use of org.hl7.fhir.dstu3.model.Property in project openmrs-module-fhir2 by openmrs.
the class FhirObservationDaoImpl method getSearchResultUuids.
@Override
public List<String> getSearchResultUuids(@Nonnull SearchParameterMap theParams) {
if (!theParams.getParameters(FhirConstants.LASTN_OBSERVATION_SEARCH_HANDLER).isEmpty()) {
Criteria criteria = getSessionFactory().getCurrentSession().createCriteria(typeToken.getRawType());
setupSearchParams(criteria, theParams);
criteria.setProjection(Projections.projectionList().add(property("uuid")).add(property("concept")).add(property("obsDatetime")));
@SuppressWarnings("unchecked") List<LastnResult> results = ((List<Object[]>) criteria.list()).stream().map(objects -> {
Map<String, Object> attributes = new HashMap<>();
attributes.put("concept", objects[1]);
return new LastnResult(objects[0], objects[2], attributes);
}).collect(Collectors.toList());
return getLastnUuids(handleGrouping(results), getMaxParameter(theParams)).stream().distinct().collect(Collectors.toList());
}
if (!theParams.getParameters(FhirConstants.LASTN_ENCOUNTERS_SEARCH_HANDLER).isEmpty()) {
ReferenceAndListParam encountersReferences = new ReferenceAndListParam();
ReferenceOrListParam referenceOrListParam = new ReferenceOrListParam();
List<String> encounters = encounterDao.getSearchResultUuids(theParams);
encounters.forEach(encounter -> referenceOrListParam.addOr(new ReferenceParam().setValue(encounter)));
encountersReferences.addAnd(referenceOrListParam);
theParams.addParameter(FhirConstants.ENCOUNTER_REFERENCE_SEARCH_HANDLER, encountersReferences);
}
return super.getSearchResultUuids(theParams);
}
use of org.hl7.fhir.dstu3.model.Property in project Gravity-SDOH-Exchange-RI by FHIR.
the class TaskPollingService method handleFinishedTask.
protected void handleFinishedTask(Bundle resultBundle, Task ehrTask, ServiceRequest ehrServiceRequest, Task cpTask, Endpoint endpoint) {
if (Task.TaskStatus.COMPLETED.equals(cpTask.getStatus())) {
ehrServiceRequest.setStatus(ServiceRequest.ServiceRequestStatus.COMPLETED);
resultBundle.addEntry(FhirUtil.createPutEntry(ehrServiceRequest));
}
// property.
if (Task.TaskStatus.COMPLETED.equals(cpTask.getStatus()) || Task.TaskStatus.CANCELLED.equals(cpTask.getStatus())) {
// Modify Task.output. If task output is of type resulting-activity and contains a Reference to a proper
// Procedure - copy output changing a Procedure reference to a local one.
List<TaskOutputComponent> cpOutputs = cpTask.getOutput().stream().filter(t -> t.getValue() instanceof CodeableConcept || (t.getValue() instanceof Reference && ((Reference) t.getValue()).getReferenceElement().getResourceType().equals(Procedure.class.getSimpleName()))).collect(Collectors.toList());
if (cpOutputs.size() == 0) {
log.warn("Not output of type 'http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/sdohcc-temporary-codes|resulting" + "-activity' with a reference to a proper Procedure is present in task with id '{}' at '{}'. " + "Expecting a reference to a Procedure resource.", cpTask.getIdElement().getIdPart(), endpoint.getAddress());
}
Map<String, Procedure> cpProcedureMap = getCpProcedures(cpOutputs, endpoint);
for (Task.TaskOutputComponent cpOutput : cpOutputs) {
Task.TaskOutputComponent ehrTaskOutput = cpOutput.copy();
if (cpOutput.getValue() instanceof Reference) {
Reference cpProcedureReference = (Reference) cpOutput.getValue();
String cpProcedureId = cpProcedureReference.getReferenceElement().getIdPart();
Procedure cpProcedure = cpProcedureMap.get(cpProcedureId);
// All Procedures have the same reason reference as ServiceRequest
Procedure resultProcedure = copyProcedure(cpProcedure, ehrTask.getFor(), ehrTask.getFocus(), ehrServiceRequest.getReasonReference());
resultProcedure.setId(IdType.newRandomUuid());
resultProcedure.addIdentifier().setSystem(endpoint.getAddress()).setValue(cpProcedureId);
// Add Procedure to result bundle
resultBundle.addEntry(FhirUtil.createPostEntry(resultProcedure));
ehrTaskOutput.setValue(FhirUtil.toReference(Procedure.class, resultProcedure.getIdElement().getIdPart(), cpProcedureReference.getDisplay()));
}
ehrTask.addOutput(ehrTaskOutput);
}
}
}
use of org.hl7.fhir.dstu3.model.Property in project Gravity-SDOH-Exchange-RI by FHIR.
