Examples with CodeableConcept org.hl7.fhir.r5.model.CodeableConcept used on opensource projects

Example 16 with CodeableConcept

use of org.hl7.fhir.r5.model.CodeableConcept in project gpconnect-demonstrator by nhsconnect.

the class FhirSectionBuilder method buildFhirSection.

public static SectionComponent buildFhirSection(Page page) {
    Coding coding = new Coding().setSystem(SystemURL.VS_GPC_RECORD_SECTION).setCode(page.getCode()).setDisplay(page.getName());
    CodeableConcept codableConcept = new CodeableConcept().addCoding(coding);
    codableConcept.setText(page.getName());
    Narrative narrative = new Narrative();
    narrative.setStatus(NarrativeStatus.GENERATED);
    narrative.setDivAsString(createHtmlContent(page));
    SectionComponent sectionComponent = new SectionComponent();
    sectionComponent.setCode(codableConcept);
    sectionComponent.setTitle(page.getName()).setCode(codableConcept).setText(narrative);
    return sectionComponent;
}

Example 17 with CodeableConcept

use of org.hl7.fhir.r5.model.CodeableConcept in project gpconnect-demonstrator by nhsconnect.

the class PopulateSlotBundle method populateBundle.

/**
 * @param bundle Bundle resource to populate
 * @param operationOutcome
 * @param planningHorizonStart Date
 * @param planningHorizonEnd Date
 * @param actorPractitioner boolean
 * @param actorLocation boolean
 * @param managingOrganisation boolean
 * @param bookingOdsCode String
 * @param bookingOrgType String eg "urgent-care"
 */
public void populateBundle(Bundle bundle, OperationOutcome operationOutcome, Date planningHorizonStart, Date planningHorizonEnd, boolean actorPractitioner, boolean actorLocation, boolean managingOrganisation, String bookingOdsCode, String bookingOrgType) {
    bundle.getMeta().addProfile(SystemURL.SD_GPC_SRCHSET_BUNDLE);
    // TODO remove hard coding pick up from providerRouting.json ?
    final String OUR_ODS_CODE = "A20047";
    // find all locations for this ODS practice code and construct Resources for them
    // #144 generalise to handle 1..n locations for a practice
    HashMap<String, BundleEntryComponent> locationEntries = new HashMap<>();
    for (LocationDetails aLocationDetail : locationSearch.findAllLocations()) {
        if (aLocationDetail.getOrgOdsCode().equals(OUR_ODS_CODE)) {
            Location aLocationResource = locationResourceProvider.getLocationById(new IdType(aLocationDetail.getId()));
            BundleEntryComponent locationEntry = new BundleEntryComponent();
            locationEntry.setResource(aLocationResource);
            // #202 use full urls
            // #215 full url removed completely
            // locationEntry.setFullUrl(serverBaseUrl + "Location/" + aLocationResource.getIdElement().getIdPart());
            locationEntries.put(aLocationResource.getIdElement().getIdPart(), locationEntry);
        }
    }
    // find the provider organization from the ods code
    List<OrganizationDetails> ourOrganizationsDetails = organizationSearch.findOrganizationDetailsByOrgODSCode(OUR_ODS_CODE);
    OrganizationDetails ourOrganizationDetails = null;
    if (!ourOrganizationsDetails.isEmpty()) {
        // at 1.2.2 these are added regardless of the status of the relevant parameter
        // Just picks the first organization. There should only be one.
        ourOrganizationDetails = ourOrganizationsDetails.get(0);
    } else {
    // do something here .. should never happen
    }
    // find the bookng organization from the ods code
    List<OrganizationDetails> bookingOrganizationsDetails = organizationSearch.findOrganizationDetailsByOrgODSCode(bookingOdsCode);
    OrganizationDetails bookingOrganizationDetails = null;
    if (!bookingOrganizationsDetails.isEmpty()) {
        // at 1.2.2 these are added regardless of the status of the relevant parameter
        // Just picks the first organization. There should only be one.
        bookingOrganizationDetails = bookingOrganizationsDetails.get(0);
    }
    HashSet<BundleEntryComponent> addedSchedule = new HashSet<>();
    HashSet<BundleEntryComponent> addedLocation = new HashSet<>();
    HashSet<String> addedPractitioner = new HashSet<>();
    HashSet<String> addedOrganization = new HashSet<>();
    // issue #165 don't add duplicate slots, hashSet contains slot id as String
    HashSet<String> addedSlot = new HashSet<>();
    // #144 process all locations
    for (String locationId : locationEntries.keySet()) {
        // process the schedules
        for (Schedule schedule : scheduleResourceProvider.getSchedulesForLocationId(locationId, planningHorizonStart, planningHorizonEnd)) {
            boolean slotsAdded = false;
            schedule.getMeta().addProfile(SystemURL.SD_GPC_SCHEDULE);
            BundleEntryComponent scheduleEntry = new BundleEntryComponent();
            scheduleEntry.setResource(schedule);
            // #202 use full urls
            // #215 full url removed completely
            // scheduleEntry.setFullUrl(serverBaseUrl + "Schedule/" + schedule.getIdElement().getIdPart());
            // This Set does not work as expected because Slot does not implement hashCode
            // so the second set call to getSlots returns different objects with the same slot id
            Set<Slot> slots = new HashSet<>();
            // 
            if (bookingOrgType.isEmpty() && bookingOdsCode.isEmpty()) {
                // OPTION 1 get slots Specfying  neither org type nor org code
                slots.addAll(slotResourceProvider.getSlotsForScheduleIdNoOrganizationTypeOrODS(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd));
            } else if (!bookingOrgType.isEmpty() && bookingOdsCode.isEmpty()) {
                // OPTION 2 organisation type only
