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EHR Team"},"license":"MIT","homepage":"https://github.com/atomic-ehr/codegen#readme","keywords":["fhir","codegen","typescript","healthcare","ehr","typeschema"],"repository":{"url":"git+https://github.com/atomic-ehr/codegen.git","type":"git"},"description":"Code generation tools for FHIR resources and TypeSchema definitions","maintainers":[{"name":"aitem","email":"muradbei@gmail.com"},{"name":"aleksandr.penskoi","email":"aleksandr.penskoi@gmail.com"},{"name":"niquola","email":"niquola@health-samurai.io"}],"readme":"# Atomic EHR Codegen\n\n[![npm canary](https://img.shields.io/npm/v/@atomic-ehr/codegen/canary.svg?label=canary)](https://www.npmjs.com/package/@atomic-ehr/codegen/v/canary)\n[![npm version](https://img.shields.io/npm/v/@atomic-ehr/codegen.svg)](https://www.npmjs.com/package/@atomic-ehr/codegen)\n[![CI](https://github.com/atomic-ehr/codegen/actions/workflows/ci.yml/badge.svg)](https://github.com/atomic-ehr/codegen/actions/workflows/ci.yml)\n[![SDK Tests](https://github.com/atomic-ehr/codegen/actions/workflows/sdk-tests.yml/badge.svg)](https://github.com/atomic-ehr/codegen/actions/workflows/sdk-tests.yml)\n\n<!-- markdown-toc start - Don't edit this section. Run M-x markdown-toc-refresh-toc -->\n**Table of Contents**\n\n- [Atomic EHR Codegen](#atomic-ehr-codegen)\n  - [Features](#features)\n  - [Guides](#guides)\n  - [Versions & Release Cycle](#versions--release-cycle)\n  - [Installation](#installation)\n  - [Quick Start](#quick-start)\n    - [Usage Examples](#usage-examples)\n  - [Architecture](#architecture)\n    - [Generator Options](#generator-options)\n    - [Input - FHIR packages & resolves canonicals](#input---fhir-packages--resolves-canonicals)\n      - [Load Local StructureDefinitions & TGZ Archives](#load-local-structuredefinitions--tgz-archives)\n    - [Intermediate - Type Schema](#intermediate---type-schema)\n      - [Tree Shaking](#tree-shaking)\n        - [Field-Level Tree Shaking](#field-level-tree-shaking)\n      - [Logical Model Promotion](#logical-model-promotion)\n      - [Resolving Schema Collisions](#resolving-schema-collisions)\n    - [Generation](#generation)\n      - [1. Writer-Based Generation (Programmatic)](#1-writer-based-generation-programmatic)\n      - [2. Mustache Template-Based Generation (Declarative)](#2-mustache-template-based-generation-declarative)\n    - [Profile Classes](#profile-classes)\n  - [Support](#support)\n\n<!-- markdown-toc end -->\n\nA powerful, extensible code generation toolkit for FHIR ([Fast Healthcare Interoperability Resources](https://www.hl7.org/fhir/)) that transforms FHIR specifications into strongly-typed code for multiple programming languages.\n\n## Features\n\n- [x] **Multi-Package Support** — Load packages from the [FHIR registry](examples/typescript-r4-us-core/), [remote TGZ files](examples/typescript-custom-packages/), or a [local folder with custom StructureDefinitions](examples/typescript-custom-packages/)\n  - Tested with hl7.fhir.r4.core, US Core, C-CDA, SQL on FHIR, etc.\n- [x] **Resources & Complex Types** — Generates typed definitions with proper inheritance\n- [x] **Value Set Bindings** — Strongly-typed enums from FHIR terminology bindings\n- [x] **Profiles** — Factory methods with auto-populated fixed values and required slices ([R4 profiles](examples/typescript-r4-us-core/profile-r4-bp.test.ts), [US Core](examples/typescript-r4-us-core/profile-us-core-patient.test.ts))\n  - Extensions — flat typed accessors (e.g. `setRace()` on US Core Patient), [standalone extension profiles](examples/typescript-r4-us-core/profile-r4-extension.test.ts)\n  - Slicing — typed get/set accessors with discriminator matching\n  - Validation — runtime `validate()` for required fields, fixed values, slice cardinality, enums, references\n- [x] **Extensible Architecture** — Three-stage pipeline: FHIR packages → [TypeSchema](https://www.health-samurai.io/articles/type-schema-a-pragmatic-approach-to-build-fhir-sdk) IR → code generation\n  - TypeSchema is a universal intermediate representation — add a new language by writing only