the class OurTaskPollingService method handleFinishedTask.
protected void handleFinishedTask(Bundle resultBundle, Task task, ServiceRequest serviceRequest, Task ourTask) {
boolean isFinished = false;
if (TaskStatus.COMPLETED.equals(ourTask.getStatus())) {
serviceRequest.setStatus(ServiceRequest.ServiceRequestStatus.COMPLETED);
resultBundle.addEntry(FhirUtil.createPutEntry(serviceRequest));
isFinished = true;
} else if (TaskStatus.CANCELLED.equals(ourTask.getStatus()) || TaskStatus.REJECTED.equals(ourTask.getStatus()) || TaskStatus.FAILED.equals(ourTask.getStatus())) {
serviceRequest.setStatus(ServiceRequest.ServiceRequestStatus.REVOKED);
resultBundle.addEntry(FhirUtil.createPutEntry(serviceRequest));
isFinished = true;
}
// property.
if (isFinished) {
// Modify Task.output. If task output is of type resulting-activity and contains a Reference to a proper
// Procedure - copy output changing a Procedure reference to a local one.
List<TaskOutputComponent> ourTaskOutputs = ourTask.getOutput().stream().filter(t -> t.getValue() instanceof CodeableConcept || (t.getValue() instanceof Reference && ((Reference) t.getValue()).getReferenceElement().getResourceType().equals(Procedure.class.getSimpleName()))).collect(Collectors.toList());
if (ourTaskOutputs.size() == 0) {
log.warn("No output of type 'http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/sdohcc-temporary-codes|resulting" + "-activity' with a reference to a proper Procedure is present in task with id '{}'. " + "Expecting a reference to a Procedure resource.", ourTask.getIdElement().getIdPart());
}
Map<String, Procedure> ourProcedureMap = getOurTaskProcedures(ourTaskOutputs);
for (TaskOutputComponent ourTaskOutput : ourTaskOutputs) {
TaskOutputComponent taskOutput = ourTaskOutput.copy();
if (ourTaskOutput.getValue() instanceof Reference) {
Reference ourProcedureReference = (Reference) ourTaskOutput.getValue();
String ourProcedureId = ourProcedureReference.getReferenceElement().getIdPart();
Procedure ourProcedure = ourProcedureMap.get(ourProcedureId);
// All Procedures have the same reason reference as ServiceRequest
Procedure resultProcedure = copyProcedure(ourProcedure, task.getFor(), task.getFocus(), serviceRequest.getReasonReference());
resultProcedure.setId(IdType.newRandomUuid());
// TODO add identifier
// resultProcedure.addIdentifier()
// .setSystem(SERVER_BASE)
// .setValue(ourProcedureId);
// Add Procedure to result bundle
resultBundle.addEntry(FhirUtil.createPostEntry(resultProcedure));
taskOutput.setValue(FhirUtil.toReference(Procedure.class, resultProcedure.getIdElement().getIdPart(), ourProcedureReference.getDisplay()));
}
task.addOutput(taskOutput);
}
}
}
use of org.hl7.fhir.dstu3.model.Property in project Gravity-SDOH-Exchange-RI by FHIR.
the class ConditionBundleToDtoConverterBase method conditionInfoToDto.
