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

Example 1 with AdditionalTestDto

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

the class AdditionalTestFacadeEjb method toDto.

public static AdditionalTestDto toDto(AdditionalTest source) {
    if (source == null) {
        return null;
    }
    AdditionalTestDto target = new AdditionalTestDto();
    DtoHelper.fillDto(target, source);
    target.setSample(SampleFacadeEjb.toReferenceDto(source.getSample()));
    target.setTestDateTime(source.getTestDateTime());
    target.setHaemoglobinuria(source.getHaemoglobinuria());
    target.setProteinuria(source.getProteinuria());
    target.setHematuria(source.getHematuria());
    target.setArterialVenousGasPH(source.getArterialVenousGasPH());
    target.setArterialVenousGasPco2(source.getArterialVenousGasPco2());
    target.setArterialVenousGasPao2(source.getArterialVenousGasPao2());
    target.setArterialVenousGasHco3(source.getArterialVenousGasHco3());
    target.setGasOxygenTherapy(source.getGasOxygenTherapy());
    target.setAltSgpt(source.getAltSgpt());
    target.setAstSgot(source.getAstSgot());
    target.setCreatinine(source.getCreatinine());
    target.setPotassium(source.getPotassium());
    target.setUrea(source.getUrea());
    target.setHaemoglobin(source.getHaemoglobin());
    target.setTotalBilirubin(source.getTotalBilirubin());
    target.setConjBilirubin(source.getConjBilirubin());
    target.setWbcCount(source.getWbcCount());
    target.setPlatelets(source.getPlatelets());
    target.setProthrombinTime(source.getPlatelets());
    target.setOtherTestResults(source.getOtherTestResults());
    return target;
}

Example 2 with AdditionalTestDto

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

the class CaseFacadeEjb method mergeCase.

