Examples with EpiDataDto de.symeda.sormas.api.epidata.EpiDataDto used on opensource projects

Example 1 with EpiDataDto

use of de.symeda.sormas.api.epidata.EpiDataDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjb method restorePseudonymizedDto.

public void restorePseudonymizedDto(CaseDataDto dto, CaseDataDto existingCaseDto, Case caze, Pseudonymizer pseudonymizer) {
    if (existingCaseDto != null) {
        boolean inJurisdiction = service.inJurisdictionOrOwned(caze);
        User currentUser = userService.getCurrentUser();
        pseudonymizer.restoreUser(caze.getReportingUser(), currentUser, dto, dto::setReportingUser);
        pseudonymizer.restoreUser(caze.getClassificationUser(), currentUser, dto, dto::setClassificationUser);
        pseudonymizer.restorePseudonymizedValues(CaseDataDto.class, dto, existingCaseDto, inJurisdiction);
        EpiDataDto epiData = dto.getEpiData();
        EpiDataDto existingEpiData = existingCaseDto.getEpiData();
        pseudonymizer.restorePseudonymizedValues(EpiDataDto.class, epiData, existingEpiData, inJurisdiction);
        epiData.getExposures().forEach(exposure -> {
            ExposureDto existingExposure = existingEpiData.getExposures().stream().filter(exp -> DataHelper.isSame(exposure, exp)).findFirst().orElse(null);
            if (existingExposure != null) {
                pseudonymizer.restorePseudonymizedValues(ExposureDto.class, exposure, existingExposure, inJurisdiction);
                pseudonymizer.restorePseudonymizedValues(LocationDto.class, exposure.getLocation(), existingExposure.getLocation(), inJurisdiction);
            }
        });
        pseudonymizer.restorePseudonymizedValues(HealthConditionsDto.class, dto.getHealthConditions(), existingCaseDto.getHealthConditions(), inJurisdiction);
        dto.getHospitalization().getPreviousHospitalizations().forEach(previousHospitalization -> existingCaseDto.getHospitalization().getPreviousHospitalizations().stream().filter(eh -> DataHelper.isSame(previousHospitalization, eh)).findFirst().ifPresent(existingPreviousHospitalization -> pseudonymizer.restorePseudonymizedValues(PreviousHospitalizationDto.class, previousHospitalization, existingPreviousHospitalization, inJurisdiction)));
        pseudonymizer.restorePseudonymizedValues(SymptomsDto.class, dto.getSymptoms(), existingCaseDto.getSymptoms(), inJurisdiction);
        pseudonymizer.restorePseudonymizedValues(MaternalHistoryDto.class, dto.getMaternalHistory(), existingCaseDto.getMaternalHistory(), inJurisdiction);
    }
}

Example 2 with EpiDataDto

use of de.symeda.sormas.api.epidata.EpiDataDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjbTest method testMergeCase.

