Search in sources :

Example 1 with Sample

use of de.symeda.sormas.backend.sample.Sample in project SORMAS-Project by hzi-braunschweig.

the class ContactJurisdictionPredicateValidator method whenLaboratoryLevel.

@Override
protected Predicate whenLaboratoryLevel() {
    final Subquery<Long> sampleContactSubquery = cq.subquery(Long.class);
    final Root<Sample> sampleRoot = sampleContactSubquery.from(Sample.class);
    final SampleJoins sampleJoins = new SampleJoins(sampleRoot);
    final Join contactJoin = sampleJoins.getContact();
    SampleJurisdictionPredicateValidator sampleJurisdictionPredicateValidator = user != null ? SampleJurisdictionPredicateValidator.withoutAssociations(cb, sampleJoins, user) : SampleJurisdictionPredicateValidator.withoutAssociations(cb, sampleJoins, userPath);
    sampleContactSubquery.where(cb.and(cb.equal(contactJoin, joins.getRoot()), sampleJurisdictionPredicateValidator.inJurisdictionOrOwned()));
    sampleContactSubquery.select(sampleRoot.get(Sample.ID));
    return cb.exists(sampleContactSubquery);
}
Also used : Sample(de.symeda.sormas.backend.sample.Sample) Join(javax.persistence.criteria.Join) SampleJoins(de.symeda.sormas.backend.sample.SampleJoins) SampleJurisdictionPredicateValidator(de.symeda.sormas.backend.sample.SampleJurisdictionPredicateValidator)

