FHIR Research Data Finder

This is a query tool that allows you search a FHIR server’s resources to select a cohort of patients, and then pull data for those patients.

Demo

Try it out on the demo page.

How to run it locally

1. Install required node packages:

    npm install
   

2. Run app in development mode (locally):

    npm start
   

Testing and building

1. Run all tests (unit + e2e)

    npm test
   

2. Build the app for production

    npm run build
   

   The generated files are in public directory, which can be moved to a production server.

3. Run visual bundle analyzer (calculate uncompressed size)

    npm run analyze
   

4. Run visual bundle analyzer (calculate gzip size)

    npm run analyze-gzip
   

Connecting to a new server that requires OAuth2

If you want to connect to your own OAuth2 server, you will need to have a server program which holds your client secret and handles OAuth login calls from RDF. Here is some sample code for the server program, for the case of a Google Health & Node.js environment:

1. app.js

const express = require('express');
const oauth2Router = require('./routes/oauth2');
const app = express();
app.use(express.json());
app.use(express.urlencoded({extended: true}));
app.use('/oauth2', oauth2Router);
module.exports = app;

2. oauth2.js (router)

const express = require('express');
const router = express.Router();
const config = require('../config.json');
const {AuthorizationCode} = require('simple-oauth2');
 const googleHealthClient = new AuthorizationCode({
  client: {
    id: config["google_health_client_id"],
    secret: config["google_health_client_secret"]
  },
  auth: {
   authorizeHost: config["google_health_authorize_host"],
   authorizePath: config["google_health_authorize_path"],
   tokenHost: config["google_health_token_host"],
   tokenPath: config["google_health_token_path"]
  }
});
const rdfHostPath = "/fhir/research-data-finder";

function getCallbackUrl(req) {
  return `${req.protocol}://${req.headers.host}${rdfHostPath}${config["google_health_callback_url"]}`;
}

/* Log in. */
router.get('/login', function (req, res) {
  const authorizationUri = googleHealthClient.authorizeURL({
    redirect_uri: getCallbackUrl(req),
    scope: config["google_health_scope"]
  });
  return res.redirect(authorizationUri);
});

/* Callback service parsing the authorization token and asking for the access token. */
router.get('/callback', async function (req, res) {
  const {code} = req.query;
  const options = {
    code,
    redirect_uri: getCallbackUrl(req)
  };
  try {
    const accessToken = await googleHealthClient.getToken(options);
    return res.status(200).json(accessToken.token);
  } catch (err) {
    const errMsg = 'Authentication failed';
    return res.status(400).send(errMsg);
  }
});

module.exports = router;

3. config.json

{
  "google_health_client_id": "my_client_id",
  "google_health_client_secret": "my_client_secret",
  "google_health_authorize_host": "https://accounts.google.com",
  "google_health_authorize_path": "/o/oauth2/v2/auth",
  "google_health_token_host": "https://www.googleapis.com",
  "google_health_token_path": "/oauth2/v4/token",
  "google_health_scope": "https://www.googleapis.com/auth/cloud-platform",
  "google_health_callback_url": "/oauth2-callback"
}