Example usage for org.hibernate ScrollMode FORWARD_ONLY

Introduction

In this page you can find the example usage for org.hibernate ScrollMode FORWARD_ONLY.

Prototype

ScrollMode FORWARD_ONLY

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Document

Requests a scrollable result that is only scrollable forwards.

Usage

From source file:org.zanata.dao.HTextFlowTargetStreamingDAO.java

License:Open Source License

/**
 *
 * @return scrollable result set of HTextFlowTarget under a project
 *         iteration, with all of its fields(locale, textflow, document,
 *         document locale, project iteration and project) eagerly fetched.
 */// www . j  ava2s  .c  o  m
public ScrollableResults getTargetsWithAllFieldsEagerlyFetchedForProjectIteration(HProjectIteration iteration) {
    Query query = getSession()
            .createQuery("from HTextFlowTarget tft " + "join fetch tft.locale " + "join fetch tft.textFlow "
                    + "join fetch tft.textFlow.document " + "join fetch tft.textFlow.document.locale "
                    + "join fetch tft.textFlow.document.projectIteration iter "
                    + "join fetch tft.textFlow.document.projectIteration.project where iter = :iteration");
    return query.setFetchSize(Integer.MIN_VALUE).setParameter("iteration", iteration)
            .scroll(ScrollMode.FORWARD_ONLY);
}

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From source file:org.zanata.search.HTextFlowTargetIndexingStrategy.java

License:Open Source License

@Override
protected ScrollableResults queryResults(int ignoredOffset, FullTextSession session) {
    // TODO move this query into something like HTextFlowTargetStreamingDAO
    Query query = session.createQuery("from HTextFlowTarget tft " + "join fetch tft.locale "
            + "join fetch tft.textFlow " + "join fetch tft.textFlow.document "
            + "join fetch tft.textFlow.document.locale " + "join fetch tft.textFlow.document.projectIteration "
            + "join fetch tft.textFlow.document.projectIteration.project");
    query.setFetchSize(Integer.MIN_VALUE);
    return query.scroll(ScrollMode.FORWARD_ONLY);
}

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From source file:org.zanata.search.SimpleClassIndexingStrategy.java

License:Open Source License

@Override
protected ScrollableResults queryResults(int offset, FullTextSession session) {
    Query query = session.createQuery("from " + getEntityType().getName());
    query.setFirstResult(offset);/*from w w  w.  j a v a  2s  . c om*/
    query.setMaxResults(MAX_QUERY_ROWS);
    return query.scroll(ScrollMode.FORWARD_ONLY);
}

---

From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java

License:Apache License

/**
 * find category terms currently used in the database by evidence
 *//* w w w  .  j  ava2 s  . c o  m*/
@Override
public Collection<CharacteristicValueObject> findEvidenceCategoryTerms() {

    Collection<CharacteristicValueObject> mgedCategory = new TreeSet<>();

    String queryString = "SELECT DISTINCT CATEGORY_URI, category FROM PHENOTYPE_ASSOCIATION "
            + "JOIN INVESTIGATION ON PHENOTYPE_ASSOCIATION.EXPERIMENT_FK = INVESTIGATION.ID "
            + "JOIN CHARACTERISTIC ON CHARACTERISTIC.INVESTIGATION_FK= INVESTIGATION.ID";
    org.hibernate.SQLQuery queryObject = this.getSessionFactory().getCurrentSession()
            .createSQLQuery(queryString);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    while (results.next()) {

        CharacteristicValueObject characteristicValueObject = new CharacteristicValueObject(-1L);
        characteristicValueObject.setCategoryUri((String) results.get(0));
        characteristicValueObject.setCategory((String) results.get(1));
        mgedCategory.add(characteristicValueObject);
    }
    results.close();

    return mgedCategory;
}

---

From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java

License:Apache License

/**
 * return the list of the owners that have evidence in the system
 *//*from  w w w  .  j a va  2  s  . c  o m*/
@Override
public Collection<String> findEvidenceOwners() {

    Set<String> owners = new HashSet<>();

    String sqlQuery = "SELECT DISTINCT sid.PRINCIPAL FROM ACLOBJECTIDENTITY aoi JOIN ACLENTRY ace ON ace.OBJECTIDENTITY_FK = "
            + "aoi.ID JOIN ACLSID sid ON sid.ID = aoi.OWNER_SID_FK WHERE aoi.OBJECT_CLASS " + "IN  "
            + PhenotypeAssociationDaoImpl.DISCRIMINATOR_CLAUSE;

