Examples with Vaccination de.symeda.sormas.backend.vaccination.Vaccination used on opensource projects

Example 1 with Vaccination

use of de.symeda.sormas.backend.vaccination.Vaccination in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjb method getExportList.

@Override
@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
public List<CaseExportDto> getExportList(CaseCriteria caseCriteria, Collection<String> selectedRows, CaseExportType exportType, int first, int max, ExportConfigurationDto exportConfiguration, Language userLanguage) {
    Boolean previousCaseManagementDataCriteria = caseCriteria.getMustHaveCaseManagementData();
    if (CaseExportType.CASE_MANAGEMENT == exportType) {
        caseCriteria.setMustHaveCaseManagementData(Boolean.TRUE);
    }
    CriteriaBuilder cb = em.getCriteriaBuilder();
    CriteriaQuery<CaseExportDto> cq = cb.createQuery(CaseExportDto.class);
    Root<Case> caseRoot = cq.from(Case.class);
    final CaseQueryContext caseQueryContext = new CaseQueryContext(cb, cq, caseRoot);
    final CaseJoins<Case> joins = (CaseJoins<Case>) caseQueryContext.getJoins();
    // Events count subquery
    Subquery<Long> eventCountSq = cq.subquery(Long.class);
    Root<EventParticipant> eventCountRoot = eventCountSq.from(EventParticipant.class);
    Join<EventParticipant, Event> event = eventCountRoot.join(EventParticipant.EVENT, JoinType.INNER);
    Join<EventParticipant, Case> resultingCase = eventCountRoot.join(EventParticipant.RESULTING_CASE, JoinType.INNER);
    eventCountSq.where(cb.and(cb.equal(resultingCase.get(Case.ID), caseRoot.get(Case.ID)), cb.isFalse(event.get(Event.DELETED)), cb.isFalse(event.get(Event.ARCHIVED)), cb.isFalse(eventCountRoot.get(EventParticipant.DELETED))));
    eventCountSq.select(cb.countDistinct(event.get(Event.ID)));
    // @formatter:off
    cq.multiselect(caseRoot.get(Case.ID), joins.getPerson().get(Person.ID), joins.getPersonAddress().get(Location.ID), joins.getEpiData().get(EpiData.ID), joins.getSymptoms().get(Symptoms.ID), joins.getHospitalization().get(Hospitalization.ID), joins.getHealthConditions().get(HealthConditions.ID), caseRoot.get(Case.UUID), caseRoot.get(Case.EPID_NUMBER), caseRoot.get(Case.DISEASE), caseRoot.get(Case.DISEASE_VARIANT), caseRoot.get(Case.DISEASE_DETAILS), caseRoot.get(Case.DISEASE_VARIANT_DETAILS), joins.getPerson().get(Person.UUID), joins.getPerson().get(Person.FIRST_NAME), joins.getPerson().get(Person.LAST_NAME), joins.getPerson().get(Person.SALUTATION), joins.getPerson().get(Person.OTHER_SALUTATION), joins.getPerson().get(Person.SEX), caseRoot.get(Case.PREGNANT), joins.getPerson().get(Person.APPROXIMATE_AGE), joins.getPerson().get(Person.APPROXIMATE_AGE_TYPE), joins.getPerson().get(Person.BIRTHDATE_DD), joins.getPerson().get(Person.BIRTHDATE_MM), joins.getPerson().get(Person.BIRTHDATE_YYYY), caseRoot.get(Case.REPORT_DATE), joins.getRegion().get(Region.NAME), joins.getDistrict().get(District.NAME), joins.getCommunity().get(Community.NAME), caseRoot.get(Case.FACILITY_TYPE), joins.getFacility().get(Facility.NAME), joins.getFacility().get(Facility.UUID), caseRoot.get(Case.HEALTH_FACILITY_DETAILS), joins.getPointOfEntry().get(PointOfEntry.NAME), joins.getPointOfEntry().get(PointOfEntry.UUID), caseRoot.get(Case.POINT_OF_ENTRY_DETAILS), caseRoot.get(Case.CASE_CLASSIFICATION), caseRoot.get(Case.CLINICAL_CONFIRMATION), caseRoot.get(Case.EPIDEMIOLOGICAL_CONFIRMATION), caseRoot.get(Case.LABORATORY_DIAGNOSTIC_CONFIRMATION), caseRoot.get(Case.NOT_A_CASE_REASON_NEGATIVE_TEST), caseRoot.get(Case.NOT_A_CASE_REASON_PHYSICIAN_INFORMATION), caseRoot.get(Case.NOT_A_CASE_REASON_DIFFERENT_PATHOGEN), caseRoot.get(Case.NOT_A_CASE_REASON_OTHER), caseRoot.get(Case.NOT_A_CASE_REASON_DETAILS), caseRoot.get(Case.INVESTIGATION_STATUS), caseRoot.get(Case.INVESTIGATED_DATE), caseRoot.get(Case.OUTCOME), caseRoot.get(Case.OUTCOME_DATE), caseRoot.get(Case.SEQUELAE), caseRoot.get(Case.SEQUELAE_DETAILS), caseRoot.get(Case.BLOOD_ORGAN_OR_TISSUE_DONATED), caseRoot.get(Case.FOLLOW_UP_STATUS), caseRoot.get(Case.FOLLOW_UP_UNTIL), caseRoot.get(Case.NOSOCOMIAL_OUTBREAK), caseRoot.get(Case.INFECTION_SETTING), caseRoot.get(Case.PROHIBITION_TO_WORK), caseRoot.get(Case.PROHIBITION_TO_WORK_FROM), caseRoot.get(Case.PROHIBITION_TO_WORK_UNTIL), caseRoot.get(Case.RE_INFECTION), caseRoot.get(Case.PREVIOUS_INFECTION_DATE), caseRoot.get(Case.REINFECTION_STATUS), caseRoot.get(Case.REINFECTION_DETAILS), // quarantine
    caseRoot.get(Case.QUARANTINE), caseRoot.get(Case.QUARANTINE_TYPE_DETAILS), caseRoot.get(Case.QUARANTINE_FROM), caseRoot.get(Case.QUARANTINE_TO), caseRoot.get(Case.QUARANTINE_HELP_NEEDED), caseRoot.get(Case.QUARANTINE_ORDERED_VERBALLY), caseRoot.get(Case.QUARANTINE_ORDERED_OFFICIAL_DOCUMENT), caseRoot.get(Case.QUARANTINE_ORDERED_VERBALLY_DATE), caseRoot.get(Case.QUARANTINE_ORDERED_OFFICIAL_DOCUMENT_DATE), caseRoot.get(Case.QUARANTINE_EXTENDED), caseRoot.get(Case.QUARANTINE_REDUCED), caseRoot.get(Case.QUARANTINE_OFFICIAL_ORDER_SENT), caseRoot.get(Case.QUARANTINE_OFFICIAL_ORDER_SENT_DATE), joins.getHospitalization().get(Hospitalization.ADMITTED_TO_HEALTH_FACILITY), joins.getHospitalization().get(Hospitalization.ADMISSION_DATE), joins.getHospitalization().get(Hospitalization.DISCHARGE_DATE), joins.getHospitalization().get(Hospitalization.LEFT_AGAINST_ADVICE), joins.getPerson().get(Person.PRESENT_CONDITION), joins.getPerson().get(Person.DEATH_DATE), joins.getPerson().get(Person.BURIAL_DATE), joins.getPerson().get(Person.BURIAL_CONDUCTOR), joins.getPerson().get(Person.BURIAL_PLACE_DESCRIPTION), // address
    joins.getPersonAddressRegion().get(Region.NAME), joins.getPersonAddressDistrict().get(District.NAME), joins.getPersonAddressCommunity().get(Community.NAME), joins.getPersonAddress().get(Location.CITY), joins.getPersonAddress().get(Location.STREET), joins.getPersonAddress().get(Location.HOUSE_NUMBER), joins.getPersonAddress().get(Location.ADDITIONAL_INFORMATION), joins.getPersonAddress().get(Location.POSTAL_CODE), joins.getPersonAddressFacility().get(Facility.NAME), joins.getPersonAddressFacility().get(Facility.UUID), joins.getPersonAddress().get(Location.FACILITY_DETAILS), // phone
    caseQueryContext.getSubqueryExpression(CaseQueryContext.PERSON_PHONE_SUBQUERY), caseQueryContext.getSubqueryExpression(CaseQueryContext.PERSON_PHONE_OWNER_SUBQUERY), caseQueryContext.getSubqueryExpression(CaseQueryContext.PERSON_EMAIL_SUBQUERY), caseQueryContext.getSubqueryExpression(CaseQueryContext.PERSON_OTHER_CONTACT_DETAILS_SUBQUERY), joins.getPerson().get(Person.EDUCATION_TYPE), joins.getPerson().get(Person.EDUCATION_DETAILS), joins.getPerson().get(Person.OCCUPATION_TYPE), joins.getPerson().get(Person.OCCUPATION_DETAILS), joins.getPerson().get(Person.ARMED_FORCES_RELATION_TYPE), joins.getEpiData().get(EpiData.CONTACT_WITH_SOURCE_CASE_KNOWN), caseRoot.get(Case.VACCINATION_STATUS), caseRoot.get(Case.POSTPARTUM), caseRoot.get(Case.TRIMESTER), eventCountSq, caseRoot.get(Case.EXTERNAL_ID), caseRoot.get(Case.EXTERNAL_TOKEN), caseRoot.get(Case.INTERNAL_TOKEN), joins.getPerson().get(Person.BIRTH_NAME), joins.getPersonBirthCountry().get(Country.ISO_CODE), joins.getPersonBirthCountry().get(Country.DEFAULT_NAME), joins.getPersonCitizenship().get(Country.ISO_CODE), joins.getPersonCitizenship().get(Country.DEFAULT_NAME), caseRoot.get(Case.CASE_IDENTIFICATION_SOURCE), caseRoot.get(Case.SCREENING_TYPE), // responsible jurisdiction
    joins.getResponsibleRegion().get(Region.NAME), joins.getResponsibleDistrict().get(District.NAME), joins.getResponsibleCommunity().get(Community.NAME), caseRoot.get(Case.CLINICIAN_NAME), caseRoot.get(Case.CLINICIAN_PHONE), caseRoot.get(Case.CLINICIAN_EMAIL), joins.getReportingUser().get(User.ID), joins.getFollowUpStatusChangeUser().get(User.ID), caseRoot.get(Case.PREVIOUS_QUARANTINE_TO), caseRoot.get(Case.QUARANTINE_CHANGE_COMMENT), JurisdictionHelper.booleanSelector(cb, service.inJurisdictionOrOwned(caseQueryContext)));
    // @formatter:on
    cq.distinct(true);