Example 2 with Sample

use of de.symeda.sormas.backend.sample.Sample 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;
}
Also used : VisitService(de.symeda.sormas.backend.visit.VisitService) PlagueType(de.symeda.sormas.api.caze.PlagueType) VisitStatus(de.symeda.sormas.api.visit.VisitStatus) CaseSimilarityCriteria(de.symeda.sormas.api.caze.CaseSimilarityCriteria) DistrictService(de.symeda.sormas.backend.infrastructure.district.DistrictService) StringUtils(org.apache.commons.lang3.StringUtils) PersonDto(de.symeda.sormas.api.person.PersonDto) TaskHelper(de.symeda.sormas.api.task.TaskHelper) AbstractCoreFacadeEjb(de.symeda.sormas.backend.common.AbstractCoreFacadeEjb) TransactionAttributeType(javax.ejb.TransactionAttributeType) CaseExportDto(de.symeda.sormas.api.caze.CaseExportDto) Duration(java.time.Duration) Map(java.util.Map) TreatmentFacadeEjb(de.symeda.sormas.backend.therapy.TreatmentFacadeEjb) DocumentRelatedEntityType(de.symeda.sormas.api.document.DocumentRelatedEntityType) PrescriptionDto(de.symeda.sormas.api.therapy.PrescriptionDto) CriteriaQuery(javax.persistence.criteria.CriteriaQuery) ParameterExpression(javax.persistence.criteria.ParameterExpression) OutbreakService(de.symeda.sormas.backend.outbreak.OutbreakService) DiseaseHelper(de.symeda.sormas.api.DiseaseHelper) CommunityService(de.symeda.sormas.backend.infrastructure.community.CommunityService) FacilityHelper(de.symeda.sormas.api.infrastructure.facility.FacilityHelper) Resource(javax.annotation.Resource) TaskPriority(de.symeda.sormas.api.task.TaskPriority) NotNull(javax.validation.constraints.NotNull) CaseIndexDetailedDto(de.symeda.sormas.api.caze.CaseIndexDetailedDto) User(de.symeda.sormas.backend.user.User) PathogenTestResultType(de.symeda.sormas.api.sample.PathogenTestResultType) CaseLogic(de.symeda.sormas.api.caze.CaseLogic) EpiDataDto(de.symeda.sormas.api.epidata.EpiDataDto) JurisdictionHelper(de.symeda.sormas.backend.util.JurisdictionHelper) SampleService(de.symeda.sormas.backend.sample.SampleService) ExternalSurveillanceToolException(de.symeda.sormas.api.externalsurveillancetool.ExternalSurveillanceToolException) Sample(de.symeda.sormas.backend.sample.Sample) Hospitalization(de.symeda.sormas.backend.hospitalization.Hospitalization) Community(de.symeda.sormas.backend.infrastructure.community.Community) QueryHelper(de.symeda.sormas.backend.util.QueryHelper) CaseClassification(de.symeda.sormas.api.caze.CaseClassification) ManualMessageLogDto(de.symeda.sormas.api.messaging.ManualMessageLogDto) FacilityFacadeEjb(de.symeda.sormas.backend.infrastructure.facility.FacilityFacadeEjb) TypedQuery(javax.persistence.TypedQuery) VisitFacadeEjbLocal(de.symeda.sormas.backend.visit.VisitFacadeEjb.VisitFacadeEjbLocal) PathogenTestType(de.symeda.sormas.api.sample.PathogenTestType) CaseListEntryDto(de.symeda.sormas.api.caze.CaseListEntryDto) Calendar(java.util.Calendar) PreviousHospitalizationDto(de.symeda.sormas.api.hospitalization.PreviousHospitalizationDto) SampleFacadeEjb(de.symeda.sormas.backend.sample.SampleFacadeEjb) ConfigFacadeEjbLocal(de.symeda.sormas.backend.common.ConfigFacadeEjb.ConfigFacadeEjbLocal) ExportHelper(de.symeda.sormas.backend.importexport.ExportHelper) EJB(javax.ejb.EJB) TaskCriteria(de.symeda.sormas.api.task.TaskCriteria) ManualMessageLogService(de.symeda.sormas.backend.common.messaging.ManualMessageLogService) HospitalizationFacadeEjbLocal(de.symeda.sormas.backend.hospitalization.HospitalizationFacadeEjb.HospitalizationFacadeEjbLocal) DataHelper(de.symeda.sormas.api.utils.DataHelper) Task(de.symeda.sormas.backend.task.Task) PointOfEntry(de.symeda.sormas.backend.infrastructure.pointofentry.PointOfEntry) PersonFacadeEjb(de.symeda.sormas.backend.person.PersonFacadeEjb) CaseOrigin(de.symeda.sormas.api.caze.CaseOrigin) AgeAndBirthDateDto(de.symeda.sormas.api.caze.AgeAndBirthDateDto) PersonService(de.symeda.sormas.backend.person.PersonService) SymptomsHelper(de.symeda.sormas.api.symptoms.SymptomsHelper) SortProperty(de.symeda.sormas.api.utils.SortProperty) Prescription(de.symeda.sormas.backend.therapy.Prescription) TravelEntryService(de.symeda.sormas.backend.travelentry.services.TravelEntryService) PrescriptionFacadeEjb(de.symeda.sormas.backend.therapy.PrescriptionFacadeEjb) AtomicLong(java.util.concurrent.atomic.AtomicLong) ExposureDto(de.symeda.sormas.api.exposure.ExposureDto) Disease(de.symeda.sormas.api.Disease) VisitDto(de.symeda.sormas.api.visit.VisitDto) HealthConditions(de.symeda.sormas.backend.clinicalcourse.HealthConditions) FeatureTypeProperty(de.symeda.sormas.api.feature