Example usage for org.hibernate Criteria createCriteria

Introduction

In this page you can find the example usage for org.hibernate Criteria createCriteria.

Prototype

public Criteria createCriteria(String associationPath) throws HibernateException;

Source Link

Document

Create a new Criteria, "rooted" at the associated entity.

Usage

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * {@inheritDoc}//www .j a  va2  s  .com
 */
@Override
@SuppressWarnings(UNCHECKED) // Hibernate operations are untyped
public List<SampleAcquisition> findMatchingSamples(AbstractAnnotationCriterion criterion, Study study) {
    if (!criterion.getEntityType().equals(EntityTypeEnum.SAMPLE)) {
        return new ArrayList<SampleAcquisition>();
    } else {
        Criteria sampleAcquisitionCrit = getCurrentSession().createCriteria(SampleAcquisition.class);
        createAnnotationValuesCriteria(criterion, sampleAcquisitionCrit,
                ANNOTATION_VALUE_COLLECTION_ASSOCIATION);
        createStudySubjectAssignmentCriteria(
                sampleAcquisitionCrit.createCriteria(STUDY_SUBJECT_ASSIGNMENT_ASSOCIATION), study);
        return sampleAcquisitionCrit.list();
    }
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * {@inheritDoc}//from w  w w .ja va 2  s  . c  o m
 */
@Override
@SuppressWarnings(UNCHECKED) // Hibernate operations are untyped
public List<StudySubjectAssignment> findMatchingSubjects(AbstractAnnotationCriterion criterion, Study study) {
    if (!criterion.getEntityType().equals(EntityTypeEnum.SUBJECT)) {
        return new ArrayList<StudySubjectAssignment>();
    }
    Criteria studySubjectAssignmentCrit = getCurrentSession().createCriteria(StudySubjectAssignment.class);
    if (criterion instanceof IdentifierCriterion) {
        studySubjectAssignmentCrit.add(AbstractAnnotationCriterionHandler.create(criterion).translate());
    } else {
        createAnnotationValuesCriteria(criterion,
                studySubjectAssignmentCrit.createCriteria("subjectAnnotationCollection"),
                ANNOTATION_VALUE_ASSOCIATION);
    }
    createStudySubjectAssignmentCriteria(studySubjectAssignmentCrit, study);
    return studySubjectAssignmentCrit.list();
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * {@inheritDoc}/*w  ww . jav  a2  s  . co  m*/
 */
@Override
@SuppressWarnings(UNCHECKED) // Hibernate operations are untyped
public Set<AbstractReporter> findReportersForGenes(Set<String> geneSymbols, ReporterTypeEnum reporterType,
        Study study, Platform platform) {
    Set<ReporterList> studyReporterLists = getStudyReporterLists(study, reporterType, platform);
    if (studyReporterLists.isEmpty()) {
        return Collections.emptySet();
    }
    Set<AbstractReporter> reporters = new HashSet<AbstractReporter>();
    Criteria criteria = getCurrentSession().createCriteria(AbstractReporter.class);
    if (!geneSymbols.isEmpty()) {
        criteria.createCriteria(GENES_ASSOCIATION).add(Restrictions.in(SYMBOL_ATTRIBUTE, geneSymbols));
    }
    criteria.add(Restrictions.in("reporterList", studyReporterLists));
    reporters.addAll(criteria.list());
    return reporters;
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * {@inheritDoc}/*from  w  w  w.j  a  va2 s  .com*/
 */
@Override
@SuppressWarnings(UNCHECKED) // Hibernate operations are untyped
public List<SegmentData> findMatchingSegmentDatasByLocation(List<SegmentData> segmentDatasToMatch, Study study,
        Platform platform) {
    Criteria segmentDataCrit = getCurrentSession().createCriteria(SegmentData.class);
    Criteria arrayDataCrit = segmentDataCrit.createCriteria("arrayData");
    Criteria reporterListsCrit = arrayDataCrit.createCriteria("reporterLists");
    reporterListsCrit.add(Restrictions.eq(PLATFORM_ASSOCIATION, platform));
    arrayDataCrit.add(Restrictions.eq(STUDY_ASSOCIATION, study));
    Junction overallOrStatement = Restrictions.disjunction();
    for (SegmentData segmentData : segmentDatasToMatch) {
        ChromosomalLocation location = segmentData.getLocation();
        overallOrStatement.add(Restrictions.conjunction()
                .add(Restrictions.eq("Location.startPosition", location.getStartPosition()))
                .add(Restrictions.eq("Location.endPosition", location.getEndPosition())));
    }
    segmentDataCrit.add(overallOrStatement);
    return segmentDataCrit.list();
