Examples with AllergyIntolerance org.hl7.fhir.dstu3.model.AllergyIntolerance used on opensource projects

Example 1 with AllergyIntolerance

use of org.hl7.fhir.dstu3.model.AllergyIntolerance in project gpconnect-demonstrator by nhsconnect.

the class StructuredAllergyIntoleranceBuilder method listResourceBuilder.

private void listResourceBuilder(ListResource buildingListResource, AllergyIntolerance allergyIntolerance, boolean isResolved) {
    ListEntryComponent comp = new ListEntryComponent();
    if (isResolved) {
        buildingListResource.addContained(allergyIntolerance);
        Reference allergyReference = new Reference("#" + allergyIntolerance.getId());
        comp.setItem(allergyReference);
    } else {
        Reference allergyReference = new Reference("AllergyIntolerance/" + allergyIntolerance.getId());
        comp.setItem(allergyReference);
    }
    buildingListResource.addEntry(comp);
}

Example 2 with AllergyIntolerance

use of org.hl7.fhir.dstu3.model.AllergyIntolerance in project gpconnect-demonstrator by nhsconnect.

the class StructuredAllergyIntoleranceBuilder method buildStructuredAllergyIntolerence.

public Bundle buildStructuredAllergyIntolerence(String NHS, Set<String> practitionerIds, Bundle bundle, Boolean includedResolved) {
    List<StructuredAllergyIntoleranceEntity> allergyData = structuredAllergySearch.getAllergyIntollerence(NHS);
    ListResource activeList = initiateListResource(NHS, ACTIVE_ALLERGIES_DISPLAY, allergyData);
    ListResource resolvedList = initiateListResource(NHS, RESOLVED_ALLERGIES_DISPLAY, allergyData);
    // This is patient 5 example 2 only
    if (allergyData.size() == 1 && allergyData.get(0).getClinicalStatus().equals(SystemConstants.NO_KNOWN)) {
        StructuredAllergyIntoleranceEntity noKnownAllergy = allergyData.get(0);
        // #214 had incorrect code and value for no known allergies
        CodeableConcept noKnownAllergies = createCoding(SystemURL.VS_LIST_EMPTY_REASON_CODE, NO_CONTENT_RECORDED, NO_CONTENT_RECORDED_DISPLAY);
        noKnownAllergies.setText("No Known Allergies");
        // activeList.setEmptyReason(noKnownAllergies);
        // see spec example 2 no known allergies positively asserted
        Reference patient = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyData.get(0).getPatientRef());
        String noKnownAllergyId = noKnownAllergy.getGuid();
        Reference allergyIntolerance = new Reference("AllergyIntolerance/" + noKnownAllergyId);
        Resource noKnownAllergyResource = createNoKnownAllergy(noKnownAllergy);
        activeList.setSubject(patient);
        // reference to AllergyIntolerance item
        activeList.addEntry().setItem(allergyIntolerance);
        activeList.setOrderedBy(createCoding(SystemURL.CS_LIST_ORDER, "event-date", "Sorted by Event Date"));
        bundle.addEntry().setResource(activeList);
        bundle.addEntry().setResource(noKnownAllergyResource);
        if (includedResolved) {
            resolvedList.setSubject(patient);
            resolvedList.setEmptyReason(noKnownAllergies);
            bundle.addEntry().setResource(resolvedList);
        }
        return bundle;
    }
    for (StructuredAllergyIntoleranceEntity allergyIntoleranceEntity : allergyData) {
        AllergyIntolerance allergyIntolerance = new AllergyIntolerance();
        allergyIntolerance.setOnset(new DateTimeType(allergyIntoleranceEntity.getOnSetDateTime()));
        allergyIntolerance.setMeta(createMeta(SystemURL.SD_CC_ALLERGY_INTOLERANCE));
        allergyIntolerance.setId(allergyIntoleranceEntity.getId().toString());
        List<Identifier> identifiers = new ArrayList<>();
        Identifier identifier1 = new Identifier().setSystem("https://fhir.nhs.uk/Id/cross-care-setting-identifier").setValue(allergyIntoleranceEntity.getGuid());
        identifiers.add(identifier1);
        allergyIntolerance.setIdentifier(identifiers);
        if (allergyIntoleranceEntity.getClinicalStatus().equals(SystemConstants.ACTIVE)) {
            allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
        } else {
            allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.RESOLVED);
        }
        if (allergyIntoleranceEntity.getCategory().equals(SystemConstants.MEDICATION)) {
            allergyIntolerance.addCategory(AllergyIntoleranceCategory.MEDICATION);
        } else {
            allergyIntolerance.addCategory(AllergyIntoleranceCategory.ENVIRONMENT);
        }
        allergyIntolerance.setVerificationStatus(AllergyIntoleranceVerificationStatus.UNCONFIRMED);
        // CODE
        codeableConceptBuilder.addConceptCode(SystemConstants.SNOMED_URL, allergyIntoleranceEntity.getConceptCode(), allergyIntoleranceEntity.getConceptDisplay()).addDescription(allergyIntoleranceEntity.getDescCode(), allergyIntoleranceEntity.getDescDisplay()).addTranslation(allergyIntoleranceEntity.getCodeTranslationRef());