                for (Slot slot : slotResourceProvider.getSlotsForScheduleId(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd)) {
                    SlotDetail slotDetail = slotSearch.findSlotByID(Long.parseLong(slot.getId()));
                    if (slotDetail.getOrganizationIds().isEmpty() && (slotDetail.getOrganizationTypes().isEmpty() || slotDetail.getOrganizationTypes().contains(bookingOrgType))) {
                        slots.add(slot);
                    }
                }
            } else if (!bookingOdsCode.isEmpty() && bookingOrgType.isEmpty()) {
                // OPTION 3 org code only
                for (Slot slot : slotResourceProvider.getSlotsForScheduleId(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd)) {
                    SlotDetail slotDetail = slotSearch.findSlotByID(Long.parseLong(slot.getId()));
                    if (slotDetail.getOrganizationTypes().isEmpty() && (slotDetail.getOrganizationIds().isEmpty() || bookingOrganizationDetails != null && slotDetail.getOrganizationIds().contains(bookingOrganizationDetails.getId()))) {
                        slots.add(slot);
                    }
                }
            } else if (!bookingOrgType.isEmpty() && !bookingOdsCode.isEmpty()) {
                // OPTION 4 both org code and org type
                for (Slot slot : slotResourceProvider.getSlotsForScheduleId(schedule.getIdElement().getIdPart(), planningHorizonStart, planningHorizonEnd)) {
                    SlotDetail slotDetail = slotSearch.findSlotByID(Long.parseLong(slot.getId()));
                    if (((slotDetail.getOrganizationTypes().isEmpty() || slotDetail.getOrganizationTypes().contains(bookingOrgType))) && (slotDetail.getOrganizationIds().isEmpty() || bookingOrganizationDetails != null && slotDetail.getOrganizationIds().contains(bookingOrganizationDetails.getId()))) {
                        slots.add(slot);
                    }
                }
            }
            // added at 1.2.2 add the organisation but only if there are some slots available
            if (slots.size() > 0 && ourOrganizationDetails != null && !addedOrganization.contains(ourOrganizationDetails.getOrgCode())) {
                addOrganisation(ourOrganizationDetails, bundle);
                addedOrganization.add(ourOrganizationDetails.getOrgCode());
            }
            String freeBusyType = "FREE";
            // process all the slots to be returned
            for (Slot slot : slots) {
                if (freeBusyType.equalsIgnoreCase(slot.getStatus().toString())) {
                    String slotId = slot.getIdElement().getIdPart();
                    if (!addedSlot.contains(slotId)) {
                        BundleEntryComponent slotEntry = new BundleEntryComponent();
                        slotEntry.setResource(slot);
                        // #202 use full urls
                        // #215 full url removed completely
                        // slotEntry.setFullUrl(serverBaseUrl + "Slot/" + slotId);
                        bundle.addEntry(slotEntry);
                        addedSlot.add(slotId);
                        slotsAdded = true;
                    }
                    if (!addedSchedule.contains(scheduleEntry)) {
                        // only add a schedule if there's a reference to it and only add it once
                        bundle.addEntry(scheduleEntry);
                        addedSchedule.add(scheduleEntry);
                    }
                    if (actorLocation == true) {
                        // only add a unique location once
                        if (!addedLocation.contains(locationEntries.get(locationId))) {
                            bundle.addEntry(locationEntries.get(locationId));
                            addedLocation.add(locationEntries.get(locationId));
                        }
                    }
                }
            // if free/busy status matches
            }
            // # 193 for each schedule only add a practitioner if there have been some slots added.
            if (slotsAdded) {
                // practitioners for this schedule
                List<Reference> practitionerActors = scheduleResourceProvider.getPractitionerReferences(schedule);
                if (!practitionerActors.isEmpty()) {
                    for (Reference practitionerActor : practitionerActors) {
                        Practitioner practitioner = practitionerResourceProvider.getPractitionerById((IdType) practitionerActor.getReferenceElement());
                        if (practitioner == null) {
                            Coding errorCoding = new Coding().setSystem(SystemURL.VS_GPC_ERROR_WARNING_CODE).setCode(SystemCode.REFERENCE_NOT_FOUND);
                            CodeableConcept errorCodableConcept = new CodeableConcept().addCoding(errorCoding);
                            errorCodableConcept.setText("Invalid Reference");
                            operationOutcome.addIssue().setSeverity(IssueSeverity.ERROR).setCode(IssueType.NOTFOUND).setDetails(errorCodableConcept);
                            throw new ResourceNotFoundException("Practitioner Reference returning null");
                        }
                        if (actorPractitioner) {
                            if (!addedPractitioner.contains(practitioner.getIdElement().getIdPart())) {
                                addPractitioner(practitioner, bundle);
                                addedPractitioner.add(practitioner.getIdElement().getIdPart());
                            }
                        }
                    }
                // for practitioner
                }
            // if non empty practitioner list
            }
        // if slots added
        }
    // for schedules
    }
// for location
}