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * {@inheritDoc}/*from   w w w.  java  2  s . com*/
 */
@Override
@SuppressWarnings(UNCHECKED) // Hibernate operations are untyped
public List<Gene> findGenesByLocation(String chromosome, Integer startPosition, Integer endPosition,
        GenomeBuildVersionEnum genomeBuildVersion) {
    String locStartPosition = "location.startPosition";
    String locEndPosition = "location.endPosition";
    Criteria geneLocationCriteria = getCurrentSession().createCriteria(GeneChromosomalLocation.class);
    // (gene.startPos <= startPosition && gene.endPos >= startPosition)
    //  || (gene.startPos >= lowerInput  && gene.startPos <= higherInput)
    Junction overallOrStatement = Restrictions.disjunction();
    overallOrStatement.add(Restrictions.conjunction().add(Restrictions.le(locStartPosition, startPosition))
            .add(Restrictions.ge(locEndPosition, startPosition)));
    overallOrStatement.add(Restrictions.conjunction().add(Restrictions.ge(locStartPosition, startPosition))
            .add(Restrictions.le(locStartPosition, endPosition)));
    geneLocationCriteria.add(overallOrStatement);
    geneLocationCriteria.add(getChromosomeRestriction(chromosome));
    geneLocationCriteria.createCriteria("geneLocationConfiguration")
            .add(Restrictions.eq("genomeBuildVersion", genomeBuildVersion));
    geneLocationCriteria.setProjection(Projections.property("geneSymbol"));
    List<String> geneSymbols = geneLocationCriteria.list();
    return geneSymbols.isEmpty() ? new ArrayList<Gene>()
            : getCurrentSession().createCriteria(Gene.class)
                    .setProjection(Projections.distinct(Projections.property(SYMBOL_ATTRIBUTE)))
                    .add(Restrictions.in(SYMBOL_ATTRIBUTE, geneSymbols)).addOrder(Order.asc(SYMBOL_ATTRIBUTE))
                    .list();
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * This function adds the values criteria for getting back the correct annotation values.
 * @param criterion - The main criterion object for the values we want.
 * @param mainAnnotationCriteria - The Criteria on the object that links directly to AbstractAnnotationValue
 * @param annotationValueRelationship - Relationship name that the above object has with AbstractAnnotationValue
 *///from w w  w.j  ava 2  s . c  o  m
private void createAnnotationValuesCriteria(AbstractAnnotationCriterion criterion,
        Criteria mainAnnotationCriteria, String annotationValueRelationship) {
    if (criterion != null && criterion.getAnnotationFieldDescriptor() != null) {
        Criteria valuesCrit = mainAnnotationCriteria.createCriteria(annotationValueRelationship);
        valuesCrit.add(Restrictions.eq(ANNOTATION_DEFINITION_ASSOCIATION,
                criterion.getAnnotationFieldDescriptor().getDefinition()));
        valuesCrit.add(AbstractAnnotationCriterionHandler.create(criterion).translate());
    }
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * Adds the criteria to the AnnotationValue object which will associate it to the given Study.
 * @param study//from   ww w .j a v  a  2  s  .c  om
 * @param entityType
 * @param abstractAnnotationValueCriteria
 */
private void addValuesToStudyCriteria(Study study, EntityTypeEnum entityType,
        Criteria abstractAnnotationValueCriteria) {
    switch (entityType) {
    case SUBJECT:
        abstractAnnotationValueCriteria.createCriteria("subjectAnnotation")
                .createCriteria("studySubjectAssignment").add(Restrictions.eq(STUDY_ASSOCIATION, study));
        break;
    case IMAGESERIES:
        abstractAnnotationValueCriteria.createCriteria("imageSeries").createCriteria("imageStudy")
                .createCriteria(STUDY_SUBJECT_ASSIGNMENT_ASSOCIATION)
                .add(Restrictions.eq(STUDY_ASSOCIATION, study));
        break;
    case IMAGE:
        abstractAnnotationValueCriteria.createCriteria("image").createCriteria("series")
                .createCriteria("imageStudy").createCriteria(STUDY_SUBJECT_ASSIGNMENT_ASSOCIATION)
                .add(Restrictions.eq(STUDY_ASSOCIATION, study));
        break;
    case SAMPLE:
        abstractAnnotationValueCriteria.createCriteria("sampleAcquisition")
                .createCriteria(STUDY_SUBJECT_ASSIGNMENT_ASSOCIATION)
                .add(Restrictions.eq(STUDY_ASSOCIATION, study));
        break;
    default:
        throw new IllegalStateException("Unknown Entity Type.");
    }
}

