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 java.util.UUID;

import org.apache.commons.lang3.StringUtils;

import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;

import eu.etaxonomy.cdm.api.service.ITermService;

import eu.etaxonomy.cdm.api.service.IVocabularyService;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.term.DefinedTermBase;

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

/**

 * This class maps a database attribute to CDM annotation added to the target class

 * TODO maybe this class should not inherit from DbSingleAttributeImportMapperBase

 * as it does not map to a single attribute

 * @author a.mueller

 * @since 01.03.2010

 */

public class DbImportAnnotationMapper

            extends DbSingleAttributeImportMapperBase<DbImportStateBase<?,?>, AnnotatableEntity>{

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

    private MarkerType ifNullMarkerType;

	/**

	 * FIXME Warning: the annotation type creation is not yet implemented

	 * @param dbAttributeString

	 * @param uuid

	 * @param label

	 * @param text

	 * @param labelAbbrev

	 * @return

	 */

    @Deprecated

	public static DbImportAnnotationMapper NewInstance(String dbAttributeString, UUID uuid, String label, String text, String labelAbbrev){

		Language language = null;

		AnnotationType annotationType = null;

		return new DbImportAnnotationMapper(dbAttributeString, language, annotationType, null);

	}

    /**

     * @param dbAttributeString

     * @param annotationType

     * @param ifNullMarkerType the type of marker to set if the annotation value is null

     * @return

     */

    public static DbImportAnnotationMapper NewInstance(String dbAttributeString, AnnotationType annotationType,

            MarkerType ifNullMarkerType) {

        return new DbImportAnnotationMapper(dbAttributeString, null, annotationType, ifNullMarkerType);

    }

	/**

	 * * FIXME Warning: the annotation type creation is not yet implemented

	 * @param dbAttributeString

	 * @param uuid

	 * @param label

	 * @param text

	 * @param labelAbbrev

	 * @return

	 */

	public static DbImportAnnotationMapper NewInstance(String dbAttributeString, UUID uuid, String label, String text, String labelAbbrev, Language language){

		AnnotationType annotationType = null;

		return new DbImportAnnotationMapper(dbAttributeString, language, annotationType, null);

	}

	/**

	 * @param dbAttributeString

	 * @param annotationType

	 * @return

	 */

	public static DbImportAnnotationMapper NewInstance(String dbAttributeString, AnnotationType annotationType){

		Language language = null;

		return NewInstance(dbAttributeString, annotationType, language);

	}

	/**

	 * @param dbAttributeString

	 * @param annotationType

	 * @param language

	 * @return

	 */

	public static DbImportAnnotationMapper NewInstance(String dbAttributeString, AnnotationType annotationType, Language language){

		return new DbImportAnnotationMapper(dbAttributeString, language, annotationType, null);

	}

	private AnnotationType annotationType;

	private Language language;

	private DbImportAnnotationMapper(String dbAttributeString, Language language, AnnotationType annotationType,

	        MarkerType ifNullMarkerType) {

		super(dbAttributeString, dbAttributeString);

		this.language = language;

		this.annotationType = annotationType;

		this.ifNullMarkerType = ifNullMarkerType;

	}

	@Override

	public void initialize(DbImportStateBase<?,?> state, Class<? extends CdmBase> destinationClass) {

		importMapperHelper.initialize(state, destinationClass);

	}

//	/**

//	 * @param service

//	 * @param state

//	 * @param tableName

//	 */

//	public void initialize(ITermService service, DbImportStateBase state, Class<? extends CdmBase> destinationClass) {

//		importMapperHelper.initialize(state, destinationClass);

//		try {

//			if (  checkDbColumnExists()){

//				if (this.annotationType == null){

//					this.annotationType = getAnnotationType(service, uuid, label, text, labelAbbrev);

//				}

//			}else{

//				ignore = true;

//			}

//		} catch (MethodNotSupportedException e) {

//			//do nothing

//		}

//	}

	@Override

	public AnnotatableEntity invoke(ResultSet rs, AnnotatableEntity annotatableEntity) throws SQLException {

		if (ignore){

			return annotatableEntity;

		}

		String dbValue = rs.getString(getSourceAttribute());

		return doInvoke(annotatableEntity, dbValue);

	}

	@Override

	protected AnnotatableEntity doInvoke(AnnotatableEntity annotatableEntity, Object dbValue){

		String strAnnotation = (String)dbValue;

		if (StringUtils.isNotBlank(strAnnotation)){

			Annotation annotation = Annotation.NewInstance(strAnnotation.trim(), annotationType, language);

			if (annotatableEntity != null){

				annotatableEntity.addAnnotation(annotation);

			}

		}else if(this.ifNullMarkerType != null){

		    annotatableEntity.addMarker(ifNullMarkerType, true);

		}

		return annotatableEntity;

	}

	protected AnnotationType getAnnotationType(CdmImportBase<?, ?> currentImport, UUID uuid, String label, String text, String labelAbbrev){

		ITermService termService = currentImport.getTermService();

		AnnotationType annotationType = (AnnotationType)termService.find(uuid);

		if (annotationType == null){

			annotationType = AnnotationType.NewInstance(text, label, labelAbbrev);

			annotationType.setUuid(uuid);

			//set vocabulary //TODO allow user defined vocabularies

			UUID uuidAnnotationTypeVocabulary = UUID.fromString("ca04609b-1ba0-4d31-9c2e-aa8eb2f4e62d");

			IVocabularyService vocService = currentImport.getVocabularyService();

			@SuppressWarnings("unchecked")

            TermVocabulary<DefinedTermBase<?>> voc = vocService.find(uuidAnnotationTypeVocabulary);

			if (voc != null){

				voc.addTerm(annotationType);

			}else{

				logger.warn("Could not find default annotation type vocabulary. Vocabulary not set for new annotation type.");

			}

			//savetermService.save(annotationType);

		}

		return annotationType;

	}

	//not used

	@Override

    public Class<String> getTypeClass(){

		return String.class;

	}

}