    Predicate filter = service.createUserFilter(cb, cq, caseRoot);
    if (caseCriteria != null) {
        Predicate criteriaFilter = service.createCriteriaFilter(caseCriteria, caseQueryContext);
        filter = CriteriaBuilderHelper.and(cb, filter, criteriaFilter);
    }
    filter = CriteriaBuilderHelper.andInValues(selectedRows, filter, cb, caseRoot.get(Case.UUID));
    if (filter != null) {
        cq.where(filter);
    }
    /*
		 * Sort by report date DESC, but also by id for stable Sorting in case of equal report dates.
		 * Since this method supports paging, values might jump between pages when sorting is unstable.
		 */
    cq.orderBy(cb.desc(caseRoot.get(Case.REPORT_DATE)), cb.desc(caseRoot.get(Case.ID)));
    List<CaseExportDto> resultList = QueryHelper.getResultList(em, cq, first, max);
    List<Long> resultCaseIds = resultList.stream().map(CaseExportDto::getId).collect(Collectors.toList());
    if (!resultList.isEmpty()) {
        Map<Long, Symptoms> symptoms = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, CaseDataDto.SYMPTOMS)) {
            List<Symptoms> symptomsList = null;
            CriteriaQuery<Symptoms> symptomsCq = cb.createQuery(Symptoms.class);
            Root<Symptoms> symptomsRoot = symptomsCq.from(Symptoms.class);
            Expression<String> symptomsIdsExpr = symptomsRoot.get(Symptoms.ID);
            symptomsCq.where(symptomsIdsExpr.in(resultList.stream().map(CaseExportDto::getSymptomsId).collect(Collectors.toList())));
            symptomsList = em.createQuery(symptomsCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            symptoms = symptomsList.stream().collect(Collectors.toMap(Symptoms::getId, Function.identity()));
        }
        Map<Long, Location> personAddresses = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, PersonDto.ADDRESS, CaseExportDto.ADDRESS_GPS_COORDINATES)) {
            CriteriaQuery<Location> personAddressesCq = cb.createQuery(Location.class);
            Root<Location> personAddressesRoot = personAddressesCq.from(Location.class);
            Expression<String> personAddressesIdsExpr = personAddressesRoot.get(Location.ID);
            personAddressesCq.where(personAddressesIdsExpr.in(resultList.stream().map(CaseExportDto::getPersonAddressId).collect(Collectors.toList())));
            List<Location> personAddressesList = em.createQuery(personAddressesCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            personAddresses = personAddressesList.stream().collect(Collectors.toMap(Location::getId, Function.identity()));
        }
        Map<Long, Integer> prescriptionCounts = null;
        Map<Long, Integer> treatmentCounts = null;
        Map<Long, Integer> clinicalVisitCounts = null;
        Map<Long, HealthConditions> healthConditions = null;
        if (exportType == null || exportType == CaseExportType.CASE_MANAGEMENT) {
            if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.NUMBER_OF_PRESCRIPTIONS)) {
                prescriptionCounts = prescriptionService.getPrescriptionCountByCases(resultCaseIds).stream().collect(Collectors.toMap(e -> (Long) e[0], e -> ((Long) e[1]).intValue()));
            }
            if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.NUMBER_OF_TREATMENTS)) {
                treatmentCounts = treatmentService.getTreatmentCountByCases(resultCaseIds).stream().collect(Collectors.toMap(e -> (Long) e[0], e -> ((Long) e[1]).intValue()));
            }
            if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.NUMBER_OF_CLINICAL_VISITS)) {
                clinicalVisitCounts = clinicalVisitService.getClinicalVisitCountByCases(resultCaseIds).stream().collect(Collectors.toMap(e -> (Long) e[0], e -> ((Long) e[1]).intValue()));
            }
            if (ExportHelper.shouldExportFields(exportConfiguration, CaseDataDto.HEALTH_CONDITIONS)) {
                List<HealthConditions> healthConditionsList = null;
                CriteriaQuery<HealthConditions> healthConditionsCq = cb.createQuery(HealthConditions.class);
                Root<HealthConditions> healthConditionsRoot = healthConditionsCq.from(HealthConditions.class);
                Expression<String> healthConditionsIdsExpr = healthConditionsRoot.get(HealthConditions.ID);
                healthConditionsCq.where(healthConditionsIdsExpr.in(resultList.stream().map(CaseExportDto::getHealthConditionsId).collect(Collectors.toList())));
                healthConditionsList = em.createQuery(healthConditionsCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
                healthConditions = healthConditionsList.stream().collect(Collectors.toMap(HealthConditions::getId, Function.identity()));
            }
        }
        Map<Long, PreviousHospitalization> firstPreviousHospitalizations = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.INITIAL_DETECTION_PLACE)) {
            List<PreviousHospitalization> prevHospsList = null;
            CriteriaQuery<PreviousHospitalization> prevHospsCq = cb.createQuery(PreviousHospitalization.class);
            Root<PreviousHospitalization> prevHospsRoot = prevHospsCq.from(PreviousHospitalization.class);
            Join<PreviousHospitalization, Hospitalization> prevHospsHospitalizationJoin = prevHospsRoot.join(PreviousHospitalization.HOSPITALIZATION, JoinType.LEFT);
            Expression<String> hospitalizationIdsExpr = prevHospsHospitalizationJoin.get(Hospitalization.ID);
            prevHospsCq.where(hospitalizationIdsExpr.in(resultList.stream().map(CaseExportDto::getHospitalizationId).collect(Collectors.toList())));
            prevHospsCq.orderBy(cb.asc(prevHospsRoot.get(PreviousHospitalization.ADMISSION_DATE)));
            prevHospsList = em.createQuery(prevHospsCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            firstPreviousHospitalizations = prevHospsList.stream().collect(Collectors.toMap(p -> p.getHospitalization().getId(), Function.identity(), (id1, id2) -> id1));
        }
        Map<Long, CaseClassification> sourceCaseClassifications = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.MAX_SOURCE_CASE_CLASSIFICATION)) {
            sourceCaseClassifications = contactService.getSourceCaseClassifications(resultCaseIds).stream().collect(Collectors.toMap(e -> (Long) e[0], e -> (CaseClassification) e[1], (c1, c2) -> c1.getSeverity() >= c2.getSeverity() ? c1 : c2));
        }
        List<Long> caseIdsWithOutbreak = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.ASSOCIATED_WITH_OUTBREAK)) {
            caseIdsWithOutbreak = outbreakService.getCaseIdsWithOutbreak(resultCaseIds);
        }
        Map<Long, List<Exposure>> exposures = null;
        if ((exportType == null || exportType == CaseExportType.CASE_SURVEILLANCE) && ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.TRAVELED, CaseExportDto.TRAVEL_HISTORY, CaseExportDto.BURIAL_ATTENDED)) {
            CriteriaQuery<Exposure> exposuresCq = cb.createQuery(Exposure.class);
            Root<Exposure> exposuresRoot = exposuresCq.from(Exposure.class);
            Join<Exposure, EpiData> exposuresEpiDataJoin = exposuresRoot.join(Exposure.EPI_DATA, JoinType.LEFT);
            Expression<String> epiDataIdsExpr = exposuresEpiDataJoin.get(EpiData.ID);
            Predicate exposuresPredicate = cb.and(epiDataIdsExpr.in(resultList.stream().map(CaseExportDto::getEpiDataId).collect(Collectors.toList())), cb.or(cb.equal(exposuresRoot.get(Exposure.EXPOSURE_TYPE), ExposureType.TRAVEL), cb.equal(exposuresRoot.get(Exposure.EXPOSURE_TYPE), ExposureType.BURIAL)));
            exposuresCq.where(exposuresPredicate);
            exposuresCq.orderBy(cb.asc(exposuresEpiDataJoin.get(EpiData.ID)));
            List<Exposure> exposureList = em.createQuery(exposuresCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            exposures = exposureList.stream().collect(Collectors.groupingBy(e -> e.getEpiData().getId()));
        }
        Map<Long, List<Sample>> samples = null;
        if ((exportType == null || exportType == CaseExportType.CASE_SURVEILLANCE) && ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.SAMPLE_INFORMATION)) {
