atomic-generate-types

FHIR Type Generation with @atomic-ehr/codegen

Generate type-safe FHIR types from StructureDefinitions. Supports TypeScript, Python, and C#. Uses tree-shaking to only include the resource types you need.

Language detection: Before setup, detect the project language from existing files (e.g., tsconfig.json → TypeScript, pyproject.toml/requirements.txt → Python, *.csproj/*.sln → C#). Use the matching language section below.

---

Setup (if not already configured)

1. Install the codegen package

The generation script is always written in TypeScript and executed with bun, tsx (installed via npm, pnpm or yarn). Install the codegen package in your project (or in a separate scripts directory for non-JS projects):

# npm
npm install -D @atomic-ehr/codegen

# pnpm
pnpm add -D @atomic-ehr/codegen

# yarn
yarn add -D @atomic-ehr/codegen

# bun
bun add -d @atomic-ehr/codegen

For npm/pnpm/yarn projects, also install tsx to run the generation script:

npm install -D tsx

2. Create the generation script

Create scripts/generate-types.ts using the template for your target language:

TypeScript

import { APIBuilder, prettyReport } from "@atomic-ehr/codegen";

const builder = new APIBuilder()
  .throwException()
  .fromPackage("<package name such as hl7.fhir.r4.core or hl7.fhir.us.core>", "<package version, such as 4.0.1 or 3.1.1>")
  .typescript({
    withDebugComment: false,
    generateProfile: false,
    openResourceTypeSet: false,
  })
  .typeSchema({
    treeShake: {
      "<package name such as hl7.fhir.r4.core or hl7.fhir.us.core>": {
        // Add the resource types you need here.
        // All dependency types (Identifier, Reference, CodeableConcept, etc.)
        // are included automatically.
        "http://hl7.org/fhir/StructureDefinition/Patient": {},
        "http://hl7.org/fhir/StructureDefinition/Bundle": {},
        "http://hl7.org/fhir/StructureDefinition/OperationOutcome": {},
      },
    },
  })
  .outputTo("./src/fhir-types")
  .cleanOutput(true);

const report = await builder.generate();
console.log(prettyReport(report));
if (!report.success) process.exit(1);

Python

import { APIBuilder, prettyReport } from "@atomic-ehr/codegen";

const builder = new APIBuilder()
  .throwException()
  .fromPackage("<package name such as hl7.fhir.r4.core or hl7.fhir.us.core>", "<package version, such as 4.0.1 or 3.1.1>")
  .python({
    rootPackageName: "fhir_types",
    fieldFormat: "snake_case",
    allowExtraFields: false,
    fhirpyClient: false,
  })
  .typeSchema({
    treeShake: {
      "<package name such as hl7.fhir.r4.core or hl7.fhir.us.core>": {
        // Add the resource types you need here.
        // All dependency types are included automatically.
        "http://hl7.org/fhir/StructureDefinition/Patient": {},
        "http://hl7.org/fhir/StructureDefinition/Bundle": {},
        "http://hl7.org/fhir/StructureDefinition/OperationOutcome": {},
      },
    },
  })
  .outputTo("./fhir_types")
  .cleanOutput(true);

const report = await builder.generate();
console.log(prettyReport(report));
if (!report.success) process.exit(1);

C#

import { APIBuilder, prettyReport } from "@atomic-ehr/codegen";

const builder = new APIBuilder()
  .throwException()
  .fromPackage("<package name such as hl7.fhir.r4.core or hl7.fhir.us.core>", "<package version, such as 4.0.1 or 3.1.1>")
  .csharp({
    rootNamespace: "Fhir.Types",
  })
  .typeSchema({
    treeShake: {
      "<package name such as hl7.fhir.r4.core or hl7.fhir.us.core>": {
        // Add the resource types you need here.
        // All dependency types are included automatically.
        "http://hl7.org/fhir/StructureDefinition/Patient": {},
        "http://hl7.org/fhir/StructureDefinition/Bundle": {},
        "http://hl7.org/fhir/StructureDefinition/OperationOutcome": {},
      },
    },
  })
  .outputTo("./FhirTypes")
  .cleanOutput(true);

const report = await builder.generate();
console.log(prettyReport(report));
if (!report.success) process.exit(1);

