fhir-validation

name

fhir-validation

description

FHIR validation specialist. Use when validating FHIR resources, profiles, or Implementation Guides against conformance rules. Covers Firely Terminal (.NET, profile-aware, free + paid QC rules), HL7 Java validator (thorough, profile-aware), and Python schema validation. Guides project assessment, runs both profile-aware validators for consistency, and supports CI/CD via FirelyTeam/firely-terminal-pipeline.

FHIR Validation Skill

Expert guidance for validating FHIR resources, profiles, and Implementation Guides. This skill assesses your project setup, selects the right validators, and runs them in the right order.

Firely Terminal commands: Only use commands that exist in Firely Terminal. This https://docs.fire.ly/projects/Firely-Terminal/Command-Reference.html is the authoritative source — do not invent command names, flags, or parameters. If you are unsure whether a command or flag exists, look it up in that file before suggesting it.

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Validation Approaches

There are three approaches. Use profile-aware validators (Firely Terminal and/or Java) for real conformance checking.

Approach	Tool	Profile-aware	Speed	Requires
Firely Terminal (.NET SDK)	fhir check / fhir validate	Yes	Fast	.NET SDK 8
HL7 Java Validator	validator_cli.jar	Yes	Slower	Java
Python fhir.resources	fhir.resources lib	No — schema only	Fastest	Python

Firely Terminal is built around an internal resource stack. All resource operations (push, validate, snapshot, etc.) act on that stack. It uses the same validation engine as Simplifier.net and Forge.

• Free tier (with Simplifier.net account): full profile-aware validation via fhir check or fhir validate
• Paid tier: adds QC business rules via .rules.yaml on top of fhir check
• No account: fhir validate loop only

HL7 Java Validator is the official HL7 reference validator — thorough but slower. Best run alongside Firely Terminal to cross-check results.

Python fhir.resources performs JSON schema validation only. It does not check profile constraints, slices, or FHIRPath invariants. Use only for in-app embedded validation where no external tool can be invoked.

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Before You Start

Three quick checks before running any validator:

1. FSH project? — if sushi-config.yaml and .fsh files in input/fsh/ are present, compile first:

   sushi build    # compiles FSH → fsh-generated/resources/
   

   Fix any SUSHI errors before validating. Never edit fsh-generated/ — it is regenerated on every build.

2. Check tooling availability (if unsure):

   dotnet --version   # .NET SDK 8+ required by Firely Terminal
   fhir --version     # Firely Terminal installation
   java -version      # Java for HL7 Java validator
   

   If fhir --version fails, Firely Terminal is not installed. Install it with dotnet tool install -g firely.terminal before proceeding.

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Phase 1 — Firely Terminal Validation

For any Firely Terminal command not shown in this skill, look it up in references/firely_terminal_commands.md before suggesting it — never guess flags or subcommands.

Install

dotnet tool install -g firely.terminal   # first time
dotnet tool update -g firely.terminal    # to update

Install dependencies

Check for package.json first. If it is missing, run fhir init to create a minimal one, then restore:

if (-not (Test-Path "package.json")) {
    fhir init    # creates a default package.json; edit name/version/dependencies as needed
}
fhir restore     # downloads declared dependencies; without this, validators may produce spurious "unknown profile" errors

Run validation

Preferred — fhir check (full profile-aware validation; also runs QC rules if .rules.yaml files are present):

Always try fhir check first. It runs full validation regardless of whether .rules.yaml files exist — the paid license only adds the QC rules layer on top.

fhir check

If not authenticated:

fhir login email=[e-mail] password=yourpassword
fhir check

Fallback — fhir validate loop (use only when no Simplifier.net account is available):

Use fhir validate [file] --push to validate a file and keep the resulting OperationOutcome on the stack for later review. On Windows, avoid absolute backslash paths — pass relative paths or use Push-Location to cd into the folder first and pass a bare filename.

# PowerShell
$folders = @("./input/resources", "./input/examples", "./fsh-generated/resources")
foreach ($folder in $folders) {
    if (Test-Path $folder) {
        Push-Location $folder
        Get-ChildItem -Filter "*.json" | ForEach-Object {
            fhir validate $_.Name --push
        }
        Pop-Location
    }
}

Review and process results

After validation, the stack contains the original resources interleaved with OperationOutcomes. Bundle and inspect:

fhir bundle      # collect all stack items into one Bundle
fhir save validation-results.json --json --pretty # Save to file for large result sets or programmatic processing

Process the saved results with Python:

import json
from pathlib import Path

def summarize_validation_results(path="validation-results.json"):
    data = json.loads(Path(path).read_text())
    entries = data.get("entry", []) if data.get("resourceType") == "Bundle" else [{"resource": data}]

    issues = []
    for entry in entries:
        resource = entry.get("resource", {})
        if resource.get("resourceType") == "OperationOutcome":
            for issue in resource.get("issue", []):
                issues.append({
                    "severity": issue.get("severity"),
                    "message": (issue.get("details") or {}).get("text") or issue.get("diagnostics", ""),
                    "location": issue.get("expression") or issue.get("location") or [],
                })

    by_severity = {}
    for i in issues:
        by_severity.setdefault(i["severity"], []).append(i)

    for severity in ("error", "warning", "information"):
        items = by_severity.get(severity, [])
        if items:
            print(f"\n{severity.upper()} ({len(items)}):")
            for i in items:
                loc = ", ".join(i["location"]) if isinstance(i["location"], list) else str(i["location"])
                print(f"  {i['message']}" + (f"  [{loc}]" if loc else ""))

summarize_validation_results()

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Phase 2 — HL7 Java Validator

Run this alongside Phase 1 to cross-check results.

