Example usage for org.hibernate Session buildLockRequest

List of usage examples for org.hibernate Session buildLockRequest

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Introduction

In this page you can find the example usage for org.hibernate Session buildLockRequest.

Prototype

LockRequest buildLockRequest(LockOptions lockOptions);

Source Link

Document

Build a LockRequest that specifies the LockMode, pessimistic lock timeout and lock scope.

Usage

From source file:ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl.java

License:Apache License

@Override
public BioAssayDimension thawLite(final BioAssayDimension bioAssayDimension) {
    if (bioAssayDimension == null)
        return null;
    if (bioAssayDimension.getId() == null)
        return bioAssayDimension;

    this.getHibernateTemplate().execute(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {
        @Override//  ww  w  .  ja  va  2  s  . co m
        public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
            session.buildLockRequest(LockOptions.NONE).lock(bioAssayDimension);
            Hibernate.initialize(bioAssayDimension);
            Hibernate.initialize(bioAssayDimension.getBioAssays());
            return null;
        }
    });
    return bioAssayDimension;
}

From source file:ubic.gemma.persistence.service.expression.bioAssayData.BioAssayDimensionDaoImpl.java

License:Apache License

@Override
public BioAssayDimension thaw(final BioAssayDimension bioAssayDimension) {
    if (bioAssayDimension == null)
        return null;
    if (bioAssayDimension.getId() == null)
        return bioAssayDimension;

    this.getHibernateTemplate().execute(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {
        @Override//from w  ww .  ja va 2  s .  c  o  m
        public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
            session.buildLockRequest(LockOptions.NONE).lock(bioAssayDimension);
            Hibernate.initialize(bioAssayDimension);
            Hibernate.initialize(bioAssayDimension.getBioAssays());

            for (BioAssay ba : bioAssayDimension.getBioAssays()) {
                if (ba != null) {
                    session.buildLockRequest(LockOptions.NONE).lock(ba);
                    Hibernate.initialize(ba);
                    Hibernate.initialize(ba.getSampleUsed());
                    Hibernate.initialize(ba.getArrayDesignUsed());
                    Hibernate.initialize(ba.getOriginalPlatform());
                    BioMaterial bm = ba.getSampleUsed();
                    session.buildLockRequest(LockOptions.NONE).lock(bm);
                    Hibernate.initialize(bm);
                    Hibernate.initialize(bm.getBioAssaysUsedIn());
                    Hibernate.initialize(bm.getFactorValues());
                }
            }
            return null;
        }
    });
    return bioAssayDimension;
}

From source file:ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDaoImpl.java

License:Apache License

@Override
public void thawRawAndProcessed(Collection<DesignElementDataVector> designElementDataVectors) {
    if (designElementDataVectors == null)
        return;//from   www.j  a v a2 s .  c  o  m

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

    Hibernate.initialize(designElementDataVectors);

    StopWatch timer = new StopWatch();
    timer.start();
    Collection<ExpressionExperiment> ees = new HashSet<>();
    Map<BioAssayDimension, Collection<DesignElementDataVector>> dims = new HashMap<>();
    Collection<CompositeSequence> cs = new HashSet<>();
    for (DesignElementDataVector vector : designElementDataVectors) {
        session.buildLockRequest(LockOptions.NONE).lock(vector);
        Hibernate.initialize(vector);
        Hibernate.initialize(vector.getQuantitationType());

        BioAssayDimension bad = vector.getBioAssayDimension();
        if (!dims.containsKey(bad)) {
            dims.put(bad, new HashSet<DesignElementDataVector>());
        }

        dims.get(bad).add(vector);
        cs.add(vector.getDesignElement());
        ees.add(vector.getExpressionExperiment());
        session.evict(vector.getQuantitationType());
        session.evict(vector);
    }

    if (timer.getTime() > designElementDataVectors.size()) {
        AbstractDao.log.info("Thaw phase 1, " + designElementDataVectors.size() + " vectors initialized in "
                + timer.getTime() + "ms ");
    }
    timer.reset();
    timer.start();

    // lightly thaw the EEs we saw
    for (ExpressionExperiment ee : ees) {
        Hibernate.initialize(ee);
        session.evict(ee);
    }

    if (timer.getTime() > 200) {
        AbstractDao.log.info("Thaw phase 2, " + ees.size() + " vector-associated expression experiments in "
                + timer.getTime() + "ms ");
    }

    timer.reset();
    timer.start();

