Example usage for org.hibernate SQLQuery scroll

List of usage examples for org.hibernate SQLQuery scroll

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Introduction

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

Prototype

ScrollableResults scroll(ScrollMode scrollMode);

Source Link

Document

Return the query results as ScrollableResults.

Usage

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  w  w  w. j a  v a2 s.  com
    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 --&gt; genes
 * @return map//w w w.  ja va2  s  .  c om
 */
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 --&gt; genes
 * @return collection/*from  w  w w.j a va2 s  .  com*/
 */
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.util.CommonQueries.java

License:Apache License

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

}

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

License:Apache License

/**
 * @param session session/*w ww.  j  av a 2  s.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;
}

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

License:Apache License

public static Collection<Long> filterProbesByPlatform(Collection<Long> probes, Collection<Long> arrayDesignIds,
        Session session) {/*from  w  w  w  .j  a va  2  s  .  co  m*/
    assert probes != null && !probes.isEmpty();
    assert arrayDesignIds != null && !arrayDesignIds.isEmpty();
    String queryString = "SELECT CS AS csid FROM GENE2CS WHERE AD IN (:adids) AND CS IN (:probes)";
    org.hibernate.SQLQuery queryObject = session.createSQLQuery(queryString);
    queryObject.addScalar("csid", LongType.INSTANCE);
    queryObject.setParameterList("probes", probes, LongType.INSTANCE);
    queryObject.setParameterList("adids", arrayDesignIds, LongType.INSTANCE);

    ScrollableResults results = queryObject.scroll(ScrollMode.FORWARD_ONLY);
    List<Long> r = new ArrayList<>();
    while (results.next()) {
        r.add(results.getLong(0));

    }
    results.close();
    return r;
}