the final generation stage\n  - Built-in generators: TypeScript, Python/Pydantic, C#, and Mustache templates\n- [x] **TypeSchema Transformations**:\n  - [x] **Tree Shaking** — include only the resources and fields you need; automatically resolves dependencies\n  - [x] **Logical Model Promotion** — promote FHIR logical models to first-class resources\n  - [ ] Renaming — custom naming conventions for generated types and fields\n- [ ] **Search Builders** — type-safe FHIR search query construction\n- [ ] **Operation Generation** — type-safe FHIR operation calls\n\n| Feature                           | TypeScript | Python  | C#   | Mustache |\n|-----------------------------------|------------|---------|------|----------|\n| Resources & Complex Types         | yes        | yes     | yes  | template |\n| Polymorphic container `Bundle<T>` | yes        | yes     | no   | no       |\n| Value Set Bindings                | inline     | limited | enum | template |\n| Primitive Extensions              | yes        | opt-in  | no   | no       |\n| Profiles                          | yes        | yes     | no   | no       |\n| Profile Validation                | yes        | yes     | no   | no       |\n\n## Guides\n\n- **[Writer Generator Guide](docs/guides/writer-generator.md)** - Build custom code generators with the Writer base class\n- **[Mustache Generator Guide](docs/guides/mustache-generator.md)** - Template-based code generation for any language\n- **[TypeSchemaIndex Guide](docs/guides/typeschema-index.md)** - Type Schema structure and utilities\n- **[Testing Generators Guide](docs/guides/testing-generators.md)** - Unit tests, snapshot testing, and best practices\n- **[Contributing Guide](CONTRIBUTING.md)** - Development setup and workflow\n\n## Versions & Release Cycle\n\n- `canary` channel - Latest development version from `main` branch\n- `latest` channel - Latest stable version, changelog: [Releases](https://github.com/atomic-ehr/codegen/releases)\n- All versions: [NPM: @atomic-ehr/codegen](https://www.npmjs.com/package/@atomic-ehr/codegen?activeTab=versions)\n\n## Installation\n\n```bash\n# Using npm\nnpm install @atomic-ehr/codegen\n\n# Using bun\nbun add @atomic-ehr/codegen\n\n# Using yarn\nyarn add @atomic-ehr/codegen\n```\n\n## Quick Start\n\n1. Write SDK generation script (`generate-types.ts`):\n\n    ```typescript\n    import { APIBuilder, prettyReport } from '@atomic-ehr/codegen';\n\n    const builder = new APIBuilder()\n        .fromPackage(\"hl7.fhir.r4.core\", \"4.0.1\")\n        .typescript({})\n        .outputTo(\"./examples/typescript-r4-us-core/fhir-types\")\n        .introspection({ typeTree: \"./type-tree.yaml\" });\n\n    const report = await builder.generate();\n    console.log(prettyReport(report));\n    ```\n\n2. Run the script with:\n\n    - `npm exec tsx generate-types.ts`\n    - `bun run generate-types.ts`\n    - `pnpm exec tsx generate-types.ts`\n\nAlternatively, drive the same pipeline from a JSON config file, with no script at all:\n\n```json\n{\n    \"version\": 1,\n    \"builders\": [\n        {\n            \"name\": \"core\",\n            \"fromPackages\": [{ \"name\": \"hl7.fhir.r4.core\", \"version\": \"4.0.1\" }],\n            \"typescript\": {},\n            \"outputTo\": \"./fhir-types\"\n        }\n    ]\n}\n```\n\n```bash\natomic-codegen generate --config ./codegen.json            # run every builder\natomic-codegen generate --config ./codegen.json --dry-run  # print the plan without generating\n```\n\nRelative paths resolve against the config file's directory, unknown keys are rejected with the full list of problems, and `outputTo` is removed before generation by default (set `\"cleanOutput\": false` to keep it). A config may hold several builders: each maps to one `APIBuilder` pipeline (`fromPackages`/`fromPackageRefs`/`localTgzPackages`/`localStructureDefinitions` inputs, `typeSchema` transformations, and `typescript`/`python`/`csharp`/`introspection` generators — see `GenerateConfigBuilder` in `src/api/generate-config.ts`). A failed builder does not stop the others, and the run exits non-zero if any failed.