use of de.symeda.sormas.api.caze.CaseClassification in project SORMAS-Project by hzi-braunschweig.
the class PersonFacadeEjb method savePersonWithoutNotifyingExternalJournal.
/**
* Saves the received person.
* This method always checks if the given source person data is outdated
* The approximate age reference date is calculated and set on the person object to be saved. In case the case classification was
* changed by saving the person,
* If the person is enrolled in the external journal, the relevant data is validated,but the external journal is not notified. The task
* of notifying the external journals falls to the caller of this method.
* Also, in case the case classification was changed, the new classification will be returned.
*
* @param source
* the person dto object to be saved
* @return a pair of objects containing:
* - the new case classification or null if it was not changed
* - the old person data from the database
* @throws ValidationRuntimeException
* if the passed source person to be saved contains invalid data
*/
@TransactionAttribute(TransactionAttributeType.REQUIRES_NEW)
public Pair<CaseClassification, PersonDto> savePersonWithoutNotifyingExternalJournal(@Valid PersonDto source) throws ValidationRuntimeException {
Person existingPerson = personService.getByUuid(source.getUuid());
PersonDto existingPersonDto = toDto(existingPerson);
List<CaseDataDto> personCases = caseFacade.getAllCasesOfPerson(source.getUuid());
computeApproximateAgeReferenceDate(existingPersonDto, source);
restorePseudonymizedDto(source, existingPerson, existingPersonDto);
validate(source);
if (existingPersonDto != null && existingPersonDto.isEnrolledInExternalJournal()) {
externalJournalService.validateExternalJournalPerson(source);
}
existingPerson = fillOrBuildEntity(source, existingPerson, true);
personService.ensurePersisted(existingPerson);
onPersonChanged(existingPersonDto, existingPerson);
CaseClassification newClassification = getNewCaseClassification(personCases);
return Pair.createPair(newClassification, existingPersonDto);
}
use of de.symeda.sormas.api.caze.CaseClassification 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;
}
use of de.symeda.sormas.api.caze.CaseClassification in project SORMAS-Project by hzi-braunschweig.
the class CaseFacadeEjb method onCaseSampleChanged.
public void onCaseSampleChanged(Case associatedCase) {
// Update case classification if the feature is enabled
if (configFacade.isFeatureAutomaticCaseClassification()) {
if (associatedCase.getCaseClassification() != CaseClassification.NO_CASE) {
Long pathogenTestsCount = pathogenTestService.countByCase(associatedCase);
if (pathogenTestsCount == 0) {
return;
}
// calculate classification
CaseDataDto newCaseDto = toDto(associatedCase);
CaseClassification classification = caseClassificationFacade.getClassification(newCaseDto);
// only update when classification by system changes - user may overwrite this
if (classification != associatedCase.getSystemCaseClassification()) {
associatedCase.setSystemCaseClassification(classification);
// really a change? (user may have already set it)
if (classification != associatedCase.getCaseClassification()) {
associatedCase.setCaseClassification(classification);
associatedCase.setClassificationUser(null);
associatedCase.setClassificationDate(new Date());
}
}
}
}
}
use of de.symeda.sormas.api.caze.CaseClassification in project SORMAS-Project by hzi-braunschweig.
the class CaseFacadeEjb method onCaseChanged.
