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.PEEvidence; import edu.monash.merc.repository.IPEEvidenceRep; 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; /** * PEEvidenceDAO class which provides the database operations for PEEvidence object. * * @author Simon Yu * <p/> * Email: xiaoming.yu@monash.edu * @version 1.0 * @since 1.0 * <p/> * Date: 23/04/12 12:54 PM */ @Scope(BeanDefinition.SCOPE_PROTOTYPE) @Repository public class PEEvidenceDAO extends HibernateGenericDAO<PEEvidence> implements IPEEvidenceRep { /** * {@inheritDoc} */ public void deletePEEvidenceById(long id) { String del_hql = "DELETE FROM " + this.persistClass.getSimpleName() + " AS ev WHERE ev.id = :id"; Query query = this.session().createQuery(del_hql); query.setLong("id", id); query.executeUpdate(); } /** * {@inheritDoc} */ public PEEvidence getPESummaryByGeneAndType(long geneId, DataType dataType) { Criteria peCriteria = this.session().createCriteria(this.persistClass); Criteria gCriteria = peCriteria.createCriteria("gene"); Criteria dtypeCriteria = peCriteria.createCriteria("tpbDataType"); gCriteria.add(Restrictions.eq("id", geneId)); Disjunction dtypeOr = Restrictions.disjunction(); //PE if (dataType.equals(DataType.PE)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_PROB.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_SAM.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_MS)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_PROB.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_SAM.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_MS_ANN)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_MS_ANN.type())); } else if (dataType.equals(DataType.PE_MS_PROB)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_MS_PROB.type())); } else if (dataType.equals(DataType.PE_MS_SAM)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_MS_SAM.type())); } else if (dataType.equals(DataType.PE_ANTI)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_ANTI_ANN)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_ANTI_ANN.type())); } else if (dataType.equals(DataType.PE_ANTI_IHC)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_ANTI_IHC_NORM)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_OTH)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_OTH_CUR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_OTH_CUR.type())); } else { //nothing to be added } peCriteria.addOrder(Order.desc("colorLevel")); peCriteria.setMaxResults(1); return (PEEvidence) peCriteria.uniqueResult(); } /** * {@inheritDoc} */ @SuppressWarnings("unchecked") public List<PEEvidence> getPEEvidencesByGeneAndType(long geneId, DataType dataType) { Criteria peCriteria = this.session().createCriteria(this.persistClass); Criteria gCriteria = peCriteria.createCriteria("gene"); Criteria dtypeCriteria = peCriteria.createCriteria("tpbDataType"); dtypeCriteria.addOrder(Order.asc("displayName")); Criteria acCriteria = peCriteria.createCriteria("identifiedAccession"); acCriteria.addOrder(Order.asc("accession")); gCriteria.add(Restrictions.eq("id", geneId)); Disjunction dtypeOr = Restrictions.disjunction(); //PE if (dataType.equals(DataType.PE)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_PROB.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_SAM.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_MS)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_PROB.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_MS_SAM.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_MS_ANN)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_MS_ANN.type())); } else if (dataType.equals(DataType.PE_MS_PROB)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_MS_PROB.type())); } else if (dataType.equals(DataType.PE_MS_SAM)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_MS_SAM.type())); } else if (dataType.equals(DataType.PE_ANTI)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_ANN.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_ANTI_ANN)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_ANTI_ANN.type())); } else if (dataType.equals(DataType.PE_ANTI_IHC)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC.type())); dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); } else if (dataType.equals(DataType.PE_ANTI_IHC_NORM)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_ANTI_IHC_NORM.type())); } else if (dataType.equals(DataType.PE_OTH)) { dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH.type())); dtypeOr.add(Restrictions.eq("dataType", DataType.PE_OTH_CUR.type())); dtypeCriteria.add(dtypeOr); } else if (dataType.equals(DataType.PE_OTH_CUR)) { dtypeCriteria.add(Restrictions.eq("dataType", DataType.PE_OTH_CUR.type())); } else { //nothing } peCriteria.addOrder(Order.desc("colorLevel")); return peCriteria.list(); } }