\n\nThe JSON `typescript` options also accept `moduleSpecifierStyle` (`\"extensionless\"` or `\"node-esm\"`) and `terminology`. For Node ESM imports and terminology output restricted to selected packages, replace `\"typescript\": {}` with:\n\n```json\n\"typescript\": {\n    \"moduleSpecifierStyle\": \"node-esm\",\n    \"terminology\": {\n        \"enabled\": true,\n        \"packages\": [\"hl7.fhir.r4.core@4.0.1\"],\n        \"packageVerification\": {\n            \"hl7.fhir.r4.core@4.0.1\": \"registry-integrity\"\n        }\n    }\n}\n```\n\nAll terminology fields are optional. When supplied, `enabled` must be a boolean, `packages` must be an array of strings, and `packageVerification` must contain string values. Unknown nested keys and invalid values are reported with their full configuration paths.\n\n### Fixing defective packages\n\nReal FHIR packages ship defects — missing dependencies, typo'd names and canonicals, bindings to unavailable ValueSets, incomplete CodeSystems. Fixes are declared, not hand-coded:\n\n- **Canonical exclusions** — drop a known-broken canonical at the package index, before codegen sees it: `canonicalManager: { patches: { indexEntry: [excludeCanonical({ package, url, reason })] } }`. Codegen ships `builtinPatches` (`src/api/builtin-patches.ts` — generation-breaking content in HL7's own packages, e.g. `hl7.fhir.r5.core` profiles that break R4-compatible generation); they apply to every loader the builder constructs, on top of your own patches, and `builtinPatches: false` is the explicit opt-out. Index exclusion removes the canonical from resolution too, so exclude whole derivation chains together — and it is applied at scan time, so drop the loader cache after changing the list. A hand-built CanonicalManager owns its wiring: apply `builtinPatches.indexEntry` explicitly (see the ccda example).\n- **Custom patches** — per-phase handlers built from the helpers on the `@atomic-ehr/fhir-canonical-manager/patch` subpath (`ensureDependency`, `renamePackage`, `replaceText`, `ensureCodes`, scoped by `inPackage`/`inResource`), passed as `new APIBuilder({ canonicalManager: { patches: {...} } })`. In the CLI config, `\"options\": { \"forceDependencies\": {...} }` pins declared dependency versions across the closure.\n- **Broken package index** — `canonicalManager: { packageIndex: \"recover\" }` heals a corrupt `.index.json` by falling back to a directory scan (always with a warning); `\"regenerate\"` ignores the shipped index entirely.\n\nLoader settings (`registry`, `packageIndex`, `dropCache`, `patches`) live under the builder's `canonicalManager` option — they configure the CanonicalManager package loader, not the generator. The old flat options are deprecated and warn.\n\nApplied fixes surface in the generation report's \"Input fixes\" section.\n\n### Usage Examples\n\nSee the [examples/](examples/) directory for working demonstrations:\n\n- **[typescript-r4-us-core/](examples/typescript-r4-us-core/)** - FHIR R4 core + US Core type generation with resource creation, profiles, and extensions\n- **[on-the-fly/ccda/](examples/on-the-fly/ccda/)** - C-CDA on FHIR type generation (logical models, generated on the fly)\n- **[python-r4-us-core/](examples/python-r4-us-core/)** - Python/Pydantic models for FHIR R4 core + US Core profiles, with the default fhirpy async client\n- **[python-r4/](examples/python-r4/)** - Python/Pydantic model generation with the simple requests-based client\n- **[csharp/](examples/csharp/)** - C# class generation with namespace configuration\n- **[mustache/](examples/mustache/)** - Java generation with Mustache templates and post-generation hooks\n- **[typescript-custom-packages/](examples/typescript-custom-packages/)** - Loading packages from local folders or remote TGZ URLs (SQL-on-FHIR)\n\nFor detailed documentation, see [examples/README.md](examples/README.md).\n\n## Architecture\n\nThe toolkit uses a three-stage architecture (details: [link](https://www.health-samurai.io/articles/type-schema-a-pragmatic-approach-to-build-fhir-sdk)):\n\n1. **Input** - FHIR packages & resolves canonicals\n2. **Intermediate representation** - TypeSchema provides a universal representation for FHIR data entities and processing utilities\n3. **Generation** - Generate code for TypeScript, Python, etc.