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

Example 1 with SampleSimilarityCriteria

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

the class SampleFacadeEjb method getSimilarSamples.

@Override
public List<SampleDto> getSimilarSamples(SampleSimilarityCriteria criteria) {
    final CriteriaBuilder cb = em.getCriteriaBuilder();
    final CriteriaQuery<Sample> cq = cb.createQuery(Sample.class);
    final Root<Sample> root = cq.from(Sample.class);
    cq.distinct(true);
    SampleQueryContext sampleQueryContext = new SampleQueryContext(cb, cq, root);
    SampleCriteria sampleCriteria = new SampleCriteria();
    sampleCriteria.caze(criteria.getCaze()).contact(criteria.getContact()).eventParticipant(criteria.getEventParticipant());
    Predicate filter = sampleService.createUserFilter(sampleQueryContext, sampleCriteria);
    filter = CriteriaBuilderHelper.and(cb, filter, sampleService.buildCriteriaFilter(sampleCriteria, sampleQueryContext));
    Predicate similarityFilter = null;
    if (criteria.getLabSampleId() != null) {
        similarityFilter = cb.equal(root.get(Sample.LAB_SAMPLE_ID), criteria.getLabSampleId());
    }
    Date sampleDateTime = criteria.getSampleDateTime();
    SampleMaterial sampleMaterial = criteria.getSampleMaterial();
    if (sampleDateTime != null && sampleMaterial != null) {
        Predicate dateAndMaterialFilter = cb.and(cb.between(root.get(Sample.SAMPLE_DATE_TIME), DateHelper.getStartOfDay(DateHelper.subtractDays(sampleDateTime, SIMILARITY_DATE_TIME_THRESHOLD)), DateHelper.getEndOfDay(DateHelper.addDays(sampleDateTime, SIMILARITY_DATE_TIME_THRESHOLD))), cb.equal(root.get(Sample.SAMPLE_MATERIAL), sampleMaterial));
        similarityFilter = CriteriaBuilderHelper.or(cb, similarityFilter, dateAndMaterialFilter);
    }
    filter = CriteriaBuilderHelper.and(cb, filter, similarityFilter);
    if (filter != null) {
        cq.where(filter);
    }
    List<Sample> samples = em.createQuery(cq).getResultList();
    if (samples.size() == 0 && (sampleDateTime == null || sampleMaterial == null)) {
        return getByCriteria(sampleCriteria);
    }
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight);
    return samples.stream().map(s -> convertToDto(s, pseudonymizer)).collect(Collectors.toList());
}

Example 2 with SampleSimilarityCriteria

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

the class AbstractLabMessageProcessingFlow method pickOrCreateSample.

private CompletionStage<ProcessingResult<PickOrCreateSampleResult>> pickOrCreateSample(Consumer<SampleSimilarityCriteria> addSampleSearchCriteria, LabMessageDto labMessage) {
    SampleSimilarityCriteria sampleCriteria = createSampleCriteria(labMessage);
    addSampleSearchCriteria.accept(sampleCriteria);
    List<SampleDto> samples = FacadeProvider.getSampleFacade().getSimilarSamples(sampleCriteria);
    PickOrCreateSampleResult result = new PickOrCreateSampleResult();
    if (samples.isEmpty()) {
        result.setNewSample(true);
        return ProcessingResult.continueWith(result).asCompletedFuture();
    }
    HandlerCallback<PickOrCreateSampleResult> callback = new HandlerCallback<>();
    handlePickOrCreateSample(samples, labMessage, callback);
    return callback.futureResult;
}

Example 3 with SampleSimilarityCriteria

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

the class AbstractLabMessageProcessingFlow method createSampleCriteria.

private SampleSimilarityCriteria createSampleCriteria(LabMessageDto labMessage) {
    SampleSimilarityCriteria sampleCriteria = new SampleSimilarityCriteria();
    sampleCriteria.setLabSampleId(labMessage.getLabSampleId());
    sampleCriteria.setSampleDateTime(labMessage.getSampleDateTime());
    sampleCriteria.setSampleMaterial(labMessage.getSampleMaterial());
    return sampleCriteria;
}

Example 4 with SampleSimilarityCriteria

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

the class SampleFacadeEjbTest method testGetSimilarSamples.