Example 18 with CodeableConcept

use of org.hl7.fhir.r5.model.CodeableConcept 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 19 with CodeableConcept

use of org.hl7.fhir.r5.model.CodeableConcept 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;
}

Example 20 with CodeableConcept

use of org.hl7.fhir.r5.model.CodeableConcept in project gpconnect-demonstrator by nhsconnect.

the class PopulateMedicationBundle method createListEntry.

private ListResource createListEntry(List<MedicationStatementDetail> medicationStatements, String nhsNumber) {
    ListResource medicationStatementsList = new ListResource();
    // #179 dont populate List.id
    // medicationStatementsList.setId(new IdType(1));
    medicationStatementsList.setMeta(new Meta().addProfile(SystemURL.SD_GPC_LIST));
    medicationStatementsList.setStatus(ListStatus.CURRENT);
    // #179 dont populate List.id
    // medicationStatementsList.setId(new IdDt(1));
    medicationStatementsList.setMode(ListMode.SNAPSHOT);
    medicationStatementsList.setTitle(SystemConstants.MEDICATION_LIST);
    medicationStatementsList.setCode(new CodeableConcept().addCoding(new Coding(SystemURL.VS_SNOMED, "933361000000108", MEDICATION_LIST)));
    medicationStatementsList.setSubject(new Reference(new IdType("Patient", 1L)).setIdentifier(new Identifier().setValue(nhsNumber).setSystem(SystemURL.ID_NHS_NUMBER)));
    medicationStatementsList.setDate(new Date());
    medicationStatementsList.setOrderedBy(new CodeableConcept().addCoding(new Coding(SystemURL.CS_LIST_ORDER, "event-date", "Sorted by Event Date")));
    medicationStatementsList.addExtension(setClinicalSetting());
    if (medicationStatements.isEmpty()) {
        medicationStatementsList.setEmptyReason(new CodeableConcept().setText(SystemConstants.NO_CONTENT));
        medicationStatementsList.setNote(Arrays.asList(new Annotation(new StringType(SystemConstants.INFORMATION_NOT_AVAILABLE))));
    }
    Set<String> warningCodes = new HashSet<>();
    medicationStatements.forEach(statement -> {
        Reference statementRef = new Reference(new IdType("MedicationStatement", statement.getId()));
        ListEntryComponent listEntryComponent = new ListEntryComponent(statementRef);
        medicationStatementsList.addEntry(listEntryComponent);
        if (statement.getWarningCode() != null) {
            warningCodes.add(statement.getWarningCode());
        }
    });
    WarningCodeExtHelper.addWarningCodeExtensions(warningCodes, medicationStatementsList, patientRepository, medicationStatementRepository, structuredAllergySearch);
    return medicationStatementsList;
}