Example usage for org.hibernate Query setReadOnly

Introduction

In this page you can find the example usage for org.hibernate Query setReadOnly.

Prototype

Query<R> setReadOnly(boolean readOnly);

Source Link

Document

Set the read-only/modifiable mode for entities and proxies loaded by this Query.

Usage

From source file:ubic.gemma.persistence.util.CommonQueries.java

License:Apache License

/**
 * @param session session/*from   w w w . ja v  a 2  s.co  m*/
 * @param eeId    experiment id
 * @return list of array designs IDs used in given expression experiment
 */
@SuppressWarnings("unchecked")
public static Collection<Long> getArrayDesignIdsUsed(Long eeId, Session session) {
    final String eeAdQuery = "select distinct ad.id from ExpressionExperiment as ee inner join "
            + "ee.bioAssays b inner join b.arrayDesignUsed ad where ee.id = :eeId";

    org.hibernate.Query queryObject = session.createQuery(eeAdQuery);
    queryObject.setCacheable(true);
    queryObject.setParameter("eeId", eeId);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    List<?> list = queryObject.list();
    return (Collection<Long>) list;
}

From source file:ubic.gemma.persistence.util.CommonQueries.java

License:Apache License

/**
 * Given a gene, get all the composite sequences that map to it.
 *
 * @param session session//from  ww w  . ja  v a 2s .c om
 * @param gene    gene
 * @return composite sequences
 */
public static Collection<CompositeSequence> getCompositeSequences(Gene gene, Session session) {

    final String csQueryString = "select distinct cs from Gene as gene"
            + " join gene.products gp, BioSequence2GeneProduct ba, CompositeSequence cs "
            + " where ba.bioSequence.id=cs.biologicalCharacteristic.id and ba.geneProduct.id = gp.id and gene.id = :gene ";

    org.hibernate.Query queryObject = session.createQuery(csQueryString);
    queryObject.setParameter("gene", gene.getId(), LongType.INSTANCE);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);
    //noinspection unchecked
    return queryObject.list();
}

From source file:ubic.gemma.persistence.util.CommonQueries.java

License:Apache License

private static Query createGetADsUsedQueryObject(Long eeId, Session session) {
    final String eeAdQuery = "select distinct ad from ExpressionExperiment as ee inner join "
            + "ee.bioAssays b inner join b.arrayDesignUsed ad inner join ad.primaryTaxon fetch all properties where ee.id = :eeId";

    Query queryObject = session.createQuery(eeAdQuery);
    queryObject.setCacheable(true);// w  w  w  .  j a  v  a 2 s  .  c  o m
    queryObject.setParameter("eeId", eeId);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);
    return queryObject;
}

From source file:ubic.gemma.persistence.util.CommonQueries.java

License:Apache License

public static Map<CompositeSequence, Collection<Gene>> getCs2GeneMap(Collection<Gene> genes,
        Collection<ArrayDesign> arrayDesigns, Session session) {

    StopWatch timer = new StopWatch();
    timer.start();/*w ww .  j  av a  2  s . c o m*/
    final String csQueryString = "select distinct cs, gene from Gene as gene"
            + " inner join gene.products gp, BioSequence2GeneProduct ba, CompositeSequence cs "
            + " where ba.bioSequence=cs.biologicalCharacteristic and ba.geneProduct = gp"
            + " and gene in (:genes) and cs.arrayDesign in (:ads) ";

    Map<CompositeSequence, Collection<Gene>> cs2gene = new HashMap<>();
    Query queryObject = session.createQuery(csQueryString);
    queryObject.setCacheable(true);
    queryObject.setParameterList("genes", genes);
    queryObject.setParameterList("ads", arrayDesigns);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    CommonQueries.addGenes(cs2gene, results);
    results.close();
    if (timer.getTime() > 200) {
        CommonQueries.log.info("Get cs2gene for " + genes.size() + " :" + timer.getTime() + "ms");
    }
    return cs2gene;

}

From source file:ubic.gemma.persistence.util.CommonQueries.java

License:Apache License

/**
 * @param genes   genes//from ww w . ja v  a  2s  .c o m
 * @param session session
 * @return map of probes to input genes they map to. Other genes those probes might detect are not included.
 */
public static Map<CompositeSequence, Collection<Gene>> getCs2GeneMap(Collection<Gene> genes, Session session) {

    StopWatch timer = new StopWatch();
    timer.start();
    final String csQueryString = "select distinct cs, gene from Gene as gene"
            + " inner join gene.products gp, BioSequence2GeneProduct ba, CompositeSequence cs "
            + " where ba.bioSequence=cs.biologicalCharacteristic and ba.geneProduct = gp"
            + " and gene in (:genes)  ";

    Map<CompositeSequence, Collection<Gene>> cs2gene = new HashMap<>();
    org.hibernate.Query queryObject = session.createQuery(csQueryString);
    queryObject.setCacheable(true);
    queryObject.setParameterList("genes", genes);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    CommonQueries.addGenes(cs2gene, results);
    results.close();
    if (timer.getTime() > 200) {
        CommonQueries.log.info("Get cs2gene for " + genes.size() + " :" + timer.getTime() + "ms");
    }
    return cs2gene;
}