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.PTMEvidence; import edu.monash.merc.repository.IPTMEvidenceRep; 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: 17/06/13 12:23 PM */ @Scope(BeanDefinition.SCOPE_PROTOTYPE) @Repository public class PTMEvidenceDAO extends HibernateGenericDAO<PTMEvidence> implements IPTMEvidenceRep { /** * {@inheritDoc} */ @Override public void deletePTMEvidenceById(long id) { String del_hql = "DELETE FROM " + this.persistClass.getSimpleName() + " AS ptev WHERE ptev.id = :id"; Query query = this.session().createQuery(del_hql); query.setLong("id", id); query.executeUpdate(); } /** * {@inheritDoc} */ @Override public PTMEvidence getPTMSummaryByGeneAndType(long geneId, DataType dataType) { Criteria ptmEvCriteria = this.session().createCriteria(this.persistClass); Criteria gCriteria = ptmEvCriteria.createCriteria("gene"); Criteria dtypeCriteria = ptmEvCriteria.createCriteria("tpbDataType"); gCriteria.add(Restrictions.eq("id", geneId)); Disjunction dtypeOr = Restrictions.disjunction(); //PTM if (dataType.equals(DataType.PTM)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PTM.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_SER.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_TYR.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_THR.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_LYS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_NTA.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PTM_PHS)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_SER.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_TYR.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_THR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PTM_PHS_SER)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_PHS_SER.type())); } else if (dataType.equals(DataType.PTM_PHS_TYR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_PHS_TYR.type())); } else if (dataType.equals(DataType.PTM_PHS_THR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_PHS_THR.type())); } else if (dataType.equals(DataType.PTM_ACE)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_LYS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_NTA.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PTM_ACE_LYS)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_ACE_LYS.type())); } else if (dataType.equals(DataType.PTM_ACE_NTA)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_ACE_NTA.type())); } else { return null; } ptmEvCriteria.addOrder(Order.desc("colorLevel")); ptmEvCriteria.setMaxResults(1); return (PTMEvidence) ptmEvCriteria.uniqueResult(); } /** * {@inheritDoc} */ @Override @SuppressWarnings("unchecked") public List<PTMEvidence> getPTMEvidencesByGeneAndType(long geneId, DataType dataType) { Criteria ptmEvCriteria = this.session().createCriteria(this.persistClass); Criteria gCriteria = ptmEvCriteria.createCriteria("gene"); Criteria dtypeCriteria = ptmEvCriteria.createCriteria("tpbDataType"); Criteria acCriteria = ptmEvCriteria.createCriteria("identifiedAccession"); acCriteria.addOrder(Order.asc("accession")); gCriteria.add(Restrictions.eq("id", geneId)); Disjunction dtypeOr = Restrictions.disjunction(); //PTM if (dataType.equals(DataType.PTM)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PTM.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_SER.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_TYR.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_THR.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_LYS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_NTA.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PTM_PHS)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_SER.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_TYR.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_PHS_THR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PTM_PHS_SER)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_PHS_SER.type())); } else if (dataType.equals(DataType.PTM_PHS_TYR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_PHS_TYR.type())); } else if (dataType.equals(DataType.PTM_PHS_THR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_PHS_THR.type())); } else if (dataType.equals(DataType.PTM_ACE)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_LYS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PTM_ACE_NTA.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PTM_ACE_LYS)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_ACE_LYS.type())); } else if (dataType.equals(DataType.PTM_ACE_NTA)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PTM_ACE_NTA.type())); } else { //nothing } ptmEvCriteria.addOrder(Order.desc("colorLevel")); return ptmEvCriteria.list(); } }