Examples with Observation gov.nih.nci.ctd2.dashboard.model.Observation used on opensource projects

Example 16 with Observation

use of gov.nih.nci.ctd2.dashboard.model.Observation in project nci-ctd2-dashboard by CBIIT.

the class ObservationController method getOneObservationsPerSubmission.

@Transactional
@RequestMapping(value = "onePerSubmissionBySubject", method = { RequestMethod.GET, RequestMethod.POST }, headers = "Accept=application/json")
public ResponseEntity<String> getOneObservationsPerSubmission(@RequestParam("subjectId") Integer subjectId, @RequestParam(value = "role", required = false, defaultValue = "") String role, @RequestParam(value = "tier", required = false, defaultValue = "0") Integer tier) {
    HttpHeaders headers = new HttpHeaders();
    headers.add("Content-Type", "application/json; charset=utf-8");
    List<ObservationWithCount> list = null;
    if (tier > 0 || role.trim().length() > 0) {
        list = onePerSubmissionBySubjectId(subjectId, role, tier);
    } else {
        Map<Observation, BigInteger> observationAndCount = dashboardDao.getOneObservationPerSubmission(subjectId);
        list = new ArrayList<ObservationWithCount>();
        for (Observation observation : observationAndCount.keySet()) {
            list.add(new ObservationWithCount(observation, observationAndCount.get(observation).intValue()));
        }
    }
    JSONSerializer jsonSerializer = new JSONSerializer().transform(new ImplTransformer(), Class.class).transform(new DateTransformer(), Date.class);
    return new ResponseEntity<String>(jsonSerializer.serialize(list), headers, HttpStatus.OK);
}

Example 17 with Observation

use of gov.nih.nci.ctd2.dashboard.model.Observation in project nci-ctd2-dashboard by CBIIT.

the class ObservationController method getObservationsBySubmissionIdAndSubjuectId.

/*
     * For a given submission, tier is decided so there is point of further
     * specifiying tier.
     */
@Transactional
@RequestMapping(value = "bySubmissionAndSubject", method = { RequestMethod.GET, RequestMethod.POST }, headers = "Accept=application/json")
public ResponseEntity<String> getObservationsBySubmissionIdAndSubjuectId(@RequestParam("submissionId") Integer submissionId, @RequestParam("subjectId") Integer subjectId, @RequestParam(value = "role", required = false, defaultValue = "") String role) {
    HttpHeaders headers = new HttpHeaders();
    headers.add("Content-Type", "application/json; charset=utf-8");
    String summaryTemplate = null;
    Set<Observation> observations = new HashSet<Observation>();
    Subject subject = dashboardDao.getEntityById(Subject.class, subjectId);
    for (ObservedSubject observedSubject : dashboardDao.findObservedSubjectBySubject(subject)) {
        Observation observation = observedSubject.getObservation();
        Submission submission = observation.getSubmission();
        if (!submission.getId().equals(submissionId)) {
            continue;
        } else if (summaryTemplate == null) {
            summaryTemplate = submission.getObservationTemplate().getObservationSummary();
        }
        String subjectRole = observedSubject.getObservedSubjectRole().getSubjectRole().getDisplayName();
        if ((role.equals("") || role.equals(subjectRole))) {
            observations.add(observation);
        }
    }
    List<ObservationWithSummary> list = new ArrayList<ObservationWithSummary>();
    for (Observation observation : observations) {
        String expanded = dashboardDao.expandSummary(observation.getId(), summaryTemplate) + " (<a class='button-link' href='#" + observation.getStableURL() + "'>details &raquo;</a>)";
        list.add(new ObservationWithSummary(observation, expanded));
    }
    JSONSerializer jsonSerializer = new JSONSerializer().transform(new ImplTransformer(), Class.class).transform(new DateTransformer(), Date.class);
    return new ResponseEntity<String>(jsonSerializer.serialize(list), headers, HttpStatus.OK);
}

Example 18 with Observation

use of gov.nih.nci.ctd2.dashboard.model.Observation in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method findObservedEvidenceRole.

@Override
public ObservedEvidenceRole findObservedEvidenceRole(String templateName, String columnName) {
    List<ObservedEvidenceRole> list = new ArrayList<ObservedEvidenceRole>();
    // first grab observation template name
    List<ObservationTemplate> otList = queryWithClass("from ObservationTemplateImpl where displayName = :templateName", "templateName", templateName);
    for (ObservationTemplate ot : otList) {
        List<ObservedEvidenceRole> oerList = query2ParamsWithClass("from ObservedEvidenceRoleImpl as oer where columnName = :columnName and " + "oer.observationTemplate = :ot", "columnName", columnName, "ot", ot);
        for (ObservedEvidenceRole o : oerList) {
            list.add(o);
        }
    }
    assert list.size() <= 1;
    return (list.size() == 1) ? list.iterator().next() : null;
}

Example 19 with Observation

use of gov.nih.nci.ctd2.dashboard.model.Observation in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method getObservations.

