Example usage for org.hibernate FetchMode JOIN

List of usage examples for org.hibernate FetchMode JOIN

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FetchMode JOIN

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Fetch using an outer join.

Usage

From source file:gcom.atendimentopublico.RepositorioAtendimentoPublicoHBM.java

License:Open Source License

/**
 * [UC1186] Gerar Relatrio Ordem de Servio Cobrana p/Resultado
 * //from ww w  .jav a 2  s. c o m
 * Pesquisar as Ordens de servios a partir de seu imvel e tipo de servio
 * 
 * @author Hugo Azevedo
 * @data 02/07/2011
 */

public Collection obterOSImovelTipoServico(Integer id, Integer tipoServico) throws ErroRepositorioException {

    Session session = HibernateUtil.getSession();
    Collection<OrdemServico> retorno = new ArrayList();

    try {

        Criteria crit = session.createCriteria(OrdemServico.class);
        crit.setFetchMode("imovel", FetchMode.JOIN);
        crit.setFetchMode("servicoTipo", FetchMode.JOIN);
        crit.setFetchMode("atendimentoMotivoEncerramento", FetchMode.JOIN);
        crit.add(Restrictions.eq("imovel.id", id));
        if (tipoServico != null && tipoServico.intValue() != -1) {
            crit.add(Restrictions.eq("servicoTipo.id", tipoServico.intValue()));
        }
        retorno = (Collection<OrdemServico>) crit.list();

    } catch (HibernateException e) {
        throw new ErroRepositorioException(e, "Erro no Hibernate");
    } finally {
        HibernateUtil.closeSession(session);
    }
    return retorno;
}

From source file:gov.nih.nci.cabio.annotations.ArrayAnnotationServiceImpl.java

License:BSD License

public List<CytobandPhysicalLocation> getCytobandPositions(String chromosomeNumber, String assembly)
        throws ApplicationException {

    DetachedCriteria criteria = DetachedCriteria.forClass(CytobandPhysicalLocation.class);

    criteria.setFetchMode("cytoband", FetchMode.JOIN);
    criteria.setFetchMode("chromosome", FetchMode.JOIN);

    criteria.add(Restrictions.eq("assembly", assembly));

    criteria.createCriteria("chromosome").add(Restrictions.eq("number", chromosomeNumber))
            .createCriteria("taxon").add(Restrictions.eq("abbreviation", taxon));

    List<CytobandPhysicalLocation> results = appService.query(criteria);
    return results;
}

From source file:gov.nih.nci.cabio.annotations.ArrayAnnotationServiceImpl.java

License:BSD License

public Collection<GeneAlias> getAliasesForGene(String symbol) throws ApplicationException {

    DetachedCriteria criteria = DetachedCriteria.forClass(Gene.class);

    criteria.setFetchMode("geneAliasCollection", FetchMode.JOIN)
            .setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY);

    criteria.add(Restrictions.eq("hugoSymbol", symbol).ignoreCase());
    criteria.createCriteria("taxon").add(Restrictions.eq("abbreviation", taxon));

    List<Gene> genes = appService.query(criteria);
    if (genes.isEmpty())
        throw new ApplicationException("No gene exists with HUGO symbol " + symbol);

    List<GeneAlias> results = new ArrayList<GeneAlias>();
    for (Gene g : genes) {
        results.addAll(g.getGeneAliasCollection());
    }/*from   w  w w  .j a va  2  s .co  m*/

    return results;
}

From source file:gov.nih.nci.caintegrator.studyQueryService.germline.SNPAssociationFindingsHandler.java

License:BSD License

protected void initializeProxies(Collection<? extends Finding> findings, Session session) {
    List<GeneBiomarker> gbObjs = new ArrayList<GeneBiomarker>();

