Examples with TissueSampleImpl gov.nih.nci.ctd2.dashboard.impl.TissueSampleImpl used on opensource projects

Example 1 with TissueSampleImpl

use of gov.nih.nci.ctd2.dashboard.impl.TissueSampleImpl in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method ontologySearchOneTerm.

private List<SubjectResult> ontologySearchOneTerm(String oneTerm, final Set<Integer> observations) {
    long t1 = System.currentTimeMillis();
    List<Integer> list = ontologySearchDiseaseContext(oneTerm);
    List<SubjectResult> entities = new ArrayList<SubjectResult>();
    Session session = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<TissueSample> query = session.createQuery("from TissueSampleImpl where code = :code");
    List<Integer> subjectIds = new ArrayList<Integer>();
    for (Integer i : list) {
        query.setParameter("code", i);
        TissueSample result = null;
        try {
            result = query.getSingleResult();
        } catch (NoResultException e) {
            log.info("Tissue sample not available for code " + i);
            continue;
        }
        int observationNumber = observationCountForTissueSample(i);
        int centerCount = centerCountForTissueSample(i);
        Set<String> roles = getRolesForSubjectId(result.getId());
        SubjectResult x = new SubjectResult(result, observationNumber, centerCount, 1, roles);
        entities.add(x);
        subjectIds.add(result.getId());
    }
    long t2 = System.currentTimeMillis();
    log.debug("disease context ontology search for '" + oneTerm + "' took " + (t2 - t1) + " milliseconds");
    log.debug("tissue sample results count: " + entities.size());
    if (observations != null) {
        List<Integer> observationIds = observationIdsForSubjectIds(subjectIds);
        observations.addAll(observationIds);
        log.debug("observations count: " + observations.size());
    }
    List<ECOTerm> ecoterms = findECOTerms(oneTerm);
    List<Integer> eco_list = ontologySearchExperimentalEvidence(ecoterms);
    int eco_list_size = eco_list.size();
    log.debug("eco list size:" + eco_list_size);
    if (eco_list_size > 0) {
        @SuppressWarnings("unchecked") org.hibernate.query.Query<ECOTerm> query2 = session.createQuery("FROM ECOTermImpl WHERE code in (:codes)");
        List<String> codes = eco_list.stream().map(x -> String.format("ECO:%07d", x)).collect(Collectors.toList());
        query2.setParameterList("codes", codes);
        List<ECOTerm> list2 = query2.list();
        for (ECOTerm x : list2) {
            int observationNumber = observationCountForEcoCode(x.getCode());
            int centerCount = centerCountForEcoCode(x.getCode());
            // no matchNumber, no roles
            SubjectResult subjectResult = new SubjectResult(x, observationNumber, centerCount, null, null);
            entities.add(subjectResult);
            if (observations != null) {
                List<Integer> observationIdsForOneECOTerm = observationIdsForEcoCode(x.getCode());
                observations.addAll(observationIdsForOneECOTerm);
            }
        }
    }
    log.debug("tissue sample results count after getting ECO term: " + entities.size());
    if (observations != null) {
        log.debug("observations count after getting ECO term: " + observations.size());
    }
    if (observations != null) {
        searchSubjectsToUpdateObservations(oneTerm, observations);
        log.debug("observationIds count after getting other subjects: " + observations.size());
    }
    session.close();
    return entities;
}