public void onCaseChanged(CaseDataDto existingCase, Case newCase, boolean syncShares) {
// If its a new case and the case is new and the geo coordinates of the case's
// health facility are null, set its coordinates to the case's report
// coordinates, if available. Else if case report coordinates are null set them
// to the facility's coordinates
Facility facility = newCase.getHealthFacility();
if (existingCase == null && facility != null && !FacilityHelper.isOtherOrNoneHealthFacility(facility.getUuid())) {
if ((facility.getLatitude() == null || facility.getLongitude() == null) && newCase.getReportLat() != null && newCase.getReportLon() != null) {
facility.setLatitude(newCase.getReportLat());
facility.setLongitude(newCase.getReportLon());
facilityService.ensurePersisted(facility);
} else if (newCase.getReportLat() == null && newCase.getReportLon() == null && newCase.getReportLatLonAccuracy() == null) {
newCase.setReportLat(facility.getLatitude());
newCase.setReportLon(facility.getLongitude());
}
}
// Clear facility type if no facility or home was selected
if (newCase.getHealthFacility() == null || FacilityDto.NONE_FACILITY_UUID.equals(newCase.getHealthFacility().getUuid())) {
newCase.setFacilityType(null);
}
// Generate epid number if missing or incomplete
FieldVisibilityCheckers fieldVisibilityCheckers = FieldVisibilityCheckers.withCountry(configFacade.getCountryLocale());
if (fieldVisibilityCheckers.isVisible(CaseDataDto.class, CaseDataDto.EPID_NUMBER) && !CaseLogic.isCompleteEpidNumber(newCase.getEpidNumber())) {
newCase.setEpidNumber(generateEpidNumber(newCase.getEpidNumber(), newCase.getUuid(), newCase.getDisease(), newCase.getReportDate(), newCase.getResponsibleDistrict().getUuid()));
}
// update the plague type based on symptoms
if (newCase.getDisease() == Disease.PLAGUE) {
PlagueType plagueType = DiseaseHelper.getPlagueTypeForSymptoms(SymptomsFacadeEjb.toDto(newCase.getSymptoms()));
if (plagueType != newCase.getPlagueType() && plagueType != null) {
newCase.setPlagueType(plagueType);
}
}
District survOffDistrict = newCase.getSurveillanceOfficer() != null ? newCase.getSurveillanceOfficer().getDistrict() : null;
if (survOffDistrict == null || (!survOffDistrict.equals(newCase.getResponsibleDistrict()) && !survOffDistrict.equals(newCase.getDistrict()))) {
setResponsibleSurveillanceOfficer(newCase);
}
updateInvestigationByStatus(existingCase, newCase);
updatePersonAndCaseByOutcome(existingCase, newCase);
updateCaseAge(existingCase, newCase);
// Change the disease of all contacts if the case disease or disease details have changed
if (existingCase != null && (newCase.getDisease() != existingCase.getDisease() || !StringUtils.equals(newCase.getDiseaseDetails(), existingCase.getDiseaseDetails()))) {
for (Contact contact : contactService.findBy(new ContactCriteria().caze(newCase.toReference()), null)) {
if (contact.getDisease() != newCase.getDisease() || !StringUtils.equals(contact.getDiseaseDetails(), newCase.getDiseaseDetails())) {
// Only do the change if it hasn't been done in the mobile app before
contact.setDisease(newCase.getDisease());
contact.setDiseaseDetails(newCase.getDiseaseDetails());
contactService.ensurePersisted(contact);
}
}
}
if (existingCase != null && (newCase.getDisease() != existingCase.getDisease() || !Objects.equals(newCase.getReportDate(), existingCase.getReportDate()) || !Objects.equals(newCase.getSymptoms().getOnsetDate(), existingCase.getSymptoms().getOnsetDate()))) {
// Update follow-up until and status of all contacts
for (Contact contact : contactService.findBy(new ContactCriteria().caze(newCase.toReference()), null)) {
contactService.updateFollowUpDetails(contact, false);
contactService.udpateContactStatus(contact);
}
for (Contact contact : contactService.getAllByResultingCase(newCase)) {
contactService.updateFollowUpDetails(contact, false);
contactService.udpateContactStatus(contact);
}
}
updateTasksOnCaseChanged(newCase, existingCase);
// Update case classification if the feature is enabled
CaseClassification classification = null;
if (configFacade.isFeatureAutomaticCaseClassification()) {
if (newCase.getCaseClassification() != CaseClassification.NO_CASE) {
// calculate classification
CaseDataDto newCaseDto = toDto(newCase);
classification = caseClassificationFacade.getClassification(newCaseDto);
// only update when classification by system changes - user may overwrite this
if (classification != newCase.getSystemCaseClassification()) {
newCase.setSystemCaseClassification(classification);
// really a change? (user may have already set it)
if (classification != newCase.getCaseClassification()) {
newCase.setCaseClassification(classification);
newCase.setClassificationUser(null);
newCase.setClassificationDate(new Date());
}
}
}
}
// calculate reference definition for cases
if (configFacade.isConfiguredCountry(CountryHelper.COUNTRY_CODE_GERMANY)) {