@Test
public void testMergeCase() throws IOException {
    useNationalUserLogin();
    // 1. Create
    // Create leadCase
    UserDto leadUser = creator.createUser("", "", "", "First", "User");
    UserReferenceDto leadUserReference = new UserReferenceDto(leadUser.getUuid());
    PersonDto leadPerson = creator.createPerson("Alex", "Miller");
    PersonReferenceDto leadPersonReference = new PersonReferenceDto(leadPerson.getUuid());
    RDCF leadRdcf = creator.createRDCF();
    CaseDataDto leadCase = creator.createCase(leadUserReference, leadPersonReference, Disease.DENGUE, CaseClassification.SUSPECT, InvestigationStatus.PENDING, new Date(), leadRdcf, (c) -> {
        c.setAdditionalDetails("Test additional details");
        c.setFollowUpComment("Test followup comment");
    });
    leadCase.setClinicianEmail("mail");
    leadCase.getEpiData().setActivityAsCaseDetailsKnown(YesNoUnknown.NO);
    getCaseFacade().save(leadCase);
    VisitDto leadVisit = creator.createVisit(leadCase.getDisease(), leadCase.getPerson(), leadCase.getReportDate());
    leadVisit.getSymptoms().setAnorexiaAppetiteLoss(SymptomState.YES);
    getVisitFacade().saveVisit(leadVisit);
    // Create otherCase
    UserDto otherUser = creator.createUser("", "", "", "Second", "User");
    UserReferenceDto otherUserReference = new UserReferenceDto(otherUser.getUuid());
    PersonDto otherPerson = creator.createPerson("Max", "Smith");
    otherPerson.setBirthWeight(2);
    getPersonFacade().savePerson(otherPerson);
    PersonReferenceDto otherPersonReference = new PersonReferenceDto(otherPerson.getUuid());
    RDCF otherRdcf = creator.createRDCF("Reg2", "Dis2", "Comm2", "Fac2", "Poe2");
    CaseDataDto otherCase = creator.createCase(otherUserReference, otherPersonReference, Disease.CHOLERA, CaseClassification.SUSPECT, InvestigationStatus.PENDING, new Date(), otherRdcf, (c) -> {
        c.setAdditionalDetails("Test other additional details");
        c.setFollowUpComment("Test other followup comment");
    });
    otherCase.setClinicianName("name");
    CaseReferenceDto otherCaseReference = getCaseFacade().getReferenceByUuid(otherCase.getUuid());
    ContactDto contact = creator.createContact(otherUserReference, otherUserReference, otherPersonReference, otherCase, new Date(), new Date(), null);
    Region region = creator.createRegion("");
    District district = creator.createDistrict("", region);
    SampleDto sample = creator.createSample(otherCaseReference, otherUserReference, creator.createFacility("", region, district, creator.createCommunity("", district)));
    TaskDto task = creator.createTask(TaskContext.CASE, TaskType.CASE_INVESTIGATION, TaskStatus.PENDING, otherCaseReference, new ContactReferenceDto(), new EventReferenceDto(), new Date(), otherUserReference);
    TreatmentDto treatment = creator.createTreatment(otherCase);
    PrescriptionDto prescription = creator.createPrescription(otherCase);
    ClinicalVisitDto visit = creator.createClinicalVisit(otherCase);
    otherCase.getEpiData().setActivityAsCaseDetailsKnown(YesNoUnknown.YES);
    final ArrayList<ActivityAsCaseDto> otherActivitiesAsCase = new ArrayList<>();
    ActivityAsCaseDto activityAsCaseDto = new ActivityAsCaseDto();
    activityAsCaseDto.setActivityAsCaseType(ActivityAsCaseType.GATHERING);
    otherActivitiesAsCase.add(activityAsCaseDto);
    otherCase.getEpiData().setActivitiesAsCase(otherActivitiesAsCase);
    getCaseFacade().save(otherCase);
    VisitDto otherVisit = creator.createVisit(otherCase.getDisease(), otherCase.getPerson(), otherCase.getReportDate());
    otherVisit.getSymptoms().setAbdominalPain(SymptomState.YES);
    getVisitFacade().saveVisit(otherVisit);
    EventDto event = creator.createEvent(otherUserReference);
    event.setDisease(otherCase.getDisease());
    getEventFacade().save(event);
    EventParticipantDto otherCaseEventParticipant = creator.createEventParticipant(event.toReference(), otherPerson, otherUserReference);
    otherCaseEventParticipant.setResultingCase(otherCaseReference);
    getEventParticipantFacade().saveEventParticipant(otherCaseEventParticipant);
    creator.createSurveillanceReport(otherUserReference, otherCaseReference);
    TravelEntryDto travelEntry = creator.createTravelEntry(otherPersonReference, otherUserReference, otherCase.getDisease(), otherRdcf.region, otherRdcf.district, otherRdcf.pointOfEntry);
    travelEntry.setResultingCase(otherCaseReference);
    travelEntry = getTravelEntryFacade().save(travelEntry);
    DocumentDto document = creator.createDocument(leadUserReference, "document.pdf", "application/pdf", 42L, DocumentRelatedEntityType.CASE, leadCase.getUuid(), "content".getBytes(StandardCharsets.UTF_8));
    DocumentDto otherDocument = creator.createDocument(leadUserReference, "other_document.pdf", "application/pdf", 42L, DocumentRelatedEntityType.CASE, otherCase.getUuid(), "other content".getBytes(StandardCharsets.UTF_8));