.FeatureTypeProperty) FieldVisibilityCheckers(de.symeda.sormas.api.utils.fieldvisibility.FieldVisibilityCheckers) PortHealthInfoFacadeEjbLocal(de.symeda.sormas.backend.caze.porthealthinfo.PortHealthInfoFacadeEjb.PortHealthInfoFacadeEjbLocal) VisitFacadeEjb(de.symeda.sormas.backend.visit.VisitFacadeEjb) CaseSelectionDto(de.symeda.sormas.api.caze.CaseSelectionDto) ContactCriteria(de.symeda.sormas.api.contact.ContactCriteria) SurveillanceReportService(de.symeda.sormas.backend.caze.surveillancereport.SurveillanceReportService) ImmunizationEntityHelper(de.symeda.sormas.backend.immunization.ImmunizationEntityHelper) Join(javax.persistence.criteria.Join) Date(java.util.Date) I18nProperties(de.symeda.sormas.api.i18n.I18nProperties) PopulationDataFacadeEjbLocal(de.symeda.sormas.backend.infrastructure.PopulationDataFacadeEjb.PopulationDataFacadeEjbLocal) Random(java.util.Random) AccessDeniedException(de.symeda.sormas.api.utils.AccessDeniedException) PortHealthInfoDto(de.symeda.sormas.api.caze.porthealthinfo.PortHealthInfoDto) PrescriptionService(de.symeda.sormas.backend.therapy.PrescriptionService) Facility(de.symeda.sormas.backend.infrastructure.facility.Facility) CriteriaBuilderHelper.or(de.symeda.sormas.backend.common.CriteriaBuilderHelper.or) CaseClassificationFacadeEjbLocal(de.symeda.sormas.backend.caze.classification.CaseClassificationFacadeEjb.CaseClassificationFacadeEjbLocal) Vaccination(de.symeda.sormas.backend.vaccination.Vaccination) VisitSummaryExportDetails(de.symeda.sormas.backend.contact.VisitSummaryExportDetails) ManagedScheduledExecutorService(javax.enterprise.concurrent.ManagedScheduledExecutorService) InfrastructureHelper(de.symeda.sormas.api.infrastructure.InfrastructureHelper) DiseaseConfigurationFacadeEjbLocal(de.symeda.sormas.backend.disease.DiseaseConfigurationFacadeEjb.DiseaseConfigurationFacadeEjbLocal) Person(de.symeda.sormas.backend.person.Person) FacilityType(de.symeda.sormas.api.infrastructure.facility.FacilityType) Timestamp(java.sql.Timestamp) Collection(java.util.Collection) InvestigationStatus(de.symeda.sormas.api.caze.InvestigationStatus) PrescriptionFacadeEjbLocal(de.symeda.sormas.backend.therapy.PrescriptionFacadeEjb.PrescriptionFacadeEjbLocal) Instant(java.time.Instant) Pseudonymizer(de.symeda.sormas.backend.util.Pseudonymizer) Collectors(java.util.stream.Collectors) Language(de.symeda.sormas.api.Language) NewCaseDateType(de.symeda.sormas.api.caze.NewCaseDateType) PatchHelper(de.symeda.sormas.backend.util.PatchHelper) Objects(java.util.Objects) CaseIndexDto(de.symeda.sormas.api.caze.CaseIndexDto) SurveillanceReportFacadeEjb(de.symeda.sormas.backend.caze.surveillancereport.SurveillanceReportFacadeEjb) ExportConfigurationDto(de.symeda.sormas.api.importexport.ExportConfigurationDto) ShareTreeCriteria(de.symeda.sormas.api.sormastosormas.ShareTreeCriteria) MessageContents(de.symeda.sormas.backend.common.messaging.MessageContents) BirthDateDto(de.symeda.sormas.api.caze.BirthDateDto) PreviousHospitalization(de.symeda.sormas.backend.hospitalization.PreviousHospitalization) ContactDto(de.symeda.sormas.api.contact.ContactDto) LocalDate(java.time.LocalDate) Order(javax.persistence.criteria.Order) ClinicalCourseDto(de.symeda.sormas.api.clinicalcourse.ClinicalCourseDto) FeatureConfigurationFacadeEjbLocal(de.symeda.sormas.backend.feature.FeatureConfigurationFacadeEjb.FeatureConfigurationFacadeEjbLocal) FacilityDto(de.symeda.sormas.api.infrastructure.facility.FacilityDto) ContactFacadeEjbLocal(de.symeda.sormas.backend.contact.ContactFacadeEjb.ContactFacadeEjbLocal) CaseFollowUpDto(de.symeda.sormas.api.caze.CaseFollowUpDto) DateHelper(de.symeda.sormas.api.utils.DateHelper) AdditionalTestDto(de.symeda.sormas.api.sample.AdditionalTestDto) CoreEntityType(de.symeda.sormas.backend.deletionconfiguration.CoreEntityType) Function(java.util.function.Function) VisitOrigin(de.symeda.sormas.api.VisitOrigin) EventParticipantService(de.symeda.sormas.backend.event.EventParticipantService) AdditionalTestFacadeEjbLocal(de.symeda.sormas.backend.sample.AdditionalTestFacadeEjb.AdditionalTestFacadeEjbLocal) Inject(javax.inject.Inject) ReinfectionDetail(de.symeda.sormas.api.caze.ReinfectionDetail) PreviousCaseDto(de.symeda.sormas.api.caze.PreviousCaseDto) TransactionAttribute(javax.ejb.TransactionAttribute) TaskStatus(de.symeda.sormas.api.task.TaskStatus) TherapyReferenceDto(de.symeda.sormas.api.therapy.TherapyReferenceDto) CriteriaBuilderHelper.and(de.symeda.sormas.backend.common.CriteriaBuilderHelper.and) SymptomsDto(de.symeda.sormas.api.symptoms.SymptomsDto) CriteriaBuilderHelper(de.symeda.sormas.backend.common.CriteriaBuilderHelper) PathogenTestDto(de.symeda.sormas.api.sample.PathogenTestDto) ExternalShareInfoService(de.symeda.sormas.backend.share.ExternalShareInfoService) LocationDto(de.symeda.sormas.api.location.LocationDto) TaskContext(de.symeda.sormas.api.task.TaskContext) Logger(org.slf4j.Logger) HospitalizationFacadeEjb(de.symeda.sormas.backend.hospitalization.HospitalizationFacadeEjb) Document(de.symeda.sormas.backend.document.Document) TherapyFacadeEjbLocal(de.symeda.sormas.backend.therapy.TherapyFacadeEjb.TherapyFacadeEjbLocal) VisitLogic.getVisitResult(de.symeda.sormas.backend.visit.VisitLogic.getVisitResult) DateTime(org.joda.time.DateTime) UserReference(de.symeda.sormas.backend.user.UserReference) RegionFacadeEjb(de.symeda.sormas.backend.infrastructure.region.RegionFacadeEjb) PresentCondition(de.symeda.sormas.api.person.PresentCondition) UserRight(de.symeda.sormas.api.user.UserRight) VisitResultDto(de.symeda.sormas.api.visit.VisitResultDto) ExternalJournalService(de.symeda.sormas.backend.externaljournal.ExternalJournalService) ContactReferenceDto(de.symeda.sormas.api.contact.ContactReferenceDto) ShareInfoHelper(de.symeda.sormas.backend.sormastosormas.share.shareinfo.ShareInfoHelper) Comparator(java.util.Comparator) Arrays(java.util.Arrays) CasePersonDto(de.symeda.sormas.api.caze.CasePersonDto) DtoHelper(de.symeda.sormas.backend.util.DtoHelper) EmbeddedSampleExportDto(de.symeda.sormas.api.caze.EmbeddedSampleExportDto) SymptomsFacadeEjbLocal(de.symeda.sormas.backend.symptoms.SymptomsFacadeEjb.SymptomsFacadeEjbLocal) Immunization(de.symeda.sormas.backend.immunization.entity.Immunization) CommunityFacadeEjb(de.symeda.sormas.backend.infrastructure.community.CommunityFacadeEjb) ExternalDataUpdateException(de.symeda.sormas.api.externaldata.ExternalDataUpdateException) MeansOfImmunization(de.symeda.sormas.api.immunization.MeansOfImmunization) ClinicalVisitCriteria(de.symeda.sormas.api.clinicalcourse.ClinicalVisitCriteria) Valid(javax.validation.Valid) BigDecimal(java.math.BigDecimal) CaseOutcome(de.symeda.sormas.api.caze.CaseOutcome) YesNoUnknown(de.symeda.sormas.api.utils.YesNoUnknown) Page(de.symeda.sormas.api.common.Page) FollowUpDto(de.symeda.sormas.api.followup.FollowUpDto) Predicate(javax.persistence.criteria.Predicate) UserFacadeEjb(de.symeda.sormas.backend.user.UserFacadeEjb) CriteriaBuilder(javax.persistence.criteria.CriteriaBuilder) JoinType(javax.persistence.criteria.JoinType) JsonNode(com.fasterxml.jackson.databind.JsonNode) Visit(de.symeda.sormas.backend.visit.Visit) EpiData(de.symeda.sormas.backend.epidata.EpiData) SormasToSormasOriginInfoFacadeEjb(de.symeda.sormas.backend.sormastosormas.origin.SormasToSormasOriginInfoFacadeEjb) EventParticipantReferenceDto(de.symeda.sormas.api.event.EventParticipantReferenceDto) FacilityService(de.symeda.sormas.backend.infrastructure.facility.FacilityService) TherapyDto(de.symeda.sormas.api.therapy.TherapyDto) Set(java.util.Set) SampleFacadeEjbLocal(de.symeda.sormas.backend.sample.SampleFacadeEjb.SampleFacadeEjbLocal) DistrictFacadeEjbLocal(de.symeda.sormas.backend.infrastructure.district.DistrictFacadeEjb.DistrictFacadeEjbLocal) PointOfEntryService(de.symeda.sormas.backend.infrastructure.pointofentry.PointOfEntryService) UserService(de.symeda.sormas.backend.user.UserService) MaternalHistoryDto(de.symeda.sormas.api.caze.maternalhistory.MaternalHistoryDto) ExternalDataDto(de.symeda.sormas.api.externaldata.ExternalDataDto) RegionReferenceDto(de.symeda.sormas.api.infrastructure.region.RegionReferenceDto) SampleCriteria(de.symeda.sormas.api.sample.SampleCriteria) EventParticipant(de.symeda.sormas.backend.event.EventParticipant) HealthConditionsDto(de.symeda.sormas.api.clinicalcourse.HealthConditionsDto) FollowUpPeriodDto(de.symeda.sormas.api.followup.FollowUpPeriodDto) CaseReferenceDefinition(de.symeda.sormas.api.caze.CaseReferenceDefinition) CaseMeasure(de.symeda.sormas.api.CaseMeasure) PersonReferenceDto(de.symeda.sormas.api.person.PersonReferenceDto) PathogenTest(de.symeda.sormas.backend.sample.PathogenTest) ArrayList(java.util.ArrayList) CaseReferenceDto(de.symeda.sormas.api.caze.CaseReferenceDto) ClinicalVisitFacadeEjb(de.symeda.sormas.backend.clinicalcourse.ClinicalVisitFacadeEjb) EpiDataFacadeEjb(de.symeda.sormas.backend.epidata.EpiDataFacadeEjb) TreatmentCriteria(de.symeda.sormas.api.therapy.TreatmentCriteria) LocalBean(javax.ejb.LocalBean) CountryHelper(de.symeda.sormas.api.CountryHelper) Root(javax.persistence.criteria.Root) PersonFacadeEjbLocal(de.symeda.sormas.backend.person.PersonFacadeEjb.PersonFacadeEjbLocal) ClinicalVisitDto(de.symeda.sormas.api.clinicalcourse.ClinicalVisitDto) MessageType(de.symeda.sormas.api.messaging.MessageType) DistrictReferenceDto(de.symeda.sormas.api.infrastructure.district.DistrictReferenceDto) MaternalHistoryFacadeEjbLocal(de.symeda.sormas.backend.caze.maternalhistory.MaternalHistoryFacadeEjb.MaternalHistoryFacadeEjbLocal) CaseFacade(de.symeda.sormas.api.caze.CaseFacade) Captions(de.symeda.sormas.api.i18n.Captions) Exposure(de.symeda.sormas.backend.exposure.Exposure) Treatment(de.symeda.sormas.backend.therapy.Treatment) CaseBulkEditData(de.symeda.sormas.api.caze.CaseBulkEditData) PrescriptionCriteria(de.symeda.sormas.api.therapy.PrescriptionCriteria) ContactService(de.symeda.sormas.backend.contact.ContactService) SampleDto(de.symeda.sormas.api.sample.SampleDto) Subquery(javax.persistence.criteria.Subquery) SymptomsFacadeEjb(de.symeda.sormas.backend.symptoms.SymptomsFacadeEjb) TravelEntry(de.symeda.sormas.backend.travelentry.TravelEntry) SurveillanceReport(de.symeda.sormas.backend.caze.surveillancereport.SurveillanceReport) SormasToSormasOriginInfo(de.symeda.sormas.backend.sormastosormas.origin.SormasToSormasOriginInfo) FeatureType(de.symeda.sormas.api.feature.FeatureType) TherapyFacadeEjb(de.symeda.sormas.backend.therapy.TherapyFacadeEjb) EventService(de.symeda.sormas.backend.event.EventService) PointOfEntryFacadeEjb(de.symeda.sormas.backend.infrastructure.pointofentry.PointOfEntryFacadeEjb) ApproximateAgeType(de.symeda.sormas.api.person.ApproximateAgeType) ClinicalVisitService(de.symeda.sormas.backend.clinicalcourse.ClinicalVisitService) AbstractDomainObject(de.symeda.sormas.backend.common.AbstractDomainObject) InfoProvider(de.symeda.sormas.api.utils.InfoProvider) LoggerFactory(org.slf4j.LoggerFactory) ExposureType(de.symeda.sormas.api.exposure.ExposureType) HealthConditionsMapper(de.symeda.sormas.backend.clinicalcourse.HealthConditionsMapper) CauseOfDeath(de.symeda.sormas.api.person.CauseOfDeath) CommunityFacadeEjbLocal(de.symeda.sormas.backend.infrastructure.community.CommunityFacadeEjb.CommunityFacadeEjbLocal) ExposureService(de.symeda.sormas.backend.exposure.ExposureService) ExternalShareInfoCountAndLatestDate(de.symeda.sormas.backend.share.ExternalShareInfoCountAndLatestDate) SormasToSormasCaseFacadeEjbLocal(de.symeda.sormas.backend.sormastosormas.entities.caze.SormasToSormasCaseFacadeEjb.SormasToSormasCaseFacadeEjbLocal) NotificationService(de.symeda.sormas.backend.common.NotificationService) TreatmentFacadeEjbLocal(de.symeda.sormas.backend.therapy.TreatmentFacadeEjb.TreatmentFacadeEjbLocal) UserRole(de.symeda.sormas.api.user.UserRole) Path(javax.persistence.criteria.Path) Contact(de.symeda.sormas.backend.contact.Contact) Stateless(javax.ejb.Stateless) PortHealthInfoFacadeEjb(de.symeda.sormas.backend.caze.porthealthinfo.PortHealthInfoFacadeEjb) DocumentService(de.symeda.sormas.backend.document.DocumentService) NotificationDeliveryFailedException(de.symeda.sormas.backend.common.messaging.NotificationDeliveryFailedException) CaseCriteria(de.symeda.sormas.api.caze.CaseCriteria) CaseDataDto(de.symeda.sormas.api.caze.CaseDataDto) Region(de.symeda.sormas.backend.infrastructure.region.Region) District(de.symeda.sormas.backend.infrastructure.district.District) AdditionalTest(de.symeda.sormas.backend.sample.AdditionalTest) SormasToSormasFacadeEjbLocal(de.symeda.sormas.backend.sormastosormas.SormasToSormasFacadeEjb.SormasToSormasFacadeEjbLocal) CommunityReferenceDto(de.symeda.sormas.api.infrastructure.community.CommunityReferenceDto) TaskType(de.symeda.sormas.api.task.TaskType) EventSummaryDetails(de.symeda.sormas.backend.event.EventSummaryDetails) List(java.util.List) MaternalHistoryFacadeEjb(de.symeda.sormas.backend.caze.maternalhistory.MaternalHistoryFacadeEjb) DistrictFacadeEjb(de.symeda.sormas.backend.infrastructure.district.DistrictFacadeEjb) DistrictDto(de.symeda.sormas.api.infrastructure.district.DistrictDto) Optional(java.util.Optional) EpiDataHelper(de.symeda.sormas.api.epidata.EpiDataHelper) Location(de.symeda.sormas.backend.location.Location) ValidationRuntimeException(de.symeda.sormas.api.utils.ValidationRuntimeException) ClinicalCourseFacadeEjb(de.symeda.sormas.backend.clinicalcourse.ClinicalCourseFacadeEjb) VaccinationFacadeEjb(de.symeda.sormas.backend.vaccination.VaccinationFacadeEjb) TaskService(de.symeda.sormas.backend.task.TaskService) HashMap(java.util.HashMap) PathogenTestFacadeEjbLocal(de.symeda.sormas.backend.sample.PathogenTestFacadeEjb.