@Override
public ObservationItem[] getObservations(String submissionId, Set<Integer> indexes) {
    // this works because observation URIs are totally based on submission URI
    List<String> uris = indexes.stream().map(i -> "observation/" + submissionId + "-" + i).collect(Collectors.toList());
    // uris.forEach(System.out::println);
    Session session = getSession();
    List<ObservationItem> list = new ArrayList<ObservationItem>();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<ObservationItem> query = session.createQuery("FROM ObservationItem WHERE uri IN (:uris)");
    query.setParameterList("uris", uris);
    try {
        list = query.getResultList();
    } catch (NoResultException e) {
        log.info("ObservationItem not available for submission ID " + submissionId);
    }
    ObservationItem[] x = list.stream().toArray(ObservationItem[]::new);
    log.debug("count of observations:" + x.length);
    session.close();
    return x;
}

Example 20 with Observation

use of gov.nih.nci.ctd2.dashboard.model.Observation in project nci-ctd2-dashboard by CBIIT.

the class DashboardDaoImpl method getEcoBrowse.

@Override
public List<EcoBrowse> getEcoBrowse() {
    Session session = getSession();
    @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> ecocodeQuery = session.createNativeQuery("SELECT ecocode, id, tier, submissionCenter_id FROM observation_template WHERE LENGTH(ecocode)>0");
    List<Object[]> ecocodeResult = ecocodeQuery.list();
    Map<String, EcoBrowse> map = new HashMap<String, EcoBrowse>();
    Map<String, Set<Integer>> mapTier1centers = new HashMap<String, Set<Integer>>();
    Map<String, Set<Integer>> mapTier2centers = new HashMap<String, Set<Integer>>();
    Map<String, Set<Integer>> mapTier3centers = new HashMap<String, Set<Integer>>();
    for (Object[] array : ecocodeResult) {
        String allcodes = (String) array[0];
        Integer templateId = (Integer) array[1];
        Integer tier = (Integer) array[2];
        Integer centerId = (Integer) array[3];
        String countSql = "SELECT COUNT(DISTINCT submission.id), COUNT(DISTINCT observation.id)" + " FROM observation JOIN submission ON observation.submission_id=submission.id" + " JOIN observation_template ON submission.observationTemplate_id=observation_template.id" + " WHERE submission.observationTemplate_id=" + templateId;
        @SuppressWarnings("unchecked") org.hibernate.query.Query<Object[]> query = session.createNativeQuery(countSql);
        Object[] result = query.getSingleResult();
        BigInteger submissionCount = (BigInteger) result[0];
        BigInteger tierCount = (BigInteger) result[1];
        String[] ecocodes = allcodes.split("\\|");
        for (String code : ecocodes) {
            EcoBrowse b = map.get(code);
            if (b == null) {
                // this term not in the map yet
                @SuppressWarnings("unchecked") org.hibernate.query.Query<ECOTerm> ecotermQuery = session.createQuery("FROM ECOTermImpl WHERE code='" + code + "'");
                ECOTerm term = ecotermQuery.getSingleResult();
                b = new EcoBrowse(term.getDisplayName(), term.getStableURL(), 0);
                map.put(code, b);
            }
            b.setNumberOfSubmissions(b.getNumberOfSubmissions() + submissionCount.intValue());
            Set<Integer> centerSet = null;
            switch(tier) {
                case 1:
                    b.setNumberOfTier1Observations(b.getNumberOfTier1Observations() + tierCount.intValue());
                    centerSet = mapTier1centers.get(code);
                    if (centerSet == null) {
                        centerSet = new HashSet<Integer>();
                        mapTier1centers.put(code, centerSet);
                    }
                    break;
                case 2:
                    b.setNumberOfTier2Observations(b.getNumberOfTier2Observations() + tierCount.intValue());
                    centerSet = mapTier2centers.get(code);
                    if (centerSet == null) {
                        centerSet = new HashSet<Integer>();
                        mapTier2centers.put(code, centerSet);
                    }
                    break;
                case 3:
                    b.setNumberOfTier3Observations(b.getNumberOfTier3Observations() + tierCount.intValue());
                    centerSet = mapTier3centers.get(code);
                    if (centerSet == null) {
                        centerSet = new HashSet<Integer>();
                        mapTier3centers.put(code, centerSet);
                    }
                    break;
                default:
                    log.error("unknow tier number " + tier);
            }
            centerSet.add(centerId);
        }
    }
    map.forEach((code, browseItem) -> {
        int tier1 = 0, tier2 = 0, tier3 = 0;
        Set<Integer> set1 = mapTier1centers.get(code);
        Set<Integer> set2 = mapTier2centers.get(code);
        Set<Integer> set3 = mapTier3centers.get(code);
        if (set1 != null)
            tier1 = set1.size();
        if (set2 != null)
            tier2 = set2.size();
        if (set3 != null)
            tier3 = set3.size();
        browseItem.setNumberOfTier1SubmissionCenters(tier1);
        browseItem.setNumberOfTier2SubmissionCenters(tier2);
        browseItem.setNumberOfTier3SubmissionCenters(tier3);
    });
    session.close();
    log.debug("map size " + map.size());
    return new ArrayList<EcoBrowse>(map.values());
}