From source file:gov.nih.nci.caintegrator.data.CaIntegrator2DaoImpl.java

License:BSD License

/**
 * {@inheritDoc}//from  ww w  . j av a 2  s .  c  om
 */
@Override
@SuppressWarnings(UNCHECKED)
public ImageDataSourceConfiguration retrieveImagingDataSourceForStudy(Study study) {
    Criteria imagingDataSourceConfigurationCrit = getCurrentSession()
            .createCriteria(ImageDataSourceConfiguration.class);
    imagingDataSourceConfigurationCrit.createCriteria("studyConfiguration")
            .add(Restrictions.eq(STUDY_ASSOCIATION, study));
    List<ImageDataSourceConfiguration> sourceList = imagingDataSourceConfigurationCrit.list();
    if (sourceList != null && !sourceList.isEmpty()) {
        return sourceList.get(0);
    }
    return null;
}

From source file:gov.nih.nci.caintegrator.data.CopyNumberAlterationCriterionConverter.java

License:BSD License

Criteria retrieveSegmentDataCriteria(Study study, Platform platform, Session currentSession) {
    Criteria segmentDataCrit = currentSession.createCriteria(SegmentData.class);
    Criteria arrayDataCrit = segmentDataCrit.createCriteria("arrayData");
    arrayDataCrit.createCriteria("reporterLists").add(Restrictions.eq("platform", platform));
    arrayDataCrit.add(Restrictions.eq("study", study));
    if (CopyNumberCriterionTypeEnum.SEGMENT_VALUE.equals(copyNumberCriterion.getCopyNumberCriterionType())) {
        addSegmentValueCriterion(segmentDataCrit);
    } else { // Calls type...
        addCallsValueCriterion(segmentDataCrit);
    }/*  ww  w  . j a va 2 s.  com*/

    addGenomicIntervalTypeToCriteria(segmentDataCrit, currentSession, platform.getGenomeVersion());
    return segmentDataCrit;
}

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

License:BSD License

private List<Population> handlePopulationCriteria(SNPFrequencyFindingCriteriaDTO findingCritDTO,
        Session session) {// w  w w  .  ja v a 2  s. co m
    String[] populationNames = findingCritDTO.getPopulationNames();
    Long studyId = findingCritDTO.getStudyCriteria().getId();

    if ((populationNames == null || populationNames.length < 1) && (studyId == null)) {
        return new ArrayList<Population>();
    }

    Criteria popCrit = session.createCriteria(Population.class);
    if (populationNames != null && populationNames.length > 0) {
        popCrit.add(Restrictions.in("name", populationNames));
    }

    boolean appendStudy = isAddStudyCriteria(findingCritDTO);
    if (appendStudy) {
        Criteria studyCrit = popCrit.createCriteria("studyCollection");
        addStudyCriteria(findingCritDTO, studyCrit, session);
    }

    List<Population> populationList = popCrit.list();
    return populationList;
}