protected T conditionInfoToDto(ConditionInfoBundleExtractor.ConditionInfoHolder conditionInfo) {
T conditionDto = newConditionDtoImpl();
Condition condition = conditionInfo.getCondition();
conditionDto.setId(condition.getIdElement().getIdPart());
conditionDto.setName(codeableConceptToStringConverter.convert(condition.getCode()));
Coding categoryCoding = FhirUtil.findCoding(condition.getCategory(), SDOHMappings.getInstance().getSystem());
// TODO remove this in future. Fow now two different categories might be used before discussed.
if (categoryCoding == null) {
categoryCoding = FhirUtil.findCoding(condition.getCategory(), "http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/SDOHCC-CodeSystemTemporaryCodes");
}
if (categoryCoding == null) {
conditionDto.getErrors().add("SDOH category is not found.");
} else {
conditionDto.setCategory(new CodingDto(categoryCoding.getCode(), categoryCoding.getDisplay()));
}
Optional<Coding> icdCodeCodingOptional = findCode(condition.getCode(), System.ICD_10);
if (icdCodeCodingOptional.isPresent()) {
Coding icdCodeCoding = icdCodeCodingOptional.get();
conditionDto.setIcdCode(new CodingDto(icdCodeCoding.getCode(), icdCodeCoding.getDisplay()));
} else {
conditionDto.getErrors().add("ICD-10 code is not found.");
}
Optional<Coding> snomedCodeCodingOptional = findCode(condition.getCode(), System.SNOMED);
if (snomedCodeCodingOptional.isPresent()) {
Coding snomedCodeCoding = snomedCodeCodingOptional.get();
conditionDto.setSnomedCode(new CodingDto(snomedCodeCoding.getCode(), snomedCodeCoding.getDisplay()));
} else {
conditionDto.getErrors().add("SNOMED-CT code is not found.");
}
QuestionnaireResponse questionnaireResponse = conditionInfo.getQuestionnaireResponse();
if (questionnaireResponse != null) {
conditionDto.setAssessmentDate(FhirUtil.toLocalDateTime(questionnaireResponse.getAuthoredElement()));
Questionnaire questionnaire = conditionInfo.getQuestionnaire();
if (questionnaire != null) {
conditionDto.setBasedOn(new ReferenceDto(questionnaireResponse.getIdElement().getIdPart(), questionnaire.getTitle()));
} else {
conditionDto.setBasedOn(new ReferenceDto(questionnaireResponse.getIdElement().getIdPart(), questionnaireResponse.getQuestionnaire()));
conditionDto.getErrors().add("Based on QuestionnaireResponse doesn't have a matching Questionnaire to get a title from. Using URL " + "instead.");
}
} else {
conditionDto.setBasedOn(new StringTypeDto(condition.getEvidenceFirstRep().getCodeFirstRep().getText()));
Reference recorder = condition.getRecorder();
conditionDto.setAuthoredBy(new ReferenceDto(recorder.getReferenceElement().getIdPart(), recorder.getDisplay()));
}
// abatement must be available for all resolved condition
if (ConditionClinicalStatusCodes.RESOLVED.toCode().equals(condition.getClinicalStatus().getCodingFirstRep().getCode())) {
if (condition.getAbatement() instanceof DateTimeType) {
conditionDto.setResolutionDate(FhirUtil.toLocalDateTime((DateTimeType) condition.getAbatement()));
} else {
conditionDto.getErrors().add("Condition is resolved but an abatement property is missing or not of a DateTimeType type.");
}
}
return conditionDto;
}
use of org.hl7.fhir.dstu3.model.Property in project Gravity-SDOH-Exchange-RI by FHIR.
the class GoalBundleToDtoConverter method convert.