\n\nThe `APIBuilder` provides a fluent interface for configuring and generating code:\n\n```typescript\nconst builder = new APIBuilder()\n\n    // Input sources (choose one or combine)\n    .fromPackage(\"hl7.fhir.r4.core\", \"4.0.1\") // NPM registry package\n    .fromPackageRef(\"https://...package.tgz\") // Remote TGZ file\n    .localStructureDefinitions({ ... })       // Loose JSON files\n\n    // Type Schema processing\n    .typeSchema({\n        treeShake: { ... },        // Include only specified types\n        promoteLogical: { ... },   // Process logical models as resources\n        resolveCollisions: { ... },// Resolve duplicate schema collisions\n    })\n\n    // Code generator (choose one)\n    .typescript({                              // TypeScript generator\n        generateProfile?: boolean,\n        withDebugComment?: boolean,\n        openResourceTypeSet?: boolean,\n        terminology?: {\n            enabled: true,\n            packageVerification: {\n                \"hl7.fhir.r4.core@4.0.1\": \"registry-integrity\",\n            },\n        },\n    })\n    .python({                                   // Python generator\n        client?: \"fhirpy\" | \"none\",            // client integration (default: fhirpy)\n        generateProfile?: boolean,             // generate profile wrapper classes\n        primitiveTypeExtension?: boolean,\n        allowExtraFields?: boolean,\n        fieldFormat?: \"snake_case\" | \"camelCase\",\n    })\n    .csharp({                                  // C# generator\n        rootNamespace: \"Fhir.Types\",\n        staticSourceDir?: \"./static\",\n    })\n\n    // Output configuration\n    .outputTo(\"./generated/types\")             // Output directory\n    .cleanOutput(true)                         // Clean before generation\n\n    // Optional: Introspection & debugging\n    .throwException()                          // Throw on errors (optional)\n    .introspection({\n        typeSchemas: \"./schemas\",              // Export TypeSchemas\n        typeTree: \"./tree.yaml\",               // Export type tree\n        fhirSchemas: \"./fhir-schemas\",         // Export FHIR schemas\n        structureDefinitions: \"./sd\"           // Export StructureDefinitions\n    })\n\n    // Execute generation\n    .generate();                                // Returns GenerationReport\n```\n\nEach method returns the builder instance, allowing method chaining. The `generate()` method executes the pipeline and returns a report with success status and generated file details.\n\n### Generator Options\n\nEach language generator accepts its own option object. All options are optional; the tables below list the defaults.\n\n**TypeScript** — `.typescript({ ... })`\n\n| Option | Type | Default | Description |\n|--------|------|---------|-------------|\n| `generateProfile` | `boolean` | `true` | Generate profile wrapper classes (factories, typed slice/extension accessors, `validate()`). |\n| `primitiveTypeExtension` | `boolean` | `true` | Emit sibling `_field` properties for [primitive element extensions](https://www.hl7.org/fhir/element.html#json). |\n| `openResourceTypeSet` | `boolean` | `false` | For resource families (`Resource`, `DomainResource`), keep the `resourceType` union open by adding a `string` fallback instead of a closed literal union. |\n| `extensionGetterDefault` | `\"flat\" \\| \"profile\" \\| \"raw\"` | `\"flat\"` | Default return shape for generated extension getters. |\n| `sliceGetterDefault` | `\"flat\" \\| \"raw\"` | `\"flat\"` | Default return shape for generated slice getters (`flat` strips discriminators, `raw` returns the full FHIR element). |\n| `lineWidth` | `number` | `120` | Maximum line width before wrapping. |\n| `withDebugComment` | `boolean` | `false` | Emit comments tracing each generated type back to its source schema. |\n| `terminology.enabled` | `boolean` | `false` | Emit a `terminology.ts` module for every package in the resolved closure. |\n| `terminology.packageVerification` | `Record<string, string>` | `{}` | Map package references such as `hl7.fhir.r4.core@4.0.1` to a closure verification state (`registry-integrity`, `unverifiable`, ...). Absent entries record `not-recorded`. |\n\nWhen terminology generation is enabled, each exported symbol includes its canonical identity, source package and version, declared content mode, and verification state. Only CodeSystems declaring `content: \"complete\"` emit code unions and display maps. ValueSet expansions are never promoted to constants, and an `unverifiable` package emits identity and provenance without concept content.\n\n**Python** — `.python({ ... })`\n\n| Option | Type | Default | Description |\n|--------|------|---------|-------------|\n| `client` | `\"fhirpy\" \\| \"none\"` | `\"fhirpy\"` | Client integration baked into the models: `\"fhirpy\"` makes models extend `FhirpyBaseModel` for the fhirpy async client; `\"none\"` emits plain Pydantic models. |\n| `fieldFormat` | `\"camelCase\" \\| \"snake_case\" \\| \"PascalCase\"` | `\"camelCase\"` | Naming convention for generated model fields. |\n| `generateProfile` | `boolean` | `false` | Generate profile wrapper classes (`create()`, typed accessors, `validate()`) around the Pydantic models. |\n| `primitiveTypeExtension` | `boolean` | `false` | Emit primitive element extension fields. |\n| `allowExtraFields` | `boolean` | `false` | Allow fields not present in the schema on generated models (Pydantic `extra`). |\n| `rootPackageName` | `string` | `\"fhir_types\"` | Root Python package name for the generated module tree. |\n| `withDebugComment` | `boolean` | `false` | Emit comments tracing each generated type back to its source schema. |\n\n> `fhirpyClient?: boolean` is **deprecated** — use `client` instead (`true` → `\"fhirpy\"`, `false` → `\"none\"`).\n\n**C#** — `.csharp({ ... })`\n\n| Option | Type | Default | Description |\n|--------|------|---------|-------------|\n| `rootNamespace` | `string` | `\"Fhir.Types\"` | Root namespace for generated classes. |\n| `staticSourceDir` | `string` | — | Directory of static `.cs` source files copied verbatim into the output. |\n| `withDebugComment` | `boolean` | `false` | Emit comments tracing each generated type back to its source schema. |\n\n### Input - FHIR packages & resolves canonicals\n\nThe input stage leverages [Canonical Manager](https://github.com/atomic-ehr/canonical-manager) to handle FHIR package management and dependency resolution. It processes FHIR packages from multiple sources (registry, local files, TGZ archives) and resolves all canonical URLs to their concrete definitions, ensuring all references between resources are properly linked before transformation.\n\nThe [`Register`](src/typeschema/register.ts) component wraps Canonical Manager specifically for codegen purposes, providing:\n\n- **Multi-package indexing** for fast canonical URL lookups across package boundaries\n- **Package-aware resolution** with automatic dependency tree traversal\n- **FHIR-to-TypeSchema conversion** using the `@atomic-ehr/fhirschema` translator\n- **Element snapshot generation** that merges inherited properties from base resources\n\n#### Load Local StructureDefinitions & TGZ Archives\n\nUse the new `localPackage` helper to point the builder at an on-disk FHIR package folder (for example, an unpublished implementation guide). If you only have loose StructureDefinition JSON files, group them under a folder and pass it to `localStructureDefinitions`. Canonical Manager handles copying, indexing, and dependency installation in both scenarios, so the API builder only needs to describe where the files live and what upstream packages they depend on.\n\n```typescript\n.localStructureDefinitions({\n    package: { name: \"example.local.structures\", version: \"0.0.1\" },\n    path: \"./custom-profiles\",\n    dependencies: [{ name: \"hl7.fhir.r4.core\", version: \"4.0.1\" }],\n})\n.localTgzPackage(\"./packages/my-custom-ig.tgz\")\n```\n\nThe example above points Canonical Manager at `./custom-profiles` and installs the HL7 R4 core dependency automatically. The `localTgzPackage` helper registers `.tgz` artifacts that Canonical Manager already knows how to unpack.