            List<Sample> samplesList = null;
            CriteriaQuery<Sample> samplesCq = cb.createQuery(Sample.class);
            Root<Sample> samplesRoot = samplesCq.from(Sample.class);
            Join<Sample, Case> samplesCaseJoin = samplesRoot.join(Sample.ASSOCIATED_CASE, JoinType.LEFT);
            Expression<String> caseIdsExpr = samplesCaseJoin.get(Case.ID);
            samplesCq.where(caseIdsExpr.in(resultCaseIds));
            samplesList = em.createQuery(samplesCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            samples = samplesList.stream().collect(Collectors.groupingBy(s -> s.getAssociatedCase().getId()));
        }
        List<VisitSummaryExportDetails> visitSummaries = null;
        if (featureConfigurationFacade.isFeatureEnabled(FeatureType.CASE_FOLLOWUP) && ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.NUMBER_OF_VISITS, CaseExportDto.LAST_COOPERATIVE_VISIT_DATE, CaseExportDto.LAST_COOPERATIVE_VISIT_SYMPTOMATIC, CaseExportDto.LAST_COOPERATIVE_VISIT_SYMPTOMS)) {
            CriteriaQuery<VisitSummaryExportDetails> visitsCq = cb.createQuery(VisitSummaryExportDetails.class);
            Root<Case> visitsCqRoot = visitsCq.from(Case.class);
            Join<Case, Visit> visitsJoin = visitsCqRoot.join(Case.VISITS, JoinType.LEFT);
            Join<Visit, Symptoms> visitSymptomsJoin = visitsJoin.join(Visit.SYMPTOMS, JoinType.LEFT);
            visitsCq.where(CriteriaBuilderHelper.and(cb, visitsCqRoot.get(AbstractDomainObject.ID).in(resultCaseIds), cb.isNotEmpty(visitsCqRoot.get(Case.VISITS))));
            visitsCq.multiselect(visitsCqRoot.get(AbstractDomainObject.ID), visitsJoin.get(Visit.VISIT_DATE_TIME), visitsJoin.get(Visit.VISIT_STATUS), visitSymptomsJoin);
            visitSummaries = em.createQuery(visitsCq).getResultList();
        }
        Map<Long, List<Immunization>> immunizations = null;
        if ((exportType == null || exportType == CaseExportType.CASE_SURVEILLANCE) && (exportConfiguration == null || exportConfiguration.getProperties().stream().anyMatch(p -> StringUtils.equalsAny(p, ExportHelper.getVaccinationExportProperties())))) {
            List<Immunization> immunizationList;
            CriteriaQuery<Immunization> immunizationsCq = cb.createQuery(Immunization.class);
            Root<Immunization> immunizationsCqRoot = immunizationsCq.from(Immunization.class);
            Join<Immunization, Person> personJoin = immunizationsCqRoot.join(Immunization.PERSON, JoinType.LEFT);
            Expression<String> personIdsExpr = personJoin.get(Person.ID);
            immunizationsCq.where(CriteriaBuilderHelper.and(cb, cb.or(cb.equal(immunizationsCqRoot.get(Immunization.MEANS_OF_IMMUNIZATION), MeansOfImmunization.VACCINATION), cb.equal(immunizationsCqRoot.get(Immunization.MEANS_OF_IMMUNIZATION), MeansOfImmunization.VACCINATION_RECOVERY)), personIdsExpr.in(resultList.stream().map(CaseExportDto::getPersonId).collect(Collectors.toList()))));
            immunizationsCq.select(immunizationsCqRoot);
            immunizationList = em.createQuery(immunizationsCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            immunizations = immunizationList.stream().collect(Collectors.groupingBy(i -> i.getPerson().getId()));
        }
        // Load latest events info
        // Adding a second query here is not perfect, but selecting the last event with a criteria query
        // doesn't seem to be possible and using a native query is not an option because of user filters
        List<EventSummaryDetails> eventSummaries = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, CaseExportDto.LATEST_EVENT_ID, CaseExportDto.LATEST_EVENT_STATUS, CaseExportDto.LATEST_EVENT_TITLE)) {
            eventSummaries = eventService.getEventSummaryDetailsByCases(resultCaseIds);
        }
        Map<Long, UserReference> caseUsers = getCaseUsersForExport(resultList, exportConfiguration);
        Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight, I18nProperties.getCaption(Captions.inaccessibleValue));
        for (CaseExportDto exportDto : resultList) {
            final boolean inJurisdiction = exportDto.getInJurisdiction();
            if (exportConfiguration == null || exportConfiguration.getProperties().contains(CaseExportDto.COUNTRY)) {
                exportDto.setCountry(configFacade.getEpidPrefix());
            }
            if (symptoms != null) {
                Optional.ofNullable(symptoms.get(exportDto.getSymptomsId())).ifPresent(symptom -> exportDto.setSymptoms(SymptomsFacadeEjb.toDto(symptom)));
            }
            if (personAddresses != null || exportConfiguration.getProperties().contains(CaseExportDto.ADDRESS_GPS_COORDINATES)) {
                Optional.ofNullable(personAddresses.get(exportDto.getPersonAddressId())).ifPresent(personAddress -> exportDto.setAddressGpsCoordinates(personAddress.buildGpsCoordinatesCaption()));
            }
            if (prescriptionCounts != null) {
                Optional.ofNullable(prescriptionCounts.get(exportDto.getId())).ifPresent(prescriptionCount -> exportDto.setNumberOfPrescriptions(prescriptionCount));
            }
            if (treatmentCounts != null) {
                Optional.ofNullable(treatmentCounts.get(exportDto.getId())).ifPresent(treatmentCount -> exportDto.setNumberOfTreatments(treatmentCount));
            }
            if (clinicalVisitCounts != null) {
                Optional.ofNullable(clinicalVisitCounts.get(exportDto.getId())).ifPresent(clinicalVisitCount -> exportDto.setNumberOfClinicalVisits(clinicalVisitCount));
            }
            if (healthConditions != null) {
                Optional.ofNullable(healthConditions.get(exportDto.getHealthConditionsId())).ifPresent(healthCondition -> exportDto.setHealthConditions(healthConditionsMapper.toDto(healthCondition)));
            }
            if (firstPreviousHospitalizations != null) {
                Optional.ofNullable(firstPreviousHospitalizations.get(exportDto.getHospitalizationId())).ifPresent(firstPreviousHospitalization -> {
                    if (firstPreviousHospitalization.getHealthFacility() != null) {
                        exportDto.setInitialDetectionPlace(FacilityHelper.buildFacilityString(firstPreviousHospitalization.getHealthFacility().getUuid(), firstPreviousHospitalization.getHealthFacility().getName(), firstPreviousHospitalization.getHealthFacilityDetails()));
                    } else {
                        exportDto.setInitialDetectionPlace(I18nProperties.getCaption(Captions.unknown));
                    }
                });
                if (StringUtils.isEmpty(exportDto.getInitialDetectionPlace())) {
                    if (!StringUtils.isEmpty(exportDto.getHealthFacility())) {
                        exportDto.setInitialDetectionPlace(exportDto.getHealthFacility());
                    } else {
                        exportDto.setInitialDetectionPlace(exportDto.getPointOfEntry());
                    }
                }
            }
            if (sourceCaseClassifications != null) {
                Optional.ofNullable(sourceCaseClassifications.get(exportDto.getId())).ifPresent(sourceCaseClassification -> exportDto.setMaxSourceCaseClassification(sourceCaseClassification));
            }
            if (caseIdsWithOutbreak != null) {
                exportDto.setAssociatedWithOutbreak(caseIdsWithOutbreak.contains(exportDto.getId()));
            }
            if (exposures != null) {
                Optional.ofNullable(exposures.get(exportDto.getEpiDataId())).ifPresent(caseExposures -> {
                    StringBuilder travelHistoryBuilder = new StringBuilder();
                    if (caseExposures.stream().anyMatch(e -> ExposureType.BURIAL.equals(e.getExposureType()))) {
                        exportDto.setBurialAttended(true);
                    }
