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

Example 1 with TissueSample

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

the class DashboardDaoImpl method ontologySearch.

/*
     * To get observation 'search' results, i.e. the intersection concept, the
     * implmentation of ontology search will be much more complex. Ideally it would
     * be better to compeltely separate the observation part, but to avoid repeating
     * the actual hierarchical searching, embedding observations here is the best
     * choice. Although the previous implementation is better for searching
     * subjects, but to cover the observation parts, we have no choice but to
     * compromise the clarity here.
     * 
     * Other points of consideration for the purpose of observation 'search': (1)
     * the ontologySearch cover the original non-ontology subject results (in
     * principle) (2) the subjects other than TissueSample and ECO term are neither
     * affected or covered by ontology search so it is not consistent.
     */
@Override
public SearchResults ontologySearch(String queryString) {
    final String[] searchTerms = parseWords(queryString);
    Set<Integer> observationsIntersection = null;
    Set<SubjectResult> subject_result = null;
    final int termCount = searchTerms.length;
    if (termCount <= 1) {
        // prevent wasting time finding observations
        subject_result = new HashSet<SubjectResult>(ontologySearchOneTerm(searchTerms[0].replace("\"", ""), null));
    } else {
        boolean first = true;
        Map<SubjectResult, Integer> subjectResultMap = new HashMap<SubjectResult, Integer>();
        for (String oneTerm : searchTerms) {
            oneTerm = oneTerm.replace("\"", "");
            log.debug("ontology search term:" + oneTerm);
            Set<Integer> observations = new HashSet<Integer>();
            List<SubjectResult> oneTermList = ontologySearchOneTerm(oneTerm, observations);
            for (SubjectResult s : oneTermList) {
                Integer matchNumber = subjectResultMap.get(s);
                if (matchNumber != null) {
                    s.matchNumber = matchNumber + 1;
                }
                subjectResultMap.put(s, s.getMatchNumber());
            }
            if (first) {
                observationsIntersection = observations;
                first = false;
            } else {
                observationsIntersection.retainAll(observations);
            }
        }
        subject_result = subjectResultMap.keySet();
    }
    SearchResults searchResults = new SearchResults();
    if (subject_result.size() > maxNumberOfSearchResults) {
        searchResults.oversized = subject_result.size();
        searchResults.subject_result = subject_result.stream().sorted(new SearchResultComparator()).limit(maxNumberOfSearchResults).collect(Collectors.toList());
        log.debug("size after limiting: " + subject_result.size());
    } else {
        searchResults.subject_result = new ArrayList<SubjectResult>(subject_result);
    }
    if (observationsIntersection != null) {
        searchResults.observation_result = observationsIntersection.stream().map(id -> this.getEntityById(Observation.class, id)).collect(Collectors.toList());
        log.debug("size of observation intersection: " + observationsIntersection.size());
    }
    return searchResults;
}

Example 2 with TissueSample

use of gov.nih.nci.ctd2.dashboard.model.TissueSample 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;
}

Example 3 with TissueSample

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

the class TissueSampleSynonymsDataFieldSetMapper method mapFieldSet.

public TissueSample mapFieldSet(FieldSet fieldSet) throws BindException {
    String nciThesaurusCode = fieldSet.readString(NCI_THESAURUS_CODE);
    TissueSample tissueSample = tissueSampleMap.get(nciThesaurusCode);
    if (tissueSample != null) {
        Synonym synonym = dashboardFactory.create(Synonym.class);
        synonym.setDisplayName(fieldSet.readString(SYNONYM));
        tissueSample.getSynonyms().add(synonym);
    }
    return tissueSample;
}

Example 4 with TissueSample

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

the class TissueSampleDataWriter method execute.

public RepeatStatus execute(StepContribution arg0, ChunkContext arg1) throws Exception {
    ArrayList<DashboardEntity> entities = new ArrayList<DashboardEntity>();
    for (TissueSample tissueSample : tissueSampleMap.values()) {
        String nciThesaurusId = getNCIThesaurusID(tissueSample);
        String stableURL = new StableURL().createURLWithPrefix("tissue", nciThesaurusId);
        tissueSample.setStableURL(stableURL);
        entities.add(tissueSample);
    }
    dashboardDao.batchSave(entities, batchSize);
    return RepeatStatus.FINISHED;
}

Example 5 with TissueSample

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

the class TissueSampleTermsDataFieldSetMapper method mapFieldSet.

public TissueSample mapFieldSet(FieldSet fieldSet) throws BindException {
    TissueSample tissueSample = dashboardFactory.create(TissueSample.class);
    tissueSample.setDisplayName(fieldSet.readString(TISSUE_SAMPLE_NAME));
    // create xref to NCI thesaurus
    String nciThesaurusCode = fieldSet.readString(NCI_THESAURUS_CODE);
    tissueSample.setCode(Integer.parseInt(nciThesaurusCode.substring(1)));
    if (!nciThesaurusCode.isEmpty()) {
        addXrefToSample(tissueSample, nciThesaurusCode, NCI_THESAURUS_DATABASE);
    }
    // create xref to NCI thesaurus (parent)
    String parents = fieldSet.readString(PARENTS);
    if (!parents.isEmpty()) {
        for (String parentThesaurusCode : parents.split(";")) {
            addXrefToSample(tissueSample, parentThesaurusCode, NCI_PARENT_THESAURUS_DATABASE);
        }
    }
    tissueSampleMap.put(nciThesaurusCode, tissueSample);
    return tissueSample;
}