    /* initialize SNPAnnotations */
    List<Long> snpAssocFindingIDs = new ArrayList<Long>();
    Collection<Long> snpAnnotsIDs = new HashSet<Long>();
    Collection<Long> populationIDs = new HashSet<Long>();
    for (Iterator<? extends Finding> iterator = findings.iterator(); iterator.hasNext();) {
        SNPAssociationFinding finding = (SNPAssociationFinding) iterator.next();
        snpAnnotsIDs.add(finding.getSnpAnnotation().getId());
        snpAssocFindingIDs.add(finding.getId());
    }/*from  w  w  w. j a va2  s .c  o m*/

    if (snpAnnotsIDs.size() > 0) {
        ArrayList arrayIDs = new ArrayList(snpAnnotsIDs);
        for (int i = 0; i < arrayIDs.size();) {
            Collection values = new ArrayList();
            int begIndex = i;
            i += IN_PARAMETERS;
            int lastIndex = (i < arrayIDs.size()) ? i : (arrayIDs.size());
            values.addAll(arrayIDs.subList(begIndex, lastIndex));
            Criteria snpAnnotcrit = session.createCriteria(SNPAnnotation.class)
                    .setFetchMode("geneBiomarkerCollection", FetchMode.JOIN).add(Restrictions.in("id", values));
            snpAnnotcrit.list();
        }
    }

    if (snpAssocFindingIDs.size() > 0) {
        ArrayList arrayIDs = new ArrayList(snpAssocFindingIDs);
        for (int i = 0; i < arrayIDs.size();) {
            Collection values = new ArrayList();
            int begIndex = i;
            i += IN_PARAMETERS;
            int lastIndex = (i < arrayIDs.size()) ? i : (arrayIDs.size());
            values.addAll(arrayIDs.subList(begIndex, lastIndex));
            Criteria snpAssocFindingCrit = session.createCriteria(SNPAssociationFinding.class)
                    .setFetchMode("oddsRatioCollection", FetchMode.JOIN).add(Restrictions.in("id", values));
            snpAssocFindingCrit.list();
        }
    }

    //        Collection findingIDs = new HashSet();
    //        for (Iterator<? extends Finding> iterator = findings.iterator(); iterator.hasNext();) {
    //           SNPAssociationFinding finding = (SNPAssociationFinding) iterator.next();
    //           findingIDs.add(finding.getId());
    //           //gbObjs.addAll(finding.getSnpAnnotation().getGeneBiomarkerCollection());
    //        }
    //
    //        Criteria crit;
    //        ArrayList<String> arrayIDs = new ArrayList<String>(findingIDs);
    //        for (int i = 0; i < arrayIDs.size();) {
    //            List<String> values = new ArrayList<String>();
    //            int begIndex = i;
    //            i += 1000 ;
    //            int lastIndex = (i < arrayIDs.size()) ? i : (arrayIDs.size());
    //            values.addAll(arrayIDs.subList(begIndex,  lastIndex));
    //            crit = session.createCriteria(SNPAnnotation.class).
    //                                      createAlias("snpAssociationFindingCollection", "findings").
    //                                      setFetchMode("geneBiomarkerCollection", FetchMode.EAGER).
    //                                      add(Restrictions.in("findings.id", values));
    //            crit.list();
    //        }
    //        //Hibernate.initialize(gbObjs);
    //        //gbObjs = null;
}

From source file:gov.nih.nci.cananolab.service.admin.impl.OwnershipTransferServiceImpl.java

License:BSD License

private Sample findFullyLoadedSampleById(String sampleId) throws Exception {
    CaNanoLabApplicationService appService = (CaNanoLabApplicationService) ApplicationServiceProvider
            .getApplicationService();//ww  w . j  a  v  a 2 s  .c  om
    // load composition and characterization separate because of Hibernate
    // join limitation
    DetachedCriteria crit = DetachedCriteria.forClass(Sample.class)
            .add(Property.forName("id").eq(new Long(sampleId)));
    Sample sample = null;