                    caseExposures.stream().filter(e -> ExposureType.TRAVEL.equals(e.getExposureType())).forEach(exposure -> travelHistoryBuilder.append(EpiDataHelper.buildDetailedTravelString(exposure.getLocation().toString(), exposure.getDescription(), exposure.getStartDate(), exposure.getEndDate(), userLanguage)).append(", "));
                    if (travelHistoryBuilder.length() > 0) {
                        exportDto.setTraveled(true);
                        travelHistoryBuilder.delete(travelHistoryBuilder.lastIndexOf(", "), travelHistoryBuilder.length() - 1);
                    }
                    exportDto.setTravelHistory(travelHistoryBuilder.toString());
                });
            }
            if (samples != null) {
                Optional.ofNullable(samples.get(exportDto.getId())).ifPresent(caseSamples -> {
                    int count = 0;
                    caseSamples.sort((o1, o2) -> o2.getSampleDateTime().compareTo(o1.getSampleDateTime()));
                    for (Sample sample : caseSamples) {
                        EmbeddedSampleExportDto sampleDto = new EmbeddedSampleExportDto(sample.getUuid(), sample.getSampleDateTime(), sample.getLab() != null ? FacilityHelper.buildFacilityString(sample.getLab().getUuid(), sample.getLab().getName(), sample.getLabDetails()) : null, sample.getPathogenTestResult());
                        switch(++count) {
                            case 1:
                                exportDto.setSample1(sampleDto);
                                break;
                            case 2:
                                exportDto.setSample2(sampleDto);
                                break;
                            case 3:
                                exportDto.setSample3(sampleDto);
                                break;
                            default:
                                exportDto.addOtherSample(sampleDto);
                        }
                    }
                });
            }
            if (immunizations != null) {
                Optional.ofNullable(immunizations.get(exportDto.getPersonId())).ifPresent(caseImmunizations -> {
                    List<Immunization> filteredImmunizations = caseImmunizations.stream().filter(i -> i.getDisease() == exportDto.getDisease()).collect(Collectors.toList());
                    if (!filteredImmunizations.isEmpty()) {
                        filteredImmunizations.sort(Comparator.comparing(i -> ImmunizationEntityHelper.getDateForComparison(i, false)));
                        Immunization mostRecentImmunization = filteredImmunizations.get(filteredImmunizations.size() - 1);
                        Integer numberOfDoses = mostRecentImmunization.getNumberOfDoses();
                        exportDto.setNumberOfDoses(numberOfDoses != null ? String.valueOf(numberOfDoses) : "");
                        if (CollectionUtils.isNotEmpty(mostRecentImmunization.getVaccinations())) {
                            List<Vaccination> sortedVaccinations = mostRecentImmunization.getVaccinations().stream().sorted(Comparator.comparing(ImmunizationEntityHelper::getVaccinationDateForComparison)).collect(Collectors.toList());
                            Vaccination firstVaccination = sortedVaccinations.get(0);
                            Vaccination lastVaccination = sortedVaccinations.get(sortedVaccinations.size() - 1);
                            exportDto.setFirstVaccinationDate(firstVaccination.getVaccinationDate());
                            exportDto.setLastVaccinationDate(lastVaccination.getVaccinationDate());
                            exportDto.setVaccineName(lastVaccination.getVaccineName());
                            exportDto.setOtherVaccineName(lastVaccination.getOtherVaccineName());
                            exportDto.setVaccineManufacturer(lastVaccination.getVaccineManufacturer());
                            exportDto.setOtherVaccineManufacturer(lastVaccination.getOtherVaccineManufacturer());
                            exportDto.setVaccinationInfoSource(lastVaccination.getVaccinationInfoSource());
                            exportDto.setVaccineAtcCode(lastVaccination.getVaccineAtcCode());
                            exportDto.setVaccineBatchNumber(lastVaccination.getVaccineBatchNumber());
                            exportDto.setVaccineUniiCode(lastVaccination.getVaccineUniiCode());
                            exportDto.setVaccineInn(lastVaccination.getVaccineInn());
                        }
                    }
                });
            }
            if (visitSummaries != null) {
                List<VisitSummaryExportDetails> visits = visitSummaries.stream().filter(v -> v.getContactId() == exportDto.getId()).collect(Collectors.toList());
                VisitSummaryExportDetails lastCooperativeVisit = visits.stream().filter(v -> v.getVisitStatus() == VisitStatus.COOPERATIVE).max(Comparator.comparing(VisitSummaryExportDetails::getVisitDateTime)).orElse(null);
                exportDto.setNumberOfVisits(visits.size());
                if (lastCooperativeVisit != null) {
                    exportDto.setLastCooperativeVisitDate(lastCooperativeVisit.getVisitDateTime());
                    SymptomsDto visitSymptoms = SymptomsFacadeEjb.toDto(lastCooperativeVisit.getSymptoms());
                    pseudonymizer.pseudonymizeDto(SymptomsDto.class, visitSymptoms, inJurisdiction, null);
                    exportDto.setLastCooperativeVisitSymptoms(SymptomsHelper.buildSymptomsHumanString(visitSymptoms, true, userLanguage));
                    exportDto.setLastCooperativeVisitSymptomatic(visitSymptoms.getSymptomatic() == null ? YesNoUnknown.UNKNOWN : (visitSymptoms.getSymptomatic() ? YesNoUnknown.YES : YesNoUnknown.NO));
                }
            }
            if (eventSummaries != null && exportDto.getEventCount() != 0) {
                eventSummaries.stream().filter(v -> v.getCaseId() == exportDto.getId()).max(Comparator.comparing(EventSummaryDetails::getEventDate)).ifPresent(eventSummary -> {
                    exportDto.setLatestEventId(eventSummary.getEventUuid());
                    exportDto.setLatestEventStatus(eventSummary.getEventStatus());
                    exportDto.setLatestEventTitle(eventSummary.getEventTitle());
                });
            }
            if (!caseUsers.isEmpty()) {
                if (exportDto.getReportingUserId() != null) {
                    UserReference user = caseUsers.get(exportDto.getReportingUserId());
                    exportDto.setReportingUserName(user.getName());
                    exportDto.setReportingUserRoles(user.getUserRoles());
                }
                if (exportDto.getFollowUpStatusChangeUserId() != null) {
                    UserReference user = caseUsers.get(exportDto.getFollowUpStatusChangeUserId());
                    exportDto.setFollowUpStatusChangeUserName(user.getName());
                    exportDto.setFollowUpStatusChangeUserRoles(user.getUserRoles());
                }
            }
            pseudonymizer.pseudonymizeDto(CaseExportDto.class, exportDto, inJurisdiction, c -> {
                pseudonymizer.pseudonymizeDto(BirthDateDto.class, c.getBirthdate(), inJurisdiction, null);
                pseudonymizer.pseudonymizeDto(EmbeddedSampleExportDto.class, c.getSample1(), inJurisdiction, null);
                pseudonymizer.pseudonymizeDto(EmbeddedSampleExportDto.class, c.getSample2(), inJurisdiction, null);
                pseudonymizer.pseudonymizeDto(EmbeddedSampleExportDto.class, c.getSample3(), inJurisdiction, null);
                pseudonymizer.pseudonymizeDtoCollection(EmbeddedSampleExportDto.class, c.getOtherSamples(), s -> inJurisdiction, null);
                pseudonymizer.pseudonymizeDto(BurialInfoDto.class, c.getBurialInfo(), inJurisdiction, null);
                pseudonymizer.pseudonymizeDto(SymptomsDto.class, c.getSymptoms(), inJurisdiction, null);
            });
        }
    }
    caseCriteria.setMustHaveCaseManagementData(previousCaseManagementDataCriteria);
    return resultList;
}