    // 2. Merge
    getCaseFacade().mergeCase(leadCase.getUuid(), otherCase.getUuid());
    // 3. Test
    CaseDataDto mergedCase = getCaseFacade().getCaseDataByUuid(leadCase.getUuid());
    // Check no values
    assertNull(mergedCase.getClassificationComment());
    // Check 'lead and other have different values'
    assertEquals(leadCase.getDisease(), mergedCase.getDisease());
    // Check 'lead has value, other has not'
    assertEquals(leadCase.getClinicianEmail(), mergedCase.getClinicianEmail());
    // Check 'lead has no value, other has'
    assertEquals(otherCase.getClinicianName(), mergedCase.getClinicianName());
    PersonDto mergedPerson = getPersonFacade().getPersonByUuid(mergedCase.getPerson().getUuid());
    // Check no values
    assertNull(mergedPerson.getBirthdateDD());
    // Check 'lead and other have different values'
    assertEquals(leadCase.getPerson().getFirstName(), mergedPerson.getFirstName());
    // Check 'lead has value, other has not'
    assertEquals(leadCase.getPerson().getLastName(), mergedPerson.getLastName());
    // Check 'lead has no value, other has'
    assertEquals(otherPerson.getBirthWeight(), mergedPerson.getBirthWeight());
    // Check merge comments
    assertEquals("Test additional details Test other additional details", mergedCase.getAdditionalDetails());
    assertEquals("Test followup comment Test other followup comment", mergedCase.getFollowUpComment());
    // 4. Test Reference Changes
    // 4.1 Contacts
    List<String> contactUuids = new ArrayList<>();
    contactUuids.add(contact.getUuid());
    assertEquals(leadCase.getUuid(), getContactFacade().getByUuids(contactUuids).get(0).getCaze().getUuid());
    // 4.2 Samples
    List<String> sampleUuids = new ArrayList<>();
    sampleUuids.add(sample.getUuid());
    assertEquals(leadCase.getUuid(), getSampleFacade().getByUuids(sampleUuids).get(0).getAssociatedCase().getUuid());
    // 4.3 Tasks
    List<String> taskUuids = new ArrayList<>();
    taskUuids.add(task.getUuid());
    assertEquals(leadCase.getUuid(), getTaskFacade().getByUuids(taskUuids).get(0).getCaze().getUuid());
    // 4.4 Treatments
    List<String> treatmentUuids = new ArrayList<>();
    treatmentUuids.add(treatment.getUuid());
    assertEquals(leadCase.getTherapy().getUuid(), getTreatmentFacade().getByUuids(treatmentUuids).get(0).getTherapy().getUuid());
    // 4.5 Prescriptions
    List<String> prescriptionUuids = new ArrayList<>();
    prescriptionUuids.add(prescription.getUuid());
    assertEquals(leadCase.getTherapy().getUuid(), getPrescriptionFacade().getByUuids(prescriptionUuids).get(0).getTherapy().getUuid());
    // 4.6 Clinical Visits
    List<String> visitUuids = new ArrayList<>();
    visitUuids.add(visit.getUuid());
    assertEquals(leadCase.getClinicalCourse().getUuid(), getClinicalVisitFacade().getByUuids(visitUuids).get(0).getClinicalCourse().getUuid());
    // 4.7 Visits;
    List<String> mergedVisits = getVisitFacade().getIndexList(new VisitCriteria().caze(mergedCase.toReference()), null, null, null).stream().map(VisitIndexDto::getUuid).collect(Collectors.toList());
    assertEquals(2, mergedVisits.size());
    assertTrue(mergedVisits.contains(leadVisit.getUuid()));
    assertTrue(mergedVisits.contains(otherVisit.getUuid()));
    // and symptoms
    assertEquals(SymptomState.YES, mergedCase.getSymptoms().getAbdominalPain());
    assertEquals(SymptomState.YES, mergedCase.getSymptoms().getAnorexiaAppetiteLoss());
    assertTrue(mergedCase.getSymptoms().getSymptomatic());
    // 4.8 Linked Events
    assertEquals(1, getEventFacade().count(new EventCriteria().caze(mergedCase.toReference())));
    // 4.8 Linked Surveillance Reports
    List<SurveillanceReportDto> surveillanceReportList = getSurveillanceReportFacade().getByCaseUuids(Collections.singletonList(mergedCase.getUuid()));
    MatcherAssert.assertThat(surveillanceReportList, hasSize(1));
    // 5 Documents
    List<DocumentDto> mergedDocuments = getDocumentFacade().getDocumentsRelatedToEntity(DocumentRelatedEntityType.CASE, leadCase.getUuid());
    assertEquals(2, mergedDocuments.size());
    List<String> documentUuids = mergedDocuments.stream().map(DocumentDto::getUuid).collect(Collectors.toList());
    assertTrue(documentUuids.contains(document.getUuid()));
    assertTrue(documentUuids.contains(otherDocument.getUuid()));
    // 10 Activities as case
    final EpiDataDto epiData = mergedCase.getEpiData();
    assertEquals(YesNoUnknown.YES, epiData.getActivityAsCaseDetailsKnown());
    final List<ActivityAsCaseDto> activitiesAsCase = epiData.getActivitiesAsCase();
    assertEquals(1, activitiesAsCase.size());
    assertEquals(ActivityAsCaseType.GATHERING, activitiesAsCase.get(0).getActivityAsCaseType());
    // Travel entry
    travelEntry = getTravelEntryFacade().getByUuid(travelEntry.getUuid());
    assertEquals(mergedCase.toReference(), travelEntry.getResultingCase());
}