\n\n### Intermediate - Type Schema\n\nType Schema serves as a universal intermediate representation that bridges FHIR's complex hierarchical structure with programming language constructs. It transforms FHIR StructureDefinitions into a flattened, code-generation-friendly format that:\n\n- **Unifies** all FHIR elements (Resources, Types, ValueSets) into a consistent structure\n- **Flattens** nested paths for direct field access without complex traversal\n- **Enriches** definitions with resolved references, value set expansions, and type dependencies\n- **Simplifies** FHIR concepts like choice types and extensions for easier code generation\n\nThis approach enables generating idiomatic code for any programming language while preserving FHIR semantics and constraints. Learn more: [Type Schema specification](https://www.health-samurai.io/articles/type-schema-a-pragmatic-approach-to-build-fhir-sdk).\n\n#### Tree Shaking\n\nTree shaking optimizes the generated output by including only the resources you explicitly need and their dependencies. Instead of generating types for an entire FHIR package (which can contain hundreds of resources), you can specify exactly which resources to include:\n\n```typescript\n.typeSchema({\n    treeShake: {\n        \"hl7.fhir.r4.core#4.0.1\": {\n            \"http://hl7.org/fhir/StructureDefinition/Patient\": {},\n            \"http://hl7.org/fhir/StructureDefinition/Observation\": {}\n        }\n    }\n})\n```\n\nThis feature automatically resolves and includes all dependencies (field types, base resources, nested types, and extension definitions used by profiles) while excluding unused resources, significantly reducing the size of generated code and improving compilation times. Reference targets are not dependencies: a field typed `Reference<\"Patient\">` does not pull the `Patient` type into the output, since the reference is rendered as a string literal.\n\n##### Field-Level Tree Shaking\n\nBeyond resource-level filtering, tree shaking supports fine-grained field selection using `selectFields` (whitelist) or `ignoreFields` (blacklist):\n\n```typescript\n.typeSchema({\n    treeShake: {\n        \"hl7.fhir.r4.core#4.0.1\": {\n            \"http://hl7.org/fhir/StructureDefinition/Patient\": {\n                selectFields: [\"id\", \"name\", \"birthDate\", \"gender\"]\n            },\n            \"http://hl7.org/fhir/StructureDefinition/Observation\": {\n                ignoreFields: [\"performer\", \"note\"]\n            }\n        }\n    }\n})\n```\n\n**Configuration Rules:**\n\n- `selectFields`: Only includes the specified fields (whitelist approach)\n- `ignoreFields`: Removes specified fields, keeps everything else (blacklist approach)\n- These options are **mutually exclusive** - you cannot use both in the same rule\n- `ignoreExtensions`: Removes specific extensions from a profile by canonical URL\n\n**Polymorphic Field Handling:**\n\nFHIR choice types (like `multipleBirth[x]` which can be boolean or integer) are handled intelligently. Selecting/ignoring the base field affects all variants, while targeting specific variants only affects those types.\n\n##### Following Reference Targets\n\nTo also generate types for a schema's reference targets — both the base resources (`reference.resource`) and the target profiles (`reference.profiles`) — enable `followReferences` on the rule (default: `false`):\n\n```typescript\n.typeSchema({\n    treeShake: {\n        \"kbv.basis\": {\n            \"https://fhir.kbv.de/StructureDefinition/KBV_PR_Base_Condition_Diagnosis\": {\n                followReferences: true\n            }\n        }\n    }\n})\n```\n\nWith this rule, `Condition.subject` targeting `KBV_PR_Base_Patient` pulls the Patient profile (and the `Patient`/`Group` resources) into the generated output, including their regular dependencies. Following is **non-transitive**: the pulled-in types keep their own reference targets as plain string literals, so a single flag cannot drag in the whole package. If a followed target is also listed as a tree-shake root, the root's rule wins.