Example usage for org.hibernate FlushMode MANUAL

List of usage examples for org.hibernate FlushMode MANUAL

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FlushMode MANUAL

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Document

The Session is only ever flushed when Session#flush is explicitly called by the application.

Usage

From source file:ubic.gemma.persistence.persister.AbstractPersister.java

License:Apache License

@Override
@Transactional/*from   w w  w .j  a  va2  s.  c  o m*/
public boolean isTransient(Object entity) {
    if (entity == null)
        return true;
    Long id = EntityUtils.getId(entity);

    if (id == null)
        return true; // assume.

    /*
     * We normally won't get past this point; the case where it might is when the transaction has been rolled back
     * and is being retried.
     */

    if (EntityUtils.isProxy(entity)) {
        if (AbstractPersister.log.isDebugEnabled())
            AbstractPersister.log.debug("Object is a proxy: " + entity.getClass().getSimpleName() + ":" + id);
        return false;
    }

    org.hibernate.Session session = this.getSessionFactory().getCurrentSession();
    if (session.contains(entity)) {
        if (AbstractPersister.log.isDebugEnabled())
            AbstractPersister.log
                    .debug("Found object in session: " + entity.getClass().getSimpleName() + ":" + id);
        return false;
    }

    //noinspection SynchronizationOnLocalVariableOrMethodParameter // Getting desperate ...
    synchronized (entity) {
        Session sess = this.getSessionFactory().openSession();
        sess.setFlushMode(FlushMode.MANUAL);
        Object pe = sess.get(entity.getClass(), id);
        sess.close();
        if (pe != null) {
            // Common case.
            if (AbstractPersister.log.isDebugEnabled())
                AbstractPersister.log
                        .debug("Found object in store: " + entity.getClass().getSimpleName() + ":" + id);
            return false;
        }
    }

    /*
     * Hibernate has a method that, pretty much, does what we've done so far ... but probably does it better.
     */
    String bestGuessEntityName = ((SessionImplementor) session).bestGuessEntityName(entity);
    if (ForeignKeys.isNotTransient(bestGuessEntityName, entity, null, (SessionImplementor) session)) {
        AbstractPersister.log.info("Hibernate says object is not transient: " + bestGuessEntityName + ":" + id);
        return false;
    }

    /*
     * The ID is filled in, but it probably is a survivor of a rolled-back transaction. It doesn't matter what we
     * return, it's not guaranteed to be right.
     */
    AbstractPersister.log.info("Object has ID but we can't tell if it is persistent: "
            + entity.getClass().getSimpleName() + ":" + id);
    return true;

}

From source file:ubic.gemma.persistence.service.AbstractDao.java

License:Apache License

/**
 * Lists all entities whose given property matches the given value.
 *
 * @param  propertyName  the name of property to be matched.
 * @param  propertyValue the value to look for.
 * @return               a list of entities whose properties matched the given value.
 *//* w  w  w . java  2  s .  c  o m*/
@SuppressWarnings("unchecked")
protected T findOneByProperty(String propertyName, Object propertyValue) {

    /*
     * Disable flush to avoid NonNullability constraint failures, etc. prematurely when running this during object
     * creation. This effectively makes this method read-only even in a read-write context. (the same setup might be
     * needed for other methods)
     */
    FlushMode fm = this.getSessionFactory().getCurrentSession().getFlushMode();
    this.getSessionFactory().getCurrentSession().setFlushMode(FlushMode.MANUAL);
    Criteria criteria = this.getSessionFactory().getCurrentSession().createCriteria(this.elementClass);
    criteria.add(Restrictions.eq(propertyName, propertyValue));
    criteria.setMaxResults(1);

    //noinspection unchecked
    T result = (T) criteria.uniqueResult();
    this.getSessionFactory().getCurrentSession().setFlushMode(fm);
    return result;
}

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

License:Apache License

@Override
public Map<Long, Map<Long, DiffExprGeneSearchResult>> findDiffExAnalysisResultIdsInResultSets(
        Collection<DiffExResultSetSummaryValueObject> resultSets, Collection<Long> geneIds) {

    Map<Long, Map<Long, DiffExprGeneSearchResult>> results = new HashMap<>();