Example 3 with EpiDataDto

use of de.symeda.sormas.api.epidata.EpiDataDto in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjbTest method testCloneCaseActivityAsCaseIsCloned.

@Test
public void testCloneCaseActivityAsCaseIsCloned() {
    useNationalUserLogin();
    // 1. Create
    // Create aCase
    UserDto user = creator.createUser("", "", "", "", "");
    UserReferenceDto userReferenceDto = new UserReferenceDto(user.getUuid());
    PersonDto person = creator.createPerson("Max", "Smith");
    person.setBirthWeight(2);
    getPersonFacade().savePerson(person);
    PersonReferenceDto personReferenceDto = new PersonReferenceDto(person.getUuid());
    RDCF rdcf = creator.createRDCF();
    CaseDataDto aCase = creator.createCase(userReferenceDto, personReferenceDto, Disease.CHOLERA, CaseClassification.SUSPECT, InvestigationStatus.PENDING, new Date(), rdcf, (c) -> {
        c.setAdditionalDetails("Test other additional details");
        c.setFollowUpComment("Test other followup comment");
    });
    aCase.setClinicianName("name");
    aCase.getEpiData().setActivityAsCaseDetailsKnown(YesNoUnknown.YES);
    final ArrayList<ActivityAsCaseDto> otherActivitiesAsCase = new ArrayList<>();
    ActivityAsCaseDto activityAsCaseDto = new ActivityAsCaseDto();
    activityAsCaseDto.setActivityAsCaseType(ActivityAsCaseType.GATHERING);
    otherActivitiesAsCase.add(activityAsCaseDto);
    aCase.getEpiData().setActivitiesAsCase(otherActivitiesAsCase);
    CaseDataDto caseDataDto = getCaseFacade().save(aCase);
    // 2. Clone
    CaseDataDto clonedCase = getCaseFacade().cloneCase(caseDataDto);
    final EpiDataDto epiData = clonedCase.getEpiData();
    assertEquals(YesNoUnknown.YES, epiData.getActivityAsCaseDetailsKnown());
    final List<ActivityAsCaseDto> activitiesAsCase = epiData.getActivitiesAsCase();
    assertEquals(1, activitiesAsCase.size());
    assertEquals(ActivityAsCaseType.GATHERING, activitiesAsCase.get(0).getActivityAsCaseType());
}

Example 4 with EpiDataDto

use of de.symeda.sormas.api.epidata.EpiDataDto in project SORMAS-Project by hzi-braunschweig.

the class EpiDataPseudonymizationTest method createCaseWEpiData.

