Example usage for org.hibernate LockOptions NONE

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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.analysis.expression.diff.ExpressionAnalysisResultSetDaoImpl.java

License:Apache License

@Override
public void remove(ExpressionAnalysisResultSet resultSet) {

    // Wipe references
    resultSet.setResults(new HashSet<DifferentialExpressionAnalysisResult>());
    this.update(resultSet);

    // Clear session
    Session session = this.getSessionFactory().getCurrentSession();
    session.flush();/*w  w w.j a  va2  s.c o  m*/
    session.clear();
    session.buildLockRequest(LockOptions.NONE).lock(resultSet);
    int contrastsDone = 0;
    int resultsDone = 0;

    // Remove results - Not using DifferentialExpressionResultDaoImpl.remove() for speed
    {
        AbstractDao.log.info("Bulk removing dea results...");

        // Delete contrasts
        //language=MySQL
        final String nativeDeleteContrastsQuery = "DELETE c FROM CONTRAST_RESULT c, DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT d"
                + " WHERE d.RESULT_SET_FK = :rsid AND d.ID = c.DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT_FK";
        SQLQuery q = session.createSQLQuery(nativeDeleteContrastsQuery);
        q.setParameter("rsid", resultSet.getId());
        contrastsDone += q.executeUpdate(); // cannot use the limit clause for this multi-table remove.

        // Delete AnalysisResults
        //language=MySQL
        String nativeDeleteARQuery = "DELETE d FROM DIFFERENTIAL_EXPRESSION_ANALYSIS_RESULT d WHERE d.RESULT_SET_FK = :rsid  ";
        q = session.createSQLQuery(nativeDeleteARQuery);
        q.setParameter("rsid", resultSet.getId());
        resultsDone += q.executeUpdate();

        AbstractDao.log
                .info("Deleted " + contrastsDone + " contrasts, " + resultsDone + " results. Flushing...");
        session.flush();
        session.clear();
    }

    // Remove result set
    AbstractDao.log.info("Removing result set " + resultSet.getId());
    super.remove(resultSet);
    this.getSessionFactory().getCurrentSession().flush();
}

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From source file:ubic.gemma.persistence.service.analysis.expression.ExpressionExperimentSetDaoImpl.java

License:Apache License

@Override
public void thaw(final ExpressionExperimentSet expressionExperimentSet) {
    this.getSessionFactory().getCurrentSession().buildLockRequest(LockOptions.NONE)
            .lock(expressionExperimentSet);
    Hibernate.initialize(expressionExperimentSet);
    Hibernate.initialize(expressionExperimentSet.getTaxon());
    Hibernate.initialize(expressionExperimentSet.getExperiments());
}

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From source file:ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDaoImpl.java

License:Apache License

@Override
public void removeBiologicalCharacteristics(final ArrayDesign arrayDesign) {
    if (arrayDesign == null) {
        throw new IllegalArgumentException("Array design cannot be null");
    }/*from  ww w .  j a va  2 s. c o  m*/
    Session session = this.getSessionFactory().getCurrentSession();
    session.buildLockRequest(LockOptions.NONE).lock(arrayDesign);

    int count = 0;
    for (CompositeSequence cs : arrayDesign.getCompositeSequences()) {
        cs.setBiologicalCharacteristic(null);
        session.update(cs);
        session.evict(cs);
        if (++count % ArrayDesignDaoImpl.LOGGING_UPDATE_EVENT_COUNT == 0) {
            AbstractDao.log.info("Cleared sequence association for " + count + " composite sequences");
        }
    }

}

---

From source file:ubic.gemma.persistence.service.expression.bioAssay.BioAssayDaoImpl.java

License:Apache License

@Override
public void thaw(final BioAssay bioAssay) {
    try {//from w  w w.  ja  va  2 s. c o  m
        this.getSessionFactory().getCurrentSession().doWork(new Work() {
            @Override
            public void execute(Connection connection) {
                BioAssayDaoImpl.this.getSession().buildLockRequest(LockOptions.NONE).lock(bioAssay);
                Hibernate.initialize(bioAssay.getArrayDesignUsed());
                Hibernate.initialize(bioAssay.getOriginalPlatform());
                BioMaterial bm = bioAssay.getSampleUsed();
                BioAssayDaoImpl.this.getSession().buildLockRequest(LockOptions.NONE).lock(bm);
                Hibernate.initialize(bm);
                Hibernate.initialize(bm.getBioAssaysUsedIn());
                Hibernate.initialize(bm.getFactorValues());
                BioAssayDaoImpl.this.getSession().evict(bm);
                BioAssayDaoImpl.this.getSession().evict(bioAssay);
            }
        });
    } catch (Throwable th) {
        throw new RuntimeException(
                "Error performing 'BioAssayDao.thawRawAndProcessed(BioAssay bioAssay)' --> " + th, th);
    }
}

---

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//from   w  w w . j av  a 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());
            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  w w .j  av  a2 s .com*/
        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;// www.  j  a  v  a2  s . com

    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);// www  .j a va 2s  . co 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());
    }
}

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

License:Apache License

/**
 * @param ee  ee//  w w  w.  j av  a  2s  .c  o m
 * @param obs obs
 * @return Given an ExpressionExperimentSubset and vectors from the source experiment, give vectors that include
 * just the
 * data for the subset.
 */
private Collection<DoubleVectorValueObject> sliceSubSet(ExpressionExperimentSubSet ee,
        Collection<DoubleVectorValueObject> obs) {

    Collection<DoubleVectorValueObject> sliced = new HashSet<>();
    if (obs == null || obs.isEmpty())
        return sliced;

    this.getSessionFactory().getCurrentSession().buildLockRequest(LockOptions.NONE).lock(ee);
    Hibernate.initialize(ee.getBioAssays());
    List<BioAssayValueObject> sliceBioAssays = new ArrayList<>();

    DoubleVectorValueObject exemplar = obs.iterator().next();

    BioAssayDimensionValueObject bad = new BioAssayDimensionValueObject(-1L);
    bad.setName("Subset of :" + exemplar.getBioAssayDimension().getName());
    bad.setDescription("Subset slice");
    bad.setSourceBioAssayDimension(exemplar.getBioAssayDimension());
    bad.setIsSubset(true);
    Collection<Long> subsetBioAssayIds = EntityUtils.getIds(ee.getBioAssays());

    for (BioAssayValueObject ba : exemplar.getBioAssays()) {
        if (!subsetBioAssayIds.contains(ba.getId())) {
            continue;
        }

        sliceBioAssays.add(ba);
    }

    bad.addBioAssays(sliceBioAssays);
    for (DoubleVectorValueObject vec : obs) {
        DoubleVectorValueObject s = new DoubleVectorValueObject(ee, vec, bad);
        sliced.add(s);
    }

    return sliced;
}

---

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 w  w. ja  v  a  2 s  .c o m*/
    Hibernate.initialize(bioMaterial.getSourceTaxon());
    Hibernate.initialize(bioMaterial.getBioAssaysUsedIn());
    Hibernate.initialize(bioMaterial.getTreatments());
    Hibernate.initialize(bioMaterial.getFactorValues());
}

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