Example 2 with Vaccination

use of de.symeda.sormas.backend.vaccination.Vaccination in project SORMAS-Project by hzi-braunschweig.

the class ImmunizationFacadeEjb method fillOrBuildEntity.

protected Immunization fillOrBuildEntity(@NotNull ImmunizationDto source, Immunization target, boolean checkChangeDate) {
    target = DtoHelper.fillOrBuildEntity(source, target, Immunization::new, checkChangeDate);
    target.setDisease(source.getDisease());
    target.setDiseaseDetails(source.getDiseaseDetails());
    target.setPerson(personService.getByReferenceDto(source.getPerson()));
    target.setReportDate(source.getReportDate());
    target.setReportingUser(userService.getByReferenceDto(source.getReportingUser()));
    target.setArchived(source.isArchived());
    target.setImmunizationStatus(source.getImmunizationStatus());
    target.setMeansOfImmunization(source.getMeansOfImmunization());
    target.setMeansOfImmunizationDetails(source.getMeansOfImmunizationDetails());
    target.setImmunizationManagementStatus(source.getImmunizationManagementStatus());
    target.setExternalId(source.getExternalId());
    target.setResponsibleRegion(regionService.getByReferenceDto(source.getResponsibleRegion()));
    target.setResponsibleDistrict(districtService.getByReferenceDto(source.getResponsibleDistrict()));
    target.setResponsibleCommunity(communityService.getByReferenceDto(source.getResponsibleCommunity()));
    target.setCountry(countryService.getByReferenceDto(source.getCountry()));
    target.setFacilityType(source.getFacilityType());
    target.setHealthFacility(facilityService.getByReferenceDto(source.getHealthFacility()));
    target.setHealthFacilityDetails(source.getHealthFacilityDetails());
    target.setStartDate(source.getStartDate());
    target.setEndDate(source.getEndDate());
    target.setNumberOfDoses(source.getNumberOfDoses());
    target.setNumberOfDosesDetails(source.getNumberOfDosesDetails());
    target.setPreviousInfection(source.getPreviousInfection());
    target.setLastInfectionDate(source.getLastInfectionDate());
    target.setAdditionalDetails(source.getAdditionalDetails());
    target.setPositiveTestResultDate(source.getPositiveTestResultDate());
    target.setRecoveryDate(source.getRecoveryDate());
    target.setValidFrom(source.getValidFrom());
    target.setValidUntil(source.getValidUntil());
    target.setRelatedCase(caseService.getByReferenceDto(source.getRelatedCase()));
    List<Vaccination> vaccinationEntities = new ArrayList<>();
    for (VaccinationDto vaccinationDto : source.getVaccinations()) {
        Vaccination vaccination = vaccinationFacade.fromDto(vaccinationDto, checkChangeDate);
        vaccination.setImmunization(target);
        vaccinationEntities.add(vaccination);
    }
    target.getVaccinations().clear();
    target.getVaccinations().addAll(vaccinationEntities);
    if (source.getSormasToSormasOriginInfo() != null) {
        target.setSormasToSormasOriginInfo(originInfoFacade.fromDto(source.getSormasToSormasOriginInfo(), checkChangeDate));
    }
    return target;
}

Example 3 with Vaccination

use of de.symeda.sormas.backend.vaccination.Vaccination in project SORMAS-Project by hzi-braunschweig.

the class ReceivedImmunizationProcessor method handleReceivedData.

@Override
public void handleReceivedData(SormasToSormasImmunizationDto sharedData, Immunization existingData) {
    updateReportingUser(sharedData.getEntity(), existingData);
    handleIgnoredProperties(sharedData.getEntity(), immunizationFacadeEjb.toDto(existingData));
    ImmunizationDto im = sharedData.getEntity();
    im.getVaccinations().forEach(vaccination -> {
        Vaccination existingVaccination;
        if (existingData == null) {
            existingVaccination = null;
        } else {
            existingVaccination = existingData.getVaccinations().stream().filter(v -> v.getUuid().equals(vaccination.getUuid())).findFirst().orElse(null);
        }
        UserReferenceDto reportingUser;
        if (existingVaccination == null) {
            reportingUser = userService.getCurrentUser().toReference();
        } else {
            reportingUser = existingVaccination.getReportingUser().toReference();
        }
        vaccination.setReportingUser(reportingUser);
    });
}

Example 4 with Vaccination

use of de.symeda.sormas.backend.vaccination.Vaccination in project SORMAS-Project by hzi-braunschweig.

the class EventParticipantFacadeEjb method getExportList.

