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Example 1 with ConditionDto

use of org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto 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;
}
Also used : Condition(org.hl7.fhir.r4.model.Condition) CodingDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.CodingDto) ReferenceDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ReferenceDto) DateTimeType(org.hl7.fhir.r4.model.DateTimeType) Questionnaire(org.hl7.fhir.r4.model.Questionnaire) StringTypeDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.StringTypeDto) Coding(org.hl7.fhir.r4.model.Coding) Reference(org.hl7.fhir.r4.model.Reference) QuestionnaireResponse(org.hl7.fhir.r4.model.QuestionnaireResponse)

Example 2 with ConditionDto

use of org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto 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;
}
Also used : Converter(org.springframework.core.convert.converter.Converter) GoalDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.GoalDto) Goal(org.hl7.fhir.r4.model.Goal) ReferenceDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ReferenceDto) CodeableConcept(org.hl7.fhir.r4.model.CodeableConcept) Condition(org.hl7.fhir.r4.model.Condition) Reference(org.hl7.fhir.r4.model.Reference) Function(java.util.function.Function) Collectors(java.util.stream.Collectors) Task(org.hl7.fhir.r4.model.Task) CodingDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.CodingDto) List(java.util.List) GoalAchievement(org.hl7.fhir.r4.model.codesystems.GoalAchievement) TaskInfoDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.TaskInfoDto) Coding(org.hl7.fhir.r4.model.Coding) Map(java.util.Map) Optional(java.util.Optional) Bundle(org.hl7.fhir.r4.model.Bundle) ConditionDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto) System(org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System) SDOHMappings(org.hl7.gravity.refimpl.sdohexchange.sdohmappings.SDOHMappings) ServiceRequest(org.hl7.fhir.r4.model.ServiceRequest) FhirUtil(org.hl7.gravity.refimpl.sdohexchange.util.FhirUtil) Condition(org.hl7.fhir.r4.model.Condition) GoalDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.GoalDto) ReferenceDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ReferenceDto) Task(org.hl7.fhir.r4.model.Task) Optional(java.util.Optional) Reference(org.hl7.fhir.r4.model.Reference) TaskInfoDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.TaskInfoDto) ServiceRequest(org.hl7.fhir.r4.model.ServiceRequest) CodingDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.CodingDto) Goal(org.hl7.fhir.r4.model.Goal) Coding(org.hl7.fhir.r4.model.Coding) ConditionDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto)

Example 3 with ConditionDto

use of org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto in project Gravity-SDOH-Exchange-RI by FHIR.

the class SupportService method listProblems.