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

    Map<Long, DiffExResultSetSummaryValueObject> resultSetIdsMap = EntityUtils.getIdMap(resultSets,
            "getResultSetId");

    Map<Long, Collection<Long>> foundInCache = this.fillFromCache(results, resultSetIdsMap.keySet(), geneIds);

    if (!foundInCache.isEmpty()) {
        AbstractDao.log.info("Results for " + foundInCache.size() + " resultsets found in cache");
    } else {//from   w ww  .j a v a2s  . c om
        AbstractDao.log.info("No results were in the cache");
    }

    Collection<Long> resultSetsNeeded = this.stripUnneededResultSets(foundInCache, resultSetIdsMap.keySet(),
            geneIds);

    // Are we finished?
    if (resultSetsNeeded.isEmpty()) {
        AbstractDao.log.info("All results were in the cache.");
        return results;
    }

    AbstractDao.log.info(foundInCache.size() + "/" + resultSetIdsMap.size()
            + " resultsSets had at least some cached results; still need to query " + resultSetsNeeded.size());

    assert !resultSetsNeeded.isEmpty();

    org.hibernate.SQLQuery queryObject = session.createSQLQuery(
            DifferentialExpressionResultDaoImpl.fetchBatchDifferentialExpressionAnalysisResultsByResultSetsAndGeneQuery);

    /*
     * These values have been tweaked to probe for performance issues.
     */
    int resultSetBatchSize = 50;
    int geneBatchSize = 100;

    if (resultSetsNeeded.size() > geneIds.size()) {
        resultSetBatchSize = Math.min(500, resultSetsNeeded.size());
        AbstractDao.log.info("Batching by result sets (" + resultSetsNeeded.size() + " resultSets); "
                + geneIds.size() + " genes; batch size=" + resultSetBatchSize);

    } else {
        geneBatchSize = Math.min(200, geneIds.size());
        AbstractDao.log.info("Batching by genes (" + geneIds.size() + " genes); " + resultSetsNeeded.size()
                + " resultSets; batch size=" + geneBatchSize);
    }

    final int numResultSetBatches = (int) Math.ceil(resultSetsNeeded.size() / resultSetBatchSize);

    queryObject.setFlushMode(FlushMode.MANUAL);

    StopWatch timer = new StopWatch();
    timer.start();
    int numResults = 0;
    long timeForFillingNonSig = 0;

    Map<Long, Map<Long, DiffExprGeneSearchResult>> resultsFromDb = new HashMap<>();

    int numResultSetBatchesDone = 0;

    // Iterate over batches of resultSets
    for (Collection<Long> resultSetIdBatch : new BatchIterator<>(resultSetsNeeded, resultSetBatchSize)) {

        if (AbstractDao.log.isDebugEnabled())
            AbstractDao.log.debug("Starting batch of resultsets: "
                    + StringUtils.abbreviate(StringUtils.join(resultSetIdBatch, ","), 100));

        /*
         * Get the probes using the CommonQueries gene2cs. Otherwise we (in effect) end up doing this over and over
         * again.
         */
        Map<Long, Collection<Long>> cs2GeneIdMap = this.getProbesForGenesInResultSetBatch(session, geneIds,
                resultSetIdsMap, resultSetIdBatch);

        queryObject.setParameterList("rs_ids", resultSetIdBatch);

        int numGeneBatchesDone = 0;
        final int numGeneBatches = (int) Math.ceil(cs2GeneIdMap.size() / geneBatchSize);

        StopWatch innerQt = new StopWatch();

        // iterate over batches of probes (genes)
        for (Collection<Long> probeBatch : new BatchIterator<>(cs2GeneIdMap.keySet(), geneBatchSize)) {

            if (AbstractDao.log.isDebugEnabled())
                AbstractDao.log.debug("Starting batch of probes: "
                        + StringUtils.abbreviate(StringUtils.join(probeBatch, ","), 100));

