Examples with PersistentCollection org.hibernate.collection.PersistentCollection used on opensource projects

Example 1 with PersistentCollection

use of org.hibernate.collection.PersistentCollection in project Gemma by PavlidisLab.

the class ArrayDesignDaoImpl method thaw.

@Override
public ArrayDesign thaw(final ArrayDesign arrayDesign) {
    if (arrayDesign.getId() == null) {
        throw new IllegalArgumentException("Cannot thawRawAndProcessed a non-persistent array design");
    }
    /*
         * Thaw basic stuff
         */
    StopWatch timer = new StopWatch();
    timer.start();
    ArrayDesign result = this.thawLite(arrayDesign);
    if (timer.getTime() > 1000) {
        AbstractDao.log.info("Thaw array design stage 1: " + timer.getTime() + "ms");
    }
    timer.stop();
    timer.reset();
    timer.start();
    /*
         * Thaw the composite sequences.
         */
    AbstractDao.log.info("Start initialize composite sequences");
    Hibernate.initialize(result.getCompositeSequences());
    if (timer.getTime() > 1000) {
        AbstractDao.log.info("Thaw array design stage 2: " + timer.getTime() + "ms");
    }
    timer.stop();
    timer.reset();
    timer.start();
    /*
         * Thaw the biosequences in batches
         */
    Collection<CompositeSequence> thawed = new HashSet<>();
    Collection<CompositeSequence> batch = new HashSet<>();
    long lastTime = timer.getTime();
    for (CompositeSequence cs : result.getCompositeSequences()) {
        batch.add(cs);
        if (batch.size() == 1000) {
            long t = timer.getTime();
            if (t > 10000 && t - lastTime > 1000) {
                AbstractDao.log.info("Thaw Batch : " + t);
            }
            List bb = this.thawBatchOfProbes(batch);
            // noinspection unchecked
            thawed.addAll((Collection<? extends CompositeSequence>) bb);
            lastTime = timer.getTime();
            batch.clear();
        }
        this.getSessionFactory().getCurrentSession().evict(cs);
    }
    if (!batch.isEmpty()) {
        // tail end
        List bb = this.thawBatchOfProbes(batch);
        // noinspection unchecked
        thawed.addAll((Collection<? extends CompositeSequence>) bb);
    }
    result.getCompositeSequences().clear();
    result.getCompositeSequences().addAll(thawed);
    /*
         * This is a bit ugly, but necessary to avoid 'dirty collection' errors later.
         */
    if (result.getCompositeSequences() instanceof PersistentCollection)
        ((PersistentCollection) result.getCompositeSequences()).clearDirty();
    if (timer.getTime() > 1000) {
        AbstractDao.log.info("Thaw array design stage 3: " + timer.getTime());
    }
    return result;
}