    // load composition and characterization separate because of
    // Hibernate join limitation
    crit.setFetchMode("primaryPointOfContact", FetchMode.JOIN);
    crit.setFetchMode("primaryPointOfContact.organization", FetchMode.JOIN);
    crit.setFetchMode("otherPointOfContactCollection", FetchMode.JOIN);
    crit.setFetchMode("otherPointOfContactCollection.organization", FetchMode.JOIN);
    crit.setFetchMode("keywordCollection", FetchMode.JOIN);
    crit.setFetchMode("publicationCollection", FetchMode.JOIN);
    crit.setFetchMode("publicationCollection.authorCollection", FetchMode.JOIN);
    crit.setFetchMode("publicationCollection.keywordCollection", FetchMode.JOIN);
    crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);

    List result = appService.query(crit);
    if (!result.isEmpty()) {
        sample = (Sample) result.get(0);
    }
    if (sample == null) {
        throw new NotExistException("Sample doesn't exist in the database");
    }

    // fully load composition
    SampleComposition comp = this.loadComposition(sample.getId().toString());
    sample.setSampleComposition(comp);

    // fully load characterizations
    List<Characterization> chars = this.loadCharacterizations(sample.getId().toString());
    if (chars != null && !chars.isEmpty()) {
        sample.setCharacterizationCollection(new HashSet<Characterization>(chars));
    } else {
        sample.setCharacterizationCollection(null);
    }
    return sample;
}

From source file:gov.nih.nci.cananolab.service.admin.impl.OwnershipTransferServiceImpl.java

License:BSD License

private SampleComposition loadComposition(String sampleId) throws Exception {
    SampleComposition composition = null;

    CaNanoLabApplicationService appService = (CaNanoLabApplicationService) ApplicationServiceProvider
            .getApplicationService();//from  w w w. ja  v  a  2s.  c om
    DetachedCriteria crit = DetachedCriteria.forClass(SampleComposition.class);
    crit.createAlias("sample", "sample");
    crit.add(Property.forName("sample.id").eq(new Long(sampleId)));
    crit.setFetchMode("nanomaterialEntityCollection", FetchMode.JOIN);
    crit.setFetchMode("nanomaterialEntityCollection.fileCollection", FetchMode.JOIN);
    crit.setFetchMode("nanomaterialEntityCollection.fileCollection.keywordCollection", FetchMode.JOIN);
    crit.setFetchMode("nanomaterialEntityCollection.composingElementCollection", FetchMode.JOIN);
    crit.setFetchMode("nanomaterialEntityCollection.composingElementCollection.inherentFunctionCollection",
            FetchMode.JOIN);
    crit.setFetchMode(
            "nanomaterialEntityCollection.composingElementCollection.inherentFunctionCollection.targetCollection",
            FetchMode.JOIN);
    crit.setFetchMode("functionalizingEntityCollection", FetchMode.JOIN);
    crit.setFetchMode("functionalizingEntityCollection.fileCollection", FetchMode.JOIN);
    crit.setFetchMode("functionalizingEntityCollection.fileCollection.keywordCollection", FetchMode.JOIN);
    crit.setFetchMode("functionalizingEntityCollection.functionCollection", FetchMode.JOIN);
    crit.setFetchMode("functionalizingEntityCollection.functionCollection.targetCollection", FetchMode.JOIN);
    crit.setFetchMode("functionalizingEntityCollection.activationMethod", FetchMode.JOIN);
    crit.setFetchMode("chemicalAssociationCollection", FetchMode.JOIN);
    crit.setFetchMode("chemicalAssociationCollection.fileCollection", FetchMode.JOIN);
    crit.setFetchMode("chemicalAssociationCollection.fileCollection.keywordCollection", FetchMode.JOIN);
    crit.setFetchMode("chemicalAssociationCollection.associatedElementA", FetchMode.JOIN);
    crit.setFetchMode("chemicalAssociationCollection.associatedElementB", FetchMode.JOIN);
    crit.setFetchMode("fileCollection", FetchMode.JOIN);
    crit.setFetchMode("fileCollection.keywordCollection", FetchMode.JOIN);
    crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
    List result = appService.query(crit);

    if (!result.isEmpty()) {
        composition = (SampleComposition) result.get(0);
    }
    return composition;
}

