fhir-developer-skill

# FHIR Developer Skill

## Quick Reference

### HTTP Status Codes
| Code | When to Use |
|------|-------------|
| `200 OK` | Successful read, update, or search |
| `201 Created` | Successful create (include `Location` header) |
| `204 No Content` | Successful delete |
| `400 Bad Request` | Malformed JSON, wrong resourceType |
| `401 Unauthorized` | Missing, expired, revoked, or malformed token (RFC 6750) |
| `403 Forbidden` | Valid token but insufficient scopes |
| `404 Not Found` | Resource doesn't exist |
| `412 Precondition Failed` | If-Match ETag mismatch (NOT 400!) |
| `422 Unprocessable Entity` | Missing required fields, invalid enum values, business rule violations |

### Required Fields by Resource (FHIR R4)
| Resource | Required Fields | Everything Else |
|----------|-----------------|-----------------|
| Patient | *(none)* | All optional |
| Observation | `status`, `code` | Optional |
| Encounter | `status`, `class` | Optional (including `subject`, `period`) |
| Condition | `subject` | Optional (including `code`, `clinicalStatus`) |
| MedicationRequest | `status`, `intent`, `medication[x]`, `subject` | Optional |
| Medication | *(none)* | All optional |
| Bundle | `type` | Optional |

---

## Required vs Optional Fields (CRITICAL)

**Only validate fields with cardinality starting with "1" as required.**

| Cardinality | Required? |
|-------------|-----------|
| `0..1`, `0..*` | NO |
| `1..1`, `1..*` | YES |

**Common mistake**: Making `subject` or `period` required on Encounter. They are 0..1 (optional).

---

## Value Sets (Enum Values)

Invalid enum values must return `422 Unprocessable Entity`.

### Patient.gender
`male | female | other | unknown`

### Observation.status
`registered | preliminary | final | amended | corrected | cancelled | entered-in-error | unknown`

### Encounter.status
`planned | arrived | triaged | in-progress | onleave | finished | cancelled | entered-in-error | unknown`

### Encounter.class (Common Codes)
| Code | Display | Use |
|------|---------|-----|
| `AMB` | ambulatory | Outpatient visits |
| `IMP` | inpatient encounter | Hospital admissions |
| `EMER` | emergency | Emergency department |
| `VR` | virtual | Telehealth |

### Condition.clinicalStatus
`active | recurrence | relapse | inactive | remission | resolved`

### Condition.verificationStatus
`unconfirmed | provisional | differential | confirmed | refuted | entered-in-error`

### MedicationRequest.status
`active | on-hold | cancelled | completed | entered-in-error | stopped | draft | unknown`

### MedicationRequest.intent
`proposal | plan | order | original-order | reflex-order | filler-order | instance-order | option`

### Bundle.type
`document | message | transaction | transaction-response | batch | batch-response | history | searchset | collection`

---

## Validation Pattern

**Python/FastAPI:**
```python
from fastapi import FastAPI
from fastapi.responses import JSONResponse

app = FastAPI()

def operation_outcome(severity: str, code: str, diagnostics: str):
    return {
        "resourceType": "OperationOutcome",
        "issue": [{"severity": severity, "code": code, "diagnostics": diagnostics}]
    }

VALID_OBS_STATUS = {"registered", "preliminary", "final", "amended",
                    "corrected", "cancelled", "entered-in-error", "unknown"}

@app.post("/Observation", status_code=201)
async def create_observation(data: dict):
    if not data.get("status"):
        return JSONResponse(status_code=422, content=operation_outcome(
            "error", "required", "Observation.status is required"
        ), media_type="application/fhir+json")

    if data["status"] not in VALID_OBS_STATUS:
        return JSONResponse(status_code=422, content=operation_outcome(
            "error", "value", f"Invalid status '{data['status']}'"
        ), media_type="application/fhir+json")
    # ... create resource
```

**TypeScript/Express:**
```typescript
const VALID_OBS_STATUS = new Set(['registered', 'preliminary', 'final', 'amended',
  'corrected', 'cancelled', 'entered-in-error', 'unknown']);

app.post('/Observation', (req, res) => {
  if (!req.body.status) {
    return res.status(422).contentType('application/fhir+json')
      .json(operationOutcome('error', 'required', 'Observation.status is required'));
  }
  if (!VALID_OBS_STATUS.has(req.body.status)) {
    return res.status(422).contentType('application/fhir+json')
      .json(operationOutcome('error', 'value', `Invalid status '${req.body.status}'`));
  }
  // ... create resource
});
```

**Pydantic v2 Models** (use `Literal`, not `const=True`):
```python
from typing import Literal
from pydantic import BaseModel

class Patient(BaseModel):
    resourceType: Literal["Patient"] = "Patient"
    id: str | None = None
    gender: Literal["male", "female", "other", "unknown"] | None = None
```