@Override
public List<GoalDto> convert(Bundle bundle) {
List<GoalDto> result = FhirUtil.getFromBundle(bundle, Goal.class).stream().map(goal -> {
GoalDto goalDto = new GoalDto();
goalDto.setId(goal.getIdElement().getIdPart());
if (goal.hasDescription() && goal.getDescription().hasText()) {
goalDto.setName(goal.getDescription().getText());
} else {
goalDto.getErrors().add("Goal description.text not found. Name cannot be set.");
}
if (goal.hasAchievementStatus()) {
goalDto.setAchievementStatus(GoalAchievement.fromCode(goal.getAchievementStatus().getCodingFirstRep().getCode()));
} else {
goalDto.getErrors().add("No achievement status available.");
}
// TODO reused from HealthConcernBundleToDtoConverter class. Refactor!
Coding categoryCoding = FhirUtil.findCoding(goal.getCategory(), SDOHMappings.getInstance().getSystem());
// TODO remove this in future. Fow now two different categories might be used before discussed.
if (categoryCoding == null) {
categoryCoding = FhirUtil.findCoding(goal.getCategory(), "http://hl7.org/fhir/us/sdoh-clinicalcare/CodeSystem/SDOHCC-CodeSystemTemporaryCodes");
}
if (categoryCoding == null) {
goalDto.getErrors().add("SDOH category is not found.");
} else {
goalDto.setCategory(new CodingDto(categoryCoding.getCode(), categoryCoding.getDisplay()));
}
Optional<Coding> snomedCodeCodingOptional = findCode(goal.getDescription(), System.SNOMED);
if (snomedCodeCodingOptional.isPresent()) {
Coding snomedCodeCoding = snomedCodeCodingOptional.get();
goalDto.setSnomedCode(new CodingDto(snomedCodeCoding.getCode(), snomedCodeCoding.getDisplay()));
} else {
goalDto.getErrors().add("SNOMED-CT code is not found.");
}
if (goal.hasExpressedBy()) {
Reference expressedBy = goal.getExpressedBy();
goalDto.setAddedBy(new ReferenceDto(expressedBy.getReferenceElement().getIdPart(), expressedBy.getDisplay()));
} else {
goalDto.getErrors().add("Goal expressedBy property is missing. addedBy will be null.");
}
goalDto.setStartDate(FhirUtil.toLocalDate(goal.getStartDateType()));
// TODO this is invalid. To clarify!
if (goal.getLifecycleStatus() == Goal.GoalLifecycleStatus.COMPLETED) {
if (goal.hasStatusDate()) {
goalDto.setEndDate(FhirUtil.toLocalDate(goal.getStatusDateElement()));
} else {
goalDto.getErrors().add("Goal statusDate must be set when the lifecycleStatus is COMPLETED. endDate will be null.");
}
}
goalDto.setComments(goal.getNote().stream().map(annotationToDtoConverter::convert).collect(Collectors.toList()));
goalDto.setProblems(goal.getAddresses().stream().filter(ref -> Condition.class.getSimpleName().equals(ref.getReferenceElement().getResourceType())).map(ref -> (Condition) ref.getResource()).map(cond -> new ConditionDto(cond.getIdElement().getIdPart(), codeableConceptToStringConverter.convert(cond.getCode()))).collect(Collectors.toList()));
return goalDto;
}).collect(Collectors.toList());
// TODO refactor. method too long.
// TODO refactor. Almost the same fragmen exists in a ProblemInfoBundleExtractor
Map<String, GoalDto> idToDtoMap = result.stream().collect(Collectors.toMap(g -> g.getId(), Function.identity()));
for (Task task : FhirUtil.getFromBundle(bundle, Task.class)) {
if (!task.hasFocus() || !(task.getFocus().getResource() instanceof ServiceRequest)) {
continue;
}
ServiceRequest sr = (ServiceRequest) task.getFocus().getResource();
sr.getSupportingInfo().stream().filter(ref -> Goal.class.getSimpleName().equals(ref.getReferenceElement().getResourceType()) && idToDtoMap.containsKey(ref.getReferenceElement().getIdPart())).forEach(ref -> idToDtoMap.get(ref.getReferenceElement().getIdPart()).getTasks().add(new TaskInfoDto(task.getIdElement().getIdPart(), task.getDescription(), task.getStatus())));
}
return result;
}
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