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Intro

The Medplum CLI (Command Line Interface) is a set of command line tools to quickly deploy Medplum web applications and Medplum bots.

Installation​

Add globally:

npm install --global @medplum/cli

Or add as a package dependency:

npm install @medplum/cli

Authentication​

Use one of these authentication options:

  1. Stored credentials in ~/.medplum/credentials. You can use the medplum login command (see below) to automatically create this file.
  2. Client credentials in environment variables MEDPLUM_CLIENT_ID and MEDPLUM_CLIENT_SECRET. dotenv is enabled, so you can store them in a .env file.
  3. Client credentials in optional command flags.
  • --client-id <clientId>
    • FHIR server client id
  • --client-secret <clientSecret>
    • FHIR server client id

Usage​

If installed globally, you can use the medplum command directly:

medplum <command> <args>

If installed as a package dependency, you can use the medplum command via npx:

npx medplum <command> <args>

By default, the medplum command uses the Medplum hosted API at "https://api.medplum.com". If you want to use the medplum command against your own self-hosted server, you can use the MEDPLUM_BASE_URL environment variable. dotenv is enabled, so you can store this value in a .env file.

optional flags​

  • --base-url <baseUrl>
    • FHIR server base url
  • --fhir-url-path <fhirUrlPath>
    • FHIR server url path
  • --tokenUrl <tokenUrl>
    • FHIR server token url
  • --authorizeUrl <authorizeUrl>
    • FHIR server authorize url

Auth​

login​

The login command opens a web browser to a Medplum authentication page.

On successful login, the command writes credentials to disk at ~/.medplum/credentials.

The medplum command will then load those credentials on all future runs.

Example:

medplum login

whoami​

The whoami command displays whether the client is authenticated, and, if so, the name of the current user and current Medplum project.

medplum whoami

RESTful Operations​

The medplum command can be used as a convenient tool for basic Medplum CRUD and RESTful operations.

While all API endpoints are available to any command line HTTP client such as curl or wget, there are a few advantages to using the medplum command:

  1. Authentication and credentials - login once using the login command, and the Authorization header will be set automatically.
  2. URL prefixes - adds the base URL (i.e., "https://api.medplum.com") and FHIR path prefix (i.e., "fhir/R4/").
  3. Pretty print - formats the JSON with spaces and newlines.
  4. Medplum extended mode - adds the X-Medplum HTTP header for private Medplum fields.

get​

Makes an HTTP GET request.

medplum get <url>

Example: Search for patients:

medplum get 'Patient?name=homer'

Example: Read patient by ID:

medplum get Patient/$id

flags​

  • --as-transaction
    • Convert the output response to a transaction bundle

post​

Makes an HTTP POST request.

medplum post <url> <body>

Example: Create a patient:

medplum post Patient '{"resourceType":"Patient","name":[{"family":"Simpson"}]}'

Example: Invoke a FHIR operation:

medplum post 'Patient/$validate' '{"resourceType":"Patient","name":[{"family":"Simpson"}]}'

put​

Makes an HTTP PUT request.

medplum put <url> <body>

Example: Update a patient:

medplum put Patient/$id '{"resourceType":"Patient","name":[{"family":"Simpson"}]}'

patch​

Makes an HTTP PATCH request.

medplum patch <url> <body>

Example: Update a patient with JSONPatch:

medplum patch Patient/$id '[{"op":"add","path":"/active","value":[true]}]'

delete​

Makes an HTTP DELETE request.

medplum delete <url>

Example: Delete patient by ID:

medplum delete Patient/$id

Project​

project will have administration commands for visibilty and management

current​

Sees your current project

medplum project current

list​

Sees your list of project ids and names

medplum project list

switch​

Switching to another project from the current one

medplum project switch <projectId>

invite​

Invite a user to a project

medplum project invite <firstName> <lastName> <email>

optional flags for invite​

  • --send-email

    • If you want to send the email when inviting the user

  • --admin

    • If the user you are inviting is an admin

  • --role -r <role>

    • The type of role the new user will have
    • Choices are Patient, Practitioner, and RelatedPerson
      • Default will be Practitioner

AWS​

aws includes commands for creating and managing AWS resources.