PathogenTestFacadeEjbLocal) SurveillanceReportDto(de.symeda.sormas.api.caze.surveillancereport.SurveillanceReportDto) CaseExportType(de.symeda.sormas.api.caze.CaseExportType) CollectionUtils(org.apache.commons.collections.CollectionUtils) IterableHelper(de.symeda.sormas.backend.util.IterableHelper) FacilityFacadeEjbLocal(de.symeda.sormas.backend.infrastructure.facility.FacilityFacadeEjb.FacilityFacadeEjbLocal) Symptoms(de.symeda.sormas.backend.symptoms.Symptoms) TreatmentService(de.symeda.sormas.backend.therapy.TreatmentService) Expression(javax.persistence.criteria.Expression) BurialInfoDto(de.symeda.sormas.api.caze.BurialInfoDto) SormasToSormasOriginInfoFacadeEjbLocal(de.symeda.sormas.backend.sormastosormas.origin.SormasToSormasOriginInfoFacadeEjb.SormasToSormasOriginInfoFacadeEjbLocal) ModelConstants(de.symeda.sormas.backend.util.ModelConstants) EpiDataService(de.symeda.sormas.backend.epidata.EpiDataService) CaseJoins(de.symeda.sormas.utils.CaseJoins) ClinicalVisit(de.symeda.sormas.backend.clinicalcourse.ClinicalVisit) EpiDataFacadeEjbLocal(de.symeda.sormas.backend.epidata.EpiDataFacadeEjb.EpiDataFacadeEjbLocal) Validations(de.symeda.sormas.api.i18n.Validations) ClinicalVisitFacadeEjbLocal(de.symeda.sormas.backend.clinicalcourse.ClinicalVisitFacadeEjb.ClinicalVisitFacadeEjbLocal) MessageSubject(de.symeda.sormas.backend.common.messaging.MessageSubject) Pair(de.symeda.sormas.api.utils.DataHelper.Pair) PathogenTestService(de.symeda.sormas.backend.sample.PathogenTestService) MapCaseDto(de.symeda.sormas.api.caze.MapCaseDto) RegionService(de.symeda.sormas.backend.infrastructure.region.RegionService) TimeUnit(java.util.concurrent.TimeUnit) Event(de.symeda.sormas.backend.event.Event) NotificationType(de.symeda.sormas.api.user.NotificationType) MessagingService(de.symeda.sormas.backend.common.messaging.MessagingService) Country(de.symeda.sormas.backend.infrastructure.country.Country) SormasToSormasShareInfo(de.symeda.sormas.backend.sormastosormas.share.shareinfo.SormasToSormasShareInfo) ClinicalCourseFacadeEjbLocal(de.symeda.sormas.backend.clinicalcourse.ClinicalCourseFacadeEjb.ClinicalCourseFacadeEjbLocal) Strings(de.symeda.sormas.api.i18n.Strings) ExternalSurveillanceToolGatewayFacadeEjbLocal(de.symeda.sormas.backend.externalsurveillancetool.ExternalSurveillanceToolGatewayFacadeEjb.ExternalSurveillanceToolGatewayFacadeEjbLocal) Collections(java.util.Collections) ClinicalCourseReferenceDto(de.symeda.sormas.api.clinicalcourse.ClinicalCourseReferenceDto) TreatmentDto(de.symeda.sormas.api.therapy.TreatmentDto) SymptomsDto(de.symeda.sormas.api.symptoms.SymptomsDto) Pseudonymizer(de.symeda.sormas.backend.util.Pseudonymizer) ImmunizationEntityHelper(de.symeda.sormas.backend.immunization.ImmunizationEntityHelper) Predicate(javax.persistence.criteria.Predicate) ArrayList(java.util.ArrayList) List(java.util.List) CriteriaBuilder(javax.persistence.criteria.CriteriaBuilder) Immunization(de.symeda.sormas.backend.immunization.entity.Immunization) MeansOfImmunization(de.symeda.sormas.api.immunization.MeansOfImmunization) Exposure(de.symeda.sormas.backend.exposure.Exposure) UserReference(de.symeda.sormas.backend.user.UserReference) EventSummaryDetails(de.symeda.sormas.backend.event.EventSummaryDetails) AtomicLong(java.util.concurrent.atomic.AtomicLong) PreviousHospitalization(de.symeda.sormas.backend.hospitalization.PreviousHospitalization) Person(de.symeda.sormas.backend.person.Person) EventParticipant(de.symeda.sormas.backend.event.EventParticipant) Symptoms(de.symeda.sormas.backend.symptoms.Symptoms) Visit(de.symeda.sormas.backend.visit.Visit) ClinicalVisit(de.symeda.sormas.backend.clinicalcourse.ClinicalVisit) Vaccination(de.symeda.sormas.backend.vaccination.Vaccination) VisitSummaryExportDetails(de.symeda.sormas.backend.contact.VisitSummaryExportDetails) EpiData(de.symeda.sormas.backend.epidata.EpiData) CaseJoins(de.symeda.sormas.utils.CaseJoins) CaseClassification(de.symeda.sormas.api.caze.CaseClassification) Sample(de.symeda.sormas.backend.sample.Sample) Hospitalization(de.symeda.sormas.backend.hospitalization.Hospitalization) PreviousHospitalization(de.symeda.sormas.backend.hospitalization.PreviousHospitalization) HealthConditions(de.symeda.sormas.backend.clinicalcourse.HealthConditions) CaseExportDto(de.symeda.sormas.api.caze.CaseExportDto) EmbeddedSampleExportDto(de.symeda.sormas.api.caze.EmbeddedSampleExportDto) Event(de.symeda.sormas.backend.event.Event) Location(de.symeda.sormas.backend.location.Location) TransactionAttribute(javax.ejb.TransactionAttribute)