private void mergeCase(CaseDataDto leadCaseData, CaseDataDto otherCaseData, boolean cloning) {
    // 1 Merge Dtos
    // 1.1 Case
    copyDtoValues(leadCaseData, otherCaseData, cloning);
    save(leadCaseData, !cloning, true, true, false);
    // 1.2 Person - Only merge when the persons have different UUIDs
    if (!cloning && !DataHelper.equal(leadCaseData.getPerson().getUuid(), otherCaseData.getPerson().getUuid())) {
        PersonDto leadPerson = personFacade.getPersonByUuid(leadCaseData.getPerson().getUuid());
        PersonDto otherPerson = personFacade.getPersonByUuid(otherCaseData.getPerson().getUuid());
        personFacade.mergePerson(leadPerson, otherPerson);
    } else {
        assert (DataHelper.equal(leadCaseData.getPerson().getUuid(), otherCaseData.getPerson().getUuid()));
    }
    // 2 Change CaseReference
    Case leadCase = service.getByUuid(leadCaseData.getUuid());
    Case otherCase = service.getByUuid(otherCaseData.getUuid());
    // 2.1 Contacts
    List<Contact> contacts = contactService.findBy(new ContactCriteria().caze(otherCase.toReference()), null);
    for (Contact contact : contacts) {
        if (cloning) {
            ContactDto newContact = ContactDto.build(leadCase.toReference(), leadCase.getDisease(), leadCase.getDiseaseDetails(), leadCase.getDiseaseVariant());
            newContact.setPerson(new PersonReferenceDto(contact.getPerson().getUuid()));
            DtoHelper.copyDtoValues(newContact, contactFacade.toDto(contact), cloning);
            contactFacade.save(newContact, false, false);
        } else {
            // simply move existing entities to the merge target
            contact.setCaze(leadCase);
            contactService.ensurePersisted(contact);
        }
    }
    // 2.2 Samples
    List<Sample> samples = sampleService.findBy(new SampleCriteria().caze(otherCase.toReference()), null);
    for (Sample sample : samples) {
        if (cloning) {
            SampleDto newSample = SampleDto.build(sample.getReportingUser().toReference(), leadCase.toReference());
            DtoHelper.copyDtoValues(newSample, SampleFacadeEjb.toDto(sample), cloning);
            sampleFacade.saveSample(newSample, false, true, true);
            // 2.2.1 Pathogen Tests
            for (PathogenTest pathogenTest : sample.getPathogenTests()) {
                PathogenTestDto newPathogenTest = PathogenTestDto.build(newSample.toReference(), pathogenTest.getLabUser().toReference());
                DtoHelper.copyDtoValues(newPathogenTest, PathogenTestFacadeEjbLocal.toDto(pathogenTest), cloning);
                sampleTestFacade.savePathogenTest(newPathogenTest);
            }
            for (AdditionalTest additionalTest : sample.getAdditionalTests()) {
                AdditionalTestDto newAdditionalTest = AdditionalTestDto.build(newSample.toReference());
                DtoHelper.copyDtoValues(newAdditionalTest, AdditionalTestFacadeEjbLocal.toDto(additionalTest), cloning);
                additionalTestFacade.saveAdditionalTest(newAdditionalTest);
            }
        } else {
            // simply move existing entities to the merge target
            sample.setAssociatedCase(leadCase);
            sampleService.ensurePersisted(sample);
        }
    }
    // 2.3 Tasks
    if (!cloning) {
        // simply move existing entities to the merge target
        List<Task> tasks = taskService.findBy(new TaskCriteria().caze(new CaseReferenceDto(otherCase.getUuid())), true);
        for (Task task : tasks) {
            task.setCaze(leadCase);
            taskService.ensurePersisted(task);
        }
    }
    // 3 Change Therapy Reference
    // 3.1 Treatments
    List<Treatment> treatments = treatmentService.findBy(new TreatmentCriteria().therapy(new TherapyReferenceDto(otherCase.getTherapy().getUuid())));
    TherapyReferenceDto leadCaseTherapyReference = new TherapyReferenceDto(leadCase.getTherapy().getUuid());
    for (Treatment treatment : treatments) {
        if (cloning) {
            TreatmentDto newTreatment = TreatmentDto.build(leadCaseTherapyReference);
            DtoHelper.copyDtoValues(newTreatment, TreatmentFacadeEjb.toDto(treatment), cloning);
            treatmentFacade.saveTreatment(newTreatment);
        } else {
            // simply move existing entities to the merge target
            treatment.setTherapy(leadCase.getTherapy());
            treatmentService.ensurePersisted(treatment);
        }
    }
    // 3.2 Prescriptions
    List<Prescription> prescriptions = prescriptionService.findBy(new PrescriptionCriteria().therapy(new TherapyReferenceDto(otherCase.getTherapy().getUuid())));
