Java tutorial
/* * Copyright (c) 2011-2013, Monash e-Research Centre * (Monash University, Australia) * All rights reserved. * * Redistribution and use in source and binary forms, with or without * modification, are permitted provided that the following conditions are met: * * Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * * Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the distribution. * * Neither the name of the Monash University nor the names of its * contributors may be used to endorse or promote products derived from * this software without specific prior written permission. * * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; * without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. * See the GNU Affero General Public License for more details. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * * You should have received a copy of the GNU Affero General Public License along with * this program. If not, see <http://www.gnu.org/licenses/>. */ package edu.monash.merc.dao; import edu.monash.merc.common.name.ChromType; import edu.monash.merc.common.name.DbAcType; import edu.monash.merc.domain.Accession; import edu.monash.merc.domain.Gene; import edu.monash.merc.repository.IGeneRep; import org.hibernate.Criteria; import org.hibernate.Query; import org.hibernate.criterion.Projections; import org.hibernate.criterion.Restrictions; import org.springframework.beans.factory.config.BeanDefinition; import org.springframework.context.annotation.Scope; import org.springframework.stereotype.Repository; import java.util.Date; import java.util.List; /** * GeneDAO class which provides the database operations for Gene object. * * @author Simon Yu * <p/> * Email: xiaoming.yu@monash.edu * @version 1.0 * @since 1.0 * <p/> * Date: 21/05/12 12:20 PM */ @Scope(BeanDefinition.SCOPE_PROTOTYPE) @Repository public class GeneDAO extends HibernateGenericDAO<Gene> implements IGeneRep { /** * {@inheritDoc} */ public void deleteGeneById(long id) { String del_hql = "DELETE FROM " + this.persistClass.getSimpleName() + " AS g WHERE g.id = :id"; Query query = this.session().createQuery(del_hql); query.setLong("id", id); query.executeUpdate(); } /** * {@inheritDoc} */ public Gene getGeneByEnsgAndDbVersion(String ensgAccession, String dbSource, Date versionTime) { Criteria qCriteria = this.session().createCriteria(this.persistClass); Criteria dbsCriteria = qCriteria.createCriteria("dbSource"); qCriteria.add(Restrictions.eq("ensgAccession", ensgAccession).ignoreCase()) .add(Restrictions.eq("createdTime", versionTime)); dbsCriteria.add(Restrictions.eq("dbName", dbSource).ignoreCase()); return (Gene) qCriteria.uniqueResult(); } // @SuppressWarnings("unchecked") // public List<Gene> getGeneByDBSChromVersion(DbAcType dbAcType, ChromType chromType, Date versionTime) { // // String gQueryStr = "SELECT DISTINCT(g) FROM Gene g JOIN g.accessions acs JOIN acs.dbSource dbs WHERE dbs.dbName =:dbName AND g.createdTime =:createdTime AND g.chromosome = :chromosome"; // // String gQueryStr = "SELECT g FROM Gene g JOIN g.dbSource dbs WHERE dbs.dbName = :dbName AND g.createdTime = :createdTime AND g.chromosome = :chromosome"; // Query gQuery = this.session().createQuery(gQueryStr); // gQuery.setString("dbName", dbAcType.type()); // gQuery.setString("chromosome", chromType.chm()); // gQuery.setTimestamp("createdTime", versionTime); // return gQuery.list(); // } /** * {@inheritDoc} */ @SuppressWarnings("unchecked") public List<Gene> getGenesByDBSChromVersion(DbAcType dbAcType, ChromType chromType, Date versionTime) { String gQueryBase = "SELECT g FROM Gene g JOIN g.dbSource dbs WHERE dbs.dbName = :dbName AND g.createdTime = :createdTime AND "; List<String> allNamedChroms = ChromType.allNamedChmTypes(); if (chromType.equals(ChromType.CHMOTHER)) { gQueryBase += "g.chromosome NOT IN (:chromosomes)"; } else { gQueryBase += "g.chromosome = :chromosome"; } Query gQuery = this.session().createQuery(gQueryBase); gQuery.setString("dbName", dbAcType.type()); if (chromType.equals(ChromType.CHMOTHER)) { gQuery.setParameterList("chromosomes", allNamedChroms); } else { gQuery.setString("chromosome", chromType.chm()); } gQuery.setTimestamp("createdTime", versionTime); return gQuery.list(); } /** * {@inheritDoc} */ @SuppressWarnings("unchecked") public List<Gene> getGenesByTLGeneId(long tlGeneId) { String sgQueryStr = "SELECT DISTINCT(g) FROM Gene g JOIN g.tlGenes tlgs WHERE tlgs.id = :tlGeneId"; Query sgQuery = this.session().createQuery(sgQueryStr); sgQuery.setLong("tlGeneId", tlGeneId); return sgQuery.list(); } /** * {@inheritDoc} */ @SuppressWarnings("unchecked") public List<Accession> getAllAssociatedAccessionsByGeneId(long geneId) { String acQueryStr = "SELECT DISTINCT(gacs) FROM Gene g JOIN g.accessions gacs WHERE g.id = :geneId"; Query acQuery = this.session().createQuery(acQueryStr); acQuery.setLong("geneId", geneId); return acQuery.list(); } }