Example usage for org.hibernate SQLQuery setLong

List of usage examples for org.hibernate SQLQuery setLong

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Introduction

In this page you can find the example usage for org.hibernate SQLQuery setLong.

Prototype

@Deprecated
@SuppressWarnings("unchecked")
default Query<R> setLong(int position, long val)

Source Link

Document

Bind a positional long-valued parameter.

Usage

From source file:org.linagora.linshare.core.repository.hibernate.ContainerQuotaRepositoryImpl.java

License:Open Source License

public List<Long> getQuotaIdforAccountQuotaInSubDomains(AbstractDomain domain, QuotaType type,
        ContainerQuotaType containerType) {
    HibernateCallback<List<Long>> action = new HibernateCallback<List<Long>>() {
        public List<Long> doInHibernate(final Session session) throws HibernateException, SQLException {
            StringBuilder sb = new StringBuilder();
            sb.append("SELECT DISTINCT child.id AS child_id FROM quota AS father");
            sb.append(" JOIN quota AS child");
            sb.append(" ON child.domain_parent_id = father.domain_id");
            sb.append(" AND child.quota_type = :domainType ");
            sb.append(" AND father.domain_parent_id = :domainId ");
            sb.append(" AND father.default_account_quota_override = false");
            if (containerType != null) {
                sb.append(" AND father.container_type = :containerType");
            }//from w w w  . j  a  v  a2  s  .  c o m
            sb.append(" WHERE father.quota_type = :domainType");
            if (containerType != null) {
                sb.append(" AND child.container_type = :containerType");
            }
            sb.append(" AND child.account_quota_override = false");
            sb.append(";");
            final SQLQuery query = session.createSQLQuery(sb.toString());
            query.setLong("domainId", domain.getPersistenceId());
            query.addScalar("child_id", LongType.INSTANCE);
            query.setString("domainType", type.name());
            if (containerType != null) {
                query.setString("containerType", containerType.name());
            }
            @SuppressWarnings("unchecked")
            List<Long> res = query.list();
            logger.debug("child_ids :" + res);
            return res;
        }
    };
    return getHibernateTemplate().execute(action);
}

From source file:org.linagora.linshare.core.repository.hibernate.GenericQuotaRepositoryImpl.java

License:Open Source License

public List<Long> getQuotaIdforDefaultQuotaInSubDomains(AbstractDomain domain, Long quota, QuotaType type,
        ContainerQuotaType containerType) {
    HibernateCallback<List<Long>> action = new HibernateCallback<List<Long>>() {
        public List<Long> doInHibernate(final Session session) throws HibernateException, SQLException {
            StringBuilder sb = new StringBuilder();
            sb.append("SELECT DISTINCT child.id AS child_id FROM quota AS father");
            sb.append(" JOIN quota AS child");
            sb.append(" ON child.domain_parent_id = father.domain_id");
            sb.append(" AND child.quota_type = :domainType ");
            sb.append(" AND father.domain_parent_id = :domainId ");
            sb.append(" AND father.default_quota_override = false");
            sb.append(" WHERE father.quota_type = :domainType");
            if (containerType != null) {
                sb.append(" AND child.container_type = :containerType");
            }/*ww w . j  a  v a 2s  .  co m*/
            sb.append(" AND child.default_quota_override = false");
            sb.append(";");
            final SQLQuery query = session.createSQLQuery(sb.toString());
            query.setLong("domainId", domain.getPersistenceId());
            query.addScalar("child_id", LongType.INSTANCE);
            query.setString("domainType", type.name());
            if (containerType != null) {
                query.setString("containerType", containerType.name());
            }
            @SuppressWarnings("unchecked")
            List<Long> res = query.list();
            logger.debug("child_ids :" + res);
            return res;
        }
    };
    return getHibernateTemplate().execute(action);
}

From source file:org.linagora.linshare.core.repository.hibernate.GenericQuotaRepositoryImpl.java