    SQLQuery queryObject = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);

    while (results.next()) {
        String owner = (String) results.get(0);
        owners.add(owner);
    }

    return owners;
}

---

From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java

License:Apache License

@Override
public Set<Long> findPrivateEvidenceId(Long taxonId, Integer limit) {

    String limitAbs;/*from   ww  w  .j  av a 2 s .  c o m*/
    String orderBy;

    if (limit < 0) {
        limitAbs = "limit " + limit * -1;
        orderBy = "order by LAST_UPDATED asc ";
    } else {
        orderBy = "order by LAST_UPDATED desc ";
        limitAbs = "limit " + limit;
    }

    Set<Long> ids = new HashSet<>();

    String sqlQuery = "select distinct phen.ID ";
    sqlQuery += this.getPhenotypesGenesAssociationsBeginQuery(false);

    if (!SecurityUtil.isUserAdmin()) { // admins have no restrictions.
        if (!sqlQuery.trim().endsWith("where")) {
            sqlQuery += " AND ";
        }
        sqlQuery += EntityUtils.addGroupAndUserNameRestriction(true, false);
    }

    if (taxonId != null) {
        if (!sqlQuery.trim().endsWith("where")) {
            sqlQuery += " AND ";
        }
        sqlQuery += " tax.ID = :taxonId ";
    }

    sqlQuery += orderBy + limitAbs;

    SQLQuery queryObject = this.getSessionFactory().getCurrentSession().createSQLQuery(sqlQuery);

    if (taxonId != null) {
        queryObject.setParameter("taxonId", taxonId);
    }

    EntityUtils.addUserAndGroupParameters(queryObject, this.getSessionFactory());

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);

    while (results.next()) {
        Long phenotypeId = ((BigInteger) results.get(0)).longValue();
        ids.add(phenotypeId);
    }

    results.close();
    return ids;
}

---

From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java

License:Apache License

/**
 * @param queryObject execute sqlQuery and populate phenotypesGenesAssociations is : phenotype --> genes
 * @return map//w ww .  j  av  a  2 s  .c  o  m
 */
private Map<String, Set<Integer>> populateGenesAssociations(SQLQuery queryObject) {
    Map<String, Set<Integer>> phenotypesGenesAssociations = new HashMap<>();
    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    while (results.next()) {

        Integer geneNcbiId = (Integer) results.get(0);
        String valueUri = (String) results.get(1);

        EntityUtils.populateMapSet(phenotypesGenesAssociations, valueUri, geneNcbiId);
    }
    results.close();
    return phenotypesGenesAssociations;
}

---

From source file:ubic.gemma.persistence.service.association.phenotype.PhenotypeAssociationDaoImpl.java

License:Apache License

/**
 * @param queryObject execute sqlQuery and populate phenotypesGenesAssociations is : phenotype --> genes
 * @return collection//from   www  .ja  va 2 s. c o  m
 */
private Collection<GeneEvidenceValueObject> populateGenesWithPhenotypes(SQLQuery queryObject) {
    StopWatch sw = new StopWatch();
    sw.start();

    // we accumulate the phenotypes for a gene in one VO
    Map<Long, GeneEvidenceValueObject> genesWithPhenotypes = new HashMap<>();

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    while (results.next()) {
        /* 0: gene id 1: ncbi id 2: name 3: symbol 4: taxon id 5: taxon name 6: characteristic value URI */
        Long geneId = ((BigInteger) results.get(0)).longValue();
        Integer nbciGeneId = (Integer) results.get(1);
        String officialName = (String) results.get(2);
        String officialSymbol = (String) results.get(3);
        Long taxonId = ((BigInteger) results.get(4)).longValue();
        String taxonCommonName = (String) results.get(5);
        String valueUri = (String) results.get(6);

        if (genesWithPhenotypes.get(geneId) != null) {
            genesWithPhenotypes.get(geneId).getPhenotypesValueUri().add(valueUri);
        } else {
            GeneEvidenceValueObject g = new GeneEvidenceValueObject(geneId);
            g.setNcbiId(nbciGeneId);
            g.setOfficialName(officialName);
            g.setOfficialSymbol(officialSymbol);
            g.setTaxonCommonName(taxonCommonName);
            g.setTaxonId(taxonId);
            g.getPhenotypesValueUri().add(valueUri);
            genesWithPhenotypes.put(geneId, g);
        }
    }
    results.close();

    if (sw.getTime() > 500) {
        PhenotypeAssociationDaoImpl.log
                .info("Get " + genesWithPhenotypes.size() + " genes with phenotypes: " + sw.getTime() + "ms");
    }

    return genesWithPhenotypes.values();
}

---

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);//from  ww  w.  j a v  a 2s  . co 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.util.CommonQueries.java

License:Apache License

/**
 * @param session      session//w ww  .  j a  v a  2 s. c  o  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;

}

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