Examples with PathogenTestResultType de.symeda.sormas.api.sample.PathogenTestResultType used on opensource projects

Example 1 with PathogenTestResultType

use of de.symeda.sormas.api.sample.PathogenTestResultType in project SORMAS-Project by hzi-braunschweig.

the class TestEntityCreator method createSampleTest.

public static PathogenTest createSampleTest(Sample sample) {
    PathogenTestType pathogenTestType = PathogenTestType.RAPID_TEST;
    PathogenTestResultType pathogenTestResultType = PathogenTestResultType.NEGATIVE;
    Date sampleTestDateTime = new Date();
    PathogenTest pathogenTest = DatabaseHelper.getSampleTestDao().build(sample);
    pathogenTest.setTestType(pathogenTestType);
    pathogenTest.setTestResult(pathogenTestResultType);
    pathogenTest.setTestDateTime(sampleTestDateTime);
    try {
        DatabaseHelper.getSampleTestDao().saveAndSnapshot(pathogenTest);
        DatabaseHelper.getSampleTestDao().accept(pathogenTest);
    } catch (DaoException e) {
        throw new RuntimeException(e);
    }
    return DatabaseHelper.getSampleTestDao().queryForIdWithEmbedded(pathogenTest.getId());
}

Example 2 with PathogenTestResultType

use of de.symeda.sormas.api.sample.PathogenTestResultType in project SORMAS-Project by hzi-braunschweig.

the class SampleFacadeEjbTest method testGetNewTestResultCountByResultType.

@Test
public void testGetNewTestResultCountByResultType() {
    RDCFEntities rdcf = creator.createRDCFEntities();
    UserReferenceDto user = creator.createUser(rdcf).toReference();
    PersonReferenceDto person1 = creator.createPerson("Heinz", "First").toReference();
    PersonReferenceDto person2 = creator.createPerson("Heinz", "Second").toReference();
    CaseDataDto case1 = creator.createCase(user, person1, rdcf);
    CaseDataDto case2 = creator.createCase(user, person2, rdcf);
    List<Long> caseIds = getCaseService().getAllIds(null);
    // no existing samples
    SampleFacade sampleFacade = getSampleFacade();
    Map<PathogenTestResultType, Long> resultMap = sampleFacade.getNewTestResultCountByResultType(caseIds);
    assertEquals(new Long(0), resultMap.values().stream().collect(Collectors.summingLong(Long::longValue)));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.INDETERMINATE, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.NEGATIVE, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.PENDING, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.POSITIVE, null));
    // one pending sample with in one case
    Facility lab = creator.createFacility("facility", rdcf.region, rdcf.district, rdcf.community);
    creator.createSample(case1.toReference(), user, lab);
    resultMap = sampleFacade.getNewTestResultCountByResultType(caseIds);
    assertEquals(new Long(1), resultMap.values().stream().collect(Collectors.summingLong(Long::longValue)));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.INDETERMINATE, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.NEGATIVE, null));
    assertEquals(new Long(1), resultMap.getOrDefault(PathogenTestResultType.PENDING, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.POSITIVE, null));
    // one pending sample in each of two cases
    creator.createSample(case2.toReference(), user, lab);
    resultMap = sampleFacade.getNewTestResultCountByResultType(caseIds);
    assertEquals(new Long(2), resultMap.values().stream().collect(Collectors.summingLong(Long::longValue)));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.INDETERMINATE, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.NEGATIVE, null));
    assertEquals(new Long(2), resultMap.getOrDefault(PathogenTestResultType.PENDING, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.POSITIVE, null));
    // one pending sample in each of two cases
    // and one positive sample in one of the two cases
    SampleDto sample = creator.createSample(case1.toReference(), user, lab);
    sample.setPathogenTestResult(PathogenTestResultType.POSITIVE);
    sampleFacade.saveSample(sample);
    resultMap = sampleFacade.getNewTestResultCountByResultType(caseIds);
    assertEquals(new Long(2), resultMap.values().stream().collect(Collectors.summingLong(Long::longValue)));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.INDETERMINATE, null));
    assertNull(resultMap.getOrDefault(PathogenTestResultType.NEGATIVE, null));
    assertEquals(new Long(1), resultMap.getOrDefault(PathogenTestResultType.PENDING, null));
    assertEquals(new Long(1), resultMap.getOrDefault(PathogenTestResultType.POSITIVE, null));
}

Example 3 with PathogenTestResultType

use of de.symeda.sormas.api.sample.PathogenTestResultType in project SORMAS-Project by hzi-braunschweig.

the class PathogenTestEditFragment method onAfterLayoutBinding.