public List<ConditionDto> listProblems() {
    Assert.notNull(SmartOnFhirContext.get().getPatient(), "Patient id cannot be null.");
    Bundle conditionsBundle = ehrClient.search().forResource(Condition.class).sort().descending(Constants.PARAM_LASTUPDATED).where(Condition.PATIENT.hasId(SmartOnFhirContext.get().getPatient())).where(new StringClientParam(Constants.PARAM_PROFILE).matches().value(SDOHProfiles.CONDITION)).where(Condition.CLINICAL_STATUS.exactly().code(ConditionClinicalStatusCodes.ACTIVE.toCode())).where(Condition.CATEGORY.exactly().systemAndCode(UsCoreConditionCategory.PROBLEMLISTITEM.getSystem(), UsCoreConditionCategory.PROBLEMLISTITEM.toCode())).returnBundle(Bundle.class).execute();
    return FhirUtil.getFromBundle(conditionsBundle, Condition.class).stream().map(condition -> new ConditionToDtoConverter().convert(condition)).collect(Collectors.toList());
}
Also used : Condition(org.hl7.fhir.r4.model.Condition) Constants(ca.uhn.fhir.rest.api.Constants) RequiredArgsConstructor(lombok.RequiredArgsConstructor) Autowired(org.springframework.beans.factory.annotation.Autowired) Condition(org.hl7.fhir.r4.model.Condition) UsCoreConditionCategory(org.hl7.gravity.refimpl.sdohexchange.fhir.UsCoreConditionCategory) IBaseBundle(org.hl7.fhir.instance.model.api.IBaseBundle) GoalToInfoDtoConverter(org.hl7.gravity.refimpl.sdohexchange.dto.converter.GoalToInfoDtoConverter) Task(org.hl7.fhir.r5.model.Task) TaskQueryFactory(org.hl7.gravity.refimpl.sdohexchange.fhir.query.TaskQueryFactory) Strings(com.google.common.base.Strings) GoalInfoDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.GoalInfoDto) Service(org.springframework.stereotype.Service) GoalQueryFactory(org.hl7.gravity.refimpl.sdohexchange.fhir.query.GoalQueryFactory) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) StringClientParam(ca.uhn.fhir.rest.gclient.StringClientParam) HealthcareServiceBundleToDtoConverter(org.hl7.gravity.refimpl.sdohexchange.dto.converter.HealthcareServiceBundleToDtoConverter) SDOHProfiles(org.hl7.gravity.refimpl.sdohexchange.fhir.SDOHProfiles) HealthConcernQueryFactory(org.hl7.gravity.refimpl.sdohexchange.fhir.query.HealthConcernQueryFactory) HealthcareServiceDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.HealthcareServiceDto) OrganizationDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.OrganizationDto) OrganizationToDtoConverter(org.hl7.gravity.refimpl.sdohexchange.dto.converter.OrganizationToDtoConverter) Goal(org.hl7.fhir.r4.model.Goal) IQuery(ca.uhn.fhir.rest.gclient.IQuery) ConditionClinicalStatusCodes(org.hl7.gravity.refimpl.sdohexchange.fhir.ConditionClinicalStatusCodes) ReferenceDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ReferenceDto) ActiveResourcesDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ActiveResourcesDto) Collectors(java.util.stream.Collectors) Organization(org.hl7.fhir.r4.model.Organization) List(java.util.List) SmartOnFhirContext(com.healthlx.smartonfhir.core.SmartOnFhirContext) HealthcareService(org.hl7.fhir.r4.model.HealthcareService) ConditionToDtoConverter(org.hl7.gravity.refimpl.sdohexchange.dto.converter.ConditionToDtoConverter) Bundle(org.hl7.fhir.r4.model.Bundle) ConditionDto(org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto) OrganizationTypeCode(org.hl7.gravity.refimpl.sdohexchange.codes.OrganizationTypeCode) ProblemQueryFactory(org.hl7.gravity.refimpl.sdohexchange.fhir.query.ProblemQueryFactory) Questionnaire(org.hl7.fhir.r4.model.Questionnaire) FhirUtil(org.hl7.gravity.refimpl.sdohexchange.util.FhirUtil) Assert(org.springframework.util.Assert) StringClientParam(ca.uhn.fhir.rest.gclient.StringClientParam) IBaseBundle(org.hl7.fhir.instance.model.api.IBaseBundle) Bundle(org.hl7.fhir.r4.model.Bundle) ConditionToDtoConverter(org.hl7.gravity.refimpl.sdohexchange.dto.converter.ConditionToDtoConverter)

Aggregations

Condition (org.hl7.fhir.r4.model.Condition)3 ReferenceDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.ReferenceDto)3 List (java.util.List)2 Collectors (java.util.stream.Collectors)2 Bundle (org.hl7.fhir.r4.model.Bundle)2 Coding (org.hl7.fhir.r4.model.Coding)2 Goal (org.hl7.fhir.r4.model.Goal)2 Questionnaire (org.hl7.fhir.r4.model.Questionnaire)2 Reference (org.hl7.fhir.r4.model.Reference)2 CodingDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.CodingDto)2 ConditionDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto)2 FhirUtil (org.hl7.gravity.refimpl.sdohexchange.util.FhirUtil)2 Constants (ca.uhn.fhir.rest.api.Constants)1 IGenericClient (ca.uhn.fhir.rest.client.api.IGenericClient)1 IQuery (ca.uhn.fhir.rest.gclient.IQuery)1 StringClientParam (ca.uhn.fhir.rest.gclient.StringClientParam)1 Strings (com.google.common.base.Strings)1 SmartOnFhirContext (com.healthlx.smartonfhir.core.SmartOnFhirContext)1 Map (java.util.Map)1 Optional (java.util.Optional)1