From source file:gov.nih.nci.cananolab.service.admin.impl.OwnershipTransferServiceImpl.java

License:BSD License

private List<Characterization> loadCharacterizations(String sampleId) throws Exception {
    List<Characterization> chars = new ArrayList<Characterization>();

    CaNanoLabApplicationService appService = (CaNanoLabApplicationService) ApplicationServiceProvider
            .getApplicationService();/*from w  ww. j a  va2  s .  c om*/
    DetachedCriteria crit = DetachedCriteria.forClass(Characterization.class);
    crit.createAlias("sample", "sample");
    crit.add(Property.forName("sample.id").eq(new Long(sampleId)));
    // fully load characterization
    crit.setFetchMode("pointOfContact", FetchMode.JOIN);
    crit.setFetchMode("pointOfContact.organization", FetchMode.JOIN);
    crit.setFetchMode("protocol", FetchMode.JOIN);
    crit.setFetchMode("protocol.file", FetchMode.JOIN);
    crit.setFetchMode("protocol.file.keywordCollection", FetchMode.JOIN);
    crit.setFetchMode("experimentConfigCollection", FetchMode.JOIN);
    crit.setFetchMode("experimentConfigCollection.technique", FetchMode.JOIN);
    crit.setFetchMode("experimentConfigCollection.instrumentCollection", FetchMode.JOIN);
    crit.setFetchMode("findingCollection", FetchMode.JOIN);
    crit.setFetchMode("findingCollection.datumCollection", FetchMode.JOIN);
    crit.setFetchMode("findingCollection.datumCollection.conditionCollection", FetchMode.JOIN);
    crit.setFetchMode("findingCollection.fileCollection", FetchMode.JOIN);
    crit.setFetchMode("findingCollection.fileCollection.keywordCollection", FetchMode.JOIN);
    crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
    List results = appService.query(crit);

    for (int i = 0; i < results.size(); i++) {
        Characterization achar = (Characterization) results.get(i);
        chars.add(achar);
    }
    return chars;
}

From source file:gov.nih.nci.cananolab.service.protocol.helper.ProtocolServiceHelper.java

License:BSD License

public List<Protocol> findProtocolsBy(String protocolType, String protocolName, String protocolAbbreviation,
        String fileTitle) throws Exception {
    List<Protocol> protocols = new ArrayList<Protocol>();
    CaNanoLabApplicationService appService = (CaNanoLabApplicationService) ApplicationServiceProvider
            .getApplicationService();/*from w w  w. ja v  a  2  s.  co  m*/
    DetachedCriteria crit = DetachedCriteria.forClass(Protocol.class);
    crit.createAlias("file", "file", CriteriaSpecification.LEFT_JOIN);

    crit.setFetchMode("file.keywordCollection", FetchMode.JOIN);
    if (!StringUtils.isEmpty(protocolType)) {
        // case insensitive
        crit.add(Restrictions.ilike("type", protocolType, MatchMode.EXACT));
    }
    if (!StringUtils.isEmpty(protocolName)) {
        TextMatchMode protocolNameMatchMode = new TextMatchMode(protocolName);
        crit.add(Restrictions.ilike("name", protocolNameMatchMode.getUpdatedText(),
                protocolNameMatchMode.getMatchMode()));
    }
    if (!StringUtils.isEmpty(protocolAbbreviation)) {
        TextMatchMode protocolAbbreviationMatchMode = new TextMatchMode(protocolAbbreviation);
        crit.add(Restrictions.ilike("abbreviation", protocolAbbreviationMatchMode.getUpdatedText(),
                protocolAbbreviationMatchMode.getMatchMode()));
    }
    if (!StringUtils.isEmpty(fileTitle)) {
        TextMatchMode titleMatchMode = new TextMatchMode(fileTitle);
        crit.add(Restrictions.ilike("file.title", titleMatchMode.getUpdatedText(),
                titleMatchMode.getMatchMode()));
    }
    crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
    List results = appService.query(crit);
    for (int i = 0; i < results.size(); i++) {
        Protocol protocol = (Protocol) results.get(i);
        if (springSecurityAclService.currentUserHasReadPermission(protocol.getId(),
                SecureClassesEnum.PROTOCOL.getClazz())
                || springSecurityAclService.currentUserHasWritePermission(protocol.getId(),
                        SecureClassesEnum.PROTOCOL.getClazz())) {
            protocols.add(protocol);
        } else {
            logger.debug("User doesn't have access ot protocol with id " + protocol.getId());
        }
    }
    return protocols;
}

