Examples with StructuredAllergyIntoleranceEntity uk.gov.hscic.patient.structuredAllergyIntolerance.StructuredAllergyIntoleranceEntity used on opensource projects

Example 1 with StructuredAllergyIntoleranceEntity

use of uk.gov.hscic.patient.structuredAllergyIntolerance.StructuredAllergyIntoleranceEntity in project gpconnect-demonstrator by nhsconnect.

the class WarningCodeExtHelper method addWarningCodeExtensions.

/**
 * confidential items are per record but the other two are global values per
 * patient
 *
 * @param warningCodes
 * @param list
 * @param patientRepository
 * @param medicationStatementRepository
 * @param structuredAllergySearch
 */
public static void addWarningCodeExtensions(Set<String> warningCodes, ListResource list, PatientRepository patientRepository, MedicationStatementRepository medicationStatementRepository, StructuredAllergySearch structuredAllergySearch) {
    String NHS = list.getSubject().getIdentifier().getValue();
    PatientEntity patientEntity = patientRepository.findByNhsNumber(NHS);
    List<MedicationStatementEntity> medicationStatements = medicationStatementRepository.findByPatientId(patientEntity.getId());
    for (MedicationStatementEntity medicationStatement : medicationStatements) {
        setFlags(medicationStatement.getWarningCode());
    }
    List<StructuredAllergyIntoleranceEntity> allergies = structuredAllergySearch.getAllergyIntollerence(NHS);
    for (StructuredAllergyIntoleranceEntity allergy : allergies) {
        setFlags(allergy.getWarningCode());
    }
    // check medication_statements for either of the global flags
    if (dataInTransit) {
        warningCodes.add(DATA_IN_TRANSIT);
    }
    if (dataAwaitingFiling) {
        warningCodes.add(DATA_AWAITING_FILING);
    }
    StringBuilder sb = new StringBuilder();
    warningCodes.forEach(warningCode -> {
        if (warningCode != null) {
            String warningCodeDisplay = "";
            Annotation annotation = new Annotation();
            switch(warningCode) {
                case CONFIDENTIAL_ITEMS:
                    warningCodeDisplay = "Confidential Items";
                    // #266
                    annotation.setText(CONFIDENTIAL_ITEMS_NOTE);
                    // list.addNote(annotation);
                    sb.append("\r\n").append(annotation.getText());
                    break;
                case DATA_IN_TRANSIT:
                    warningCodeDisplay = "Data in Transit";
                    Calendar cal = new GregorianCalendar();
                    Date now = new Date();
                    cal.setTime(now);
                    // a week before now
                    cal.add(Calendar.DAY_OF_YEAR, -7);
                    // #266
                    annotation.setText(String.format(DATA_IN_TRANSIT_NOTE, DATE_FORMAT.format(cal.getTime())));
                    // list.addNote(annotation);
                    sb.append("\r\n").append(annotation.getText());
                    break;
                case DATA_AWAITING_FILING:
                    warningCodeDisplay = "Data Awaiting Filing";
                    // #266
                    annotation.setText(DATA_AWAITING_FILING_NOTE);
                    // list.addNote(annotation);
                    sb.append("\r\n").append(annotation.getText());
                    break;
                default:
                    break;
            }
            // #182
            Extension warningExt = new Extension(SystemURL.WARNING_CODE, new CodeType(warningCode));
            list.addExtension(warningExt);
        }
    });
    // cardinality of note 0..1 #266
    if (sb.length() > 0) {
        Annotation annotation = null;
        if (list.getNote().size() > 0) {
            annotation = list.getNote().get(0);
            annotation.setText(annotation.getText());
            annotation.setText(annotation.getText() + sb.toString());
        } else {
            annotation = new Annotation();
            list.addNote(annotation);
            annotation.setText(sb.toString().replaceFirst("^\r\n", ""));
        }
    }
}

Example 2 with StructuredAllergyIntoleranceEntity

use of uk.gov.hscic.patient.structuredAllergyIntolerance.StructuredAllergyIntoleranceEntity 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 StructuredAllergyIntoleranceEntity

use of uk.gov.hscic.patient.structuredAllergyIntolerance.StructuredAllergyIntoleranceEntity in project gpconnect-demonstrator by nhsconnect.

the class StructuredAllergyIntoleranceBuilder method setClinicalSetting.

private Extension setClinicalSetting(List<StructuredAllergyIntoleranceEntity> allergyIntoleranceEntity) {
    String warningCode = null;
    for (StructuredAllergyIntoleranceEntity structuredAllergyIntoleranceEntity : allergyIntoleranceEntity) {
        warningCode = structuredAllergyIntoleranceEntity.getWarningCode();
    }
    CodeableConcept codeableConcept = new CodeableConcept();
    Coding coding = new Coding(SystemConstants.SNOMED_URL, "1060971000000108", "General practice service");
    codeableConcept.setCoding(Collections.singletonList(coding));
    return warningCode != null ? new Extension(SystemURL.CLINICAL_SETTING, codeableConcept) : null;
}