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.DataType; import edu.monash.merc.domain.TEEvidence; import edu.monash.merc.repository.ITEEvidenceRep; import org.hibernate.Criteria; import org.hibernate.Query; import org.hibernate.criterion.Disjunction; import org.hibernate.criterion.Order; 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.List; /** * @author Simon Yu * <p/> * Email: xiaoming.yu@monash.edu * @version 1.0 * @since 1.0 * <p/> * Date: 8/07/13 12:37 PM */ @Scope(BeanDefinition.SCOPE_PROTOTYPE) @Repository public class TEEvidenceDAO extends HibernateGenericDAO<TEEvidence> implements ITEEvidenceRep { @Override public void deleteTEEvidenceById(long id) { String del_hql = "DELETE FROM " + this.persistClass.getSimpleName() + " AS te WHERE te.id = :id"; Query query = this.session().createQuery(del_hql); query.setLong("id", id); query.executeUpdate(); } @Override public TEEvidence getTESummaryByGeneAndType(long seneId, DataType dataType) { Criteria teEvCriteria = this.session().createCriteria(this.persistClass); Criteria gCriteria = teEvCriteria.createCriteria("gene"); Criteria dtypeCriteria = teEvCriteria.createCriteria("tpbDataType"); gCriteria.add(Restrictions.eq("id", seneId)); Disjunction dtypeOr = Restrictions.disjunction(); //TE if (dataType.equals(DataType.TE)) { dtypeOr.add(Restrictions.eq("dataType", DataType.TE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA_PROP.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.TE_MA)) { dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA_PROP.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.TE_MA_PROP)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.TE_MA_PROP.type())); } else if (dataType.equals(DataType.TE_OTH)) { dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.TE_OTH_CUR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.TE_OTH_CUR.type())); } else { //nothing } teEvCriteria.addOrder(Order.desc("colorLevel")); teEvCriteria.setMaxResults(1); return (TEEvidence) teEvCriteria.uniqueResult(); } @SuppressWarnings("unchecked") @Override public List<TEEvidence> getTEEvidencesByGeneAndType(long geneId, DataType dataType) { Criteria teEvCriteria = this.session().createCriteria(this.persistClass); Criteria gCriteria = teEvCriteria.createCriteria("gene"); Criteria dtypeCriteria = teEvCriteria.createCriteria("tpbDataType"); Criteria acCriteria = teEvCriteria.createCriteria("identifiedAccession"); acCriteria.addOrder(Order.asc("accession")); gCriteria.add(Restrictions.eq("id", geneId)); Disjunction dtypeOr = Restrictions.disjunction(); //TE if (dataType.equals(DataType.TE)) { dtypeOr.add(Restrictions.eq("dataType", DataType.TE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA_PROP.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.TE_MA)) { dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_MA_PROP.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.TE_MA_PROP)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.TE_MA_PROP.type())); } else if (dataType.equals(DataType.TE_OTH)) { dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.TE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.TE_OTH_CUR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.TE_OTH_CUR.type())); } else { //nothing } teEvCriteria.addOrder(Order.desc("colorLevel")); return teEvCriteria.list(); } }