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

Example 1 with ObservedSubjectRole

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

the class DashboardDaoImpl method findObservedSubjectRole.

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

Example 2 with ObservedSubjectRole

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

the class ControlledVocabularyPerColumnFieldSetMapper method mapFieldSet.

public ControlledVocabulary mapFieldSet(FieldSet fieldSet) throws BindException {
    String templateName = fieldSet.readString(TEMPLATE_NAME);
    ObservationTemplate observationTemplate = observationTemplateNameMap.get(templateName);
    if (observationTemplate == null)
        return new ControlledVocabulary(null, null, null);
    if (subjectRoleCache == null)
        subjectRoleCache = new HashMap<String, SubjectRole>();
    if (evidenceRoleCache == null)
        evidenceRoleCache = new HashMap<String, EvidenceRole>();
    String subject = fieldSet.readString(SUBJECT);
    String evidence = fieldSet.readString(EVIDENCE);
    if (subject.length() > 0) {
        String subjectRoleStr = fieldSet.readString(ROLE);
        SubjectRole subjectRole = subjectRoleCache.get(subjectRoleStr);
        if (subjectRole == null) {
            subjectRole = dashboardFactory.create(SubjectRole.class);
            subjectRole.setDisplayName(subjectRoleStr);
            subjectRoleCache.put(subjectRoleStr, subjectRole);
        }
        ObservedSubjectRole observedSubjectRole = dashboardFactory.create(ObservedSubjectRole.class);
        observedSubjectRole.setSubjectRole(subjectRole);
        observedSubjectRole.setColumnName(fieldSet.readString(COLUMN_NAME));
        observedSubjectRole.setDisplayText(fieldSet.readString(DISPLAY_TEXT));
        observedSubjectRole.setObservationTemplate(observationTemplate);
        return new ControlledVocabulary(observationTemplate, subjectRole, observedSubjectRole);
    } else if (evidence.length() > 0) {
        String evidenceRoleStr = fieldSet.readString(ROLE);
        EvidenceRole evidenceRole = evidenceRoleCache.get(evidenceRoleStr);
        if (evidenceRole == null) {
            evidenceRole = dashboardFactory.create(EvidenceRole.class);
            evidenceRole.setDisplayName(evidenceRoleStr);
            evidenceRoleCache.put(evidenceRoleStr, evidenceRole);
        }
        ObservedEvidenceRole observedEvidenceRole = dashboardFactory.create(ObservedEvidenceRole.class);
        observedEvidenceRole.setEvidenceRole(evidenceRole);
        observedEvidenceRole.setColumnName(fieldSet.readString(COLUMN_NAME));
        observedEvidenceRole.setDisplayText(fieldSet.readString(DISPLAY_TEXT));
        observedEvidenceRole.setObservationTemplate(observationTemplate);
        observedEvidenceRole.setAttribute(getObservedEvidenceRoleAttribute(fieldSet.readString(MIME_TYPE), fieldSet.readString(NUMERIC_UNITS)));
        return new ControlledVocabulary(observationTemplate, evidenceRole, observedEvidenceRole);
    }
    return new ControlledVocabulary(null, null, null);
}

Example 3 with ObservedSubjectRole

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

the class ObservationController method getBySubjectId.

private List<Observation> getBySubjectId(Integer subjectId, String role, Integer tier) {
    Subject subject = dashboardDao.getEntityById(Subject.class, subjectId);
    if (subject != null) {
        Set<Observation> observations = new HashSet<Observation>();
        for (ObservedSubject observedSubject : dashboardDao.findObservedSubjectBySubject(subject)) {
            ObservedSubjectRole observedSubjectRole = observedSubject.getObservedSubjectRole();
            String subjectRole = observedSubjectRole.getSubjectRole().getDisplayName();
            Integer observationTier = observedSubject.getObservation().getSubmission().getObservationTemplate().getTier();
            if ((role.equals("") || role.equals(subjectRole)) && (tier == 0 || tier == observationTier)) {
                observations.add(observedSubject.getObservation());
            }
        }
        List<Observation> list = new ArrayList<Observation>(observations);
        Collections.sort(list, new Comparator<Observation>() {

            @Override
            public int compare(Observation o1, Observation o2) {
                Integer tier2 = o2.getSubmission().getObservationTemplate().getTier();
                Integer tier1 = o1.getSubmission().getObservationTemplate().getTier();
                return tier2 - tier1;
            }
        });
        return list;
    } else {
        return new ArrayList<Observation>();
    }
}