\n\nTo enable it for every tree-shake root at once, use `treeShakeDefaults` (a rule's own `followReferences` still wins over the default):\n\n```typescript\n.typeSchema({\n    treeShake: { ... },\n    treeShakeDefaults: { followReferences: true }\n})\n```\n\n#### Logical Model Promotion\n\nSome implementation guides expose logical models (logical-kind StructureDefinitions) that are intended to be used like resources in generated SDKs. The code generator supports promoting selected logical models to behave as resources during generation.\n\nUse the programmatic API via `APIBuilder`:\n\n```typescript\nconst builder = new APIBuilder({})\n  .fromPackage(\"my.custom.pkg\", \"4.0.1\")\n  .typeSchema({\n    promoteLogical: {\n      \"my.custom.pkg\": [\n        \"http://example.org/StructureDefinition/MyLogicalModel\"\n      ]\n    }\n  })\n```\n\n#### Resolving Schema Collisions\n\nWhen multiple StructureDefinitions produce the same binding (e.g. `ObservationCategory` from both `Observation` and `ObservationDefinition`), the schemas may differ in strength or value set. By default the generator picks the most common variant and emits a warning:\n\n```\n! ts: 'urn:fhir:binding:ObservationCategory' from 'shared' has 2 versions (#duplicateSchema)\n```\n\nTo fix this, add `resolveCollisions` to `.typeSchema()` specifying which source should win for each binding URL:\n\n```typescript\n.typeSchema({\n    resolveCollisions: {\n        \"urn:fhir:binding:ObservationCategory\": {\n            package: \"hl7.fhir.r4.core#4.0.1\",\n            canonical: \"http://hl7.org/fhir/StructureDefinition/Observation\",\n        },\n    },\n})\n```\n\n- **`package`** — the FHIR package ID (`name#version`) that contains the preferred source\n- **`canonical`** — the StructureDefinition URL that should provide the authoritative binding\n\nThe generated `README.md` report (from `.introspection()`) lists all collisions with version details and includes a ready-to-paste `resolveCollisions` config for any unresolved ones. Example output:\n\n```markdown\n## Schema Collisions\n\n- `urn:fhir:binding:CommunicationReason` (2 versions)\n  - Version 1 (selected): Communication (hl7.fhir.r4.core#4.0.1)\n  - Version 2: CommunicationRequest (hl7.fhir.r4.core#4.0.1)\n- `urn:fhir:binding:ProcessPriority` (2 versions)\n  - Version 1 (auto): Claim (hl7.fhir.r4.core#4.0.1), CoverageEligibilityRequest (hl7.fhir.r4.core#4.0.1)\n  - Version 2: ExplanationOfBenefit (hl7.fhir.r4.core#4.0.1)\n\n### Suggested `resolveCollisions` config\n\n.typeSchema({\n    resolveCollisions: {\n        \"urn:fhir:binding:ProcessPriority\": {\n            package: \"hl7.fhir.r4.core#4.0.1\",\n            canonical: \"http://hl7.org/fhir/StructureDefinition/Claim\",\n        },\n    },\n})\n```\n\n- **(selected)** — resolved by your `resolveCollisions` config\n- **(auto)** — picked automatically (most common variant); add to config to make explicit\n\n### Generation\n\nThe generation stage transforms Type Schema into target language code using two complementary approaches:\n\n#### 1. Writer-Based Generation (Programmatic)\n\nFor languages with built-in support (TypeScript, Python, C#), extend the `Writer` class to implement language-specific generators:\n\n- **FileSystemWriter**: Base class providing file I/O, directory management, and buffer handling (both disk and in-memory modes)\n- **Writer**: Extends FileSystemWriter with code formatting utilities (indentation, blocks, comments, line management)\n- **Language Writers** (`TypeScript`, `Python`, `CSharp`): Implement language-specific generation logic by traversing TypeSchema index and generating corresponding types, interfaces, or classes (see also: [Type Schema: Python SDK for FHIR](https://www.health-samurai.io/articles/type-schema-python-sdk-for-fhir))\n\nEach language writer maintains full control over output formatting while leveraging high-level abstractions for common code patterns. Writers follow language idioms and best practices, with optimized output for production use.