@Test
public void testGetSimilarSamples() {
    TestDataCreator.RDCF rdcf = creator.createRDCF();
    UserDto officer = creator.createUser(rdcf, UserRole.SURVEILLANCE_OFFICER);
    CaseDataDto caze = creator.createCase(officer.toReference(), creator.createPerson().toReference(), rdcf);
    Date sampleDateTime1 = DateHelper.parseDate("11.02.2021", new SimpleDateFormat("dd.MM.yyyy"));
    creator.createSample(caze.toReference(), officer.toReference(), rdcf.facility, (s) -> {
        s.setLabSampleID("case_sample_id");
        s.setSampleDateTime(sampleDateTime1);
        s.setSampleMaterial(SampleMaterial.BLOOD);
    });
    Date sampleDateTime2 = DateHelper.parseDate("08.02.2021", new SimpleDateFormat("dd.MM.yyyy"));
    creator.createSample(caze.toReference(), officer.toReference(), rdcf.facility, (s) -> {
        s.setLabSampleID("case_sample_id_2");
        s.setSampleDateTime(sampleDateTime2);
        s.setSampleMaterial(SampleMaterial.BLOOD);
    });
    ContactReferenceDto contact = creator.createContact(officer.toReference(), creator.createPerson().toReference()).toReference();
    SampleDto contactSample = creator.createSample(contact, sampleDateTime1, new Date(), officer.toReference(), SampleMaterial.BLOOD, rdcf.facility);
    EventParticipantDto eventParticipant = creator.createEventParticipant(creator.createEvent(officer.toReference()).toReference(), creator.createPerson(), officer.toReference());
    SampleDto eventParticipantSample = creator.createSample(eventParticipant.toReference(), sampleDateTime1, new Date(), officer.toReference(), SampleMaterial.BLOOD, rdcf.facility);
    SampleSimilarityCriteria criteria = new SampleSimilarityCriteria();
    criteria.caze(caze.toReference());
    criteria.setLabSampleId("case_sample_id");
    List<SampleDto> similarSamples = getSampleFacade().getSimilarSamples(criteria);
    MatcherAssert.assertThat(similarSamples, hasSize(1));
    // should return all samples for unknown lab sample id and missing date and material
    criteria.setLabSampleId("unknown_id");
    similarSamples = getSampleFacade().getSimilarSamples(criteria);
    MatcherAssert.assertThat(similarSamples, hasSize(2));
    criteria.setSampleMaterial(SampleMaterial.BLOOD);
    criteria.setSampleDateTime(DateHelper.addDays(sampleDateTime2, 1));
    similarSamples = getSampleFacade().getSimilarSamples(criteria);
    MatcherAssert.assertThat(similarSamples, hasSize(2));
    criteria.setSampleDateTime(DateHelper.subtractDays(sampleDateTime2, 1));
    similarSamples = getSampleFacade().getSimilarSamples(criteria);
    MatcherAssert.assertThat(similarSamples, hasSize(1));
    criteria.setSampleDateTime(DateHelper.addDays(sampleDateTime1, 3));
    similarSamples = getSampleFacade().getSimilarSamples(criteria);
    MatcherAssert.assertThat(similarSamples, hasSize(0));
    criteria.setSampleDateTime(DateHelper.subtractDays(sampleDateTime2, 3));
    similarSamples = getSampleFacade().getSimilarSamples(criteria);
    MatcherAssert.assertThat(similarSamples, hasSize(0));
    // contact samples
    SampleSimilarityCriteria contactSampleCriteria = new SampleSimilarityCriteria().contact(contact);
    contactSampleCriteria.setSampleDateTime(sampleDateTime1);
    contactSampleCriteria.setSampleMaterial(SampleMaterial.BLOOD);
    List<SampleDto> contactSimilarSamples = getSampleFacade().getSimilarSamples(contactSampleCriteria);
    MatcherAssert.assertThat(contactSimilarSamples, hasSize(1));
    MatcherAssert.assertThat(contactSimilarSamples.get(0).getUuid(), is(contactSample.getUuid()));
    // event participant samples
    SampleSimilarityCriteria eventParticipantSampleCriteria = new SampleSimilarityCriteria().eventParticipant(eventParticipant.toReference());
    eventParticipantSampleCriteria.setSampleDateTime(sampleDateTime1);
    eventParticipantSampleCriteria.setSampleMaterial(SampleMaterial.BLOOD);
    List<SampleDto> eventParticipantSimilarSamples = getSampleFacade().getSimilarSamples(eventParticipantSampleCriteria);
    MatcherAssert.assertThat(eventParticipantSimilarSamples, hasSize(1));
    MatcherAssert.assertThat(eventParticipantSimilarSamples.get(0).getUuid(), is(eventParticipantSample.getUuid()));
}

Example 5 with SampleSimilarityCriteria

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

the class LabMessageController method createSampleCriteria.

private SampleSimilarityCriteria createSampleCriteria(LabMessageDto labMessageDto) {
    SampleSimilarityCriteria sampleCriteria = new SampleSimilarityCriteria();
    sampleCriteria.setLabSampleId(labMessageDto.getLabSampleId());
    sampleCriteria.setSampleDateTime(labMessageDto.getSampleDateTime());
    sampleCriteria.setSampleMaterial(labMessageDto.getSampleMaterial());
    return sampleCriteria;
}