    for (Prescription prescription : prescriptions) {
        if (cloning) {
            PrescriptionDto newPrescription = PrescriptionDto.buildPrescription(leadCaseTherapyReference);
            DtoHelper.copyDtoValues(newPrescription, PrescriptionFacadeEjb.toDto(prescription), cloning);
            prescriptionFacade.savePrescription(newPrescription);
        } else {
            // simply move existing entities to the merge target
            prescription.setTherapy(leadCase.getTherapy());
            prescriptionService.ensurePersisted(prescription);
        }
    }
    // 4 Change Clinical Course Reference
    // 4.1 Clinical Visits
    List<ClinicalVisit> clinicalVisits = clinicalVisitService.findBy(new ClinicalVisitCriteria().clinicalCourse(new ClinicalCourseReferenceDto(otherCase.getClinicalCourse().getUuid())));
    for (ClinicalVisit clinicalVisit : clinicalVisits) {
        if (cloning) {
            ClinicalVisitDto newClinicalVisit = ClinicalVisitDto.build(leadCaseData.getClinicalCourse().toReference(), leadCase.getDisease());
            DtoHelper.copyDtoValues(newClinicalVisit, ClinicalVisitFacadeEjb.toDto(clinicalVisit), cloning);
            clinicalVisitFacade.saveClinicalVisit(newClinicalVisit, leadCase.getUuid(), false);
        } else {
            // simply move existing entities to the merge target
            clinicalVisit.setClinicalCourse(leadCase.getClinicalCourse());
            clinicalVisitService.ensurePersisted(clinicalVisit);
        }
    }
    // (set the person and the disease of the visit, saveVisit does the rest)
    for (VisitDto otherVisit : otherCase.getVisits().stream().map(VisitFacadeEjb::toDto).collect(Collectors.toList())) {
        otherVisit.setPerson(leadCaseData.getPerson());
        otherVisit.setDisease(leadCaseData.getDisease());
        visitFacade.saveVisit(otherVisit);
    }
    // 6 Documents
    List<Document> documents = documentService.getRelatedToEntity(DocumentRelatedEntityType.CASE, otherCase.getUuid());
    for (Document document : documents) {
        document.setRelatedEntityUuid(leadCaseData.getUuid());
        documentService.ensurePersisted(document);
    }
    // 7 Persist Event links through eventparticipants
    Set<EventParticipant> eventParticipants = otherCase.getEventParticipants();
    for (EventParticipant eventParticipant : eventParticipants) {
        eventParticipant.setResultingCase(leadCase);
        eventParticipantService.ensurePersisted(eventParticipant);
    }
    otherCase.getEventParticipants().clear();
    // 8 Exposures - Make sure there are no two probable infection environments
    // if there are more than 2 exposures marked as probable infection environment, find the one that originates from the otherCase and set it to false
    // the one originating from the otherCase should always be found at the higher index
    List<Exposure> probableExposuresList = leadCase.getEpiData().getExposures().stream().filter(Exposure::isProbableInfectionEnvironment).collect(Collectors.toList());
    while (probableExposuresList.size() >= 2) {
        // should never be > 2, but still make sure to set all but one exposures to false
        probableExposuresList.get(probableExposuresList.size() - 1).setProbableInfectionEnvironment(false);
        exposureService.ensurePersisted(probableExposuresList.get(probableExposuresList.size() - 1));
        probableExposuresList.remove(probableExposuresList.size() - 1);
    }
    // 9 Reports
    List<SurveillanceReport> surveillanceReports = surveillanceReportService.getByCaseUuids(Collections.singletonList(otherCase.getUuid()));
    surveillanceReports.forEach(surveillanceReport -> {
        SurveillanceReportDto surveillanceReportDto = SurveillanceReportFacadeEjb.toDto(surveillanceReport);
        surveillanceReportDto.setCaze(leadCase.toReference());
        surveillanceReportFacade.saveSurveillanceReport(surveillanceReportDto);
    });
    // 10 Activity as case
    final EpiData otherEpiData = otherCase.getEpiData();
    if (otherEpiData != null && YesNoUnknown.YES == otherEpiData.getActivityAsCaseDetailsKnown() && CollectionUtils.isNotEmpty(otherEpiData.getActivitiesAsCase())) {
        final EpiData leadEpiData = leadCase.getEpiData();
        leadEpiData.setActivityAsCaseDetailsKnown(YesNoUnknown.YES);
        epiDataService.ensurePersisted(leadEpiData);
    }
    // Travel entries reference
    List<TravelEntry> travelEntries = travelEntryService.getAllByResultingCase(otherCase);
    travelEntries.forEach(t -> {
        t.setResultingCase(leadCase);
        travelEntryService.ensurePersisted(t);
    });
}