\n\n**When to use**: Full control needed, complex generation logic, performance-critical, language has a dedicated writer, production-grade output\n\n#### 2. Mustache Template-Based Generation (Declarative)\n\nFor custom languages or formats, use Mustache templates to define code generation rules without programming:\n\n- **Template Files**: Declarative Mustache templates that describe output structure\n- **Configuration**: JSON config file controlling type filtering, naming, and post-generation hooks\n- **ViewModels**: Type Schema automatically transformed into template-friendly data structures\n\nTemplates enable flexible code generation for any language or format (Go, Rust, GraphQL, documentation, configs) by describing the output format rather than implementing generation logic.\n\n**When to use**: Custom language support, quick prototyping, template-driven customization, non-code output\n\n---\n\n### Profile Classes\n\nWhen generating TypeScript with `generateProfile: true`, the generator creates profile wrapper classes that provide a fluent API for working with FHIR profiles. These classes handle complex profile constraints like slicing and extensions automatically.\n\nResource profile classes expose `static readonly resourceType` alongside `canonicalUrl`, `from()` and `createResource()`. A generic FHIR client can use the class itself as a structural descriptor. The resource type comes from the resolved snapshot base; Extension and datatype profile classes do not expose `resourceType`.\n\n```typescript\nimport { observation_bodyweightProfile } from \"./profiles/Observation_observation_bodyweight\";\n\nobservation_bodyweightProfile.resourceType; // \"Observation\"\nobservation_bodyweightProfile.canonicalUrl; // \"http://hl7.org/fhir/StructureDefinition/bodyweight\"\n```\n\n```typescript\nimport { observation_bpProfile as bpProfile } from \"./profiles/Observation_observation_bp\";\n\n// create() auto-sets fixed values (code, meta.profile) and required slice stubs\nconst bp = bpProfile.create({\n    status: \"final\",\n    subject: { reference: \"Patient/pt-1\" },\n});\n\n// Slice setters — discriminator values (LOINC codes) applied automatically\n// Single-variant choice types (value[x] → valueQuantity) are flattened:\nbp.setVSCat({ text: \"Vital Signs\" })\n    .setSystolicBP({ value: 120, unit: \"mmHg\" })\n    .setDiastolicBP({ value: 80, unit: \"mmHg\" })\n    .setEffectiveDateTime(\"2024-06-15\");\n\nbp.validate(); // [] — valid\n\n// Get plain FHIR JSON — ready for API calls, storage, etc.\nconst obs = bp.toResource();\n// obs.component[0].valueQuantity.value === 120\n// obs.component[0].code.coding[0].code === \"8480-6\"\n```\n\n**Slicing & Choice Type Flattening:**\n\n```typescript\n// Flat getter (default) — discriminator stripped, choice type flattened\nbp.getSystolicBP();        // { value: 120, unit: \"mmHg\" }\n\n// Raw getter — full FHIR element including discriminator values\nbp.getSystolicBP('raw');   // { code: { coding: [...] }, valueQuantity: { value: 120, ... } }\n```\n\n**Wrapping Existing Resources:**\n\n```typescript\n// Wrap any resource to read slices\nconst bp2 = bpProfile.from(existingObservation);\nbp2.getSystolicBP();       // { value: 120, unit: \"mmHg\" }\nbp2.getVSCat();            // { text: \"Vital Signs\" }\nbp2.getEffectiveDateTime(); // \"2024-06-15\"\n```\n\n**Validation:**\n\n```typescript\nconst errors = bp.validate();\n// [] — empty means valid\n// [\"effective: at least one of effectiveDateTime, effectivePeriod is required\"]\n```\n\nSee [examples/typescript-r4-us-core/](examples/typescript-r4-us-core/) for R4 and US Core profile tests.\n\nPython (`generateProfile: true`) produces equivalent profile classes — `create()`, typed accessors, and `validate()` — wrapping a Pydantic model via `_resource`. See [examples/python-r4-us-core/](examples/python-r4-us-core/).\n\n## Support\n\n- [Issue Tracker](https://github.com/atomic-ehr/codegen/issues)\n\n---\n\nBuilt by the Atomic Healthcare team\n","readmeFilename":"README.md"}