@Override
public List<EventParticipantExportDto> getExportList(EventParticipantCriteria eventParticipantCriteria, Collection<String> selectedRows, int first, int max, Language userLanguage, ExportConfigurationDto exportConfiguration) {
    CriteriaBuilder cb = em.getCriteriaBuilder();
    CriteriaQuery<EventParticipantExportDto> cq = cb.createQuery(EventParticipantExportDto.class);
    Root<EventParticipant> eventParticipant = cq.from(EventParticipant.class);
    EventParticipantQueryContext eventParticipantQueryContext = new EventParticipantQueryContext(cb, cq, eventParticipant);
    EventParticipantJoins<EventParticipant> joins = (EventParticipantJoins<EventParticipant>) eventParticipantQueryContext.getJoins();
    Join<EventParticipant, Person> person = joins.getPerson();
    PersonQueryContext personQueryContext = new PersonQueryContext(cb, cq, person);
    Join<Person, Location> address = joins.getAddress();
    Join<Person, Country> birthCountry = person.join(Person.BIRTH_COUNTRY, JoinType.LEFT);
    Join<Person, Country> citizenship = person.join(Person.CITIZENSHIP, JoinType.LEFT);
    Join<EventParticipant, Event> event = joins.getEvent();
    Join<Event, Location> eventLocation = joins.getEventAddress();
    Join<EventParticipant, Case> resultingCase = joins.getResultingCase();
    cq.multiselect(eventParticipant.get(EventParticipant.ID), person.get(Person.ID), person.get(Person.UUID), eventParticipant.get(EventParticipant.UUID), person.get(Person.NATIONAL_HEALTH_ID), person.get(Location.ID), JurisdictionHelper.booleanSelector(cb, service.inJurisdictionOrOwned(eventParticipantQueryContext)), event.get(Event.UUID), event.get(Event.EVENT_STATUS), event.get(Event.EVENT_INVESTIGATION_STATUS), event.get(Event.DISEASE), event.get(Event.TYPE_OF_PLACE), event.get(Event.START_DATE), event.get(Event.END_DATE), event.get(Event.EVENT_TITLE), event.get(Event.EVENT_DESC), eventLocation.join(Location.REGION, JoinType.LEFT).get(Region.NAME), eventLocation.join(Location.DISTRICT, JoinType.LEFT).get(District.NAME), eventLocation.join(Location.COMMUNITY, JoinType.LEFT).get(Community.NAME), eventLocation.get(Location.CITY), eventLocation.get(Location.STREET), eventLocation.get(Location.HOUSE_NUMBER), person.get(Person.FIRST_NAME), person.get(Person.LAST_NAME), person.get(Person.SALUTATION), person.get(Person.OTHER_SALUTATION), person.get(Person.SEX), eventParticipant.get(EventParticipant.INVOLVEMENT_DESCRIPTION), person.get(Person.APPROXIMATE_AGE), person.get(Person.APPROXIMATE_AGE_TYPE), person.get(Person.BIRTHDATE_DD), person.get(Person.BIRTHDATE_MM), person.get(Person.BIRTHDATE_YYYY), person.get(Person.PRESENT_CONDITION), person.get(Person.DEATH_DATE), person.get(Person.BURIAL_DATE), person.get(Person.BURIAL_CONDUCTOR), person.get(Person.BURIAL_PLACE_DESCRIPTION), joins.getAddressRegion().get(Region.NAME), joins.getAddressDistrict().get(District.NAME), joins.getAddressCommunity().get(Community.NAME), address.get(Location.CITY), address.get(Location.STREET), address.get(Location.HOUSE_NUMBER), address.get(Location.ADDITIONAL_INFORMATION), address.get(Location.POSTAL_CODE), personQueryContext.getSubqueryExpression(PersonQueryContext.PERSON_PHONE_SUBQUERY), personQueryContext.getSubqueryExpression(PersonQueryContext.PERSON_EMAIL_SUBQUERY), resultingCase.get(Case.UUID), person.get(Person.BIRTH_NAME), birthCountry.get(Country.ISO_CODE), birthCountry.get(Country.DEFAULT_NAME), citizenship.get(Country.ISO_CODE), citizenship.get(Country.DEFAULT_NAME), eventParticipant.get(EventParticipant.VACCINATION_STATUS));
    Predicate filter = service.buildCriteriaFilter(eventParticipantCriteria, eventParticipantQueryContext);
    filter = CriteriaBuilderHelper.andInValues(selectedRows, filter, cb, eventParticipant.get(EventParticipant.UUID));
    cq.where(filter);
    List<EventParticipantExportDto> eventParticipantResultList = QueryHelper.getResultList(em, cq, first, max);
    if (!eventParticipantResultList.isEmpty()) {
        Map<String, Long> eventParticipantContactCount = getContactCountPerEventParticipant(eventParticipantResultList.stream().map(EventParticipantExportDto::getEventParticipantUuid).collect(Collectors.toList()), eventParticipantCriteria);
        Map<Long, Location> personAddresses = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, PersonDto.ADDRESS, CaseExportDto.ADDRESS_GPS_COORDINATES)) {
            CriteriaQuery<Location> personAddressesCq = cb.createQuery(Location.class);
            Root<Location> personAddressesRoot = personAddressesCq.from(Location.class);
            Expression<String> personAddressesIdsExpr = personAddressesRoot.get(Location.ID);
            personAddressesCq.where(personAddressesIdsExpr.in(eventParticipantResultList.stream().map(EventParticipantExportDto::getPersonAddressId).collect(Collectors.toList())));
            List<Location> personAddressesList = em.createQuery(personAddressesCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            personAddresses = personAddressesList.stream().collect(Collectors.toMap(Location::getId, Function.identity()));
        }
        Map<Long, List<Sample>> samples = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, EventParticipantExportDto.SAMPLE_INFORMATION)) {
            List<Sample> samplesList = null;
            CriteriaQuery<Sample> samplesCq = cb.createQuery(Sample.class);
            Root<Sample> samplesRoot = samplesCq.from(Sample.class);
            Join<Sample, EventParticipant> samplesEventParticipantJoin = samplesRoot.join(Sample.ASSOCIATED_EVENT_PARTICIPANT, JoinType.LEFT);
            Expression<String> eventParticipantIdsExpr = samplesEventParticipantJoin.get(EventParticipant.ID);
            samplesCq.where(eventParticipantIdsExpr.in(eventParticipantResultList.stream().map(EventParticipantExportDto::getId).collect(Collectors.toList())));
            samplesList = em.createQuery(samplesCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            samples = samplesList.stream().collect(Collectors.groupingBy(s -> s.getAssociatedEventParticipant().getId()));
        }
        Map<Long, List<Immunization>> immunizations = null;
        if (exportConfiguration == null || exportConfiguration.getProperties().stream().anyMatch(p -> StringUtils.equalsAny(p, ExportHelper.getVaccinationExportProperties()))) {
            List<Immunization> immunizationList;
            CriteriaQuery<Immunization> immunizationsCq = cb.createQuery(Immunization.class);
            Root<Immunization> immunizationsCqRoot = immunizationsCq.from(Immunization.class);
            Join<Immunization, Person> personJoin = immunizationsCqRoot.join(Immunization.PERSON, JoinType.LEFT);
            Expression<String> personIdsExpr = personJoin.get(Person.ID);
            immunizationsCq.where(CriteriaBuilderHelper.and(cb, cb.or(cb.equal(immunizationsCqRoot.get(Immunization.MEANS_OF_IMMUNIZATION), MeansOfImmunization.VACCINATION), cb.equal(immunizationsCqRoot.get(Immunization.MEANS_OF_IMMUNIZATION), MeansOfImmunization.VACCINATION_RECOVERY)), personIdsExpr.in(eventParticipantResultList.stream().map(EventParticipantExportDto::getPersonId).collect(Collectors.toList()))));
            immunizationList = em.createQuery(immunizationsCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            immunizations = immunizationList.stream().collect(Collectors.groupingBy(i -> i.getPerson().getId()));
        }
        Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight, I18nProperties.getCaption(Captions.inaccessibleValue));
        for (EventParticipantExportDto exportDto : eventParticipantResultList) {
            final boolean inJurisdiction = exportDto.getInJurisdiction();
            if (personAddresses != null) {
                Optional.ofNullable(personAddresses.get(exportDto.getPersonAddressId())).ifPresent(personAddress -> exportDto.setAddressGpsCoordinates(personAddress.buildGpsCoordinatesCaption()));
            }
            if (samples != null) {
                Optional.ofNullable(samples.get(exportDto.getId())).ifPresent(eventParticipantSamples -> {
                    int count = 0;
                    for (Sample sample : eventParticipantSamples) {
                        EmbeddedSampleExportDto sampleDto = new EmbeddedSampleExportDto(sample.getUuid(), sample.getSampleDateTime(), sample.getLab() != null ? FacilityHelper.buildFacilityString(sample.getLab().getUuid(), sample.getLab().getName(), sample.getLabDetails()) : null, sample.getPathogenTestResult());
                        exportDto.addEventParticipantSample(sampleDto);
                    }
                });
            }
            if (immunizations != null) {
                Optional.ofNullable(immunizations.get(exportDto.getPersonId())).ifPresent(epImmunizations -> {
                    List<Immunization> filteredImmunizations = epImmunizations.stream().filter(i -> i.getDisease() == exportDto.getEventDisease()).collect(Collectors.toList());
                    filteredImmunizations.sort(Comparator.comparing(i -> ImmunizationEntityHelper.getDateForComparison(i, false)));
                    Immunization mostRecentImmunization = filteredImmunizations.get(filteredImmunizations.size() - 1);
                    exportDto.setVaccinationDoses(String.valueOf(mostRecentImmunization.getNumberOfDoses()));
                    if (CollectionUtils.isNotEmpty(mostRecentImmunization.getVaccinations())) {
                        List<Vaccination> sortedVaccinations = mostRecentImmunization.getVaccinations().stream().sorted(Comparator.comparing(ImmunizationEntityHelper::getVaccinationDateForComparison)).collect(Collectors.toList());
                        Vaccination firstVaccination = sortedVaccinations.get(0);
                        Vaccination lastVaccination = sortedVaccinations.get(sortedVaccinations.size() - 1);
                        exportDto.setFirstVaccinationDate(firstVaccination.getVaccinationDate());
                        exportDto.setLastVaccinationDate(lastVaccination.getVaccinationDate());
                        exportDto.setVaccineName(lastVaccination.getVaccineName());
                        exportDto.setOtherVaccineName(lastVaccination.getOtherVaccineName());
                        exportDto.setVaccineManufacturer(lastVaccination.getVaccineManufacturer());
                        exportDto.setOtherVaccineManufacturer(lastVaccination.getOtherVaccineManufacturer());
                        exportDto.setVaccinationInfoSource(lastVaccination.getVaccinationInfoSource());
                        exportDto.setVaccineAtcCode(lastVaccination.getVaccineAtcCode());
                        exportDto.setVaccineBatchNumber(lastVaccination.getVaccineBatchNumber());
                        exportDto.setVaccineUniiCode(lastVaccination.getVaccineUniiCode());
                        exportDto.setVaccineInn(lastVaccination.getVaccineInn());
                    }
                });
            }
            Optional.ofNullable(eventParticipantContactCount.get(exportDto.getEventParticipantUuid())).ifPresent(exportDto::setContactCount);
            pseudonymizer.pseudonymizeDto(EventParticipantExportDto.class, exportDto, inJurisdiction, (c) -> {
                pseudonymizer.pseudonymizeDto(BirthDateDto.class, c.getBirthdate(), inJurisdiction, null);
                pseudonymizer.pseudonymizeDtoCollection(EmbeddedSampleExportDto.class, c.getEventParticipantSamples(), s -> inJurisdiction, null);
                pseudonymizer.pseudonymizeDto(BurialInfoDto.class, c.getBurialInfo(), inJurisdiction, null);
            });
        }
    }
    return eventParticipantResultList;
}

Example 5 with Vaccination

use of de.symeda.sormas.backend.vaccination.Vaccination in project SORMAS-Project by hzi-braunschweig.

the class ContactFacadeEjb method getExportList.

