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Example 1 with ProblemInfoBundleExtractor

use of org.hl7.gravity.refimpl.sdohexchange.fhir.extract.ProblemInfoBundleExtractor 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)

Aggregations

List (java.util.List)1 Map (java.util.Map)1 Optional (java.util.Optional)1 Function (java.util.function.Function)1 Collectors (java.util.stream.Collectors)1 Bundle (org.hl7.fhir.r4.model.Bundle)1 CodeableConcept (org.hl7.fhir.r4.model.CodeableConcept)1 Coding (org.hl7.fhir.r4.model.Coding)1 Condition (org.hl7.fhir.r4.model.Condition)1 Goal (org.hl7.fhir.r4.model.Goal)1 Reference (org.hl7.fhir.r4.model.Reference)1 ServiceRequest (org.hl7.fhir.r4.model.ServiceRequest)1 Task (org.hl7.fhir.r4.model.Task)1 GoalAchievement (org.hl7.fhir.r4.model.codesystems.GoalAchievement)1 CodingDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.CodingDto)1 ConditionDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.ConditionDto)1 GoalDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.GoalDto)1 ReferenceDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.ReferenceDto)1 TaskInfoDto (org.hl7.gravity.refimpl.sdohexchange.dto.response.TaskInfoDto)1 SDOHMappings (org.hl7.gravity.refimpl.sdohexchange.sdohmappings.SDOHMappings)1