Example usage for org.hibernate ScrollableResults getLong

Introduction

In this page you can find the example usage for org.hibernate ScrollableResults getLong.

Prototype

Long getLong(int col);

Source Link

Document

Convenience method to read a long.

Usage

From source file:org.dcm4chee.archive.query.impl.StudyQuery.java

License:LGPL

@Override
public Attributes toAttributes(ScrollableResults results, QueryContext context) {
    Long studyPk = results.getLong(0);
    Integer numberOfInstancesI = results.getInteger(1);
    int numberOfStudyRelatedInstances;
    int numberOfStudyRelatedSeries;
    String modalitiesInStudy;/*from  w ww. j  a v a  2  s.co  m*/
    String sopClassesInStudy;
    String retrieveAETs;
    Availability availability;
    int numberOfStudyVisibleInstances;
    Date studyLastUpdateTime;
    if (numberOfInstancesI != null) {
        numberOfStudyRelatedInstances = numberOfInstancesI;
        if (numberOfStudyRelatedInstances == 0)
            return null;

        numberOfStudyRelatedSeries = results.getInteger(2);
        modalitiesInStudy = results.getString(3);
        sopClassesInStudy = results.getString(4);
        retrieveAETs = results.getString(5);
        availability = (Availability) results.get(6);
        numberOfStudyVisibleInstances = results.getInteger(7);
        studyLastUpdateTime = results.getDate(8);
    } else {
        StudyQueryAttributes studyView = context.getQueryService().createStudyView(studyPk,
                context.getQueryParam());
        numberOfStudyRelatedInstances = studyView.getNumberOfInstances();
        if (numberOfStudyRelatedInstances == 0)
            return null;

        numberOfStudyRelatedSeries = studyView.getNumberOfSeries();
        modalitiesInStudy = studyView.getRawModalitiesInStudy();
        sopClassesInStudy = studyView.getRawSOPClassesInStudy();
        retrieveAETs = studyView.getRawRetrieveAETs();
        availability = studyView.getAvailability();
        numberOfStudyVisibleInstances = studyView.getNumberOfVisibleInstances();
        studyLastUpdateTime = studyView.getLastUpdateTime();
    }

    byte[] studyByteAttributes = results.getBinary(9);
    byte[] patientByteAttributes = results.getBinary(10);
    Attributes patientAttrs = new Attributes();
    Attributes studyAttrs = new Attributes();
    Utils.decodeAttributes(patientAttrs, patientByteAttributes);
    Utils.decodeAttributes(studyAttrs, studyByteAttributes);
    Attributes attrs = Utils.mergeAndNormalize(patientAttrs, studyAttrs);
    ArchiveDeviceExtension ade = context.getArchiveAEExtension().getApplicationEntity().getDevice()
            .getDeviceExtension(ArchiveDeviceExtension.class);
    Utils.setStudyQueryAttributes(attrs, numberOfStudyRelatedSeries, numberOfStudyRelatedInstances,
            modalitiesInStudy, sopClassesInStudy, numberOfStudyVisibleInstances,
            ade.getPrivateDerivedFields().findStudyNumberOfVisibleInstancesTag(), studyLastUpdateTime,
            ade.getPrivateDerivedFields().findStudyUpdateTimeTag());
    Utils.setRetrieveAET(attrs, retrieveAETs);
    Utils.setAvailability(attrs, availability);
    return attrs;
}

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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 {/* w  ww. j a v a2s .  com*/
        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);
}

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

License:Apache License

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

    /*//from ww w  . j a v  a  2s  . c  o  m
     * 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);
}

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

License:Apache License

@Override
public Map<Taxon, Long> getPerTaxonCount() {

    Map<Taxon, Long> taxonCount = new LinkedHashMap<>();
    String queryString = "select t, count(distinct ee) from ExpressionExperiment "
            + "ee inner join ee.bioAssays as ba inner join ba.sampleUsed su "
            + "inner join su.sourceTaxon t group by t order by t.scientificName ";

    // it is important to cache this, as it gets called on the home page. Though it's actually fast.
    org.hibernate.Query queryObject = this.getSessionFactory().getCurrentSession().createQuery(queryString);
    queryObject.setCacheable(true);/*from   ww  w  . j  a  va  2  s. com*/
    ScrollableResults list = queryObject.scroll();
    while (list.next()) {
        Taxon taxon = (Taxon) list.get(0);
        Long count = list.getLong(1);

        taxonCount.put(taxon, count);

    }
    return taxonCount;

}

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

License:Apache License

private static void addGeneIds(Map<Long, Collection<Long>> cs2genes, ScrollableResults results) {
    while (results.next()) {
        Long csid = results.getLong(0);
        Long geneId = results.getLong(1);

        if (!cs2genes.containsKey(csid)) {
            cs2genes.put(csid, new HashSet<Long>());
        }/*from ww  w. j a v  a2  s  . co  m*/
        cs2genes.get(csid).add(geneId);
    }
}

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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) {//w ww .ja va2s .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;
}

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