License:Open Source License

public List<Long> getQuotaIdforQuotaInSubDomains(AbstractDomain domain, Long quota, QuotaType type,
        ContainerQuotaType containerType) {
    HibernateCallback<List<Long>> action = new HibernateCallback<List<Long>>() {
        public List<Long> doInHibernate(final Session session) throws HibernateException, SQLException {
            StringBuilder sb = new StringBuilder();
            sb.append("SELECT DISTINCT child.id AS child_id FROM quota AS father");
            sb.append(" JOIN quota AS child");
            sb.append(" ON child.domain_parent_id = father.domain_id");
            sb.append(" AND child.quota_type = :domainType ");
            sb.append(" AND father.domain_parent_id = :domainId ");
            sb.append(" AND father.quota_override = false");
            if (containerType != null) {
                sb.append(" AND father.container_type = :containerType");
            }// w ww.j  a v a 2 s.com
            sb.append(" WHERE father.quota_type = :domainType");
            if (containerType != null) {
                sb.append(" AND child.container_type = :containerType");
            }
            sb.append(" AND child.quota_override = false");
            sb.append(";");
            final SQLQuery query = session.createSQLQuery(sb.toString());
            query.setLong("domainId", domain.getPersistenceId());
            query.addScalar("child_id", LongType.INSTANCE);
            query.setString("domainType", type.name());
            if (containerType != null) {
                query.setString("containerType", containerType.name());
            }
            @SuppressWarnings("unchecked")
            List<Long> res = query.list();
            logger.debug("child_ids :" + res);
            return res;
        }
    };
    return getHibernateTemplate().execute(action);
}

From source file:org.mousephenotype.dcc.utils.persistence.HibernateManager.java

License:Apache License

public <T> List<T> nativeQuery(String query, Class<T> clazz,
        com.google.common.collect.Table<String, Class, Object> parameters) {
    this.refreshSession();
    Transaction transaction = null;/*from   w  ww . jav  a 2 s . c om*/
    List<T> result = null;
    try {
        transaction = session.beginTransaction();
        SQLQuery sqlQuery = session.createSQLQuery(query).addEntity(clazz);
        if (parameters != null) {
            for (com.google.common.collect.Table.Cell<String, Class, Object> entry : parameters.cellSet()) {
                if (entry.getColumnKey().equals(String.class)) {
                    sqlQuery.setString(entry.getRowKey(), (String) entry.getValue());
                    continue;
                }
                if (entry.getColumnKey().equals(Long.class)) {
                    sqlQuery.setLong(entry.getRowKey(), (Long) entry.getValue());
                    continue;
                }
                if (entry.getColumnKey().equals(BigInteger.class)) {
                    sqlQuery.setBigInteger(entry.getRowKey(), (BigInteger) entry.getValue());
                    continue;
                }
                logger.error("Type {} not registered", entry.getValue().getClass());
            }
        }

        result = sqlQuery.list();
        transaction.commit();
    } catch (RuntimeException ex) {
        if (transaction != null) {
            logger.error("rolling back transaction {}", ex);
            transaction.rollback();
        }
    }
    return result;
}

From source file:org.mousephenotype.dcc.utils.persistence.HibernateManager.java

License:Apache License

public List nativeQuery(String query, Map<String, org.hibernate.type.Type> scalars,
        com.google.common.collect.Table<String, Class, Object> parameters) {

    this.refreshSession();
    Transaction transaction = null;//from  w  ww. j  a va  2 s .  c  o m
    List result = null;
    try {
        transaction = session.beginTransaction();
        SQLQuery sqlQuery = session.createSQLQuery(query);
        if (scalars != null) {
            for (Map.Entry<String, org.hibernate.type.Type> entry : scalars.entrySet()) {
                sqlQuery.addScalar(entry.getKey(), entry.getValue());
            }
        }
        if (parameters != null) {
            for (com.google.common.collect.Table.Cell<String, Class, Object> entry : parameters.cellSet()) {
                if (entry.getColumnKey().equals(String.class)) {
                    sqlQuery.setString(entry.getRowKey(), (String) entry.getValue());
                    continue;
                }
                if (entry.getColumnKey().equals(Long.class)) {
                    sqlQuery.setLong(entry.getRowKey(), (Long) entry.getValue());
                    continue;
                }
                if (entry.getColumnKey().equals(BigInteger.class)) {
                    sqlQuery.setBigInteger(entry.getRowKey(), (BigInteger) entry.getValue());
                    continue;
                }
                logger.error("Type {} not registered", entry.getValue().getClass());
            }
        }

        result = sqlQuery.list();
        transaction.commit();
    } catch (RuntimeException ex) {
        if (transaction != null) {
            logger.error("rolling back transaction {}", ex);
            transaction.rollback();
        }
    }
    return result;
}