Example 3 with Sample

use of de.symeda.sormas.backend.sample.Sample 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);
    });
}
Also used : AdditionalTest(de.symeda.sormas.backend.sample.AdditionalTest) Prescription(de.symeda.sormas.backend.therapy.Prescription) TravelEntry(de.symeda.sormas.backend.travelentry.TravelEntry) PrescriptionCriteria(de.symeda.sormas.api.therapy.PrescriptionCriteria) Task(de.symeda.sormas.backend.task.Task) SurveillanceReport(de.symeda.sormas.backend.caze.surveillancereport.SurveillanceReport) PersonReferenceDto(de.symeda.sormas.api.person.PersonReferenceDto) ClinicalVisitCriteria(de.symeda.sormas.api.clinicalcourse.ClinicalVisitCriteria) PathogenTestDto(de.symeda.sormas.api.sample.PathogenTestDto) Document(de.symeda.sormas.backend.document.Document) TreatmentDto(de.symeda.sormas.api.therapy.TreatmentDto) ContactCriteria(de.symeda.sormas.api.contact.ContactCriteria) ContactDto(de.symeda.sormas.api.contact.ContactDto) PrescriptionDto(de.symeda.sormas.api.therapy.PrescriptionDto) TreatmentCriteria(de.symeda.sormas.api.therapy.TreatmentCriteria) TaskCriteria(de.symeda.sormas.api.task.TaskCriteria) EpiData(de.symeda.sormas.backend.epidata.EpiData) ClinicalCourseReferenceDto(de.symeda.sormas.api.clinicalcourse.ClinicalCourseReferenceDto) PersonDto(de.symeda.sormas.api.person.PersonDto) CasePersonDto(de.symeda.sormas.api.caze.CasePersonDto) Sample(de.symeda.sormas.backend.sample.Sample) SampleCriteria(de.symeda.sormas.api.sample.SampleCriteria) TherapyReferenceDto(de.symeda.sormas.api.therapy.TherapyReferenceDto) Exposure(de.symeda.sormas.backend.exposure.Exposure) PathogenTest(de.symeda.sormas.backend.sample.PathogenTest) ClinicalVisit(de.symeda.sormas.backend.clinicalcourse.ClinicalVisit) Contact(de.symeda.sormas.backend.contact.Contact) Treatment(de.symeda.sormas.backend.therapy.Treatment) ClinicalVisitDto(de.symeda.sormas.api.clinicalcourse.ClinicalVisitDto) VisitDto(de.symeda.sormas.api.visit.VisitDto) ClinicalVisitDto(de.symeda.sormas.api.clinicalcourse.ClinicalVisitDto) SurveillanceReportDto(de.symeda.sormas.api.caze.surveillancereport.SurveillanceReportDto) SampleDto(de.symeda.sormas.api.sample.SampleDto) CaseReferenceDto(de.symeda.sormas.api.caze.CaseReferenceDto) EventParticipant(de.symeda.sormas.backend.event.EventParticipant) AdditionalTestDto(de.symeda.sormas.api.sample.AdditionalTestDto)

Example 4 with Sample

use of de.symeda.sormas.backend.sample.Sample in project SORMAS-Project by hzi-braunschweig.

the class CaseService method createUserFilter.

@SuppressWarnings("rawtypes")
public Predicate createUserFilter(CriteriaBuilder cb, CriteriaQuery cq, From<?, Case> casePath, CaseUserFilterCriteria userFilterCriteria) {
    User currentUser = getCurrentUser();
    if (currentUser == null) {
        return null;
    }
    Predicate filterResponsible = null;
    Predicate filter = null;
    final JurisdictionLevel jurisdictionLevel = currentUser.getCalculatedJurisdictionLevel();
    if (jurisdictionLevel != JurisdictionLevel.NATION && !currentUser.hasAnyUserRole(UserRole.REST_USER, UserRole.REST_EXTERNAL_VISITS_USER)) {
        // whoever created the case or is assigned to it is allowed to access it
        if (userFilterCriteria == null || (userFilterCriteria.getIncludeCasesFromOtherJurisdictions())) {
            filterResponsible = cb.equal(casePath.get(Case.REPORTING_USER).get(User.ID), currentUser.getId());
            filterResponsible = cb.or(filterResponsible, cb.equal(casePath.get(Case.SURVEILLANCE_OFFICER).get(User.ID), currentUser.getId()));
            filterResponsible = cb.or(filterResponsible, cb.equal(casePath.get(Case.CASE_OFFICER).get(User.ID), currentUser.getId()));
        }
        switch(jurisdictionLevel) {
            case REGION:
                final Region region = currentUser.getRegion();
                if (region != null) {
                    filter = CriteriaBuilderHelper.or(cb, filter, cb.equal(casePath.get(Case.REGION).get(Region.ID), region.getId()), cb.equal(casePath.get(Case.RESPONSIBLE_REGION).get(Region.ID), region.getId()));
                }
                break;
            case DISTRICT:
                final District district = currentUser.getDistrict();
                if (district != null) {
                    filter = CriteriaBuilderHelper.or(cb, filter, cb.equal(casePath.get(Case.DISTRICT).get(District.ID), district.getId()), cb.equal(casePath.get(Case.RESPONSIBLE_DISTRICT).get(District.ID), district.getId()));
                }
                break;
            case HEALTH_FACILITY:
                final Facility healthFacility = currentUser.getHealthFacility();
                if (healthFacility != null) {
                    filter = CriteriaBuilderHelper.or(cb, filter, cb.equal(casePath.get(Case.HEALTH_FACILITY).get(Facility.ID), healthFacility.getId()));
                }
                break;
            case COMMUNITY:
                final Community community = currentUser.getCommunity();
                if (community != null) {
                    filter = CriteriaBuilderHelper.or(cb, filter, cb.equal(casePath.get(Case.COMMUNITY).get(Community.ID), community.getId()), cb.equal(casePath.get(Case.RESPONSIBLE_COMMUNITY).get(Community.ID), community.getId()));
                }
                break;
            case POINT_OF_ENTRY:
                final PointOfEntry pointOfEntry = currentUser.getPointOfEntry();
                if (pointOfEntry != null) {
                    filter = CriteriaBuilderHelper.or(cb, filter, cb.equal(casePath.get(Case.POINT_OF_ENTRY).get(PointOfEntry.ID), pointOfEntry.getId()));
                }
                break;
            case LABORATORY:
                final Subquery<Long> sampleSubQuery = cq.subquery(Long.class);
                final Root<Sample> sampleRoot = sampleSubQuery.from(Sample.class);
                final SampleJoins joins = new SampleJoins(sampleRoot);
                final Join cazeJoin = joins.getCaze();
                sampleSubQuery.where(cb.and(cb.equal(cazeJoin, casePath), sampleService.createUserFilterWithoutAssociations(cb, joins)));
                sampleSubQuery.select(sampleRoot.get(Sample.ID));
                filter = CriteriaBuilderHelper.or(cb, filter, cb.exists(sampleSubQuery));
                break;
            default:
        }
        // get all cases based on the user's contact association
        if (userFilterCriteria == null || (!userFilterCriteria.isExcludeCasesFromContacts() && Boolean.TRUE.equals(userFilterCriteria.getIncludeCasesFromOtherJurisdictions()))) {
            filter = CriteriaBuilderHelper.or(cb, filter, contactService.createUserFilterWithoutCase(new ContactQueryContext(cb, cq, casePath.join(Case.CONTACTS, JoinType.LEFT))));
        }
        // all users (without specific restrictions) get access to cases that have been made available to the whole country
        if ((userFilterCriteria == null || userFilterCriteria.getIncludeCasesFromOtherJurisdictions()) && !featureConfigurationFacade.isFeatureDisabled(FeatureType.NATIONAL_CASE_SHARING)) {
            filter = CriteriaBuilderHelper.or(cb, filter, cb.isTrue(casePath.get(Case.SHARED_TO_COUNTRY)));
        }
    }
    // only show cases of a specific disease if a limited disease is set
    if (currentUser.getLimitedDisease() != null) {
        filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(casePath.get(Case.DISEASE), currentUser.getLimitedDisease()));
    }
    // port health users can only see port health cases
    if (UserRole.isPortHealthUser(currentUser.getUserRoles())) {
        filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(casePath.get(Case.CASE_ORIGIN), CaseOrigin.POINT_OF_ENTRY));
    }
    filter = CriteriaBuilderHelper.or(cb, filter, filterResponsible);
    return filter;
}
Also used : User(de.symeda.sormas.backend.user.User) Sample(de.symeda.sormas.backend.sample.Sample) ContactQueryContext(de.symeda.sormas.backend.contact.ContactQueryContext) JurisdictionLevel(de.symeda.sormas.api.user.JurisdictionLevel) Join(javax.persistence.criteria.Join) Predicate(javax.persistence.criteria.Predicate) Region(de.symeda.sormas.backend.infrastructure.region.Region) Facility(de.symeda.sormas.backend.infrastructure.facility.Facility) PointOfEntry(de.symeda.sormas.backend.infrastructure.pointofentry.PointOfEntry) District(de.symeda.sormas.backend.infrastructure.district.District) SampleJoins(de.symeda.sormas.backend.sample.SampleJoins) Community(de.symeda.sormas.backend.infrastructure.community.Community)