        allergyIntolerance.setCode(codeableConceptBuilder.build());
        codeableConceptBuilder.clear();
        allergyIntolerance.setAssertedDate(allergyIntoleranceEntity.getAssertedDate());
        Reference patient = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyIntoleranceEntity.getPatientRef());
        allergyIntolerance.setPatient(patient);
        Annotation noteAnnotation = new Annotation(new StringType(allergyIntoleranceEntity.getNote()));
        allergyIntolerance.setNote(Collections.singletonList(noteAnnotation));
        AllergyIntoleranceReactionComponent reaction = new AllergyIntoleranceReactionComponent();
        // MANIFESTATION
        List<CodeableConcept> theManifestation = new ArrayList<>();
        codeableConceptBuilder.addConceptCode(SystemConstants.SNOMED_URL, allergyIntoleranceEntity.getManifestationCoding(), allergyIntoleranceEntity.getManifestationDisplay()).addDescription(allergyIntoleranceEntity.getManifestationDescCoding(), allergyIntoleranceEntity.getManifestationDescDisplay()).addTranslation(allergyIntoleranceEntity.getManTranslationRef());
        theManifestation.add(codeableConceptBuilder.build());
        codeableConceptBuilder.clear();
        reaction.setManifestation(theManifestation);
        reaction.setDescription(allergyIntoleranceEntity.getNote());
        // SEVERITY
        try {
            reaction.setSeverity(AllergyIntoleranceSeverity.fromCode(allergyIntoleranceEntity.getSeverity()));
        } catch (FHIRException e) {
            throw OperationOutcomeFactory.buildOperationOutcomeException(new UnprocessableEntityException("Unknown severity: " + allergyIntoleranceEntity.getSeverity()), SystemCode.INVALID_RESOURCE, IssueType.INVALID);
        }
        // EXPOSURE
        CodeableConcept exposureRoute = new CodeableConcept();
        reaction.setExposureRoute(exposureRoute);
        allergyIntolerance.addReaction(reaction);
        // RECORDER
        final Reference refValue = new Reference();
        final Identifier identifier = new Identifier();
        final String recorder = allergyIntoleranceEntity.getRecorder();
        // This is just an example to demonstrate using Reference element instead of Identifier element
        if (recorder.equals(patient2NhsNo.trim())) {
            Reference rec = new Reference(SystemConstants.PATIENT_REFERENCE_URL + allergyIntoleranceEntity.getPatientRef());
            allergyIntolerance.setRecorder(rec);
        } else if (patientRepository.findByNhsNumber(recorder) != null) {
            identifier.setSystem(SystemURL.ID_NHS_NUMBER);
            identifier.setValue(recorder);
            refValue.setIdentifier(identifier);
            allergyIntolerance.setRecorder(refValue);
        } else if (practitionerSearch.findPractitionerByUserId(recorder) != null) {
            refValue.setReference("Practitioner/" + recorder);
            allergyIntolerance.setRecorder(refValue);
            practitionerIds.add(recorder);
        }
        // CLINICAL STATUS
        List<Extension> extensions = new ArrayList<>();
        if (allergyIntolerance.getClinicalStatus().getDisplay().contains("Active")) {
            listResourceBuilder(activeList, allergyIntolerance, false);
            bundle.addEntry().setResource(allergyIntolerance);
        } else if (allergyIntolerance.getClinicalStatus().getDisplay().equals("Resolved") && includedResolved.equals(true)) {
            listResourceBuilder(resolvedList, allergyIntolerance, true);
            allergyIntolerance.setLastOccurrence(allergyIntoleranceEntity.getEndDate());
            final Extension allergyEndExtension = createAllergyEndExtension(allergyIntoleranceEntity);
            extensions.add(allergyEndExtension);
        }
        if (!extensions.isEmpty()) {
            allergyIntolerance.setExtension(extensions);
        }
        // ASSERTER
        Reference asserter = allergyIntolerance.getAsserter();
        if (asserter != null && asserter.getReference() != null && asserter.getReference().startsWith("Practitioner")) {
            String[] split = asserter.getReference().split("/");
            practitionerIds.add(split[1]);
        }
    }
    if (!activeList.hasEntry()) {
        addEmptyListNote(activeList);
        addEmptyReasonCode(activeList);
    }
    bundle.addEntry().setResource(activeList);
    if (includedResolved && !resolvedList.hasEntry()) {
        addEmptyListNote(resolvedList);
        addEmptyReasonCode(resolvedList);
    }
    if (includedResolved) {
        bundle.addEntry().setResource(resolvedList);
    }
    return bundle;
}

