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octoshikarioctoshikari
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chore: progress with profile generation
1 parent 774c4ba commit 602075d

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Lines changed: 25817 additions & 1032 deletions

‎atomic-codegen.config.js‎

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@@ -14,7 +14,7 @@ export default defineConfig({
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typescript: {
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includeDocuments: true,
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namingConvention: "PascalCase",
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includeProfiles: false,
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includeProfiles: true,
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includeExtensions: false,
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generateIndex: true,
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strictMode: true,

‎examples/typescript-us-core/.gitignore‎

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fhir-types

‎examples/typescript-us-core/demo.ts‎

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/**
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* FHIR R4 Resource Creation Demo
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*
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* This file demonstrates how to:
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* 1. Create a Patient resource
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* 2. Create an Observation resource
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* 3. Create a body weight observation with profiles
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* 4. Use attach and extract functions for FHIR profiles
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* 5. Bundle them together in a FHIR Bundle
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*/
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import type { Bundle, BundleEntry } from "./fhir-types/hl7-fhir-r4-core/Bundle";
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import type { CodeableConcept } from "./fhir-types/hl7-fhir-r4-core/CodeableConcept";
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import type { Coding } from "./fhir-types/hl7-fhir-r4-core/Coding";
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import type { Observation, ObservationReferenceRange } from "./fhir-types/hl7-fhir-r4-core/Observation";
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import type { Address, ContactPoint, HumanName, Identifier, Patient } from "./fhir-types/hl7-fhir-r4-core/Patient";
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import type { Quantity } from "./fhir-types/hl7-fhir-r4-core/Quantity";
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import type { Reference } from "./fhir-types/hl7-fhir-r4-core/Reference";
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function createPatient(): Patient {
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const identifier: Identifier = {
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system: "http://hospital.example.org/identifiers/patient",
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value: "12345",
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use: "official",
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};
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const name: HumanName = {
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family: "Smith",
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given: ["John", "Jacob"],
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use: "official",
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prefix: ["Mr."],
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};
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const telecom: ContactPoint[] = [
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{
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system: "phone",
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value: "555-555-5555",
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use: "home",
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},
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{
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system: "email",
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value: "john.smith@example.com",
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use: "work",
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},
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];
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const address: Address = {
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line: ["123 Main St"],
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city: "Anytown",
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state: "CA",
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postalCode: "12345",
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country: "USA",
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use: "home",
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};
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const patient: Patient = {
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resourceType: "Patient",
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id: "pt-1",
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identifier: [identifier],
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active: true,
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name: [name],
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telecom: telecom,
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gender: "male",
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birthDate: "1974-12-25",
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address: [address],
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};
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return patient;
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}
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function createObservation(patientId: string): Observation {
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const glucoseCoding: Coding = {
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system: "http://loinc.org",
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code: "15074-8",
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display: "Glucose [Moles/volume] in Blood",
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};
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const glucoseConcept: CodeableConcept = {
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coding: [glucoseCoding],
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text: "Blood glucose measurement",
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};
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const referenceRange: ObservationReferenceRange = {
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low: {
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value: 3.1,
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unit: "mmol/L",
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system: "http://unitsofmeasure.org",
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code: "mmol/L",
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},
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high: {
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value: 6.2,
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unit: "mmol/L",
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system: "http://unitsofmeasure.org",
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code: "mmol/L",
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},
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text: "3.1 to 6.2 mmol/L",
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};
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const glucoseValue: Quantity = {
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value: 6.3,
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unit: "mmol/L",
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system: "http://unitsofmeasure.org",
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code: "mmol/L",
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};
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const patientReference: Reference<"Patient"> = {
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reference: `Patient/${patientId}`,
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display: "John Smith",
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};
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const observation: Observation = {
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resourceType: "Observation",
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id: "glucose-obs-1",
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status: "final",
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category: [
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{
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coding: [
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{
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system: "http://terminology.hl7.org/CodeSystem/observation-category",
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code: "laboratory",
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display: "Laboratory",
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},
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],
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text: "Laboratory",
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},
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],
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code: glucoseConcept,
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subject: patientReference,
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effectiveDateTime: "2023-03-15T09:30:00Z",
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issued: "2023-03-15T10:15:00Z",
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valueQuantity: glucoseValue,
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referenceRange: [referenceRange],
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};
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return observation;
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}
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function createBodyWeightObservation(patientId: string): Observation {
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const baseObservation: Observation = {
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resourceType: "Observation",
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id: "example-genetics-1",
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status: "final",
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code: {
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coding: [
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{
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code: "29463-7",
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system: "http://loinc.org",
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display: "Body weight",
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},
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],
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},
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};
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const bodyweightProfile: observation_bodyweight = {
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__profileUrl: "http://hl7.org/fhir/StructureDefinition/bodyweight",
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status: baseObservation.status,
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category: [
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{
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coding: [
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{