3. Add the script to package.json

{
  "scripts": {
    "generate-types": "bun run scripts/generate-types.ts"
  }
}

For npm/pnpm/yarn projects (using tsx instead of bun):

{
  "scripts": {
    "generate-types": "tsx scripts/generate-types.ts"
  }
}

4. Add to .gitignore

.codegen-cache/

5. Additional setup per language

TypeScript — ensure tsconfig.json has the required compiler options for generated imports:

{
  "compilerOptions": {
    "moduleResolution": "bundler",
    "allowImportingTsExtensions": true
  }
}

Python — the generator creates a requirements.txt inside the output directory listing pydantic>=2.11.0 and other deps. Install them:

pip install pydantic>=2.11.0

For mypy support, add the Pydantic plugin to mypy.ini:

[mypy]
plugins = pydantic.mypy

C# — no additional setup needed. Generated files include Usings.cs with necessary using statements.

6. Run generation

# bun
bun run generate-types

# npm
npm run generate-types

# pnpm
pnpm run generate-types

Commit the generated files — they are the project's FHIR type definitions.

---

APIBuilder reference

Loading FHIR packages

Important: Only load packages that the user explicitly requires. Avoid adding unnecessary packages — especially core packages, which should be pulled in as dependencies of the user's IG rather than loaded directly.

// FHIR R4 base
.fromPackage("hl7.fhir.r4.core", "4.0.1")

// Implementation Guides (optional) — load from tgz URL
.fromPackageRef("https://fs.get-ig.org/-/hl7.fhir.us.core-7.0.0.tgz")
.fromPackageRef("https://fs.get-ig.org/-/fhir.r4.ukcore.stu2-2.0.2.tgz")

// Local StructureDefinition JSON files (custom resources/profiles)
.localStructureDefinitions({
  package: { name: "my-org.custom-profiles", version: "0.0.1" },
  path: "./fhir/custom-profiles",
  dependencies: [{ name: "hl7.fhir.r4.core", version: "4.0.1" }],
})

// Local tgz archive (unpublished IG built by FHIR IG Publisher)
.localTgzPackage("./fhir/my-org.custom-ig-0.1.0.tgz")

Language-specific options

TypeScript — .typescript()

.typescript({
  withDebugComment: false,       // omit debug comments in generated files
  generateProfile: false,        // set true when loading IGs with constrained profiles
  openResourceTypeSet: false,    // stricter resource type unions
})

Python — .python()

.python({
  rootPackageName: "fhir_types",  // Python package name
  fieldFormat: "snake_case",      // "snake_case" | "PascalCase" | "camelCase"
  allowExtraFields: false,        // Pydantic model_config extra="allow"|"forbid"
  fhirpyClient: false,           // generate fhirpy-compatible base model
})

C# — .csharp()

.csharp({
  rootNamespace: "Fhir.Types",   // .NET namespace for generated classes
})

Tree-shaking

Tree-shaking controls which resource types are generated. Without it, ALL FHIR resources are included (~150+ files). With it, only the listed types and their transitive dependencies are generated.

.typeSchema({
  treeShake: {
    "<package-name>": {
      "<StructureDefinition canonical URL>": {},
      // ...
    },
  },
})

StructureDefinition URL patterns:

Source	Pattern	Example
FHIR R4 base	http://hl7.org/fhir/StructureDefinition/{ResourceType}	http://hl7.org/fhir/StructureDefinition/Patient
US Core	http://hl7.org/fhir/us/core/StructureDefinition/{profile}	http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
UK Core	https://fhir.hl7.org.uk/StructureDefinition/{profile}	https://fhir.hl7.org.uk/StructureDefinition/UKCore-Patient

Common FHIR R4 resource types:

"http://hl7.org/fhir/StructureDefinition/Patient": {},
"http://hl7.org/fhir/StructureDefinition/Encounter": {},
"http://hl7.org/fhir/StructureDefinition/Observation": {},
"http://hl7.org/fhir/StructureDefinition/Condition": {},
"http://hl7.org/fhir/StructureDefinition/Procedure": {},
"http://hl7.org/fhir/StructureDefinition/MedicationRequest": {},
"http://hl7.org/fhir/StructureDefinition/DiagnosticReport": {},
"http://hl7.org/fhir/StructureDefinition/AllergyIntolerance": {},
"http://hl7.org/fhir/StructureDefinition/Immunization": {},
"http://hl7.org/fhir/StructureDefinition/Location": {},
"http://hl7.org/fhir/StructureDefinition/Organization": {},
"http://hl7.org/fhir/StructureDefinition/Practitioner": {},
"http://hl7.org/fhir/StructureDefinition/Bundle": {},
"http://hl7.org/fhir/StructureDefinition/OperationOutcome": {},
"http://hl7.org/fhir/StructureDefinition/Questionnaire": {},
"http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse": {},

Output options

.outputTo("./src/fhir-types")   // output directory
.cleanOutput(true)               // delete output dir before regenerating

---

What gets generated

TypeScript

For each resource type, a .ts file is generated containing:

• Main interface — e.g., Patient, Encounter, Bundle
• BackboneElement interfaces — nested structures like EncounterLocation, PatientContact, BundleEntry
• Type guard function — e.g., isPatient(resource), isEncounter(resource)
• Re-exports of dependency types (Identifier, Reference, CodeableConcept, etc.)
• Barrel export — index.ts re-exports everything for convenience

Generated types include FHIR value set enums:

status: ("planned" | "arrived" | "triaged" | "in-progress" | "onleave" | "finished" | "cancelled" | "entered-in-error" | "unknown");
subject?: Reference<"Group" | "Patient">;

Python

For each resource type, a .py file is generated containing:

• Pydantic BaseModel class — e.g., Patient(DomainResource), Encounter(DomainResource)
• Nested backbone classes — e.g., EncounterLocation, PatientContact
• Literal types for closed enums — e.g., Literal["planned", "arrived", ...]
• Field aliases for JSON round-tripping — Field(alias="originalName", serialization_alias="originalName")
• to_json() / from_json() methods on each resource
• __init__.py barrel with model_rebuild() calls for forward-reference resolution
• resource_families.py — runtime polymorphic validators
• requirements.txt — pydantic>=2.11.0 and other deps

FHIR primitive type mapping: boolean → bool, decimal → float, integer → int, string-like → str.

C#

For each resource type, a .cs file is generated containing:

• Public class — e.g., Patient : DomainResource
• Nested backbone classes within the parent class
• Nullable properties for optional fields — public string? Id { get; set; }
• Enum definitions with [Description("value")] attributes in *Enums.cs
• ResourceDictionary.cs — Dictionary<Type, string> mapping types to FHIR resource names
• Helper.cs — JSON serializer options (camelCase, null-ignoring)
• Client.cs — FHIR REST client with Search<T>, Read<T>, Create<T>, Update<T>, Delete<T>
• Usings.cs — global using statements

FHIR primitive type mapping: boolean → bool, decimal → decimal, integer → int, unsignedInt/positiveInt → long, string-like → string.

---

Custom resources and profiles

You can generate types for custom FHIR resources or profiles that are not part of a published IG. Place your StructureDefinition JSON files in a local folder and load them with .localStructureDefinitions().

Loading local StructureDefinitions

import { APIBuilder, prettyReport } from "@atomic-ehr/codegen";

