ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl.java Source code

Introduction

Here is the source code for ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl.java

Source

/*
 * The Gemma project.
 *
 * Copyright (c) 2006-2007 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.genome.sequenceAnalysis;

import org.apache.commons.lang3.StringUtils;
import org.hibernate.Criteria;
import org.hibernate.Hibernate;
import org.hibernate.LockOptions;
import org.hibernate.SessionFactory;
import org.hibernate.criterion.Restrictions;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.orm.hibernate3.HibernateTemplate;
import org.springframework.stereotype.Repository;
import ubic.gemma.model.genome.Gene;
import ubic.gemma.model.genome.biosequence.BioSequence;
import ubic.gemma.model.genome.gene.GeneProduct;
import ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation;
import ubic.gemma.persistence.service.AbstractDao;
import ubic.gemma.persistence.util.BusinessKey;

import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;

/**
 * <p>
 * Base Spring DAO Class: is able to create, update, remove, load, and find objects of type
 * <code>BlatAssociation</code>.
 * </p>
 *
 * @see BlatAssociation
 */
@Repository
public class BlatAssociationDaoImpl extends AbstractDao<BlatAssociation> implements BlatAssociationDao {

    @Autowired
    public BlatAssociationDaoImpl(SessionFactory sessionFactory) {
        super(BlatAssociation.class, sessionFactory);
    }

    @Override
    public Collection<BlatAssociation> find(BioSequence bioSequence) {
        BusinessKey.checkValidKey(bioSequence);
        Criteria queryObject = super.getSessionFactory().getCurrentSession().createCriteria(BlatAssociation.class);
        BusinessKey.attachCriteria(queryObject, bioSequence, "bioSequence");
        //noinspection unchecked
        return queryObject.list();
    }

    @Override
    public Collection<BlatAssociation> find(Gene gene) {

        if (gene.getProducts().size() == 0) {
            throw new IllegalArgumentException("Gene has no products");
        }

        Collection<BlatAssociation> result = new HashSet<>();

        for (GeneProduct geneProduct : gene.getProducts()) {

            BusinessKey.checkValidKey(geneProduct);

            Criteria queryObject = super.getSessionFactory().getCurrentSession()
                    .createCriteria(BlatAssociation.class);
            Criteria innerQuery = queryObject.createCriteria("geneProduct");
            if (StringUtils.isNotBlank(geneProduct.getNcbiGi())) {
                innerQuery.add(Restrictions.eq("ncbiGi", geneProduct.getNcbiGi()));
            }
            if (StringUtils.isNotBlank(geneProduct.getName())) {
                innerQuery.add(Restrictions.eq("name", geneProduct.getName()));
            }

            //noinspection unchecked
            result.addAll(queryObject.list());
        }

        return result;

    }

    @Override
    public void thaw(final Collection<BlatAssociation> blatAssociations) {
        if (blatAssociations == null)
            return;
        HibernateTemplate templ = this.getHibernateTemplate();
        templ.executeWithNativeSession(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {
            @Override
            public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
                for (Object object : blatAssociations) {
                    BlatAssociation blatAssociation = (BlatAssociation) object;
                    if ((blatAssociation).getId() == null)
                        continue;
                    BlatAssociationDaoImpl.this.thawBlatAssociation(session, blatAssociation);
                    session.evict(blatAssociation);
                }
                return null;
            }

        });
    }

    @Override
    public void thaw(final BlatAssociation blatAssociation) {
        if (blatAssociation == null)
            return;
        if (blatAssociation.getId() == null)
            return;
        HibernateTemplate templ = this.getHibernateTemplate();
        templ.executeWithNativeSession(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {
            @Override
            public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
                BlatAssociationDaoImpl.this.thawBlatAssociation(session, blatAssociation);
                return null;
            }
        });
    }

    @Override
    public Collection<BlatAssociation> find(Collection<GeneProduct> gps) {
        //noinspection unchecked
        return gps.isEmpty() ? Collections.emptySet()
                : this.getSessionFactory().getCurrentSession()
                        .createQuery("select b from BlatAssociation b join b.geneProduct gp where gp in (:gps)")
                        .setParameterList("gps", gps).list();
    }

    private void thawBlatAssociation(org.hibernate.Session session, BlatAssociation blatAssociation) {
        session.buildLockRequest(LockOptions.NONE).lock(blatAssociation);
        Hibernate.initialize(blatAssociation.getBioSequence());
        Hibernate.initialize(blatAssociation.getGeneProduct());
        Hibernate.initialize(blatAssociation.getBlatResult());
        Hibernate.initialize(blatAssociation.getBlatResult().getTargetChromosome());
    }

}