Example 3 with AdditionalTestDto

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

the class AdditionalTestList method reload.

@Override
public void reload() {
    List<AdditionalTestDto> additionalTests = ControllerProvider.getAdditionalTestController().getAdditionalTestsBySample(sampleUuid);
    setEntries(additionalTests);
    if (!additionalTests.isEmpty()) {
        showPage(1);
    } else {
        listLayout.removeAllComponents();
        updatePaginationLayout();
        Label noAdditionalTestsLabel = new Label(I18nProperties.getString(Strings.infoNoAdditionalTests));
        listLayout.addComponent(noAdditionalTestsLabel);
    }
}

Example 4 with AdditionalTestDto

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

the class SormasToSormasEventFacadeEjbTest method testSaveSharedEventsWithSamples.

@Test
public void testSaveSharedEventsWithSamples() throws SormasToSormasException, SormasToSormasValidationException {
    FacilityDto remoteLab = FacilityDto.build();
    remoteLab.setName("Test Lab");
    FacilityDto localLab = creator.createFacility("Test Lab", rdcf.region, rdcf.district, null, FacilityType.LABORATORY);
    EventDto event = createEventDto(rdcf);
    UserDto sampleUser = UserDto.build();
    EventParticipantDto eventParticipant = createEventParticipantDto(event.toReference(), sampleUser.toReference(), rdcf);
    SampleDto sample = createSample(eventParticipant.toReference(), sampleUser.toReference(), remoteLab.toReference());
    sample.setLabSampleID("Test lab sample id");
    PathogenTestDto pathogenTest = PathogenTestDto.build(sample, sampleUser);
    pathogenTest.setTestDateTime(new Date());
    pathogenTest.setLab(remoteLab.toReference());
    pathogenTest.setTestType(PathogenTestType.RAPID_TEST);
    pathogenTest.setTestResult(PathogenTestResultType.PENDING);
    AdditionalTestDto additionalTest = AdditionalTestDto.build(sample.toReference());
    additionalTest.setTestDateTime(new Date());
    additionalTest.setHaemoglobin(0.2F);
    additionalTest.setConjBilirubin(0.3F);
    SormasToSormasDto shareData = new SormasToSormasDto();
    shareData.setOriginInfo(createSormasToSormasOriginInfo(DEFAULT_SERVER_ID, false));
    shareData.setEvents(Collections.singletonList(new SormasToSormasEventDto(event)));
    shareData.setEventParticipants(Collections.singletonList(new SormasToSormasEventParticipantDto(eventParticipant)));
    shareData.setSamples(Collections.singletonList(new SormasToSormasSampleDto(sample, Collections.singletonList(pathogenTest), Collections.singletonList(additionalTest))));
    SormasToSormasEncryptedDataDto encryptedData = encryptShareData(shareData);
    getSormasToSormasEventFacade().saveSharedEntities(encryptedData);
    SampleDto savedSample = getSampleFacade().getSampleByUuid(sample.getUuid());
    assertThat(savedSample, is(notNullValue()));
    assertThat(savedSample.getAssociatedEventParticipant(), is(eventParticipant.toReference()));
    assertThat(savedSample.getSampleMaterial(), is(SampleMaterial.BLOOD));
    assertThat(savedSample.getLab(), is(localLab.toReference()));
    assertThat(savedSample.getLabSampleID(), is("Test lab sample id"));
    assertThat(savedSample.getSormasToSormasOriginInfo().getOrganizationId(), is(DEFAULT_SERVER_ID));
    assertThat(savedSample.getSormasToSormasOriginInfo().getSenderName(), is("John doe"));
    PathogenTestDto savedPathogenTest = getPathogenTestFacade().getByUuid(pathogenTest.getUuid());
    assertThat(savedPathogenTest, is(notNullValue()));
    assertThat(savedPathogenTest.getLab(), is(localLab.toReference()));
    assertThat(savedPathogenTest.getTestType(), is(PathogenTestType.RAPID_TEST));
    assertThat(savedPathogenTest.getTestResult(), is(PathogenTestResultType.PENDING));
    AdditionalTestDto savedAdditionalTest = getAdditionalTestFacade().getByUuid(additionalTest.getUuid());
    assertThat(savedAdditionalTest, is(notNullValue()));
    assertThat(savedAdditionalTest.getHaemoglobin(), is(0.2F));
    assertThat(savedAdditionalTest.getConjBilirubin(), is(0.3F));
}

Example 5 with AdditionalTestDto

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

the class SampleFacadeEjbTest method testAllSamplesDeletionWithMultipleAdditionalTest.

