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

Example 1 with SampleCriteria

use of de.symeda.sormas.api.sample.SampleCriteria 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);
    SampleJoins<Sample> joins = new SampleJoins<>(root);
    SampleCriteria sampleCriteria = new SampleCriteria();
    sampleCriteria.caze(criteria.getCaze()).contact(criteria.getContact()).eventParticipant(criteria.getEventParticipant());
    Predicate filter = sampleService.createUserFilter(cq, cb, joins, sampleCriteria);
    filter = CriteriaBuilderHelper.and(cb, filter, sampleService.buildCriteriaFilter(sampleCriteria, cb, joins));
    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 SampleCriteria

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

the class SampleFacadeEjb method getByCriteria.

private List<SampleDto> getByCriteria(SampleCriteria criteria) {
    final CriteriaBuilder cb = em.getCriteriaBuilder();
    final CriteriaQuery<Sample> cq = cb.createQuery(Sample.class);
    final Root<Sample> root = cq.from(Sample.class);
    SampleJoins<Sample> joins = new SampleJoins<>(root);
    Predicate filter = sampleService.createUserFilter(cq, cb, joins, criteria);
    filter = CriteriaBuilderHelper.and(cb, filter, sampleService.buildCriteriaFilter(criteria, cb, joins));
    if (filter != null) {
        cq.where(filter);
    }
    List<Sample> samples = em.createQuery(cq).getResultList();
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight);
    return samples.stream().map(s -> convertToDto(s, pseudonymizer)).collect(Collectors.toList());
}

Example 3 with SampleCriteria

use of de.symeda.sormas.api.sample.SampleCriteria 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 4 with SampleCriteria

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

the class SampleController method caseSampleCountOf.

public int caseSampleCountOf(SampleDto sample) {
    CaseReferenceDto cazeRef = sample.getAssociatedCase();
    if (cazeRef == null) {
        return 0;
    } else {
        SampleCriteria sampleCriteria = new SampleCriteria();
        sampleCriteria.caze(cazeRef);
        return (int) FacadeProvider.getSampleFacade().count(sampleCriteria);
    }
}

Example 5 with SampleCriteria

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

the class SampleGridFilterForm method onApplyClick.

private void onApplyClick(EpiWeekAndDateFilterComponent<DateFilterOption> weekAndDateFilter) {
    SampleCriteria criteria = getValue();
    DateFilterOption dateFilterOption = (DateFilterOption) weekAndDateFilter.getDateFilterOptionFilter().getValue();
    Date fromDate, toDate;
    if (dateFilterOption == DateFilterOption.DATE) {
        Date dateFrom = weekAndDateFilter.getDateFromFilter().getValue();
        fromDate = dateFrom != null ? DateHelper.getStartOfDay(dateFrom) : null;
        Date dateTo = weekAndDateFilter.getDateToFilter().getValue();
        toDate = dateFrom != null ? DateHelper.getEndOfDay(dateTo) : null;
    } else {
        fromDate = DateHelper.getEpiWeekStart((EpiWeek) weekAndDateFilter.getWeekFromFilter().getValue());
        toDate = DateHelper.getEpiWeekEnd((EpiWeek) weekAndDateFilter.getWeekToFilter().getValue());
    }
    if ((fromDate != null && toDate != null) || (fromDate == null && toDate == null)) {
        criteria.reportDateBetween(fromDate, toDate, dateFilterOption);
    } else {
        weekAndDateFilter.setNotificationsForMissingFilters();
    }
}