@Override
public List<ContactExportDto> getExportList(ContactCriteria contactCriteria, Collection<String> selectedRows, int first, int max, ExportConfigurationDto exportConfiguration, Language userLanguage) {
    final CriteriaBuilder cb = em.getCriteriaBuilder();
    final CriteriaQuery<ContactExportDto> cq = cb.createQuery(ContactExportDto.class);
    final Root<Contact> contact = cq.from(Contact.class);
    final ContactQueryContext contactQueryContext = new ContactQueryContext(cb, cq, contact);
    final ContactJoins<Contact> joins = (ContactJoins) contactQueryContext.getJoins();
    cq.multiselect(contact.get(Contact.ID), joins.getPerson().get(Person.ID), contact.get(Contact.UUID), joins.getCaze().get(Case.UUID), joins.getCaze().get(Case.CASE_CLASSIFICATION), contact.get(Contact.DISEASE), contact.get(Contact.DISEASE_DETAILS), contact.get(Contact.CONTACT_CLASSIFICATION), contact.get(Contact.MULTI_DAY_CONTACT), contact.get(Contact.FIRST_CONTACT_DATE), contact.get(Contact.LAST_CONTACT_DATE), contact.get(Contact.CREATION_DATE), joins.getPerson().get(Person.UUID), joins.getPerson().get(Person.FIRST_NAME), joins.getPerson().get(Person.LAST_NAME), joins.getPerson().get(Person.SALUTATION), joins.getPerson().get(Person.OTHER_SALUTATION), joins.getPerson().get(Person.SEX), joins.getPerson().get(Person.BIRTHDATE_DD), joins.getPerson().get(Person.BIRTHDATE_MM), joins.getPerson().get(Person.BIRTHDATE_YYYY), joins.getPerson().get(Person.APPROXIMATE_AGE), joins.getPerson().get(Person.APPROXIMATE_AGE_TYPE), contact.get(Contact.REPORT_DATE_TIME), contact.get(Contact.CONTACT_IDENTIFICATION_SOURCE), contact.get(Contact.CONTACT_IDENTIFICATION_SOURCE_DETAILS), contact.get(Contact.TRACING_APP), contact.get(Contact.TRACING_APP_DETAILS), contact.get(Contact.CONTACT_PROXIMITY), contact.get(Contact.CONTACT_STATUS), contact.get(Contact.COMPLETENESS), contact.get(Contact.FOLLOW_UP_STATUS), contact.get(Contact.FOLLOW_UP_UNTIL), contact.get(Contact.QUARANTINE), contact.get(Contact.QUARANTINE_TYPE_DETAILS), contact.get(Contact.QUARANTINE_FROM), contact.get(Contact.QUARANTINE_TO), contact.get(Contact.QUARANTINE_HELP_NEEDED), contact.get(Contact.QUARANTINE_ORDERED_VERBALLY), contact.get(Contact.QUARANTINE_ORDERED_OFFICIAL_DOCUMENT), contact.get(Contact.QUARANTINE_ORDERED_VERBALLY_DATE), contact.get(Contact.QUARANTINE_ORDERED_OFFICIAL_DOCUMENT_DATE), contact.get(Contact.QUARANTINE_EXTENDED), contact.get(Contact.QUARANTINE_REDUCED), contact.get(Contact.QUARANTINE_OFFICIAL_ORDER_SENT), contact.get(Contact.QUARANTINE_OFFICIAL_ORDER_SENT_DATE), contact.get(Contact.PROHIBITION_TO_WORK), contact.get(Contact.PROHIBITION_TO_WORK_FROM), contact.get(Contact.PROHIBITION_TO_WORK_UNTIL), joins.getPerson().get(Person.PRESENT_CONDITION), joins.getPerson().get(Person.DEATH_DATE), joins.getAddressRegion().get(Region.NAME), joins.getAddressDistrict().get(District.NAME), joins.getAddressCommunity().get(Community.NAME), joins.getAddress().get(Location.CITY), joins.getAddress().get(Location.STREET), joins.getAddress().get(Location.HOUSE_NUMBER), joins.getAddress().get(Location.ADDITIONAL_INFORMATION), joins.getAddress().get(Location.POSTAL_CODE), joins.getAddressFacility().get(Facility.NAME), joins.getAddressFacility().get(Facility.UUID), joins.getAddress().get(Location.FACILITY_DETAILS), ((Expression<String>) contactQueryContext.getSubqueryExpression(ContactQueryContext.PERSON_PHONE_SUBQUERY)), ((Expression<String>) contactQueryContext.getSubqueryExpression(ContactQueryContext.PERSON_PHONE_OWNER_SUBQUERY)), ((Expression<String>) contactQueryContext.getSubqueryExpression(ContactQueryContext.PERSON_EMAIL_SUBQUERY)), ((Expression<String>) contactQueryContext.getSubqueryExpression(ContactQueryContext.PERSON_OTHER_CONTACT_DETAILS_SUBQUERY)), joins.getPerson().get(Person.OCCUPATION_TYPE), joins.getPerson().get(Person.OCCUPATION_DETAILS), joins.getPerson().get(Person.ARMED_FORCES_RELATION_TYPE), joins.getRegion().get(Region.NAME), joins.getDistrict().get(District.NAME), joins.getCommunity().get(Community.NAME), joins.getEpiData().get(EpiData.ID), joins.getEpiData().get(EpiData.CONTACT_WITH_SOURCE_CASE_KNOWN), contact.get(Contact.RETURNING_TRAVELER), contact.get(Contact.VACCINATION_STATUS), contact.get(Contact.EXTERNAL_ID), contact.get(Contact.EXTERNAL_TOKEN), contact.get(Contact.INTERNAL_TOKEN), joins.getPerson().get(Person.BIRTH_NAME), joins.getPersonBirthCountry().get(Country.ISO_CODE), joins.getPersonBirthCountry().get(Country.DEFAULT_NAME), joins.getPersonCitizenship().get(Country.ISO_CODE), joins.getPersonCitizenship().get(Country.DEFAULT_NAME), joins.getReportingDistrict().get(District.NAME), joins.getPerson().get(Person.SYMPTOM_JOURNAL_STATUS), joins.getReportingUser().get(User.ID), joins.getFollowUpStatusChangeUser().get(User.ID), contact.get(Contact.PREVIOUS_QUARANTINE_TO), contact.get(Contact.QUARANTINE_CHANGE_COMMENT), jurisdictionSelector(contactQueryContext));
    cq.distinct(true);
    Predicate filter = listCriteriaBuilder.buildContactFilter(contactCriteria, contactQueryContext);
    filter = CriteriaBuilderHelper.andInValues(selectedRows, filter, cb, contact.get(Contact.UUID));
    if (filter != null) {
        cq.where(filter);
    }
    cq.orderBy(cb.desc(contact.get(Contact.REPORT_DATE_TIME)), cb.desc(contact.get(Contact.ID)));
    List<ContactExportDto> exportContacts = QueryHelper.getResultList(em, cq, first, max);
    List<String> resultContactsUuids = exportContacts.stream().map(ContactExportDto::getUuid).collect(Collectors.toList());
    if (!exportContacts.isEmpty()) {
        List<Long> exportContactIds = exportContacts.stream().map(e -> e.getId()).collect(Collectors.toList());
        List<VisitSummaryExportDetails> visitSummaries = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, ContactExportDto.NUMBER_OF_VISITS, ContactExportDto.LAST_COOPERATIVE_VISIT_DATE, ContactExportDto.LAST_COOPERATIVE_VISIT_SYMPTOMATIC, ContactExportDto.LAST_COOPERATIVE_VISIT_SYMPTOMS)) {
            CriteriaQuery<VisitSummaryExportDetails> visitsCq = cb.createQuery(VisitSummaryExportDetails.class);
            Root<Contact> visitsCqRoot = visitsCq.from(Contact.class);
            ContactJoins<Contact> visitContactJoins = new ContactJoins(visitsCqRoot);
            visitsCq.where(CriteriaBuilderHelper.and(cb, contact.get(AbstractDomainObject.ID).in(exportContactIds), cb.isNotEmpty(visitsCqRoot.get(Contact.VISITS))));
            visitsCq.multiselect(visitsCqRoot.get(AbstractDomainObject.ID), visitContactJoins.getVisits().get(Visit.VISIT_DATE_TIME), visitContactJoins.getVisits().get(Visit.VISIT_STATUS), visitContactJoins.getVisitSymptoms(), jurisdictionSelector(new ContactQueryContext(cb, cq, visitsCqRoot)));
            visitSummaries = em.createQuery(visitsCq).getResultList();
        }
        Map<Long, List<Exposure>> exposures = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, ContactExportDto.TRAVELED, ContactExportDto.TRAVEL_HISTORY, ContactExportDto.BURIAL_ATTENDED)) {
            CriteriaQuery<Exposure> exposuresCq = cb.createQuery(Exposure.class);
            Root<Exposure> exposuresRoot = exposuresCq.from(Exposure.class);
            Join<Exposure, EpiData> exposuresEpiDataJoin = exposuresRoot.join(Exposure.EPI_DATA, JoinType.LEFT);
            Expression<String> epiDataIdsExpr = exposuresEpiDataJoin.get(EpiData.ID);
            Predicate exposuresPredicate = cb.and(epiDataIdsExpr.in(exportContacts.stream().map(ContactExportDto::getEpiDataId).collect(Collectors.toList())), cb.or(cb.equal(exposuresRoot.get(Exposure.EXPOSURE_TYPE), ExposureType.TRAVEL), cb.equal(exposuresRoot.get(Exposure.EXPOSURE_TYPE), ExposureType.BURIAL)));
            exposuresCq.where(exposuresPredicate);
            exposuresCq.orderBy(cb.asc(exposuresEpiDataJoin.get(EpiData.ID)));
            List<Exposure> exposureList = em.createQuery(exposuresCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            exposures = exposureList.stream().collect(Collectors.groupingBy(e -> e.getEpiData().getId()));
        }
        Map<Long, List<Immunization>> immunizations = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, ExportHelper.getVaccinationExportProperties())) {
            List<Immunization> immunizationList;
            CriteriaQuery<Immunization> immunizationsCq = cb.createQuery(Immunization.class);
            Root<Immunization> immunizationsCqRoot = immunizationsCq.from(Immunization.class);