private CaseDataDto createCaseWEpiData(UserDto user, TestDataCreator.RDCF rdcf) {
    CaseDataDto caze = creator.createCase(user.toReference(), rdcf, c -> {
        EpiDataDto epiData = c.getEpiData();
        ExposureDto exposure = ExposureDto.build(ExposureType.ANIMAL_CONTACT);
        exposure.setAnimalCondition(AnimalCondition.DEAD);
        exposure.setDescription("Test description");
        exposure.getLocation().setDetails("Test location details");
        epiData.getExposures().add(exposure);
        ExposureDto exposure2 = ExposureDto.build(ExposureType.ANIMAL_CONTACT);
        exposure2.setTypeOfAnimal(TypeOfAnimal.OTHER);
        exposure2.setTypeOfAnimalDetails("Test other animal details");
        epiData.getExposures().add(exposure2);
        ExposureDto exposure3 = ExposureDto.build(ExposureType.TRAVEL);
        exposure3.setBodyOfWater(YesNoUnknown.YES);
        exposure3.setWaterSource(WaterSource.OTHER);
        exposure3.setWaterSourceDetails("Test water source details");
        epiData.getExposures().add(exposure3);
        ExposureDto exposure4 = ExposureDto.build(ExposureType.ANIMAL_CONTACT);
        exposure4.setAnimalContactType(AnimalContactType.OTHER);
        exposure4.setAnimalContactTypeDetails("Test animal contact type details");
        epiData.getExposures().add(exposure4);
        ExposureDto burial = ExposureDto.build(ExposureType.BURIAL);
        burial.setDeceasedPersonName("John Smith");
        burial.setDeceasedPersonRelation("Test burial relation");
        LocationDto address = new LocationDto();
        address.setRegion(rdcf.region);
        address.setDistrict(rdcf.district);
        address.setCommunity(rdcf.community);
        address.setCity("Test City");
        burial.setLocation(address);
        epiData.getExposures().add(burial);
        ExposureDto travel = ExposureDto.build(ExposureType.TRAVEL);
        travel.getLocation().setDetails("Test travel destination");
        epiData.getExposures().add(travel);
        ExposureDto gathering = ExposureDto.build(ExposureType.GATHERING);
        gathering.setLocation(address);
        gathering.setDescription("Test gathering description");
        epiData.getExposures().add(gathering);
    });
    return caze;
}

Example 5 with EpiDataDto

use of de.symeda.sormas.api.epidata.EpiDataDto in project SORMAS-Project by hzi-braunschweig.

the class EpiDataPseudonymizationTest method getEpiDataInJurisdiction.

@Test
public void getEpiDataInJurisdiction() {
    CaseDataDto caseWEpiData = createCaseWEpiData(user2, rdcf2);
    CaseDataDto savedCase = getCaseFacade().getCaseDataByUuid(caseWEpiData.getUuid());
    EpiDataDto epiData = savedCase.getEpiData();
    assertThat(epiData.getExposures().get(0).getDescription(), is("Test description"));
    assertThat(epiData.getExposures().get(0).getLocation().getDetails(), is("Test location details"));
    assertThat(epiData.getExposures().get(1).getTypeOfAnimalDetails(), is("Test other animal details"));
    assertThat(epiData.getExposures().get(2).getWaterSourceDetails(), is("Test water source details"));
    assertThat(epiData.getExposures().get(3).getAnimalContactTypeDetails(), is("Test animal contact type details"));
    ExposureDto burial = epiData.getExposures().get(4);
    assertThat(burial.getDeceasedPersonName(), is("John Smith"));
    assertThat(burial.getDeceasedPersonRelation(), is("Test burial relation"));
    LocationDto burialAddress = burial.getLocation();
    assertThat(burialAddress.getCommunity(), is(rdcf2.community));
    assertThat(burialAddress.getCity(), is("Test City"));
    ExposureDto travel = epiData.getExposures().get(5);
    assertThat(travel.getLocation().getDetails(), is("Test travel destination"));
    ExposureDto gathering = epiData.getExposures().get(6);
    assertThat(gathering.getDescription(), is("Test gathering description"));
    LocationDto gatheringAddress = gathering.getLocation();
    assertThat(gatheringAddress.getCommunity(), is(rdcf2.community));
    assertThat(gatheringAddress.getCity(), is("Test City"));
}