            // would it help to sort the probeBatch/
            List<Long> pbL = new Vector<>(probeBatch);
            Collections.sort(pbL);

            queryObject.setParameterList("probe_ids", pbL);

            innerQt.start();
            List<?> queryResult = queryObject.list();
            innerQt.stop();

            if (innerQt.getTime() > 2000) {
                // show the actual query with params.
                AbstractDao.log.info("Query time: " + innerQt.getTime() + "ms:\n "
                        + queryObject.getQueryString().replace(":probe_ids", StringUtils.join(probeBatch, ","))
                                .replace(":rs_ids", StringUtils.join(resultSetIdBatch, ",")));
            }
            innerQt.reset();

            /*
             * Each query tuple are the probe, result, resultsSet, qvalue, pvalue.
             */
            for (Object o : queryResult) {
                // Long resultSetId = ( ( BigInteger )((Object[])o)[2] ).longValue();
                // if (!resultSetId.equals)
                numResults += this.processResultTuple(o, resultsFromDb, cs2GeneIdMap);
            }

            if (timer.getTime() > 5000 && AbstractDao.log.isInfoEnabled()) {
                AbstractDao.log.info("Batch time: " + timer.getTime() + "ms; Fetched DiffEx " + numResults
                        + " results so far. " + numResultSetBatchesDone + "/" + numResultSetBatches
                        + " resultset batches completed. " + numGeneBatchesDone + "/" + numGeneBatches
                        + " gene batches done.");
                timer.reset();
                timer.start();
            }

            // Check if task was cancelled.
            if (Thread.currentThread().isInterrupted()) {
                throw new TaskCancelledException("Search was cancelled");
            }

            numGeneBatchesDone++;

            if (DifferentialExpressionResultDaoImpl.CORRECTED_PVALUE_THRESHOLD_TO_BE_CONSIDERED_DIFF_EX < 1.0) {
                timeForFillingNonSig += this.fillNonSignificant(pbL, resultSetIdsMap, resultsFromDb,
                        resultSetIdBatch, cs2GeneIdMap, session);
            }
        } // over probes.

        // Check if task was cancelled.
        if (Thread.currentThread().isInterrupted()) {
            throw new TaskCancelledException("Search was cancelled");
        }

        numResultSetBatchesDone++;

    }

    if (timer.getTime() > 1000 && AbstractDao.log.isInfoEnabled()) {
        AbstractDao.log.info("Fetching DiffEx from DB took total of " + timer.getTime() + " ms : geneIds="
                + StringUtils.abbreviate(StringUtils.join(geneIds, ","), 50) + " result set="
                + StringUtils.abbreviate(StringUtils.join(resultSetsNeeded, ","), 50));
        if (timeForFillingNonSig > 100) {
            AbstractDao.log.info("Filling in non-significant values: " + timeForFillingNonSig + "ms in total");
        }
    }

    // Add the DB results to the cached results.
    this.addToCache(resultsFromDb, resultSetsNeeded, geneIds);

    for (Long resultSetId : resultsFromDb.keySet()) {
        Map<Long, DiffExprGeneSearchResult> geneResults = resultsFromDb.get(resultSetId);
        if (results.containsKey(resultSetId)) {
            results.get(resultSetId).putAll(geneResults);
        } else {
            results.put(resultSetId, geneResults);
        }
    }

    return results;
}

From source file:ubic.gemma.persistence.service.common.auditAndSecurity.UserDaoImpl.java

License:Apache License

@Override
public User findByUserName(final String userName) {
    Session session = this.getSessionFactory().getCurrentSession();

    //noinspection unchecked
    List<User> users = session.createCriteria(User.class).setFlushMode(FlushMode.MANUAL)
            .add(Restrictions.eq("userName", userName)).list();

    if (users.isEmpty()) {
        return null;
    } else if (users.size() > 1) {
        throw new IllegalStateException("Multiple users with name=" + userName);
    }/*w w  w. jav  a  2s. co m*/
    User u = users.get(0);
    session.setReadOnly(u, true); // TESTING
    return u;
}

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

License:Apache License

@Override
public BioAssayDimension find(BioAssayDimension bioAssayDimension) {

    if (bioAssayDimension.getBioAssays().isEmpty()) {
        throw new IllegalArgumentException("BioAssayDimension had no BioAssays");
    }/*from   w ww . j  a  v a  2s  .co  m*/