    // thaw the bioassayDimensions we saw -- usually one, more rarely two.
    for (BioAssayDimension bad : dims.keySet()) {

        BioAssayDimension tbad = (BioAssayDimension) this.getSessionFactory().getCurrentSession().createQuery(
                "select distinct bad from BioAssayDimension bad join fetch bad.bioAssays ba join fetch ba.sampleUsed "
                        + "bm join fetch ba.arrayDesignUsed left join fetch bm.factorValues fetch all properties where bad.id= :bad ")
                .setParameter("bad", bad.getId()).uniqueResult();

        assert tbad != null;
        assert !dims.get(tbad).isEmpty();

        for (DesignElementDataVector v : designElementDataVectors) {
            if (v.getBioAssayDimension().getId().equals(tbad.getId())) {
                v.setBioAssayDimension(tbad);
            }
        }
    }

    if (timer.getTime() > 1000) {
        AbstractDao.log.info("Thaw phase 3, " + dims.size() + " vector-associated bioassaydimensions in "
                + timer.getTime() + "ms ");
    }
    timer.reset();
    timer.start();

    // thaw the designelements we saw. SLOW
    long lastTime = 0;
    int count = 0;
    for (CompositeSequence de : cs) {
        BioSequence seq = de.getBiologicalCharacteristic();
        if (seq == null)
            continue;
        session.buildLockRequest(LockOptions.NONE).lock(seq);
        Hibernate.initialize(seq);

        // is this really necessary?
        ArrayDesign arrayDesign = de.getArrayDesign();
        Hibernate.initialize(arrayDesign);

        if (++count % 10000 == 0) {
            if (timer.getTime() - lastTime > 1000) {
                AbstractDao.log
                        .info("Thawed " + count + " vector-associated probes " + timer.getTime() + " ms");
            }
            lastTime = timer.getTime();
        }
    }

    timer.stop();
    if (designElementDataVectors.size() >= 2000 || timer.getTime() > 200) {
        AbstractDao.log.info(
                "Thaw phase 4 " + cs.size() + " vector-associated probes thawed in " + timer.getTime() + "ms");
    }
}

From source file:ubic.gemma.persistence.service.expression.bioAssayData.DesignElementDataVectorDaoImpl.java

License:Apache License

@Override
public void thaw(T designElementDataVector) {
    Session session = this.getHibernateTemplate().getSessionFactory().getCurrentSession();
    BioSequence seq = designElementDataVector.getDesignElement().getBiologicalCharacteristic();
    if (seq != null) {
        session.buildLockRequest(LockOptions.NONE).lock(seq);
        Hibernate.initialize(seq);/*from  ww w  . j a va2  s  .  c o m*/
    }

    ArrayDesign arrayDesign = designElementDataVector.getDesignElement().getArrayDesign();
    Hibernate.initialize(arrayDesign);

    // thaw the bioassays.
    for (BioAssay ba : designElementDataVector.getBioAssayDimension().getBioAssays()) {
        ba = (BioAssay) session.get(BioAssay.class, ba.getId());
        Hibernate.initialize(ba.getArrayDesignUsed());
        Hibernate.initialize(ba.getSampleUsed());
        Hibernate.initialize(ba.getOriginalPlatform());
    }
}

From source file:ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDaoImpl.java

License:Apache License

@Override
public void thaw(final BioMaterial bioMaterial) {
    Session session = this.getSessionFactory().getCurrentSession();
    session.buildLockRequest(LockOptions.NONE).lock(bioMaterial);
    Hibernate.initialize(bioMaterial);//from  w ww.  ja  v a2s. c om
    Hibernate.initialize(bioMaterial.getSourceTaxon());
    Hibernate.initialize(bioMaterial.getBioAssaysUsedIn());
    Hibernate.initialize(bioMaterial.getTreatments());
    Hibernate.initialize(bioMaterial.getFactorValues());
}

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  av  a 2  s. com
        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);/*w  w  w .j  a v a 2  s.c o m*/
    }
}

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;/*ww  w  .  ja v a  2s .  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.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/* w w  w. ja va 2s .  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);
}