Setup

Locate an existing validator_cli.jar anywhere in the project first:

# PowerShell
$jarItem = Get-ChildItem -Recurse -Filter "validator_cli.jar" -ErrorAction SilentlyContinue | Select-Object -First 1
if ($jarItem) {
    $jar = $jarItem.FullName -replace '\\', '/'
} else {
    New-Item -ItemType Directory -Force -Path "./input-cache" | Out-Null
    Invoke-WebRequest -Uri "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar" `
      -OutFile "./input-cache/validator_cli.jar"
    $jar = "./input-cache/validator_cli.jar"
}

Run validation

# Validate against base FHIR spec
java -jar $jar patient.json -version 4.0.1

# Validate against a specific IG and profile
java -jar $jar patient.json `
    -version 4.0.1 `
    -ig hl7.fhir.us.core#6.1.0 `
    -profile http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient

# Validate multiple files
Get-ChildItem ./input/resources -Filter *.json | ForEach-Object {
    java -jar $jar $_.FullName -version 4.0.1
}

Local conformance resources (-ig) guidance

When validating against local project conformance artifacts, do not use -ig .. Point -ig to concrete folders that actually contain IG resources (for example StructureDefinition-*.json, ValueSet-*.json, CodeSystem-*.json).

Typical local folders to include when they exist:

• ./fsh-generated/resources (compiled FSH output)
• ./input/resources (hand-authored conformance resources)
• ./package (IG Publisher package output, if present)

Use one -ig per folder or package:

java -jar $jar $OUTPUT_FILE `
    -version 4.0.1 `
    -ig ./fsh-generated/resources `
    -ig ./input/resources `
    -ig "nictiz.fhir.nl.r4.zib2020#0.12.0-beta.4" `
    -ig "nictiz.fhir.nl.r4.nl-core#0.12.0-beta.4"

PowerShell helper to add only existing local IG folders:

$candidateIgDirs = @("./fsh-generated/resources", "./input/resources", "./package")
$igArgs = @()
foreach ($dir in $candidateIgDirs) {
        if (Test-Path $dir) {
                $igArgs += @("-ig", $dir)
        }
}

java -jar $jar $OUTPUT_FILE -version 4.0.1 `
    @igArgs `
    -ig "nictiz.fhir.nl.r4.zib2020#0.12.0-beta.4" `
    -ig "nictiz.fhir.nl.r4.nl-core#0.12.0-beta.4"

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Cross-Checking Results

After running both validators, compare their output:

• Issues flagged by both validators — high confidence, real conformance problems; prioritise fixing these
• Issues flagged by only one validator — investigate; may be a validator-specific edge case or tool difference
• Report any discrepancies clearly so the user can decide which to act on

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Fixing Errors in FSH Projects

If the project uses FSH (SUSHI), never edit files in fsh-generated/ — that folder is deleted and regenerated on every sushi build. All fixes must be made in the .fsh source files under input/fsh/.

Tracing an error back to its FSH source

Validation errors reference the generated JSON file (e.g. fsh-generated/resources/StructureDefinition-MyProfile.json). The naming pattern is {ResourceType}-{id}.json. To find the FSH source:

1. Note the resource id from the error (e.g. MyProfile)
2. Search for it in input/fsh/: Get-ChildItem input/fsh -Recurse -Filter *.fsh | Select-String 'Id: MyProfile'
3. The containing .fsh file is where the fix goes

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Python — In-App / Embedded Validation Only

Use fhir.resources only when validation logic must be embedded inside an application without invoking external tools. This is schema-only — profiles, slices, and FHIRPath invariants are not checked.

from fhir.resources import get_fhir_model_class

def validate_resource_schema(resource_data: dict) -> bool:
    """Schema-level validation only. Use Firely Terminal or Java validator for full conformance."""
    try:
        resource_type = resource_data.get('resourceType')
        resource_class = get_fhir_model_class(resource_type)
        resource_class(**resource_data)
        return True
    except Exception as e:
        print(f"Validation error: {e}")
        return False

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CI/CD

Validation can be automated in CI/CD pipelines using the official FirelyTeam/firely-terminal-pipeline GitHub Action, which runs Firely Terminal (and optionally the Java validator) on every push or pull request.

See references/firely_terminal.md for a full workflow example, or the source documentation at https://github.com/FirelyTeam/firely-terminal-pipeline.

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References

• Authoritative Firely Terminal command reference (all commands, parameters, and documentation): https://docs.fire.ly/projects/Firely-Terminal/Command-Reference.html
• references/firely_terminal.md — workflow guide including, quality control, CI/CD GitHub Actions setup
• Firely Terminal docs: https://docs.fire.ly/projects/Firely-Terminal/
• firely-terminal-pipeline: https://github.com/FirelyTeam/firely-terminal-pipeline