    Criteria queryObject = this.getSessionFactory().getCurrentSession().createCriteria(BioAssayDimension.class);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    if (StringUtils.isNotBlank(bioAssayDimension.getName())) {
        queryObject.add(Restrictions.eq("name", bioAssayDimension.getName()));
    }

    if (StringUtils.isNotBlank(bioAssayDimension.getDescription())) {
        queryObject.add(Restrictions.eq("description", bioAssayDimension.getDescription()));
    }

    queryObject.add(Restrictions.sizeEq("bioAssays", bioAssayDimension.getBioAssays().size()));

    Collection<String> names = new HashSet<>();
    for (BioAssay bioAssay : bioAssayDimension.getBioAssays()) {
        names.add(bioAssay.getName());
    }
    queryObject.createCriteria("bioAssays").add(Restrictions.in("name", names));

    BioAssayDimension candidate = (BioAssayDimension) queryObject.uniqueResult();

    if (candidate == null)
        return null;

    // Now check that the bioassays and order are exactly the same.
    Collection<BioAssay> desiredBioAssays = bioAssayDimension.getBioAssays();
    Collection<BioAssay> candidateBioAssays = candidate.getBioAssays();

    assert desiredBioAssays.size() == candidateBioAssays.size();

    Iterator<BioAssay> dit = desiredBioAssays.iterator();
    Iterator<BioAssay> cit = candidateBioAssays.iterator();

    while (dit.hasNext()) {
        BioAssay d = dit.next();
        BioAssay c = cit.next();
        if (!c.equals(d))
            return null;
    }

    return candidate;

}

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

License:Apache License

/**
 * @param  ee      ee//from   www.  j  a v a  2  s .  c o  m
 * @param  cs2gene Map of probes to genes.
 * @return         map of vectors to gene ids.
 */
Map<T, Collection<Long>> getVectorsForProbesInExperiments(Long ee, Map<Long, Collection<Long>> cs2gene) {

    // Do not do in clause for experiments, as it can't use the indices
    //language=HQL
    String queryString = "select dedv, dedv.designElement.id from ProcessedExpressionDataVector dedv fetch all properties"
            + " where dedv.designElement.id in ( :cs ) and dedv.expressionExperiment.id = :eeId ";

    Session session = this.getSessionFactory().getCurrentSession();
    org.hibernate.Query queryObject = session.createQuery(queryString);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    Map<T, Collection<Long>> dedv2genes = new HashMap<>();
    StopWatch timer = new StopWatch();
    timer.start();

    queryObject.setLong("eeId", ee);

    int batchSize = 100;
    for (Collection<Long> batch : new BatchIterator<>(cs2gene.keySet(), batchSize)) {
        this.getVectorsBatch(cs2gene, queryObject, dedv2genes, batch);
    }

    if (timer.getTime() > Math.max(200, 20 * dedv2genes.size())) {
        AbstractDao.log.info("Fetched " + dedv2genes.size() + " vectors for " + cs2gene.size() + " probes in "
                + timer.getTime() + "ms\n" + "Vector query was: " + queryString);

    }
    return dedv2genes;
}

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

License:Apache License

Map<T, Collection<Long>> getVectorsForProbesInExperiments(Map<Long, Collection<Long>> cs2gene) {

    //language=HQL
    String queryString = "select dedv, dedv.designElement.id from ProcessedExpressionDataVector dedv fetch all properties"
            + " where dedv.designElement.id in ( :cs ) ";

    Session session = this.getSessionFactory().getCurrentSession();
    org.hibernate.Query queryObject = session.createQuery(queryString);
    queryObject.setReadOnly(true);//from   w ww .ja  v  a 2s . com
    queryObject.setFlushMode(FlushMode.MANUAL);

    Map<T, Collection<Long>> dedv2genes = new HashMap<>();
    StopWatch timer = new StopWatch();
    timer.start();

    int batchSize = 100;
    for (Collection<Long> batch : new BatchIterator<>(cs2gene.keySet(), batchSize)) {
        this.getVectorsBatch(cs2gene, queryObject, dedv2genes, batch);
    }

    if (timer.getTime() > Math.max(200, 20 * dedv2genes.size())) {
        AbstractDao.log.info("Fetched " + dedv2genes.size() + " vectors for " + cs2gene.size() + " probes in "
                + timer.getTime() + "ms\n" + "Vector query was: " + queryString);

