Examples with UserService de.symeda.sormas.backend.user.UserService used on opensource projects

Example 1 with UserService

use of de.symeda.sormas.backend.user.UserService in project SORMAS-Project by hzi-braunschweig.

the class SampleFacadeEjb method getSimilarSamples.

@Override
public List<SampleDto> getSimilarSamples(SampleSimilarityCriteria criteria) {
    final CriteriaBuilder cb = em.getCriteriaBuilder();
    final CriteriaQuery<Sample> cq = cb.createQuery(Sample.class);
    final Root<Sample> root = cq.from(Sample.class);
    cq.distinct(true);
    SampleJoins<Sample> joins = new SampleJoins<>(root);
    SampleCriteria sampleCriteria = new SampleCriteria();
    sampleCriteria.caze(criteria.getCaze()).contact(criteria.getContact()).eventParticipant(criteria.getEventParticipant());
    Predicate filter = sampleService.createUserFilter(cq, cb, joins, sampleCriteria);
    filter = CriteriaBuilderHelper.and(cb, filter, sampleService.buildCriteriaFilter(sampleCriteria, cb, joins));
    Predicate similarityFilter = null;
    if (criteria.getLabSampleId() != null) {
        similarityFilter = cb.equal(root.get(Sample.LAB_SAMPLE_ID), criteria.getLabSampleId());
    }
    Date sampleDateTime = criteria.getSampleDateTime();
    SampleMaterial sampleMaterial = criteria.getSampleMaterial();
    if (sampleDateTime != null && sampleMaterial != null) {
        Predicate dateAndMaterialFilter = cb.and(cb.between(root.get(Sample.SAMPLE_DATE_TIME), DateHelper.getStartOfDay(DateHelper.subtractDays(sampleDateTime, SIMILARITY_DATE_TIME_THRESHOLD)), DateHelper.getEndOfDay(DateHelper.addDays(sampleDateTime, SIMILARITY_DATE_TIME_THRESHOLD))), cb.equal(root.get(Sample.SAMPLE_MATERIAL), sampleMaterial));
        similarityFilter = CriteriaBuilderHelper.or(cb, similarityFilter, dateAndMaterialFilter);
    }
    filter = CriteriaBuilderHelper.and(cb, filter, similarityFilter);
    if (filter != null) {
        cq.where(filter);
    }
    List<Sample> samples = em.createQuery(cq).getResultList();
    if (samples.size() == 0 && (sampleDateTime == null || sampleMaterial == null)) {
        return getByCriteria(sampleCriteria);
    }
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight);
    return samples.stream().map(s -> convertToDto(s, pseudonymizer)).collect(Collectors.toList());
}

Example 2 with UserService

use of de.symeda.sormas.backend.user.UserService in project SORMAS-Project by hzi-braunschweig.

the class SampleFacadeEjb method getByCriteria.

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

Example 3 with UserService

use of de.symeda.sormas.backend.user.UserService 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 4 with UserService

use of de.symeda.sormas.backend.user.UserService in project SORMAS-Project by hzi-braunschweig.

the class SurveillanceReportFacadeEjb method getIndexList.

@Override
public List<SurveillanceReportDto> getIndexList(SurveillanceReportCriteria criteria, Integer first, Integer max) {
    CriteriaBuilder cb = em.getCriteriaBuilder();
    CriteriaQuery<SurveillanceReport> cq = cb.createQuery(SurveillanceReport.class);
    Root<SurveillanceReport> root = cq.from(SurveillanceReport.class);
    Predicate filter = service.buildCriteriaFilter(criteria, cb, root);
    if (filter != null) {
        cq.where(filter);
    }
    cq.orderBy(cb.desc(root.get(SurveillanceReport.CREATION_DATE)));
    List<SurveillanceReport> resultList = QueryHelper.getResultList(em, cq, first, max);
    List<SurveillanceReportDto> reports = resultList.stream().map(SurveillanceReportFacadeEjb::toDto).collect(Collectors.toList());
    User currentUser = userService.getCurrentUser();
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight, I18nProperties.getCaption(Captions.inaccessibleValue));
    pseudonymizer.pseudonymizeDtoCollection(SurveillanceReportDto.class, reports, reportDto -> {
        Optional<SurveillanceReport> report = resultList.stream().filter(r -> r.getUuid().equals(r.getUuid())).findFirst();
        return report.isPresent() ? caseService.inJurisdictionOrOwned(report.get().getCaze()) : false;
    }, (reportDto, inJurisdiction) -> {
        Optional<SurveillanceReport> report = resultList.stream().filter(r -> r.getUuid().equals(r.getUuid())).findFirst();
        report.ifPresent(surveillanceReport -> pseudonymizer.pseudonymizeUser(surveillanceReport.getCreatingUser(), currentUser, reportDto::setCreatingUser));
    });
    return reports;
}

Example 5 with UserService

use of de.symeda.sormas.backend.user.UserService in project SORMAS-Project by hzi-braunschweig.

the class VisitFacadeEjb method getVisitsByContactAndPeriod.

@Override
public List<VisitDto> getVisitsByContactAndPeriod(ContactReferenceDto contactRef, Date begin, Date end) {
    Contact contact = contactService.getByReferenceDto(contactRef);
    Pseudonymizer pseudonymizer = Pseudonymizer.getDefault(userService::hasRight);
    return contact.getVisits().stream().filter(visit -> visit.getVisitDateTime().after(begin) && visit.getVisitDateTime().before(end)).map(visit -> convertToDto(visit, pseudonymizer)).collect(Collectors.toList());
}