Examples with Property org.hl7.fhir.r4.elementmodel.Property used on opensource projects

Example 6 with Property

use of org.hl7.fhir.r4.elementmodel.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);
}

Example 7 with Property

use of org.hl7.fhir.r4.elementmodel.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);
        }
    }
}

Example 8 with Property

use of org.hl7.fhir.r4.elementmodel.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);
        }
    }
}

Example 9 with Property

use of org.hl7.fhir.r4.elementmodel.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;
}

Example 10 with Property

use of org.hl7.fhir.r4.elementmodel.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;
}