boolean fulfilled = evaluateFulfilledCondition(toDto(newCase), classification);
newCase.setCaseReferenceDefinition(fulfilled ? CaseReferenceDefinition.FULFILLED : CaseReferenceDefinition.NOT_FULFILLED);
}
// are not empty
if (!newCase.getHospitalization().getPreviousHospitalizations().isEmpty() && YesNoUnknown.YES != newCase.getHospitalization().getHospitalizedPreviously()) {
newCase.getHospitalization().setHospitalizedPreviously(YesNoUnknown.YES);
}
if (!newCase.getEpiData().getExposures().isEmpty() && !YesNoUnknown.YES.equals(newCase.getEpiData().getExposureDetailsKnown())) {
newCase.getEpiData().setExposureDetailsKnown(YesNoUnknown.YES);
}
// Update completeness value
newCase.setCompleteness(null);
// changed
if (existingCase != null && existingCase.getCaseClassification() != newCase.getCaseClassification()) {
try {
String message = String.format(I18nProperties.getString(MessageContents.CONTENT_CASE_CLASSIFICATION_CHANGED), DataHelper.getShortUuid(newCase.getUuid()), newCase.getCaseClassification().toString());
notificationService.sendNotifications(NotificationType.CASE_CLASSIFICATION_CHANGED, JurisdictionHelper.getCaseRegions(newCase), null, MessageSubject.CASE_CLASSIFICATION_CHANGED, message);
} catch (NotificationDeliveryFailedException e) {
logger.error("NotificationDeliveryFailedException when trying to notify supervisors about the change of a case classification. ");
}
}
// Unspecified VHF case has changed
if (existingCase != null && existingCase.getDisease() == Disease.UNSPECIFIED_VHF && existingCase.getDisease() != newCase.getDisease()) {
try {
String message = String.format(I18nProperties.getString(MessageContents.CONTENT_DISEASE_CHANGED), DataHelper.getShortUuid(newCase.getUuid()), existingCase.getDisease().toString(), newCase.getDisease().toString());
notificationService.sendNotifications(NotificationType.DISEASE_CHANGED, JurisdictionHelper.getCaseRegions(newCase), null, MessageSubject.DISEASE_CHANGED, message);
} catch (NotificationDeliveryFailedException e) {
logger.error("NotificationDeliveryFailedException when trying to notify supervisors about the change of a case disease.");
}
}
// If the case is a newly created case or if it was not in a CONFIRMED status
// and now the case is in a CONFIRMED status, notify related surveillance officers
Set<CaseClassification> confirmedClassifications = CaseClassification.getConfirmedClassifications();
if ((existingCase == null || !confirmedClassifications.contains(existingCase.getCaseClassification())) && confirmedClassifications.contains(newCase.getCaseClassification())) {
sendConfirmedCaseNotificationsForEvents(newCase);
}
if (existingCase != null && syncShares && sormasToSormasFacade.isFeatureConfigured()) {
syncSharesAsync(new ShareTreeCriteria(existingCase.getUuid()));
}
// This logic should be consistent with CaseDataForm.onQuarantineEndChange
if (existingCase != null && existingCase.getQuarantineTo() != null && !existingCase.getQuarantineTo().equals(newCase.getQuarantineTo())) {
newCase.setPreviousQuarantineTo(existingCase.getQuarantineTo());
}
if (existingCase == null) {
vaccinationFacade.updateVaccinationStatuses(newCase);
}
// On German systems, correct and clean up reinfection data
if (configFacade.isConfiguredCountry(CountryHelper.COUNTRY_CODE_GERMANY)) {
newCase.setReinfectionDetails(cleanUpReinfectionDetails(newCase.getReinfectionDetails()));
newCase.setReinfectionStatus(CaseLogic.calculateReinfectionStatus(newCase.getReinfectionDetails()));
}
}
use of de.symeda.sormas.api.caze.CaseClassification in project SORMAS-Project by hzi-braunschweig.
the class TestEntityCreator method createCase.
public static Case createCase(Person person) {
Disease disease = Disease.EVD;
Region region = DatabaseHelper.getRegionDao().queryUuid(TestHelper.REGION_UUID);
District district = DatabaseHelper.getDistrictDao().queryUuid(TestHelper.DISTRICT_UUID);
Community community = DatabaseHelper.getCommunityDao().queryUuid(TestHelper.COMMUNITY_UUID);
Facility facility = DatabaseHelper.getFacilityDao().queryUuid(TestHelper.FACILITY_UUID);
CaseClassification caseClassification = CaseClassification.SUSPECT;
InvestigationStatus investigationStatus = InvestigationStatus.PENDING;
Case caze = DatabaseHelper.getCaseDao().build(person);
caze.setDisease(disease);
caze.setResponsibleRegion(region);
caze.setResponsibleDistrict(district);
caze.setResponsibleCommunity(community);
caze.setHealthFacility(facility);
caze.setFacilityType(FacilityType.HOSPITAL);
caze.setCaseClassification(caseClassification);
caze.setInvestigationStatus(investigationStatus);
caze.setReportDate(new Date());
try {
DatabaseHelper.getCaseDao().saveAndSnapshot(caze);
DatabaseHelper.getCaseDao().accept(caze);
} catch (DaoException e) {
throw new RuntimeException(e);
}
return DatabaseHelper.getCaseDao().queryForIdWithEmbedded(caze.getId());
}
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