---

## Coding Systems (URLs)

| System | URL |
|--------|-----|
| LOINC | `http://loinc.org` |
| SNOMED CT | `http://snomed.info/sct` |
| RxNorm | `http://www.nlm.nih.gov/research/umls/rxnorm` |
| ICD-10 | `http://hl7.org/fhir/sid/icd-10` |
| v3-ActCode | `http://terminology.hl7.org/CodeSystem/v3-ActCode` |
| Observation Category | `http://terminology.hl7.org/CodeSystem/observation-category` |
| Condition Clinical | `http://terminology.hl7.org/CodeSystem/condition-clinical` |
| Condition Ver Status | `http://terminology.hl7.org/CodeSystem/condition-ver-status` |

### Common LOINC Codes (Vital Signs)
| Code | Description |
|------|-------------|
| `8867-4` | Heart rate |
| `8480-6` | Systolic blood pressure |
| `8462-4` | Diastolic blood pressure |
| `8310-5` | Body temperature |
| `2708-6` | Oxygen saturation (SpO2) |

---

## Data Type Patterns

### Coding (direct) vs CodeableConcept (wrapped)

**Coding** - Used by `Encounter.class`:
```json
{"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", "code": "AMB"}
```

**CodeableConcept** - Used by `Observation.code`, `Condition.code`:
```json
{"coding": [{"system": "http://loinc.org", "code": "8480-6"}], "text": "Systolic BP"}
```

### Reference
```json
{"reference": "Patient/123", "display": "John Smith"}
```

### Identifier
```json
{"system": "http://hospital.example.org/mrn", "value": "12345"}
```

---

## Common Mistakes

| Mistake | Correct Approach |
|---------|------------------|
| Making `subject` or `period` required on Encounter | Both are 0..1 (optional). Only `status` and `class` are required |
| Using CodeableConcept for `Encounter.class` | `class` uses Coding directly: `{"system": "...", "code": "AMB"}` |
| Returning 400 for ETag mismatch | Use `412 Precondition Failed` for If-Match failures |
| Returning 400 for invalid enum values | Use `422 Unprocessable Entity` for validation errors |
| Forgetting Content-Type header | Always set `Content-Type: application/fhir+json` |
| Missing Location header on create | Return `Location: /Patient/{id}` with 201 Created |

---

## Resource Structures

For complete JSON examples of all resources, see **[references/resource-examples.md](references/resource-examples.md)**.

Quick reference for error responses:

```json
{
  "resourceType": "OperationOutcome",
  "issue": [{"severity": "error", "code": "not-found", "diagnostics": "Patient/123 not found"}]
}
```

---

## RESTful Endpoints

```
POST   /[ResourceType]              # Create (returns 201 + Location header)
GET    /[ResourceType]/[id]         # Read
PUT    /[ResourceType]/[id]         # Update
DELETE /[ResourceType]/[id]         # Delete (returns 204)
GET    /[ResourceType]?param=value  # Search (returns Bundle)
GET    /metadata                    # CapabilityStatement
POST   /                            # Bundle transaction/batch
```

---

## Conditional Operations

**If-Match** (optimistic locking):
- Client sends: `If-Match: W/"1"`
- Mismatch returns `412 Precondition Failed`

**If-None-Exist** (conditional create):
- Client sends: `If-None-Exist: identifier=http://mrn|12345`
- Match exists: return existing (200)
- No match: create new (201)

---

## Reference Files

For detailed guidance, see:

- **[Resource Examples](references/resource-examples.md)**: Complete JSON structures for Patient, Observation, Encounter, Condition, MedicationRequest, OperationOutcome, CapabilityStatement
- **[SMART on FHIR Authorization](references/smart-auth.md)**: OAuth flows, scope syntax (v1/v2), backend services, scope enforcement
- **[Pagination](references/pagination.md)**: Search result pagination, `_count`/`_offset` parameters, link relations
- **[Bundle Operations](references/bundles.md)**: Transaction vs batch semantics, atomicity, processing order

---

## Implementation Checklist

1. Set `Content-Type: application/fhir+json` on all responses
2. Return `meta.versionId` and `meta.lastUpdated` on resources
3. Return `Location` header on create: `/Patient/{id}`
4. Return `ETag` header: `W/"{versionId}"`
5. Use OperationOutcome for all error responses
6. Validate required fields → 422 for missing
7. Validate enum values → 422 for invalid
8. Search returns Bundle with `type: "searchset"`

---

## Quick Start Script

To scaffold a new FHIR API project with correct Pydantic v2 patterns:

```bash
python scripts/setup_fhir_project.py my_fhir_api
```

Creates a FastAPI project with correct models, OperationOutcome helpers, and Patient CRUD endpoints.