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

License:Apache License

@Override
public List<Double> findGeneInResultSets(Gene gene, ExpressionAnalysisResultSet resultSet,
        Collection<Long> arrayDesignIds, Integer limit) {

    StopWatch timer = new StopWatch();
    timer.start();/*from w ww  .  j a v  a  2s  . c  o  m*/

    List<Double> results;

    Session session = this.getSessionFactory().getCurrentSession();
    org.hibernate.SQLQuery queryObject = session
            .createSQLQuery(DifferentialExpressionResultDaoImpl.fetchResultsByResultSetAndGeneQuery);

    queryObject.setLong("gene_id", gene.getId());
    queryObject.setLong("rs_id", resultSet.getId());

    if (limit != null) {
        queryObject.setMaxResults(limit);
    }

    queryObject.addScalar("CORRECTED_PVALUE", new DoubleType());
    //noinspection unchecked
    results = queryObject.list();

    timer.stop();
    if (AbstractDao.log.isDebugEnabled())
        AbstractDao.log.debug("Fetching probeResults from resultSet " + resultSet.getId() + " for gene "
                + gene.getId() + "and " + arrayDesignIds.size() + "arrays took : " + timer.getTime() + " ms");

    return results;
}

From source file:ubic.gemma.persistence.service.association.coexpression.CoexpressionDaoImpl.java

License:Apache License

@Override
public Map<SupportDetails, Gene2GeneCoexpression> initializeFromOldData(Gene gene, Map<Long, Gene> geneIdMap,
        Map<NonPersistentNonOrderedCoexpLink, SupportDetails> linksSoFar, Set<Long> skipGenes) {

    Session sess = this.getSessionFactory().getCurrentSession();
    LinkCreator c = new LinkCreator(gene.getTaxon());
    String geneLinkTableName = CoexpressionQueryUtils.getGeneLinkTableName(gene.getTaxon());
    String oldGeneLinkTableName = geneLinkTableName.replace("COEX", "CO_EX");
    assert oldGeneLinkTableName.contains("CO_EX");

    int BATCH_SIZE = 1024;

    /*/*from  www.j a  v a  2s . c  om*/
     * Query the old table
     */
    SQLQuery oldLinkQuery = sess.createSQLQuery("select FIRST_GENE_FK, SECOND_GENE_FK, EFFECT from "
            + oldGeneLinkTableName + " where FIRST_GENE_FK=?");
    List<Object[]> oldLinks = oldLinkQuery.setLong(0, gene.getId()).list();

    if (oldLinks.isEmpty()) {
        return null;
    }

    Map<SupportDetails, Gene2GeneCoexpression> linksToSave = new LinkedHashMap<>();

    /*
     * Make new links.
     */
    Collection<NonPersistentNonOrderedCoexpLink> links = new HashSet<>();
    int i = 0;
    for (Object[] o : oldLinks) {
        Long fgid = ((BigInteger) o[0]).longValue();
        Long sgid = ((BigInteger) o[1]).longValue();

        if (skipGenes != null && (skipGenes.contains(fgid) || skipGenes.contains(sgid))) {
            continue;
        }

        Double eff = (Double) o[2];

        if (fgid.equals(sgid)) {
            continue;
        }

        assert geneIdMap.containsKey(fgid);
        assert geneIdMap.containsKey(sgid);

        Gene2GeneCoexpression g2g = c.create(eff, fgid, sgid);