@Test
public void testAllSamplesDeletionWithMultipleAdditionalTest() {
    Date since = new Date();
    RDCFEntities rdcf = creator.createRDCFEntities("Region", "District", "Community", "Facility");
    UserDto user = creator.createUser(rdcf.region.getUuid(), rdcf.district.getUuid(), rdcf.facility.getUuid(), "Surv", "Sup", UserRole.SURVEILLANCE_SUPERVISOR);
    PersonDto secondCazePerson = creator.createPerson("SecondCase", "SecondPerson");
    CaseDataDto secondCaze = creator.createCase(user.toReference(), secondCazePerson.toReference(), Disease.ACUTE_VIRAL_HEPATITIS, CaseClassification.NOT_CLASSIFIED, InvestigationStatus.PENDING, new Date(), rdcf);
    SampleDto thirdSample = creator.createSample(secondCaze.toReference(), new Date(), new Date(), user.toReference(), SampleMaterial.BLOOD, rdcf.facility);
    SampleDto forthSample = creator.createSample(secondCaze.toReference(), new Date(), new Date(), user.toReference(), SampleMaterial.BLOOD, rdcf.facility);
    PathogenTestDto secondSamplePathogenTest = creator.createPathogenTest(thirdSample.toReference(), PathogenTestType.RAPID_TEST, secondCaze.getDisease(), new Date(), rdcf.facility, user.toReference(), PathogenTestResultType.INDETERMINATE, "Indeterminate", true);
    PathogenTestDto thirdSamplePathogenTest = creator.createPathogenTest(forthSample.toReference(), PathogenTestType.CQ_VALUE_DETECTION, secondCaze.getDisease(), new Date(), rdcf.facility, user.toReference(), PathogenTestResultType.NOT_DONE, "Not done", true);
    AdditionalTestDto secondSampleAdditionalTest = creator.createAdditionalTest(thirdSample.toReference());
    AdditionalTestDto thirdSampleAdditionalTest = creator.createAdditionalTest(forthSample.toReference());
    // Database should contain the created sample, sample test and additional tests
    assertNotNull(getSampleTestFacade().getByUuid(secondSamplePathogenTest.getUuid()));
    assertNotNull(getSampleTestFacade().getByUuid(thirdSamplePathogenTest.getUuid()));
    assertNotNull(getAdditionalTestFacade().getByUuid(secondSampleAdditionalTest.getUuid()));
    assertNotNull(getAdditionalTestFacade().getByUuid(thirdSampleAdditionalTest.getUuid()));
    getSampleFacade().deleteAllSamples(Arrays.asList(thirdSample.getUuid(), forthSample.getUuid()));
    // Sample and pathogen test should be marked as deleted, additional tests should be deleted
    List<String> sampleUuids = getSampleFacade().getDeletedUuidsSince(since);
    assertTrue(sampleUuids.contains(thirdSample.getUuid()));
    assertTrue(sampleUuids.contains(forthSample.getUuid()));
    assertTrue(getSampleTestFacade().getDeletedUuidsSince(since).contains(secondSamplePathogenTest.getUuid()));
    assertTrue(getSampleTestFacade().getDeletedUuidsSince(since).contains(thirdSamplePathogenTest.getUuid()));
    assertNull(getAdditionalTestFacade().getByUuid(secondSampleAdditionalTest.getUuid()));
    assertNull(getAdditionalTestFacade().getByUuid(thirdSampleAdditionalTest.getUuid()));
}