Example usage for org.hibernate FlushMode MANUAL

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In this page you can find the example usage for org.hibernate FlushMode MANUAL.

Prototype

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.service.genome.taxon.TaxonDaoImpl.java

License:Apache License

@Override
public Taxon find(Taxon taxon) {

    BusinessKey.checkValidKey(taxon);//from   w  w w .j ava2  s  .  c o m

    Criteria queryObject = this.getSessionFactory().getCurrentSession().createCriteria(Taxon.class)
            .setReadOnly(true);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);
    BusinessKey.addRestrictions(queryObject, taxon);

    List<?> results = queryObject.list();
    Object result = null;
    if (results != null) {
        if (results.size() > 1) {
            throw new org.springframework.dao.InvalidDataAccessResourceUsageException(
                    "More than one instance of '" + taxon.getClass().getName()
                            + "' was found when executing query");
        } else if (results.size() == 1) {
            result = results.iterator().next();
        }
    }
    return (Taxon) result;

}

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

License:Apache License

/**
 * @param ees     collection of expression experiments.
 * @param session session/*from  w w  w  .  j a  v a  2s. c om*/
 * @return map of array designs to the experiments they were used in.
 */
public static Map<ArrayDesign, Collection<Long>> getArrayDesignsUsed(Collection<Long> ees, Session session) {
    Map<ArrayDesign, Collection<Long>> eeAdMap = new HashMap<>();

    // Safety 1st....
    if (ees == null || ees.isEmpty())
        return eeAdMap;

    final String eeAdQuery = "select distinct ee.id,ad from ExpressionExperiment as ee inner join "
            + "ee.bioAssays b inner join b.arrayDesignUsed ad fetch all properties where ee.id in (:ees)";

    org.hibernate.Query queryObject = session.createQuery(eeAdQuery);
    queryObject.setParameterList("ees", ees);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    List<?> qr = queryObject.list();
    for (Object o : qr) {
        Object[] ar = (Object[]) o;
        Long ee = (Long) ar[0];
        ArrayDesign ad = (ArrayDesign) ar[1];
        if (!eeAdMap.containsKey(ad)) {
            eeAdMap.put(ad, new HashSet<Long>());
        }
        eeAdMap.get(ad).add(ee);
    }

    return eeAdMap;
}

---

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

License:Apache License

/**
 * @param ees     experiments//  ww w .j a  va2  s .  c  o  m
 * @param session session
 * @return map of experiment to collection of array design ids. If any of the ids given are for subsets, then the
 * key in the return value will be for the subset, not the source experiment (so it is consistent with the
 * input)
 */
public static Map<Long, Collection<Long>> getArrayDesignsUsedEEMap(Collection<Long> ees, Session session) {
    Map<Long, Collection<Long>> ee2ads = new HashMap<>();

    if (ees == null || ees.isEmpty())
        return ee2ads;

    final String eeAdQuery = "select distinct ee.id,ad.id from ExpressionExperiment as ee inner join "
            + "ee.bioAssays b inner join b.arrayDesignUsed ad where ee.id in (:ees)";

    org.hibernate.Query queryObject = session.createQuery(eeAdQuery);
    queryObject.setParameterList("ees", ees);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    List<?> qr = queryObject.list();
    ee2ads = CommonQueries.addAllAds(ee2ads, qr);

    if (ee2ads.size() < ees.size()) {
        // ids might be invalid, but also might be subsets. Note that the output key is for the subset, not the
        // source.
        String subsetQuery = "select distinct ees.id,ad.id from ExpressionExperimentSubSet as ees join ees.sourceExperiment ee "
                + " join ee.bioAssays b join b.arrayDesignUsed ad where ees.id in (:ees)";
        //noinspection unchecked
        Collection<Long> possibleEEsubsets = ListUtils.removeAll(ees, ee2ads.keySet());
        // note: CollectionUtils.removeAll has a bug.

        qr = session.createQuery(subsetQuery).setParameterList("ees", possibleEEsubsets).list();
        ee2ads = CommonQueries.addAllAds(ee2ads, qr);
    }

    return ee2ads;
}

---

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

License:Apache License

/**
 * @param session session/*from  w w  w.  j  a v a 2 s  .c  om*/
 * @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  w  ww.  j  a  v  a 2s.c o m*/
 * @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);//  ww  w  .  j ava2 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

/**
 * @param session      session/* w  ww  .  j ava2s  .  co m*/
 * @param genes        genes
 * @param arrayDesigns array design
 * @return map of probe IDs to collections of gene IDs.
 */
public static Map<Long, Collection<Long>> getCs2GeneIdMap(Collection<Long> genes, Collection<Long> arrayDesigns,
        Session session) {

    Map<Long, Collection<Long>> cs2genes = new HashMap<>();

    String queryString = "SELECT CS AS csid, GENE AS geneId FROM GENE2CS g WHERE g.GENE IN (:geneIds) AND g.AD IN (:ads)";
    SQLQuery queryObject = session.createSQLQuery(queryString);
    queryObject.addScalar("csid", LongType.INSTANCE);
    queryObject.addScalar("geneId", LongType.INSTANCE);
    queryObject.setParameterList("ads", arrayDesigns);
    queryObject.setParameterList("geneIds", genes);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    CommonQueries.addGeneIds(cs2genes, results);
    results.close();

    return cs2genes;

}

---

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();/*from w w w . j  a v  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  w w  w .  ja v  a  2s  . c om
 * @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;
}

---

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

License:Apache License

/**
 * @param session session/*  www  .  j  a v  a  2s .c o  m*/
 * @param probes  probes
 * @return map of probes to all the genes 'detected' by those probes. Probes that don't map to genes will have an
 * empty gene collection.
 */
public static Map<Long, Collection<Long>> getCs2GeneMapForProbes(Collection<Long> probes, Session session) {
    if (probes.isEmpty())
        return new HashMap<>();

    Map<Long, Collection<Long>> cs2genes = new HashMap<>();

    String queryString = "SELECT CS AS csid, GENE AS geneId FROM GENE2CS g WHERE g.CS IN (:probes) ";
    org.hibernate.SQLQuery queryObject = session.createSQLQuery(queryString);
    queryObject.addScalar("csid", LongType.INSTANCE);
    queryObject.addScalar("geneId", LongType.INSTANCE);
    queryObject.setParameterList("probes", probes, LongType.INSTANCE);
    queryObject.setReadOnly(true);
    queryObject.setFlushMode(FlushMode.MANUAL);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    CommonQueries.addGeneIds(cs2genes, results);
    results.close();

    return cs2genes;
}

---

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