        /*
         * Check if we already have a link like this for the reverse - if so, reuse the supportdetails; the keys of
         * linksSoFar are id-less, so equals() is by genes and direction.
         */
        SupportDetails sdOfFlipped = linksSoFar
                .get(new NonPersistentNonOrderedCoexpLink(geneIdMap.get(fgid), geneIdMap.get(sgid), eff > 0));

        SupportDetails sd;
        if (sdOfFlipped != null) {
            sd = sdOfFlipped;
        } else {
            // we haven't saved the flipped link already so make a new support details.
            sd = c.createSupportDetails(geneIdMap.get(fgid), geneIdMap.get(sgid), eff > 0);
            sess.save(sd);
        }

        g2g.setNumDatasetsSupporting(0);
        g2g.setSupportDetails(sd);

        assert sd.getId() != null;
        linksToSave.put(sd, g2g);

        links.add(new NonPersistentNonOrderedCoexpLink(g2g));

        if (i++ % BATCH_SIZE == 0) {
            sess.flush();
            sess.clear();
        }
    }

    for (SupportDetails sd : linksToSave.keySet()) {
        assert sd.getId() != null;
        sess.save(linksToSave.get(sd));
        if (i++ % BATCH_SIZE == 0) {
            sess.flush();
            sess.clear();
        }
    }

    this.updateGeneCoexpressedWith(links);

    return linksToSave;
}

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

License:Apache License

@Override
public Collection<ExpressionExperiment> findByExpressedGene(Gene gene, Double rank) {

    //language=MySQL
    final String queryString = "SELECT DISTINCT ee.ID AS eeID FROM "
            + "GENE2CS g2s, COMPOSITE_SEQUENCE cs, PROCESSED_EXPRESSION_DATA_VECTOR dedv, INVESTIGATION ee "
            + "WHERE g2s.CS = cs.ID AND cs.ID = dedv.DESIGN_ELEMENT_FK AND dedv.EXPRESSION_EXPERIMENT_FK = ee.ID"
            + " AND g2s.gene = :geneID AND dedv.RANK_BY_MEAN >= :rank";

    Collection<Long> eeIds;

    try {/*  ww w  . j a  v  a  2  s . c om*/
        Session session = this.getSessionFactory().getCurrentSession();
        org.hibernate.SQLQuery queryObject = session.createSQLQuery(queryString);
        queryObject.setLong("geneID", gene.getId());
        queryObject.setDouble("rank", rank);
        queryObject.addScalar("eeID", new LongType());
        ScrollableResults results = queryObject.scroll();

        eeIds = new HashSet<>();

        // Post Processing
        while (results.next())
            eeIds.add(results.getLong(0));

        session.clear();
    } catch (org.hibernate.HibernateException ex) {
        throw super.convertHibernateAccessException(ex);
    }

    return this.load(eeIds);
}

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

License:Apache License

@Override
public Collection<ExpressionExperiment> findByGene(Gene gene) {

    /*// www .  j a  va  2  s  . c om
     * uses GENE2CS table.
     */
    //language=MySQL
    final String queryString = "SELECT DISTINCT ee.ID AS eeID FROM "
            + "GENE2CS g2s, COMPOSITE_SEQUENCE cs, ARRAY_DESIGN ad, BIO_ASSAY ba, INVESTIGATION ee "
            + "WHERE g2s.CS = cs.ID AND ad.ID = cs.ARRAY_DESIGN_FK AND ba.ARRAY_DESIGN_USED_FK = ad.ID AND"
            + " ba.EXPRESSION_EXPERIMENT_FK = ee.ID AND g2s.GENE = :geneID";

    Collection<Long> eeIds;

    Session session = this.getSessionFactory().getCurrentSession();
    org.hibernate.SQLQuery queryObject = session.createSQLQuery(queryString);
    queryObject.setLong("geneID", gene.getId());
    queryObject.addScalar("eeID", new LongType());
    ScrollableResults results = queryObject.scroll();

    eeIds = new HashSet<>();

    while (results.next()) {
        eeIds.add(results.getLong(0));
    }

    return this.load(eeIds);
}