const builder = new APIBuilder()
  .throwException()
  .fromPackage("hl7.fhir.r4.core", "4.0.1")
  .localStructureDefinitions({
    package: { name: "my-org.custom-profiles", version: "0.0.1" },
    path: "./fhir/custom-profiles",   // folder containing StructureDefinition JSON files
    dependencies: [{ name: "hl7.fhir.r4.core", version: "4.0.1" }],
  })
  .typescript({                       // or .python() / .csharp()
    withDebugComment: false,
    generateProfile: true,            // enable for custom profiles
    openResourceTypeSet: false,
  })
  .typeSchema({
    treeShake: {
      "hl7.fhir.r4.core": {
        "http://hl7.org/fhir/StructureDefinition/Bundle": {},
        "http://hl7.org/fhir/StructureDefinition/OperationOutcome": {},
      },
      "my-org.custom-profiles": {
        "http://my-org.example.com/StructureDefinition/MyCustomPatient": {},
        "http://my-org.example.com/StructureDefinition/CustomObservation": {},
      },
    },
  })
  .outputTo("./src/fhir-types")
  .cleanOutput(true);

const report = await builder.generate();
console.log(prettyReport(report));
if (!report.success) process.exit(1);

Folder structure for custom profiles

fhir/custom-profiles/
  StructureDefinition-MyCustomPatient.json
  StructureDefinition-CustomObservation.json

Each file must be a valid FHIR StructureDefinition JSON resource. The canonical URL in each file (e.g., "url": "http://my-org.example.com/StructureDefinition/MyCustomPatient") is what you reference in the treeShake config.

Loading a local tgz package

If you have an unpublished IG built by the FHIR IG Publisher (produces a .tgz archive), load it directly:

.localTgzPackage("./fhir/my-org.custom-ig-0.1.0.tgz")

This works the same as .fromPackageRef() but for local archives.

---

Example: Adding an Implementation Guide

To generate US Core profiled types alongside base R4 (TypeScript example — replace .typescript() with .python() or .csharp() for other languages):

import { APIBuilder, prettyReport } from "@atomic-ehr/codegen";

const builder = new APIBuilder()
  .throwException()
  .fromPackage("hl7.fhir.r4.core", "4.0.1")
  .fromPackageRef("https://fs.get-ig.org/-/hl7.fhir.us.core-7.0.0.tgz")
  .typescript({
    withDebugComment: false,
    generateProfile: true,        // enable for IG profiles
    openResourceTypeSet: false,
  })
  .typeSchema({
    treeShake: {
      "hl7.fhir.r4.core": {
        "http://hl7.org/fhir/StructureDefinition/Bundle": {},
        "http://hl7.org/fhir/StructureDefinition/OperationOutcome": {},
      },
      "hl7.fhir.us.core": {
        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient": {},
        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis": {},
        "http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab": {},
      },
    },
  })
  .outputTo("./src/fhir-types")
  .cleanOutput(true);

const report = await builder.generate();
console.log(prettyReport(report));
if (!report.success) process.exit(1);

---

Import patterns

TypeScript

// Direct file import (preferred — explicit about what you use)
import type { Patient } from "./fhir-types/hl7-fhir-r4-core/Patient";
import type { Encounter, EncounterLocation } from "./fhir-types/hl7-fhir-r4-core/Encounter";
import type { Bundle, BundleEntry } from "./fhir-types/hl7-fhir-r4-core/Bundle";

// Barrel import (convenient for grabbing many types)
import type { Patient, Encounter, Location, Bundle } from "./fhir-types/hl7-fhir-r4-core";

// Type guards (value imports, not type-only)
import { isPatient, isEncounter } from "./fhir-types/hl7-fhir-r4-core";

Python

# Direct import
from fhir_types.hl7_fhir_r4_core.patient import Patient
from fhir_types.hl7_fhir_r4_core.encounter import Encounter, EncounterLocation
from fhir_types.hl7_fhir_r4_core.bundle import Bundle, BundleEntry

# Package import
from fhir_types.hl7_fhir_r4_core import Patient, Encounter, Bundle

C#

using Fhir.Types;
using Fhir.Types.Hl7FhirR4Core;

var patient = new Patient { /* ... */ };
var encounter = new Encounter { /* ... */ };

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Workflow for adding a new resource type

1. Edit scripts/generate-types.ts — add the StructureDefinition URL to treeShake
2. Run npm run generate-types (or bun run generate-types, pnpm run generate-types)
3. Import the new type in your code
4. Run typecheck / linter to verify
5. Commit the updated generated types directory