Examples with ClinicalCourseReferenceDto de.symeda.sormas.api.clinicalcourse.ClinicalCourseReferenceDto used on opensource projects

Example 1 with ClinicalCourseReferenceDto

use of de.symeda.sormas.api.clinicalcourse.ClinicalCourseReferenceDto 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);
        t.setPerson(leadCase.getPerson());
        travelEntryService.ensurePersisted(t);
    });
}

Example 2 with ClinicalCourseReferenceDto

use of de.symeda.sormas.api.clinicalcourse.ClinicalCourseReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class CaseService method deletePermanent.

@Override
public void deletePermanent(Case caze) {
    // Delete all tasks associated with this case
    Optional.ofNullable(caze.getTasks()).ifPresent(tl -> tl.forEach(t -> taskService.deletePermanent(t)));
    // Delete all samples that are only associated with this case
    caze.getSamples().stream().filter(sample -> sample.getAssociatedContact() == null && sample.getAssociatedEventParticipant() == null).forEach(sample -> sampleService.deletePermanent(sample));
    caze.getVisits().stream().forEach(visit -> {
        if (visit.getContacts() == null || visit.getContacts().isEmpty()) {
            visitService.deletePermanent(visit);
        } else {
            visit.setCaze(null);
            visitService.ensurePersisted(visit);
        }
    });
    // Delete surveillance reports related to this case
    surveillanceReportService.getByCaseUuids(Collections.singletonList(caze.getUuid())).forEach(s -> surveillanceReportService.deletePermanent(s));
    // Delete documents related to this case
    documentService.getRelatedToEntity(DocumentRelatedEntityType.CASE, caze.getUuid()).forEach(d -> documentService.markAsDeleted(d));
    // Delete clinical management data
    if (caze.getTherapy() != null) {
        TherapyReferenceDto therapy = new TherapyReferenceDto(caze.getTherapy().getUuid());
        List<Treatment> treatments = treatmentService.findBy(new TreatmentCriteria().therapy(therapy));
        treatments.forEach(t -> treatmentService.deletePermanent(t));
        prescriptionService.findBy(new PrescriptionCriteria().therapy(therapy)).forEach(p -> prescriptionService.deletePermanent(p));
    }
    if (caze.getClinicalCourse() != null) {
        ClinicalCourseReferenceDto clinicalCourse = new ClinicalCourseReferenceDto(caze.getClinicalCourse().getUuid());
        List<ClinicalVisit> cvs = clinicalVisitService.findBy(new ClinicalVisitCriteria().clinicalCourse(clinicalCourse));
        cvs.forEach(c -> clinicalVisitService.deletePermanent(c));
    }
    // Remove the case from any S2S share info referencing it
    sormasToSormasShareInfoService.getByAssociatedEntity(SormasToSormasShareInfo.CAZE, caze.getUuid()).forEach(s -> {
        s.setCaze(null);
        if (sormasToSormasShareInfoFacade.hasAnyEntityReference(s)) {
            sormasToSormasShareInfoService.ensurePersisted(s);
        } else {
            sormasToSormasShareInfoService.deletePermanent(s);
        }
    });
    // Remove the case from any external share info referencing it
    externalShareInfoService.getShareInfoByCase(caze.getUuid()).forEach(e -> {
        externalShareInfoService.deletePermanent(e);
    });
    // Remove the case from all cases in which it has been set as a duplicate
    getCasesSetAsDuplicate(caze.getId()).forEach(c -> {
        c.setDuplicateOf(null);
        ensurePersisted(c);
    });
    caseFacade.deleteCaseInExternalSurveillanceTool(caze);
    deleteCaseLinks(caze);
    super.deletePermanent(caze);
}

Example 3 with ClinicalCourseReferenceDto

use of de.symeda.sormas.api.clinicalcourse.ClinicalCourseReferenceDto in project SORMAS-Project by hzi-braunschweig.

the class CaseService method delete.

@Override
public void delete(Case caze) {
    // Mark all contacts associated with this case as deleted and remove this case
    // from any contacts where it is set as the resulting case
    List<Contact> contacts = contactService.findBy(new ContactCriteria().caze(caze.toReference()), null);
    for (Contact contact : contacts) {
        contactService.delete(contact);
    }
    contacts = contactService.getAllByResultingCase(caze);
    for (Contact contact : contacts) {
        contact.setResultingCase(null);
        externalJournalService.handleExternalJournalPersonUpdateAsync(contact.getPerson().toReference());
        contactService.ensurePersisted(contact);
    }
    caze.getSamples().stream().filter(sample -> sample.getAssociatedContact() == null && sample.getAssociatedEventParticipant() == null).forEach(sample -> sampleService.delete(sample));
    // Delete all tasks associated with this case
    List<Task> tasks = taskService.findBy(new TaskCriteria().caze(new CaseReferenceDto(caze.getUuid())), true);
    for (Task task : tasks) {
        taskService.delete(task);
    }
    // Delete all prescriptions/treatments/clinical visits
    if (caze.getTherapy() != null) {
        TherapyReferenceDto therapy = new TherapyReferenceDto(caze.getTherapy().getUuid());
        treatmentService.findBy(new TreatmentCriteria().therapy(therapy)).stream().forEach(t -> treatmentService.delete(t));
        prescriptionService.findBy(new PrescriptionCriteria().therapy(therapy)).stream().forEach(p -> prescriptionService.delete(p));
    }
    if (caze.getClinicalCourse() != null) {
        ClinicalCourseReferenceDto clinicalCourse = new ClinicalCourseReferenceDto(caze.getClinicalCourse().getUuid());
        clinicalVisitService.findBy(new ClinicalVisitCriteria().clinicalCourse(clinicalCourse)).stream().forEach(c -> clinicalVisitService.delete(c));
    }
    // Remove all events linked to case by removing the case_id from event participant
    caze.getEventParticipants().stream().forEach(eventParticipant -> eventParticipant.setResultingCase(null));
    // Unlink TravelEntries where this case is set as the resulting case
    List<TravelEntry> travelEntries = travelEntryService.getAllByResultingCase(caze);
    for (TravelEntry travelEntry : travelEntries) {
        travelEntry.setResultingCase(null);
        travelEntryService.ensurePersisted(travelEntry);
    }
    // Unlink Immunizations where this case is set as the related case
    immunizationService.unlinkRelatedCase(caze);
    // Mark the case as deleted
    super.delete(caze);
}