Example 3 with AllergyIntolerance

use of org.hl7.fhir.dstu3.model.AllergyIntolerance in project gpconnect-demonstrator by nhsconnect.

the class StructuredAllergyIntoleranceBuilder method createNoKnownAllergy.

/**
 * This relates to the positively asserted this patient has no know
 * allergies as opposed to the the negatively asserted no allergies recorded
 * patient 5 example 2 from the spec
 *
 * @param allergyIntoleranceEntity object from the db
 * @return the allergy intolerance resource
 */
private AllergyIntolerance createNoKnownAllergy(StructuredAllergyIntoleranceEntity allergyIntoleranceEntity) {
    AllergyIntolerance allergyIntolerance = new AllergyIntolerance();
    allergyIntolerance.setId(allergyIntoleranceEntity.getGuid());
    allergyIntolerance.setAssertedDate(allergyIntoleranceEntity.getAssertedDate());
    // db has clinical status of "no known" which is not a valid value
    allergyIntolerance.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
    allergyIntolerance.setVerificationStatus(AllergyIntoleranceVerificationStatus.valueOf(allergyIntoleranceEntity.getVerificationStatus().toUpperCase()));
    allergyIntolerance.setType(AllergyIntoleranceType.ALLERGY);
    CodeableConcept codeableConcept = new CodeableConcept();
    Coding coding = new Coding();
    coding.setDisplay(allergyIntoleranceEntity.getConceptDisplay());
    // That's as in db under concept code 716186003
    coding.setCode(allergyIntoleranceEntity.getConceptCode());
    coding.setSystem(SystemConstants.SNOMED_URL);
    Extension extension = new Extension(SystemURL.SD_EXT_SCT_DESC_ID);
    // 3305010017
    extension.addExtension("descriptionId", new StringType(allergyIntoleranceEntity.getDescCode()));
    // NKA - No known allergy
    extension.addExtension("descriptionDisplay", new StringType(allergyIntoleranceEntity.getDescDisplay()));
    coding.addExtension(extension);
    codeableConcept.addCoding(coding);
    allergyIntolerance.setCode(codeableConcept);
    return allergyIntolerance;
}