Example usage for org.hibernate LockOptions NONE

Introduction

In this page you can find the example usage for org.hibernate LockOptions NONE.

Prototype

LockOptions NONE

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Document

Represents LockMode.NONE (timeout + scope do not apply).

Usage

From source file:ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl.java

License:Apache License

@Override
public void thaw(final Collection<CompositeSequence> compositeSequences) {
    HibernateTemplate templ = this.getHibernateTemplate();
    templ.executeWithNativeSession(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {
        @Override/*from   w w  w .  j a  v a 2  s  .  c  o  m*/
        public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
            int i = 0;
            int numToDo = compositeSequences.size();
            for (CompositeSequence cs : compositeSequences) {

                session.buildLockRequest(LockOptions.NONE).lock(cs);
                Hibernate.initialize(cs.getArrayDesign());
                session.buildLockRequest(LockOptions.NONE).lock(cs.getArrayDesign());
                Hibernate.initialize(cs.getArrayDesign().getPrimaryTaxon());

                BioSequence bs = cs.getBiologicalCharacteristic();
                if (bs == null) {
                    continue;
                }

                session.buildLockRequest(LockOptions.NONE).lock(bs);
                Hibernate.initialize(bs);
                Hibernate.initialize(bs.getTaxon());

                DatabaseEntry dbEntry = bs.getSequenceDatabaseEntry();
                if (dbEntry != null) {
                    Hibernate.initialize(dbEntry);
                    Hibernate.initialize(dbEntry.getExternalDatabase());
                    session.evict(dbEntry);
                    session.evict(dbEntry.getExternalDatabase());
                }

                if (bs.getBioSequence2GeneProduct() == null) {
                    continue;
                }

                for (BioSequence2GeneProduct bs2gp : bs.getBioSequence2GeneProduct()) {
                    if (bs2gp == null) {
                        continue;
                    }
                    GeneProduct geneProduct = bs2gp.getGeneProduct();
                    if (geneProduct != null && geneProduct.getGene() != null) {
                        Gene g = geneProduct.getGene();
                        g.getAliases().size();
                        session.evict(g);
                        session.evict(geneProduct);
                    }

                }

                if (++i % 2000 == 0) {
                    AbstractDao.log.info("Progress: " + i + "/" + numToDo + "...");
                    try {
                        Thread.sleep(10);
                    } catch (InterruptedException e) {
                        //
                    }
                }

                session.evict(bs);
            }
            session.clear();
            return null;
        }
    });

}

From source file:ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl.java

License:Apache License

private void removeBioAssays(Session session, Map<BioAssay, BioMaterial> copyOfRelations,
        Collection<BioMaterial> bioMaterialsToDelete, Collection<BioAssay> bioAssays) {
    for (BioAssay ba : bioAssays) {
        // relations to files cascade, so we only have to worry about biomaterials, which aren't cascaded from
        // anywhere. BioAssay -> BioMaterial is many-to-one, but bioassaySet (experiment) owns the bioAssay.
        BioMaterial biomaterial = ba.getSampleUsed();

        if (biomaterial == null)
            continue; // shouldn't...

        bioMaterialsToDelete.add(biomaterial);

        copyOfRelations.put(ba, biomaterial);

        session.buildLockRequest(LockOptions.NONE).lock(biomaterial);

        Hibernate.initialize(biomaterial);

        // this can easily end up with an unattached object.
        Hibernate.initialize(biomaterial.getBioAssaysUsedIn());

        biomaterial.getFactorValues().clear();
        biomaterial.getBioAssaysUsedIn().clear();

        ba.setSampleUsed(null);/*from w  w w  .java 2 s  .  c  om*/
    }
}

From source file:ubic.gemma.persistence.service.genome.gene.GeneSetDaoImpl.java

License:Apache License

@Override
public void thaw(final GeneSet geneSet) {
    if (geneSet == null || geneSet.getId() == null)
        return;/*from   www.  j  a va 2 s  .co m*/
    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 {
            session.buildLockRequest(LockOptions.NONE).lock(geneSet);
            Hibernate.initialize(geneSet);
            Hibernate.initialize(geneSet.getMembers());
            for (GeneSetMember gsm : geneSet.getMembers()) {
                Hibernate.initialize(gsm.getGene());
            }
            return null;
        }
    });

}

From source file:ubic.gemma.persistence.service.genome.sequenceAnalysis.BlatAssociationDaoImpl.java

License:Apache License

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());
}

From source file:ubic.gemma.persistence.service.genome.taxon.TaxonDaoImpl.java

License:Apache License

@Override
public void thaw(final Taxon taxon) {
    this.getSessionFactory().getCurrentSession().doWork(new Work() {
        @Override//w  w w  . j av  a  2  s  .  c  om
        public void execute(Connection connection) {
            TaxonDaoImpl.this.getSession().buildLockRequest(LockOptions.NONE).lock(taxon);
            Hibernate.initialize(taxon.getExternalDatabase());
            TaxonDaoImpl.this.getSession().evict(taxon);
        }
    });
}

From source file:ubic.gemma.persistence.util.EntityUtils.java

License:Apache License

/**
 * Expert only. Put the given entity into the Session, with LockMode.NONE
 * Based on idea from https://forum.hibernate.org/viewtopic.php?p=2284826#p2284826
 *
 * @param session Hibernate Session (use factory.getCurrentSession())
 * @param obj     the entity/*from   w  w w . ja v  a 2 s.  co m*/
 * @param clazz   the class type of the persisted entity. Don't use obj.getClass() as this might return a proxy type.
 * @param id      identifier of the obj
 */
public static void attach(Session session, Object obj, Class<?> clazz, Long id) {
    if (obj == null || id == null)
        return;
    if (!session.isOpen())
        throw new IllegalArgumentException("Illegal attempt to use a closed session");
    if (!session.contains(obj)) {

        Object oldObj = session.get(clazz, id);

        if (oldObj != null) {
            session.evict(oldObj);
        }
    }
    session.buildLockRequest(LockOptions.NONE).lock(obj);
}

From source file:ubic.gemma.security.audit.AuditAdvice.java

License:Apache License

/**
 * @param auditTrail/*from ww w  .  j a va 2 s.  c  o  m*/
 */
private void ensureInSession(AuditTrail auditTrail) {
    if (auditTrail == null)
        return;
    /*
     * Ensure we have the object in the session. It might not be, if we have flushed the session.
     */
    Session session = sessionFactory.getCurrentSession();
    if (!session.contains(auditTrail)) {
        session.buildLockRequest(LockOptions.NONE).lock(auditTrail);
    }
}