From source file:gov.nih.nci.cananolab.service.protocol.helper.ProtocolServiceHelper.java

License:BSD License

public Protocol findProtocolBy(String protocolType, String protocolName, String protocolVersion)
        throws Exception {
    // protocol type and protocol name are required
    if (StringUtils.isEmpty(protocolType) && StringUtils.isEmpty(protocolName)) {
        return null;
    }/*from   w  ww  .j  av a 2s .  c  o  m*/
    Protocol protocol = null;
    CaNanoLabApplicationService appService = (CaNanoLabApplicationService) ApplicationServiceProvider
            .getApplicationService();
    DetachedCriteria crit = DetachedCriteria.forClass(Protocol.class)
            .add(Property.forName("type").eq(protocolType).ignoreCase())
            .add(Property.forName("name").eq(protocolName).ignoreCase());
    if (!StringUtils.isEmpty(protocolVersion)) {
        crit.add(Property.forName("version").eq(protocolVersion).ignoreCase());
    }
    crit.setFetchMode("file", FetchMode.JOIN);
    crit.setFetchMode("file.keywordCollection", FetchMode.JOIN);
    crit.setResultTransformer(CriteriaSpecification.DISTINCT_ROOT_ENTITY);
    List results = appService.query(crit);
    if (results.isEmpty()) {
        return null;
    }
    if (results.size() > 1) {
        return null;
    }
    protocol = (Protocol) results.get(0);

    if (springSecurityAclService.currentUserHasReadPermission(protocol.getId(),
            SecureClassesEnum.PROTOCOL.getClazz())
            || springSecurityAclService.currentUserHasWritePermission(protocol.getId(),
                    SecureClassesEnum.PROTOCOL.getClazz())) {
        return protocol;
    } else {
        throw new NoAccessException();
    }
}

From source file:gov.nih.nci.cananolab.service.protocol.helper.ProtocolServiceHelper.java

License:BSD License

public Protocol findProtocolById(String protocolId) throws Exception {
    if (!springSecurityAclService.currentUserHasReadPermission(Long.valueOf(protocolId),
            SecureClassesEnum.PROTOCOL.getClazz())
            && !springSecurityAclService.currentUserHasWritePermission(Long.valueOf(protocolId),
                    SecureClassesEnum.PROTOCOL.getClazz())) {
        new NoAccessException("User has no access to the protocol " + protocolId);
    }/*  w ww  .  j av a  2s.  c  o m*/
    Protocol protocol = null;

    CaNanoLabApplicationService appService = (CaNanoLabApplicationService) ApplicationServiceProvider
            .getApplicationService();
    DetachedCriteria crit = DetachedCriteria.forClass(Protocol.class)
            .add(Property.forName("id").eq(new Long(protocolId)));
    crit.setFetchMode("file", FetchMode.JOIN);
    crit.setFetchMode("file.keywordCollection", FetchMode.JOIN);
    List result = appService.query(crit);
    if (!result.isEmpty()) {
        protocol = (Protocol) result.get(0);
    }
    return protocol;
}