Example usage for org.hibernate ScrollableResults close

Introduction

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

Prototype

void close();

Source Link

Document

Release resources immediately.

Usage

From source file:resource.dao.base.HQLDAO.java

public Object doInHibernate(Session session) throws HibernateException {
    if (logger.isDebugEnabled()) {
        logger.debug("doInHibernate(Session) - start"); //$NON-NLS-1$
    }//from w w  w. ja v a  2 s  .  co m

    Query queryObject = session.createQuery(queryCondition.getQueryString());
    Object[] values = queryCondition.getObjArray();
    Type[] types = queryCondition.getTypeArray();
    if (null != values) {
        for (int i = 0; i < values.length; i++) {
            if (logger.isDebugEnabled()) {
                logger.debug("i=" + i);
                logger.debug("values[i]=" + values[i]);
                logger.debug("types[i]=" + types[i]);
            }
            if (types != null) {
                queryObject.setParameter(i, values[i], types[i]);
            } else {
                queryObject.setParameter(i, values[i]);
            }
        }
    }

    ScrollableResults sr = null;
    try {
        PageQueryResult queryResult = new PageQueryResult();
        queryResult.setQueryResult(new ArrayList());
        queryResult.setTotalCount(0);

        sr = queryObject.scroll();
        if (false == sr.last()) {

            if (logger.isDebugEnabled()) {
                logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
            }
            return queryResult;
        }

        int totalCount = sr.getRowNumber();
        queryResult.setTotalCount(totalCount + 1);

        int pageSize = queryCondition.getPageSize();
        int pageIndex = queryCondition.getPageIndex() - 1;

        int startRowNum = pageIndex * pageSize;
        if (false == sr.setRowNumber(startRowNum)) {
            if (logger.isDebugEnabled()) {
                logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
            }
            return queryResult;
        }

        List list = queryResult.getQueryResult();
        for (int i = 0; i < pageSize; i++) {
            list.add(sr.get());
            if (false == sr.next()) {
                break;
            }
        }

        if (logger.isDebugEnabled()) {
            logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
        }
        return queryResult;
    } finally {
        if (null != sr)
            sr.close();
    }
}

---

From source file:resource.dao.base.HQLDAO.java

public Object doInHibernate(Session session) throws HibernateException {
    if (logger.isDebugEnabled()) {
        logger.debug("doInHibernate(Session) - start"); //$NON-NLS-1$
    }/*from   ww  w . j  a v a 2  s.c  o m*/

    SQLQuery queryObject = session.createSQLQuery(queryCondition.getQueryString());
    Object[] values = queryCondition.getObjArray();
    Type[] types = queryCondition.getTypeArray();
    if (null != values) {
        for (int i = 0; i < values.length; i++) {
            if (logger.isDebugEnabled()) {
                logger.debug("i=" + i);
                logger.debug("values[i]=" + values[i]);
                logger.debug("types[i]=" + types[i]);
            }
            if (types != null) {
                queryObject.setParameter(i, values[i], types[i]);
            } else {
                queryObject.setParameter(i, values[i]);
            }
        }
    }

    ScrollableResults sr = null;
    try {
        PageQueryResult queryResult = new PageQueryResult();
        queryResult.setQueryResult(new ArrayList());
        queryResult.setTotalCount(0);

        sr = queryObject.scroll();
        if (false == sr.last()) {

            if (logger.isDebugEnabled()) {
                logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
            }
            return queryResult;
        }

        int totalCount = sr.getRowNumber();
        queryResult.setTotalCount(totalCount + 1);

        int pageSize = queryCondition.getPageSize();
        int pageIndex = queryCondition.getPageIndex() - 1;

        int startRowNum = pageIndex * pageSize;
        if (false == sr.setRowNumber(startRowNum)) {
            if (logger.isDebugEnabled()) {
                logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
            }
            return queryResult;
        }

        List list = queryResult.getQueryResult();
        for (int i = 0; i < pageSize; i++) {
            list.add(sr.get());
            if (false == sr.next()) {
                break;
            }
        }

        if (logger.isDebugEnabled()) {
            logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
        }
        return queryResult;
    } finally {
        if (null != sr)
            sr.close();
    }
}

---

From source file:resource.dao.base.HQLDAO.java

public Object doInHibernate(Session session) throws HibernateException {
    if (logger.isDebugEnabled()) {
        logger.debug("doInHibernate(Session) - start"); //$NON-NLS-1$
    }/*  w  w w  .  ja v  a  2s . c  om*/

    Query queryObject = session.createQuery(queryCondition.getQueryString());
    Object[] values = queryCondition.getObjArray();
    Type[] types = queryCondition.getTypeArray();

    if (null != values) {
        for (int i = 0; i < values.length; i++) {
            if (logger.isDebugEnabled()) {
                logger.debug("i=" + i);
                logger.debug("values[i]=" + values[i]);
                logger.debug("types[i]=" + types[i]);
            }
            if (types != null) {
                queryObject.setParameter(i, values[i], types[i]);
            } else {
                queryObject.setParameter(i, values[i]);
            }
        }
    }

    ScrollableResults sr = null;
    try {
        RangeQueryResult queryResult = new RangeQueryResult();
        queryResult.setQueryResult(new ArrayList());
        queryResult.setTotalCount(0);

        sr = queryObject.scroll();
        if (false == sr.last()) {

            if (logger.isDebugEnabled()) {
                logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
            }
            return queryResult;
        }

        int totalCount = sr.getRowNumber();
        queryResult.setTotalCount(totalCount + 1);

        int startRowNum = queryCondition.getStart();
        if (false == sr.setRowNumber(startRowNum)) {
            if (logger.isDebugEnabled()) {
                logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
            }
            return queryResult;
        }

        List list = queryResult.getQueryResult();
        for (int i = 0; i < queryCondition.getCount(); i++) {
            list.add(sr.get());
            if (false == sr.next()) {
                break;
            }
        }

        if (logger.isDebugEnabled()) {
            logger.debug("doInHibernate(Session) - end"); //$NON-NLS-1$
        }
        return queryResult;
    } finally {
        if (null != sr)
            sr.close();
    }
}

---

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  ava  2  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

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

    String limitAbs;//  ww w  . jav  a 2 s .  co  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  w  w.  ja  v  a2 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  w ww.  j a  va  2 s . c  om*/
 */
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  www .  ja va  2s. c o  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//from w  ww.j  a v a  2  s.  c  om
 * @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 www.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;

}

---

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