toAttribute, TaxonRelationshipType relType, String relatedObjectNamespace, String relTypeAttribute) {

		super();

		//TODO make it a single attribute mapper

		this.fromAttribute = fromAttribute;

		this.toAttribute = toAttribute;

		this.relType = relType;

		this.relatedObjectNamespace = relatedObjectNamespace;

		this.relationshipTypeAttribute = relTypeAttribute;

		if (relTypeAttribute != null){

			logger.warn("Synonymrelationship type not yet implemented");

		}

		this.useTaxonRelationship = (relType != null);

	}

//************************************ METHODS *******************************************/

	@Override

    public CdmBase invoke(ResultSet rs, CdmBase cdmBase) throws SQLException {

		STATE state = getState();

		ICdmIO<?> currentImport = state.getCurrentIO();

		if (currentImport instanceof ICheckIgnoreMapper){

			boolean ignoreRecord = ((ICheckIgnoreMapper)currentImport).checkIgnoreMapper(this, rs);

			if (ignoreRecord){

				return cdmBase;

			}

		}

		TaxonBase<?> fromObject = (TaxonBase<?>)getRelatedObject(rs, fromAttribute);

		TaxonBase<?> toObject = (TaxonBase<?>)getRelatedObject(rs, toAttribute);

		String fromId = rs.getObject(fromAttribute)== null ? null: String.valueOf(rs.getObject(fromAttribute));

		String toId = rs.getObject(toAttribute) == null? null : String.valueOf(rs.getObject(toAttribute));

		if (toId == null){

			return fromObject;

		}

		Reference citation = CdmBase.deproxy(getRelatedObject(rs, citationAttribute), Reference.class);

		String microCitation = null;

		if (citationAttribute != null){

			microCitation = rs.getString(microCitationAttribute);

		}

		if (fromObject == null){

			String warning  = "The synonym (" + fromId + ") could not be found. Synonym not added to accepted taxon";

			logger.warn(warning);

			return cdmBase;

		}

		checkSynonymType(fromObject, fromId);

		if (toObject == null){

			String warning  = "The accepted taxon (" + toId + ") could not be found. Synonym not added to accepted taxon";

			logger.warn(warning);

			return cdmBase;

		}

		Taxon taxon = checkTaxonType(toObject, "Accepted taxon", toId);

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

			SynonymType relType = SynonymType.SYNONYM_OF();

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

			taxon.addSynonym(synonym, relType); //citation and micro citation not in use anymore as we do not have synonym relationships anymore

		}else if (fromObject.isInstanceOf(Taxon.class)  && this.useTaxonRelationship){

			TaxonRelationshipType type = relType;

			Taxon synonymTaxon = CdmBase.deproxy(fromObject, Taxon.class);

			synonymTaxon.addTaxonRelation(taxon, type, citation, microCitation);

		}else{

			logger.warn("Taxon is not a synonym and accepted taxa are not allowed as synonyms: " +  fromObject.getTitleCache() + "; " + fromObject.getId());

		}

		return fromObject;

	}

	/**

	 *	//TODO copied from DbImportObjectMapper. Maybe these can be merged again in future

	 * @param rs

	 * @param dbAttribute

	 * @return

	 * @throws SQLException

	 */

	protected CdmBase getRelatedObject(ResultSet rs, String dbAttribute) throws SQLException {

		CdmBase result = null;

		if (dbAttribute != null){

			Object dbValue = rs.getObject(dbAttribute);

			String id = String.valueOf(dbValue);

			DbImportStateBase<?,?> state = importMapperHelper.getState();

			result = state.getRelatedObject(relatedObjectNamespace, id);

		}

		return result;

	}

	/**

	 * Checks if cdmBase is of type Taxon

	 * @param fromObject

	 */

	private Taxon checkTaxonType(TaxonBase<?> taxonBase, String typeString, String id) {

		if (! taxonBase.isInstanceOf(Taxon.class)){

			String warning = typeString + " (" + id + ") is not of type Taxon but of type " + taxonBase.getClass().getSimpleName();

			logger.warn(warning);

			throw new IllegalArgumentException(warning);

		}

		return (CdmBase.deproxy(taxonBase, Taxon.class));

	}

	/**

	 * Checks if cdmBase is of type Synonym

	 * @param fromObject

	 */

	private TaxonBase<?> checkSynonymType(CdmBase cdmBase, String id) {

		if (! cdmBase.isInstanceOf(Synonym.class)){

			String warning = "Synonym (" + id + ") is not of type Synonym but of type " + cdmBase.getClass().getSimpleName();

			if (! this.useTaxonRelationship){

				logger.warn(warning);

				throw new IllegalArgumentException(warning);

			}else{

				logger.info(warning);

			}

		}

		return (CdmBase.deproxy(cdmBase, TaxonBase.class));

	}

}