Example 4 with ObservedSubjectRole

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

the class SubjectResponse method createInstance.

private static SubjectResponse createInstance(final Subject subject, final Filter filter, DashboardDao dashboardDao) {
    int[] tierCount = new int[3];
    Set<Integer> set = new HashSet<Integer>();
    for (ObservedSubject observedSubject : dashboardDao.findObservedSubjectBySubject(subject)) {
        ObservedSubjectRole observedSubjectRole = observedSubject.getObservedSubjectRole();
        String subjectRole = observedSubjectRole.getSubjectRole().getDisplayName();
        if (filter.rolesIncluded.size() > 0 && !filter.rolesIncluded.contains(subjectRole))
            continue;
        ObservationTemplate observatinoTemplate = observedSubject.getObservation().getSubmission().getObservationTemplate();
        Integer observationTier = observatinoTemplate.getTier();
        String centerNameBrief = observatinoTemplate.getSubmissionCenter().getStableURL().substring(7);
        if (filter.centerIncluded.size() > 0 && !filter.centerIncluded.contains(centerNameBrief))
            continue;
        if ((Arrays.asList(filter.tiersIncluded).contains(observationTier))) {
            set.add(observedSubject.getObservation().getId());
            tierCount[observationTier.intValue() - 1]++;
            if (filter.limit > 0 && set.size() >= filter.limit) {
                break;
            }
        }
    }
    List<ObservationItem> observations = dashboardDao.findObservationInfo(new ArrayList<Integer>(set));
    Set<String> roles = new TreeSet<String>();
    for (int i = 0; i < observations.size(); i++) {
        for (SubjectItem sub : observations.get(i).subject_list) {
            if (sub.getName().equals(subject.getDisplayName())) {
                roles.add(sub.getRole());
                break;
            }
        }
    }
    String[] uris = observations.stream().map(x -> x.uri).toArray(String[]::new);
    SubjectResponse subjectResponse = new SubjectResponse(subject, uris, roles.toArray(new String[0]), tierCount);
    return subjectResponse;
}

Example 5 with ObservedSubjectRole

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

the class ObservationController method onePerSubmissionBySubjectId.

private List<ObservationWithCount> onePerSubmissionBySubjectId(Integer subjectId, String role, Integer tier) {
    Subject subject = dashboardDao.getEntityById(Subject.class, subjectId);
    if (subject != null) {
        Map<Integer, Integer> submissionIds = new HashMap<Integer, Integer>();
        Map<Integer, Observation> observations = new HashMap<Integer, Observation>();
        for (ObservedSubject observedSubject : dashboardDao.findObservedSubjectBySubject(subject)) {
            Observation observation = observedSubject.getObservation();
            Submission submission = observation.getSubmission();
            Integer submissionId = submission.getId();
            ObservedSubjectRole observedSubjectRole = observedSubject.getObservedSubjectRole();
            String subjectRole = observedSubjectRole.getSubjectRole().getDisplayName();
            Integer observationTier = observedSubject.getObservation().getSubmission().getObservationTemplate().getTier();
            if ((role.equals("") || role.equals(subjectRole)) && (tier == 0 || tier == observationTier)) {
                if (!submissionIds.containsKey(submissionId)) {
                    submissionIds.put(submissionId, 1);
                    observations.put(submissionId, observation);
                } else {
                    submissionIds.put(submissionId, submissionIds.get(submissionId) + 1);
                }
            }
        }
        List<ObservationWithCount> list = new ArrayList<ObservationWithCount>();
        for (Integer submissionId : observations.keySet()) {
            Observation obs = observations.get(submissionId);
            Integer count = submissionIds.get(submissionId);
            list.add(new ObservationWithCount(obs, count));
        }
        Collections.sort(list, new Comparator<ObservationWithCount>() {

            @Override
            public int compare(ObservationWithCount o1, ObservationWithCount o2) {
                Integer tier2 = o2.observation.getSubmission().getObservationTemplate().getTier();
                Integer tier1 = o1.observation.getSubmission().getObservationTemplate().getTier();
                return tier2 - tier1;
            }
        });
        return list;
    } else {
        return new ArrayList<ObservationWithCount>();
    }
}