/**
 * Copyright © 2011-2012 EMBL - European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License"); 
 * you may not use this file except in compliance with the License.  
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.phenotype.dao;

/**
 *
 * Strain data access manager implementation.
 * 
 * @author Gautier Koscielny (EMBL-EBI) <koscieln@ebi.ac.uk>
 * @since February 2012
 */

import java.util.List;

import org.hibernate.SessionFactory;
import org.springframework.transaction.annotation.Transactional;

import uk.ac.ebi.phenotype.pojo.GenomicFeature;
import uk.ac.ebi.phenotype.pojo.Strain;



public class StrainDAOImpl extends HibernateDAOImpl implements
StrainDAO {

	public StrainDAOImpl(SessionFactory sessionFactory) {
		this.sessionFactory = sessionFactory;
	}

	@Override
	@SuppressWarnings("unchecked")
	public List<Strain> getAllStrains() {
		return getCurrentSession().createQuery("from Strain").list();
	}

	@Transactional(readOnly = true)
	@SuppressWarnings("unchecked")
	public Strain getStrainByName(String name) {
		return (Strain) getCurrentSession().createQuery("from Strain as s where s.name= ?").setString(0, name).uniqueResult();
	}

	@Transactional(readOnly = true)
	@SuppressWarnings("unchecked")
	public Strain getStrainBySynonym(String name) {
		// select mother from Cat as mother, Cat as kit
		//where kit in elements(foo.kittens)
		//return (Strain) getCurrentSession().createQuery("select strain from Strain as strain, Synonym as synonym where synonym in elements(strain.synonyms) and synonym.symbol = ?").setString(0, name).uniqueResult();
		return (Strain) getCurrentSession().createQuery("from Strain as strain left join strain.synonyms as synonym where synonym.symbol = ?").setString(0, name).uniqueResult();
	}

	@Transactional(readOnly = false)
	public void saveStrain(Strain strain) {
		getCurrentSession().saveOrUpdate(strain);

	}

}

/**
 * Copyright © 2011-2013 EMBL - European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License"); 
 * you may not use this file except in compliance with the License.  
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.phenotype.dao;

/**
 *
 * Strain data access manager implementation.
 * 
 * @author Gautier Koscielny (EMBL-EBI) <koscieln@ebi.ac.uk>
 * @since February 2012
 */

import java.util.List;

import org.hibernate.SessionFactory;
import org.springframework.transaction.annotation.Transactional;

import uk.ac.ebi.phenotype.pojo.Strain;



public class StrainDAOImpl extends HibernateDAOImpl implements
StrainDAO {

	public StrainDAOImpl(SessionFactory sessionFactory) {
		this.sessionFactory = sessionFactory;
	}

	@Override
	@SuppressWarnings("unchecked")
	public List<Strain> getAllStrains() {
		return getCurrentSession().createQuery("from Strain").list();
	}

	@Transactional(readOnly = true)
	public Strain getStrainByName(String name) {
		return (Strain) getCurrentSession().createQuery("from Strain as s where s.name= ?").setString(0, name).uniqueResult();
	}

	@Transactional(readOnly = true)
	public Strain getStrainBySynonym(String name) {
		// select mother from Cat as mother, Cat as kit
		//where kit in elements(foo.kittens)
		//return (Strain) getCurrentSession().createQuery("select strain from Strain as strain, Synonym as synonym where synonym in elements(strain.synonyms) and synonym.symbol = ?").setString(0, name).uniqueResult();
		return (Strain) getCurrentSession().createQuery("from Strain as strain left join strain.synonyms as synonym where synonym.symbol = ?").setString(0, name).uniqueResult();
	}

	@Transactional(readOnly = false)
	public void saveStrain(Strain strain) {
		getCurrentSession().saveOrUpdate(strain);

	}

}

Change copyright in Apache 2 license to 2013