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fhir-controller-cli

v1.4.0

Published

FHIR Controller CLI utilities.

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Links

Git

Maintainers

preston.leepreston.lee

Keywords

ClinicalQualityLanguageCQLCDSFHIRcqlHAPI

Readme

FHIR Controller Command Line Interface (CLI) Utilities

Build Status

The fhir-controller command line utility for interacting with remote FHIR servers from an on-premise or cloud host. This cross-platform executable provides:

  • Command line interface for FHIR server operations
  • Ability to upload a directory of Synthea FHIR output directly to a FHIR server in the correct dependency sequence
  • Upload terminology systems (SNOMED CT, LOINC, RxNorm) to FHIR servers as CodeSystem resources
  • Polling and auto-import capabilities for FHIR Controller deployments

Installation

NPM Package

# Install globally
npm install -g fhir-controller-cli

# Or use with npx (no installation required)
npx fhir-controller-cli help

Docker Image

# Get high-level subcommand help
docker run --rm p3000/fhir-controller-cli:latest help

# Example of headless polling and auto-loading by reference to a FHIR Controller stack.json file (HTTP URL)
# Data loading will be triggered whenever the server confirms the absence of a special AuditEvent import record
docker run --rm --pull always p3000/fhir-controller-cli:latest poll-auditevent-and-trigger-import http://fhir.example.com/fhir https://stack.foundry.hl7.org/stack.json -i 5

# Local manifest on the host: bind-mount the directory that contains stack.json and referenced data files, then pass the in-container path
docker run --rm --pull always -v /path/to/stack-dir:/manifest p3000/fhir-controller-cli:latest poll-auditevent-and-trigger-import http://fhir.example.com/fhir /manifest/stack.json

# Example of uploading terminology systems
docker run --rm --pull always p3000/fhir-controller-cli:latest terminology import /data/loinc.csv http://fhir.example.com/fhir /tmp/staging --system loinc
docker run --rm --pull always p3000/fhir-controller-cli:latest terminology import /data/snomed/ http://fhir.example.com/fhir /tmp/staging --system snomed
docker run --rm --pull always p3000/fhir-controller-cli:latest terminology import /data/rxnorm.csv http://fhir.example.com/fhir /tmp/staging --system rxnorm

# Advanced options examples
docker run --rm --pull always p3000/fhir-controller-cli:latest terminology import /data/loinc.csv http://fhir.example.com/fhir /tmp/staging --system loinc --batch-size 2000 --verbose
docker run --rm --pull always p3000/fhir-controller-cli:latest terminology import /data/snomed/ http://fhir.example.com/fhir /tmp/staging --system snomed --keep-temporary --replace
docker run --rm --pull always p3000/fhir-controller-cli:latest terminology import /data/rxnorm.csv http://fhir.example.com/fhir /tmp/staging --system rxnorm --dry-run

Available Commands

Synthea Upload

Upload Synthea-generated FHIR resources to a FHIR server:

# Upload Synthea directory
fhir-controller synthea-upload /path/to/synthea/output/ http://localhost:8080/fhir

# With dry-run option
fhir-controller synthea-upload /path/to/synthea/output/ http://localhost:8080/fhir --dry-run

Polling and Auto-Import

Monitor a FHIR server for AuditEvents and automatically trigger imports when the server has no matching import AuditEvent yet.

The second argument is the stack manifest (stack.json): an HTTP(S) URL, a file:// URL, or a filesystem path. Relative paths are resolved from the current working directory; a leading ~/ expands to your home directory (same as other commands). Data files listed in the manifest are loaded from the same base as the manifest (URL resolution for remote manifests, directory-relative paths for local manifests).

# Poll and import using a remote manifest URL
fhir-controller poll-auditevent-and-trigger-import http://fhir.example.com/fhir https://stack.foundry.hl7.org/stack.json

# Local manifest (and local bundle paths next to it)
fhir-controller poll-auditevent-and-trigger-import http://fhir.example.com/fhir ./config/stack.json

# Only import rows tagged for a given scenario (manifest `scenarios[].id`; rows may list that id under `scenarios`)
fhir-controller poll-auditevent-and-trigger-import http://fhir.example.com/fhir https://stack.foundry.hl7.org/stack.json --scenario partial

# Custom polling interval (seconds), verbose logging, dry run (no POST to FHIR)
fhir-controller poll-auditevent-and-trigger-import http://fhir.example.com/fhir https://stack.foundry.hl7.org/stack.json --interval 300 --verbose --dry-run

# One shot: poll once, import if the server has no matching AuditEvent, then exit (no repeat interval)
fhir-controller poll-auditevent-and-trigger-import http://fhir.example.com/fhir ./config/stack.json --exit --dry-run

Polling command options

  • --exit: run a single poll cycle (and manifest import if triggered) then exit; --interval is ignored after that one cycle
  • --scenario <scenario_id>: restrict imports to manifest data rows for that scenario; rows with no scenarios array (or an empty one) still load for every scenario
  • -i, --interval <seconds>: minimum time between polls (default 3600)
  • -v, --verbose: extra debug output
  • -d, --dry-run: log actions without uploading to the FHIR server
  • --audit-event-system / --audit-event-code: match and create the import AuditEvent type (defaults match the examples above)

Terminology Imports

The CLI supports uploading major terminology systems to FHIR servers:

  • SNOMED CT US Edition: Clinical terminology
  • LOINC: Laboratory and clinical observations
  • RxNorm: Clinical drugs and medications

CLI Options

The terminology import command supports the following options:

  • --system <system>: Terminology system to import (snomed, loinc, rxnorm) - Required
  • --dry-run: Perform a dry run without uploading any resources
  • --verbose: Enable verbose debugging mode
  • --keep-temporary: Keep temporary files after upload for debugging
  • --replace: Delete existing CodeSystem and ValueSet before importing new ones
  • --batch-size <size>: Number of concepts to process in each batch (default: 1000)
  • --skip-preprocess: Skip preprocessing stage (use most recent files in temp directory)
  • --skip-split: Skip splitting stage (use most recent files in temp directory)
  • --skip-upload: Skip upload stage (only preprocess and split)

Download Terminology Data

SNOMED CT US Edition

  • Download: https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
  • Format: .zip file (extract before use)

LOINC

  • Download from: https://loinc.org/downloads/
  • Format: .zip file (extract before use)

RxNorm

  • Download from: https://www.nlm.nih.gov/research/umls/rxnorm/
  • Format: .zip file (extract before use)
# Upload individual terminology systems

# SNOMED
fhir-controller terminology import ~/Developer/terminologies/SnomedCT_ManagedServiceUS_PRODUCTION_US1000124_20250901T120000Z http://localhost:8080/fhir tmp -v --keep-temporary --system snomed --replace

# LOINC
fhir-controller terminology import ~/Developer/terminologies/Loinc_2.81 http://localhost:8080/fhir tmp -v --keep-temporary --system loinc --replace

# RxNorm
fhir-controller terminology import ~/Developer/terminologies/RxNorm_full_09022025 http://localhost:8080/fhir tmp -v --keep-temporary --system rxnorm --replace

Development & Testing Usage

# Run the CLI directly from source
tsx src/bin/fhir-controller.ts ...

This software is released under the Apache 2.0 license. Copyright © 2017+ Preston Lee.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/preston/marketplace. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.