            Join<Immunization, Person> personJoin = immunizationsCqRoot.join(Immunization.PERSON, JoinType.LEFT);
            Expression<String> personIdsExpr = personJoin.get(Person.ID);
            immunizationsCq.where(CriteriaBuilderHelper.and(cb, cb.or(cb.equal(immunizationsCqRoot.get(Immunization.MEANS_OF_IMMUNIZATION), MeansOfImmunization.VACCINATION), cb.equal(immunizationsCqRoot.get(Immunization.MEANS_OF_IMMUNIZATION), MeansOfImmunization.VACCINATION_RECOVERY)), personIdsExpr.in(exportContacts.stream().map(ContactExportDto::getPersonId).collect(Collectors.toList()))));
            immunizationList = em.createQuery(immunizationsCq).setHint(ModelConstants.HINT_HIBERNATE_READ_ONLY, true).getResultList();
            immunizations = immunizationList.stream().collect(Collectors.groupingBy(i -> i.getPerson().getId()));
        }
        Map<String, List<ContactEventSummaryDetails>> eventSummaries = null;
        if (ExportHelper.shouldExportFields(exportConfiguration, ContactExportDto.EVENT_COUNT, ContactExportDto.LATEST_EVENT_ID, ContactExportDto.LATEST_EVENT_TITLE)) {
            // Load event count and latest events info per contact
            eventSummaries = eventService.getEventSummaryDetailsByContacts(resultContactsUuids).stream().collect(Collectors.groupingBy(ContactEventSummaryDetails::getContactUuid, Collectors.toList()));
        }
        Map<Long, UserReference> contactUsers = getContactUsersForExport(exportContacts, exportConfiguration);
        // Adding a second query here is not perfect, but selecting the last cooperative visit with a criteria query
        // doesn't seem to be possible and using a native query is not an option because of user filters
        Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight, I18nProperties.getCaption(Captions.inaccessibleValue));
        for (ContactExportDto exportContact : exportContacts) {
            boolean inJurisdiction = exportContact.getInJurisdiction();
            if (visitSummaries != null) {
                List<VisitSummaryExportDetails> visits = visitSummaries.stream().filter(v -> v.getContactId() == exportContact.getId()).collect(Collectors.toList());
                VisitSummaryExportDetails lastCooperativeVisit = visits.stream().filter(v -> v.getVisitStatus() == VisitStatus.COOPERATIVE).max(Comparator.comparing(VisitSummaryExportDetails::getVisitDateTime)).orElse(null);
                exportContact.setNumberOfVisits(visits.size());
                if (lastCooperativeVisit != null) {
                    SymptomsDto symptoms = SymptomsFacadeEjb.toDto(lastCooperativeVisit.getSymptoms());
                    pseudonymizer.pseudonymizeDto(SymptomsDto.class, symptoms, inJurisdiction, null);
                    exportContact.setLastCooperativeVisitDate(lastCooperativeVisit.getVisitDateTime());
                    exportContact.setLastCooperativeVisitSymptoms(SymptomsHelper.buildSymptomsHumanString(symptoms, true, userLanguage));
                    exportContact.setLastCooperativeVisitSymptomatic(symptoms.getSymptomatic() == null ? YesNoUnknown.UNKNOWN : (symptoms.getSymptomatic() ? YesNoUnknown.YES : YesNoUnknown.NO));
                }
            }
            if (exposures != null) {
                Optional.ofNullable(exposures.get(exportContact.getEpiDataId())).ifPresent(contactExposures -> {
                    StringBuilder travelHistoryBuilder = new StringBuilder();
                    if (contactExposures.stream().anyMatch(e -> ExposureType.BURIAL.equals(e.getExposureType()))) {
                        exportContact.setBurialAttended(true);
                    }
                    contactExposures.stream().filter(e -> ExposureType.TRAVEL.equals(e.getExposureType())).forEach(exposure -> {
                        travelHistoryBuilder.append(EpiDataHelper.buildDetailedTravelString(exposure.getLocation().toString(), exposure.getDescription(), exposure.getStartDate(), exposure.getEndDate(), userLanguage)).append(", ");
                    });
                    if (travelHistoryBuilder.length() > 0) {
                        exportContact.setTraveled(true);
                        travelHistoryBuilder.delete(travelHistoryBuilder.lastIndexOf(", "), travelHistoryBuilder.length());
                    }
                    exportContact.setTravelHistory(travelHistoryBuilder.toString());
                });
            }
            if (immunizations != null) {
                Optional.ofNullable(immunizations.get(exportContact.getPersonId())).ifPresent(contactImmunizations -> {
                    List<Immunization> filteredImmunizations = contactImmunizations.stream().filter(i -> i.getDisease() == exportContact.getDisease()).collect(Collectors.toList());
                    if (filteredImmunizations.size() > 0) {
                        filteredImmunizations.sort(Comparator.comparing(i -> ImmunizationEntityHelper.getDateForComparison(i, false)));
                        Immunization mostRecentImmunization = filteredImmunizations.get(filteredImmunizations.size() - 1);
                        Integer numberOfDoses = mostRecentImmunization.getNumberOfDoses();
                        exportContact.setNumberOfDoses(numberOfDoses != null ? String.valueOf(numberOfDoses) : "");
                        if (CollectionUtils.isNotEmpty(mostRecentImmunization.getVaccinations())) {
                            List<Vaccination> sortedVaccinations = mostRecentImmunization.getVaccinations().stream().sorted(Comparator.comparing(ImmunizationEntityHelper::getVaccinationDateForComparison)).collect(Collectors.toList());
                            Vaccination firstVaccination = sortedVaccinations.get(0);
                            Vaccination lastVaccination = sortedVaccinations.get(sortedVaccinations.size() - 1);
                            exportContact.setFirstVaccinationDate(firstVaccination.getVaccinationDate());
                            exportContact.setLastVaccinationDate(lastVaccination.getVaccinationDate());
                            exportContact.setVaccineName(lastVaccination.getVaccineName());
                            exportContact.setOtherVaccineName(lastVaccination.getOtherVaccineName());
                            exportContact.setVaccineManufacturer(lastVaccination.getVaccineManufacturer());
                            exportContact.setOtherVaccineManufacturer(lastVaccination.getOtherVaccineManufacturer());
                            exportContact.setVaccinationInfoSource(lastVaccination.getVaccinationInfoSource());
                            exportContact.setVaccineAtcCode(lastVaccination.getVaccineAtcCode());
                            exportContact.setVaccineBatchNumber(lastVaccination.getVaccineBatchNumber());
                            exportContact.setVaccineUniiCode(lastVaccination.getVaccineUniiCode());
                            exportContact.setVaccineInn(lastVaccination.getVaccineInn());
                        }
                    }
                });
            }
            if (eventSummaries != null) {
                List<ContactEventSummaryDetails> contactEvents = eventSummaries.getOrDefault(exportContact.getUuid(), Collections.emptyList());
                exportContact.setEventCount((long) contactEvents.size());
                contactEvents.stream().max(Comparator.comparing(ContactEventSummaryDetails::getEventDate)).ifPresent(eventSummary -> {
                    exportContact.setLatestEventId(eventSummary.getEventUuid());
                    exportContact.setLatestEventTitle(eventSummary.getEventTitle());
                });
            }
            if (!contactUsers.isEmpty()) {
                if (exportContact.getReportingUserId() != null) {
                    UserReference user = contactUsers.get(exportContact.getReportingUserId());
                    exportContact.setReportingUserName(user.getName());
                    exportContact.setReportingUserRoles(user.getUserRoles());
                }
                if (exportContact.getFollowUpStatusChangeUserId() != null) {
                    UserReference user = contactUsers.get(exportContact.getFollowUpStatusChangeUserId());
                    exportContact.setFollowUpStatusChangeUserName(user.getName());
                    exportContact.setFollowUpStatusChangeUserRoles(user.getUserRoles());
                }
            }
            pseudonymizer.pseudonymizeDto(ContactExportDto.class, exportContact, inJurisdiction, null);
        }
    }
    return exportContacts;
}