@Override
public void onAfterLayoutBinding(FragmentPathogenTestEditLayoutBinding contentBinding) {
    setFieldVisibilitiesAndAccesses(PathogenTestDto.class, contentBinding.mainContent);
    // Initialize ControlSpinnerFields
    contentBinding.pathogenTestTestType.initializeSpinner(testTypeList, new ValueChangeListener() {

        @Override
        public void onChange(ControlPropertyField field) {
            PathogenTestType currentTestType = (PathogenTestType) field.getValue();
            if ((PathogenTestType.PCR_RT_PCR == currentTestType && PathogenTestResultType.POSITIVE == contentBinding.pathogenTestTestResult.getValue()) || PathogenTestType.CQ_VALUE_DETECTION == currentTestType) {
                contentBinding.pathogenTestCqValue.setVisibility(View.VISIBLE);
            } else {
                contentBinding.pathogenTestCqValue.hideField(true);
            }
            if (PathogenTestType.PCR_RT_PCR == currentTestType && Disease.CORONAVIRUS == record.getTestedDisease()) {
                getContentBinding().pathogenTestPcrTestSpecification.setVisibility(View.VISIBLE);
            } else {
                getContentBinding().pathogenTestPcrTestSpecification.hideField(false);
            }
        }
    });
    contentBinding.pathogenTestPcrTestSpecification.initializeSpinner(pcrTestSpecificationList);
    contentBinding.pathogenTestTestedDiseaseVariant.initializeSpinner(diseaseVariantList);
    contentBinding.pathogenTestTestedDisease.initializeSpinner(diseaseList, new ValueChangeListener() {

        final Disease currentDisease = record.getTestedDisease();

        @Override
        public void onChange(ControlPropertyField field) {
            if (PathogenTestType.PCR_RT_PCR == record.getTestType() && Disease.CORONAVIRUS == field.getValue()) {
                getContentBinding().pathogenTestPcrTestSpecification.setVisibility(View.VISIBLE);
            } else {
                getContentBinding().pathogenTestPcrTestSpecification.hideField(false);
            }
            if (this.currentDisease == null || contentBinding.pathogenTestTestedDisease.getValue() != currentDisease) {
                updateDiseaseVariantsField(contentBinding);
            }
            testTypeList = DataUtils.toItems(Arrays.asList(PathogenTestType.values()), true, FieldVisibilityCheckers.withDisease((Disease) field.getValue()), PathogenTestType.class);
            contentBinding.pathogenTestTestType.setSpinnerData(testTypeList);
        }
    });
    contentBinding.pathogenTestTestResult.initializeSpinner(testResultList, new ValueChangeListener() {

        @Override
        public void onChange(ControlPropertyField field) {
            PathogenTestResultType currentPathogenTestResult = (PathogenTestResultType) field.getValue();
            if ((PathogenTestType.PCR_RT_PCR == contentBinding.pathogenTestTestType.getValue() && PathogenTestResultType.POSITIVE == currentPathogenTestResult) || PathogenTestType.CQ_VALUE_DETECTION == contentBinding.pathogenTestTestType.getValue()) {
                contentBinding.pathogenTestCqValue.setVisibility(View.VISIBLE);
            } else {
                contentBinding.pathogenTestCqValue.hideField(true);
            }
        }
    });
    contentBinding.pathogenTestLab.initializeSpinner(DataUtils.toItems(labList), new ValueChangeListener() {

        @Override
        public void onChange(ControlPropertyField field) {
            Facility laboratory = (Facility) field.getValue();
            if (laboratory != null && laboratory.getUuid().equals(FacilityDto.OTHER_FACILITY_UUID)) {
                contentBinding.pathogenTestLabDetails.setVisibility(View.VISIBLE);
            } else {
                contentBinding.pathogenTestLabDetails.hideField(true);
            }
        }
    });
    // // Initialize ControlDateFields
    contentBinding.pathogenTestReportDate.initializeDateField(getFragmentManager());
    contentBinding.pathogenTestTestDateTime.initializeDateTimeField(getFragmentManager());
    if (sample.getSamplePurpose() == SamplePurpose.INTERNAL) {
        contentBinding.pathogenTestLab.setRequired(false);
    }
}