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system: "http://terminology.hl7.org/CodeSystem/observation-category",
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code: "vital-signs",
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display: "Vital Signs",
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},
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],
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text: "Vital Signs",
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},
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],
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code: {
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coding: [
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{
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code: "29463-7",
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system: "http://loinc.org",
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display: "Body weight",
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},
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],
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},
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subject: {
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reference: `Patient/${patientId}`,
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display: "John Smith",
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},
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effectiveDateTime: "2023-03-15T09:30:00Z",
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valueQuantity: {
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value: 75.5,
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unit: "kg",
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system: "http://unitsofmeasure.org",
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code: "kg",
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},
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};
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console.log("Original observation:", JSON.stringify(baseObservation, null, 2));
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console.log("Body weight observation:", JSON.stringify(bodyweightProfile, null, 2));
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const bodyweightObservation = attach_observation_bodyweight_to_Observation(baseObservation, bodyweightProfile);
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console.log("Body weight observation with profile:", JSON.stringify(bodyweightObservation, null, 2));
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console.log("Validate bodyweight observation with attached profile");
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const isStatusCorrect = bodyweightObservation.status === "final";
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const isCodeCorrect =
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bodyweightObservation.code?.coding?.[0]?.code === "29463-7" &&
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bodyweightObservation.code?.coding?.[0]?.system === "http://loinc.org";
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const hasValueQuantity = bodyweightObservation.valueQuantity !== undefined;
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const isValueQuantityCorrect =
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bodyweightObservation.valueQuantity?.value === 75.5 &&
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bodyweightObservation.valueQuantity?.unit === "kg" &&
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bodyweightObservation.valueQuantity?.system === "http://unitsofmeasure.org";
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console.log("✓ Status is 'final':", isStatusCorrect);
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console.log("✓ Code is LOINC 29463-7 (Body weight):", isCodeCorrect);
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console.log("✓ Has valueQuantity:", hasValueQuantity);
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console.log("✓ ValueQuantity is correct (75.5 kg):", isValueQuantityCorrect);
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if (!isStatusCorrect || !isCodeCorrect || !hasValueQuantity || !isValueQuantityCorrect)
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throw new Error("Bodyweight observation is not valid");
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const extractedProfile = extract_observation_bodyweight_from_Observation(bodyweightObservation);
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console.log("Extracted bodyweight profile:", JSON.stringify(extractedProfile, null, 2));
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console.log("\n--- Validation: extractedProfile correctness ---");
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const isProfileUrlCorrect = extractedProfile.__profileUrl === "http://hl7.org/fhir/StructureDefinition/bodyweight";
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const isExtractedStatusCorrect = extractedProfile.status === "final";
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const isExtractedCodeCorrect = extractedProfile.code?.coding?.[0]?.code === "29463-7";
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const isExtractedValueCorrect =
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extractedProfile.valueQuantity?.value === 75.5 && extractedProfile.valueQuantity?.unit === "kg";
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const profilesMatch = JSON.stringify(bodyweightProfile) === JSON.stringify(extractedProfile);
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console.log("✓ Profile URL is correct:", isProfileUrlCorrect);
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console.log("✓ Extracted status matches:", isExtractedStatusCorrect);
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console.log("✓ Extracted code matches:", isExtractedCodeCorrect);
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console.log("✓ Extracted value matches:", isExtractedValueCorrect);
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console.log("✓ Original and extracted profiles match:", profilesMatch);
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if (!profilesMatch) throw new Error("Profile mismatch");
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return bodyweightObservation;
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}
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function createBundle(patient: Patient, observation: Observation, bodyweightObs: Observation): Bundle {
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const patientEntry: BundleEntry = {
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fullUrl: `urn:uuid:${patient.id}`,
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resource: patient,
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};
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const observationEntry: BundleEntry = {
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fullUrl: `urn:uuid:${observation.id}`,
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resource: observation,
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};
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const bodyweightEntry: BundleEntry = {
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fullUrl: `urn:uuid:${bodyweightObs.id}`,
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resource: bodyweightObs,
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};
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const bundle: Bundle = {
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resourceType: "Bundle",
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id: "bundle-1",
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type: "collection",
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entry: [patientEntry, observationEntry, bodyweightEntry],
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};
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return bundle;
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}
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function runDemo() {
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console.log("=".repeat(60));
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console.log("Creating FHIR R4 resources demo with bodyweight profile...");
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console.log("=".repeat(60));
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const patient = createPatient();
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console.log("✓ Created patient:", patient.id);
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const observation = createObservation(patient.id!);
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console.log("✓ Created glucose observation:", observation.id);
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console.log(`\n${"=".repeat(60)}`);
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console.log("Bodyweight profile attach/extract demo:");
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console.log("=".repeat(60));
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const bodyweightObs = createBodyWeightObservation(patient.id!);
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console.log("✓ Created body weight observation with profile:", bodyweightObs.id);
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const bundle = createBundle(patient, observation, bodyweightObs);
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console.log("\n✓ Created bundle with", bundle.entry?.length, "resources");
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console.log(`\n${"=".repeat(60)}`);
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console.log("Final Bundle JSON:");
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console.log("=".repeat(60));
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console.log(JSON.stringify(bundle, null, 2));
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}
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runDemo();

‎examples/typescript-us-core/generate.ts‎

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// Run this script using Bun CLI with:
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// bun run examples/typescript-us-core/generate.ts
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import { APIBuilder } from "../../src/api/builder";
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if (require.main === module) {
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console.log("📦 Generating FHIR R4 Core Types...");
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const builder = new APIBuilder()
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.verbose()
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.throwException()
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.fromPackage("hl7.fhir.us.core", "6.1.0")
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.typescript({ withDebugComment: false, withProfiles: true })
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.outputTo("./examples/typescript-us-core/fhir-types")
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.writeTypeTree("./examples/typescript-us-core/type-tree.yaml")
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.cleanOutput(true);
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const report = await builder.generate();
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console.log(report);
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if (report.success) {
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console.log("✅ FHIR R4 types generated successfully!");
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} else {
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console.error("❌ FHIR R4 types generation failed.");
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process.exit(1);
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}
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}

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