The AWS commands require AWS authentication and access credentials. Please make sure your credentials are configured before using the aws commands.

caution

The aws commands are in beta, and likely to change.

list​

List your Medplum deployments. This command lists AWS CloudFormation stacks with the medplum:environment tag.

medplum aws list

describe​

Describe a Medplum deployment. Displays select AWS resources such as ECS Cluster, ECS Service, and S3 buckets from the AWS CloudFormation stack with the corresponding medplum:environment tag.

medplum aws describe <name>

update-app​

Updates the app S3 buckeet in a Medplum deployment to the latest version.

medplum aws update-app <name>

update-server​

Updates the ECS Service in a Medplum deployment to the latest version.

medplum aws update-server <name>

Bots​

Bots Config file​

Create a Medplum config file called medplum.config.json:

{
  "bots": [
    {
      "name": "hello-world",
      "id": "f0465c2e-11d4-4c36-b834-8e86f7472b4b",
      "source": "src/index.ts",
      "dist": "dist/index.js"
    }
  ]
}

The name property is a friendly name you can use to reference the Bot in commands.

The id property refers to the Bot ID in your Medplum project.

The source property is the file path to the original source. When you "save" the Bot, the contents of this file will be saved to the Bot code property. This file can be JavaScript or TypeScript.

The dist property is the optional file path to the compiled source. If omitted, the command falls back to using the source property. When you "deploy" the Bot, the contents of this file will be deployed to the Bot runtime. This file must be JavaScript.

bot save​

Updates the code value on a Bot resource

Syntax:

npx medplum bot save <bot name>

Example:

npx medplum bot save hello-world

bot deploy​

Deploys the Bot code

Syntax:

npx medplum bot deploy <bot name>

Example:

npx medplum bot deploy hello-world

bot create​

Creates a bot and saves it

Syntax:

npx medplum bot create <bot name> <project id> <source file> <dist file>

Bots Example​

Create a Medplum config file medplum.config.json:

{
  "bots": [
    {
      "name": "hello-world",
      "id": "f0465c2e-11d4-4c36-b834-8e86f7472b4b",
      "source": "src/hello-world.ts",
      "dist": "dist/hello-world.js"
    }
  ]
}

Replace the sample id with your Bot's ID.

Write your bot in src/hello-world.ts. This can be TypeScript. It can reference @medplum/core and node-fetch:

import { MedplumClient } from '@medplum/core';
import { Resource } from '@medplum/fhirtypes';

export async function handler(medplum: MedplumClient, event: BotEvent): Promise<any> {
  console.log('Hello world');
}

You can use the Medplum CLI to save it:

npx medplum bot save hello-world

Compile with vanilla tsc (no bundler required)

npx tsc

The result will be JavaScript output in dist/hello-world.js:

export async function handler(medplum, input) {
  console.log('Hello world');
}

You can then use the Medplum CLI to deploy it.

npx medplum bot deploy hello-world

Bulk​

bulk includes commands for requesting bulk data export from a FHIR resource server. bulk also includes the functionality to import ndjson files generated by bulk data exports from other systems.

export​

bulk export handles the request flows documented at https://build.fhir.org/ig/HL7/bulk-data/export.html and downloads all attachment files.

medplum bulk export [options]
optional flags for bulk export​

  • -e, --export-level <exportLevel>

    • Export level. Defaults to system level export.

      • "Group/:id" - Group of Patients
      • "Patient" - All Patients.

  • -t, --types <types>

    • Resource types to export

  • -s, --since <since>

    • Resources will be included in the response if their state has changed after the supplied time (e.g. if Resource.meta.lastUpdated is later than the supplied _since time).

import​

bulk import imports ndjson files generated by bulk data exports.

medplum bulk import [options] <filename>
optional flags for bulk import​
  • --num-resources-per-request <numResourcesPerRequest>
    • number of resources to import per batch request. Defaults to 25.