Example 4 with PathogenTestResultType

use of de.symeda.sormas.api.sample.PathogenTestResultType in project SORMAS-Project by hzi-braunschweig.

the class SampleService method getNewTestResultCountByResultType.

public Map<PathogenTestResultType, Long> getNewTestResultCountByResultType(List<Long> caseIds) {
    if (CollectionUtils.isEmpty(caseIds)) {
        // Avoid empty IN clause
        return new HashMap<>();
    }
    // Avoid parameter limit by joining caseIds to a String instead of n parameters
    StringBuilder queryBuilder = new StringBuilder();
    // @formatter:off
    queryBuilder.append("WITH sortedsamples AS (SELECT DISTINCT ON (").append(Sample.ASSOCIATED_CASE).append("_id) ").append(Sample.ASSOCIATED_CASE).append("_id, ").append(Sample.PATHOGEN_TEST_RESULT).append(", ").append(Sample.SAMPLE_DATE_TIME).append(" FROM ").append(Sample.TABLE_NAME).append(" WHERE (").append(Sample.SPECIMEN_CONDITION).append(" IS NULL OR ").append(Sample.SPECIMEN_CONDITION).append(" = '").append(SpecimenCondition.ADEQUATE.name()).append("') AND ").append(Sample.TABLE_NAME).append(".").append(Sample.DELETED).append(" = false ORDER BY ").append(Sample.ASSOCIATED_CASE).append("_id, ").append(Sample.SAMPLE_DATE_TIME).append(" desc) SELECT sortedsamples.").append(Sample.PATHOGEN_TEST_RESULT).append(", COUNT(").append(Sample.ASSOCIATED_CASE).append("_id) FROM sortedsamples JOIN ").append(Case.TABLE_NAME).append(" ON sortedsamples.").append(Sample.ASSOCIATED_CASE).append("_id = ").append(Case.TABLE_NAME).append(".id ").append(" WHERE sortedsamples.").append(Sample.ASSOCIATED_CASE).append("_id IN (:caseIds)").append(" GROUP BY sortedsamples." + Sample.PATHOGEN_TEST_RESULT);
    if (caseIds.size() < ModelConstants.PARAMETER_LIMIT) {
        List<Object[]> results;
        Query query = em.createNativeQuery(queryBuilder.toString());
        query.setParameter("caseIds", caseIds);
        results = query.getResultList();
        return results.stream().filter(e -> e[0] != null).collect(Collectors.toMap(e -> PathogenTestResultType.valueOf((String) e[0]), e -> ((BigInteger) e[1]).longValue()));
    } else {
        List<Object[]> results = new LinkedList<>();
        IterableHelper.executeBatched(caseIds, ModelConstants.PARAMETER_LIMIT, batchedCaseIds -> {
            Query query = em.createNativeQuery(queryBuilder.toString());
            query.setParameter("caseIds", batchedCaseIds);
            results.addAll(query.getResultList());
        });
        return results.stream().filter(e -> e[0] != null).collect(Collectors.toMap(e -> PathogenTestResultType.valueOf((String) e[0]), e -> ((BigInteger) e[1]).longValue(), Long::sum));
    }
}

Example 5 with PathogenTestResultType

use of de.symeda.sormas.api.sample.PathogenTestResultType in project SORMAS-Project by hzi-braunschweig.

the class PathogenTestService method getPathogenTestResultsForCase.

public List<PathogenTestResultType> getPathogenTestResultsForCase(long caseId) {
    CriteriaBuilder cb = em.getCriteriaBuilder();
    CriteriaQuery<PathogenTestResultType> cq = cb.createQuery(PathogenTestResultType.class);
    Root<PathogenTest> root = cq.from(getElementClass());
    cq.where(cb.and(createDefaultFilter(cb, root), cb.equal(root.get(PathogenTest.SAMPLE).get(Sample.ASSOCIATED_CASE).get(Case.ID), caseId)));
    cq.select(root.get(PathogenTest.TEST_RESULT));
    List<PathogenTestResultType> result = em.createQuery(cq).getResultList();
    return result;
}