Example 5 with Sample

use of de.symeda.sormas.backend.sample.Sample in project SORMAS-Project by hzi-braunschweig.

the class CaseFacadeEjb method hasPositiveLabResult.

@Override
public boolean hasPositiveLabResult(String caseUuid) {
    final CriteriaBuilder criteriaBuilder = em.getCriteriaBuilder();
    final CriteriaQuery<Sample> query = criteriaBuilder.createQuery(Sample.class);
    final Root<Sample> sampleRoot = query.from(Sample.class);
    final Join<Sample, Case> caseJoin = sampleRoot.join(Sample.ASSOCIATED_CASE, JoinType.INNER);
    final Predicate casePredicate = criteriaBuilder.equal(caseJoin.get(AbstractDomainObject.UUID), caseUuid);
    final Predicate testPositivityPredicate = criteriaBuilder.equal(sampleRoot.get(Sample.PATHOGEN_TEST_RESULT), PathogenTestResultType.POSITIVE);
    return sampleService.exists((cb, root, cq) -> cb.and(casePredicate, testPositivityPredicate));
}
Also used : CriteriaBuilder(javax.persistence.criteria.CriteriaBuilder) Sample(de.symeda.sormas.backend.sample.Sample) Predicate(javax.persistence.criteria.Predicate)

Aggregations

Sample (de.symeda.sormas.backend.sample.Sample)27 CriteriaBuilder (javax.persistence.criteria.CriteriaBuilder)17 Predicate (javax.persistence.criteria.Predicate)17 Join (javax.persistence.criteria.Join)15 User (de.symeda.sormas.backend.user.User)13 Date (java.util.Date)12 Person (de.symeda.sormas.backend.person.Person)11 CriteriaQuery (javax.persistence.criteria.CriteriaQuery)11 Contact (de.symeda.sormas.backend.contact.Contact)10 SampleJoins (de.symeda.sormas.backend.sample.SampleJoins)10 Collections (java.util.Collections)10 List (java.util.List)10 Collectors (java.util.stream.Collectors)10 LocalBean (javax.ejb.LocalBean)10 Stateless (javax.ejb.Stateless)10 Expression (javax.persistence.criteria.Expression)10 Root (javax.persistence.criteria.Root)10 CriteriaBuilderHelper (de.symeda.sormas.backend.common.CriteriaBuilderHelper)9 EventParticipant (de.symeda.sormas.backend.event.EventParticipant)9 Community (de.symeda.sormas.backend.infrastructure.community.Community)9