ubic.gemma.persistence.service.association.Gene2GeneProteinAssociationDaoImpl.java Source code

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Here is the source code for ubic.gemma.persistence.service.association.Gene2GeneProteinAssociationDaoImpl.java

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/*
 * The Gemma project.
 *
 * Copyright (c) 2006-2008 University of British Columbia
 *
 * 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 ubic.gemma.persistence.service.association;

import org.hibernate.Criteria;
import org.hibernate.Hibernate;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Repository;
import ubic.gemma.model.association.Gene2GeneProteinAssociation;
import ubic.gemma.model.association.Gene2GeneProteinAssociationImpl;
import ubic.gemma.model.genome.Gene;
import ubic.gemma.persistence.service.AbstractDao;
import ubic.gemma.persistence.util.BusinessKey;
import ubic.gemma.persistence.util.EntityUtils;

import java.util.Collection;
import java.util.Collections;
import java.util.Comparator;

/**
 * Dao implementation for gene2geneproteinassociations.
 *
 * @author ldonnison
 */

@Repository
public class Gene2GeneProteinAssociationDaoImpl extends AbstractDao<Gene2GeneProteinAssociation>
        implements Gene2GeneProteinAssociationDao {

    @Autowired
    public Gene2GeneProteinAssociationDaoImpl(SessionFactory sessionFactory) {
        super(Gene2GeneProteinAssociation.class, sessionFactory);
    }

    @Override
    public Gene2GeneProteinAssociation create(final Gene2GeneProteinAssociation gene2GeneProteinAssociation) {
        Gene2GeneProteinAssociation old = this.find(gene2GeneProteinAssociation);
        if (old != null) {
            this.remove(old);
        }
        super.create(gene2GeneProteinAssociation);
        return gene2GeneProteinAssociation;
    }

    @Override
    public Gene2GeneProteinAssociation find(Gene2GeneProteinAssociation gene2GeneProteinAssociation) {
        try {
            Criteria queryObject = this.getSessionFactory().getCurrentSession()
                    .createCriteria(Gene2GeneProteinAssociation.class);
            // have to have gene 1 and gene 2 there
            BusinessKey.checkKey(gene2GeneProteinAssociation);

            BusinessKey.createQueryObject(queryObject, gene2GeneProteinAssociation);

            //noinspection unchecked
            java.util.List<Gene2GeneProteinAssociation> results = queryObject.list();
            Object result = null;
            if (results != null) {
                if (results.size() == 1) {
                    result = results.iterator().next();
                } else if (results.size() > 1) {
                    AbstractDao.log.error("Multiple interactions  found for " + gene2GeneProteinAssociation + ":");

                    Collections.sort(results, new Comparator<Gene2GeneProteinAssociation>() {
                        @Override
                        public int compare(Gene2GeneProteinAssociation arg0, Gene2GeneProteinAssociation arg1) {
                            return arg0.getId().compareTo(arg1.getId());
                        }
                    });
                    result = results.iterator().next();
                    AbstractDao.log.error("Returning arbitrary gene2GeneProteinAssociation: " + result);
                }
            }
            return (Gene2GeneProteinAssociation) result;
        } catch (org.hibernate.HibernateException ex) {
            throw super.convertHibernateAccessException(ex);
        }
    }

    @Override
    public Collection<Gene2GeneProteinAssociation> findProteinInteractionsForGene(Gene gene) {
        //noinspection unchecked
        return this.getSessionFactory().getCurrentSession()
                .createQuery(
                        "from Gene2GeneProteinAssociationImpl where :gene = firstGene.id or :gene = secondGene.id")
                .setLong("gene", gene.getId()).list();
    }

    @Override
    public void thaw(Gene2GeneProteinAssociation gene2GeneProteinAssociation) {
        if (gene2GeneProteinAssociation == null)
            return;
        if (gene2GeneProteinAssociation.getId() == null)
            return;

        Session session = this.getSessionFactory().getCurrentSession();

        EntityUtils.attach(session, gene2GeneProteinAssociation, Gene2GeneProteinAssociationImpl.class,
                gene2GeneProteinAssociation.getId());
        Hibernate.initialize(gene2GeneProteinAssociation);
        Hibernate.initialize(gene2GeneProteinAssociation.getFirstGene());
        Hibernate.initialize(gene2GeneProteinAssociation.getSecondGene());

        if (gene2GeneProteinAssociation.getSecondGene().getTaxon() != null
                && gene2GeneProteinAssociation.getSecondGene().getTaxon().getId() != null) {
            Hibernate.initialize(gene2GeneProteinAssociation.getSecondGene().getTaxon());
            Hibernate.initialize(gene2GeneProteinAssociation.getFirstGene().getTaxon());
        }

        session.evict(gene2GeneProteinAssociation);

    }

}