Example usage for org.hibernate ScrollableResults get

Introduction

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

Prototype

Object get(int i);

Source Link

Document

Get the ith object in the current row of results, without initializing any other results in the row.

Usage

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 ww. j  a v  a2s .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);/*ww  w  .j  av a  2  s .  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.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);// w w w .j av a 2 s  . co m
    ScrollableResults list = queryObject.scroll();
    while (list.next()) {
        Taxon taxon = (Taxon) list.get(0);
        Long count = list.getLong(1);

        taxonCount.put(taxon, count);

    }
    return taxonCount;

}

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

License:Apache License

private static void addGenes(Map<CompositeSequence, Collection<Gene>> cs2gene, ScrollableResults results) {
    while (results.next()) {
        CompositeSequence cs = (CompositeSequence) results.get(0);
        Gene g = (Gene) results.get(1);//from w  w w.  j a  va  2  s . c om
        if (!cs2gene.containsKey(cs)) {
            cs2gene.put(cs, new HashSet<Gene>());
        }
        cs2gene.get(cs).add(g);
    }
}

From source file:uit.qabpss.util.dao.orm.hibernate.QueryUtil.java

License:Open Source License

public static List<?> randomList(Query query, Dialect dialect, int total, int num, boolean unmodifiable) {

    if ((total == 0) || (num == 0)) {
        return new ArrayList<Object>();
    }//from  ww w  .j av a  2  s.com

    if (num >= total) {
        return list(query, ALL_POS, ALL_POS);
    }

    int[] scrollIds = Randomizer.getInstance().nextInt(total, num);

    List<Object> list = new ArrayList<Object>();

    ScrollableResults sr = query.scroll();

    for (int i = 0; i < scrollIds.length; i++) {
        if (sr.scroll(scrollIds[i])) {
            Object obj = sr.get(0);

            list.add(obj);

            sr.first();
        }
    }

    return list;

}

From source file:vnpt.media.efinder.model.PaginationResult.java

public PaginationResult(Query query, int page, int maxResult, int maxNavigationPage) {
    final int pageIndex = page - 1 < 0 ? 0 : page - 1;
    int fromRecordIndex = pageIndex * maxResult;
    int maxRecordIndex = fromRecordIndex + maxResult;

    ScrollableResults resultScroll = query.scroll(ScrollMode.SCROLL_INSENSITIVE);

    //resultScroll.g
    List results = new ArrayList<>();
    boolean hasResult = resultScroll.first();
    if (hasResult) {
        // Cuon toi vi tri
        hasResult = resultScroll.scroll(fromRecordIndex);
        if (hasResult) {
            do {//www  . jav a  2  s  .  co  m
                E record = (E) resultScroll.get(0);
                results.add(record);
            } while (resultScroll.next()//
                    && resultScroll.getRowNumber() >= fromRecordIndex
                    && resultScroll.getRowNumber() < maxRecordIndex);
        }

        // chuyen toi ban ghi cuoi
        resultScroll.last();
    }

    // Tong so ban ghi
    this.totalRecords = resultScroll.getRowNumber() + 1;
    this.currentPage = pageIndex + 1;
    this.list = results;
    this.maxResult = maxResult;
    this.totalPages = (this.totalRecords / this.maxResult);
    if (totalRecords % this.maxResult != 0) {
        this.totalPages = this.totalPages + 1;
    }
    this.maxNavigationPage = totalPages;

    if (maxNavigationPage < totalPages) {
        this.maxNavigationPage = maxNavigationPage;
    }

    this.calcNavigationPages();

}