    }
    return dedv2genes;
}

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

License:Apache License

private void getVectorsBatch(Map<Long, Collection<Long>> cs2gene, org.hibernate.Query queryObject,
        Map<T, Collection<Long>> dedv2genes, Collection<Long> batch) {
    queryObject.setParameterList("cs", batch);
    queryObject.setFlushMode(FlushMode.MANUAL);
    queryObject.setReadOnly(true);//ww  w. j a v  a  2s.  c  o m
    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);

    while (results.next()) {
        @SuppressWarnings("unchecked")
        T dedv = (T) results.get(0);
        Long cs = (Long) results.get(1);
        Collection<Long> associatedGenes = cs2gene.get(cs);
        if (!dedv2genes.containsKey(dedv)) {
            dedv2genes.put(dedv, associatedGenes);
        } else {
            Collection<Long> mappedGenes = dedv2genes.get(dedv);
            mappedGenes.addAll(associatedGenes);
        }
    }

    results.close();
}

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

License:Apache License

/**
 * @param limit if non-null and positive, you will get a random set of vectors for the experiment
 * @param ee    ee/*from w  ww .  j ava  2  s  .  c  o m*/
 * @return processed data vectors
 */
private Collection<ProcessedExpressionDataVector> getProcessedVectors(ExpressionExperiment ee, Integer limit) {

    if (limit == null || limit < 0) {
        return this.getProcessedVectors(ee);
    }

    StopWatch timer = new StopWatch();
    timer.start();
    List<ProcessedExpressionDataVector> result;

    Integer availableVectorCount = ee.getNumberOfDataVectors();
    if (availableVectorCount == null || availableVectorCount == 0) {
        AbstractDao.log.info("Experiment does not have vector count populated.");
        // cannot fix this here, because we're read-only.
    }

    Query q = this.getSessionFactory().getCurrentSession()
            .createQuery(" from ProcessedExpressionDataVector dedv where dedv.expressionExperiment.id = :ee");
    q.setParameter("ee", ee.getId(), LongType.INSTANCE);
    q.setMaxResults(limit);
    if (availableVectorCount != null && availableVectorCount > limit) {
        q.setFirstResult(new Random().nextInt(availableVectorCount - limit));
    }

    // we should already be read-only, so this is probably pointless.
    q.setReadOnly(true);

    // and so this probably doesn't do anything useful.
    q.setFlushMode(FlushMode.MANUAL);

    //noinspection unchecked
    result = q.list();
    if (timer.getTime() > 1000)
        AbstractDao.log
                .info("Fetch " + limit + " vectors from " + ee.getShortName() + ": " + timer.getTime() + "ms");

    if (result.isEmpty()) {
        AbstractDao.log.warn("Experiment does not have any processed data vectors");
        return result;
    }

    this.thaw(result); // needed?
    return result;
}

From source file:ubic.gemma.persistence.service.genome.biosequence.BioSequenceDaoImpl.java

License:Apache License

@SuppressWarnings("unchecked")
@Override/*w  w w .  ja  va2s  .  co  m*/
public BioSequence find(BioSequence bioSequence) {

    BusinessKey.checkValidKey(bioSequence);

    Criteria queryObject = BusinessKey.createQueryObject(this.getSessionFactory().getCurrentSession(),
            bioSequence);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);
    /*
     * this initially matches on name and taxon only.
     */
    java.util.List<?> results = queryObject.list();
    Object result = null;
    if (results != null) {
        if (results.size() > 1) {
            this.debug(bioSequence, results);

            // Try to find the best match. See BusinessKey for more
            // explanation of why this is needed.
            BioSequence match = null;
            for (BioSequence res : (Collection<BioSequence>) results) {
                if (res.equals(bioSequence)) {
                    if (match != null) {
                        AbstractDao.log.warn("More than one sequence in the database matches " + bioSequence
                                + ", returning arbitrary match: " + match);
                        break;
                    }
                    match = res;
                }
            }

            return match;

        } else if (results.size() == 1) {
            result = results.iterator().next();
        }
    }
    return (BioSequence) result;
}