search

AHRQ-CDS / AHRQ-CDS-Connect-Authoring-Tool

The CDS Authoring Tool is part of the CDS Connect project https://cds.ahrq.gov/, sponsored by the Agency for Healthcare Research and Quality (AHRQ), and developed under contract with AHRQ by MITRE's CAMH FFRDC.
https://cds.ahrq.gov/cdsconnect/authoring
Apache License 2.0
42 stars 19 forks source link
cds clinical-decision-support clinical-quality-language cql fhir

readme

CDS Connect Authoring Tool

About

The Clinical Decision Support (CDS) Authoring Tool is a web-based application aimed at simplifying the creation of production-ready CQL code. The project is based on "concept templates" (e.g. gender, HDL Cholesterol, etc.), which allow for additional clinical concepts to be included in the future. Concept modifiers are included to allow for more flexible definitions (e.g. most recent, value comparisons, etc.).

The CDS Authoring Tool is part of the CDS Connect project, sponsored by the Agency for Healthcare Research and Quality (AHRQ), and initially developed under contract with AHRQ by MITRE's Health FFRDC.

Contributions

For information about contributing to this project, please see CONTRIBUTING.

Development Details

This project uses the MERN stack: Mongo, Express, React, and NodeJS. The project is split into two components:

For specific development details of each component, including configuration, see their respective README files.

Run (Development Quick Start)

Prerequisites

First, ensure you have Node.js LTS and MongoDB installed. The CDS Authoring Tool is tested using MongoDB 6.0.x, but later versions are expected to work.

MongoDB can be run using a docker image if desired via

mkdir -p db
docker run --name=mongodb --volume=$PWD/db:/data/db -p 27017:27017 --restart=unless-stopped --detach=true mongo:6.0

This creates a local db directory and then runs a MongoDB docker container that will store files in that directory.

Install Dependencies

Each of the subprojects (api and frontend) must have the dependencies installed via npm. This can be done as follows:

cd api
npm install

After the api dependency install successfully runs, install the frontend dependencies:

cd ../frontend
npm install

After the frontend dependency install runs, go back to the root folder:

cd ..

Configure Authentication

The CDS Authoring Tool requires authentication. Currently LDAP authentication and local file authentication are supported. For local development, the simplest approach is to use local user authentication. To enable it, copy the minimal-example and example-local-users configuration files to local.json and local-users.json.

NOTE: The following example uses cp. If you are on Windows, use copy instead.

cp api/config/minimal-example.json api/config/local.json
cp api/config/example-local-users.json api/config/local-users.json

This will enable the following two users:

Of course, these default users and passwords should never be enabled on a public-facing system.

Run the API and Frontend

In one terminal, run the backend API server:

cd api
npm start

In another terminal, run the frontend server:

cd frontend
npm start

NOTE: Ensure MongoDB is running before starting the CDS Authoring Tool.

When running, the Authoring Tool will be available at http://localhost:3000/authoring.

Testing CQL Execution Results

Testing CQL execution in development requires the API to be configured to use the CQL-to-ELM Translator and also requires the Translator to be running locally.

To configure the API, edit the configuration settings in api/config/local.json to point to a local instance of the Translator:

"cqlToElm": {
  "url": "http://localhost:8080/cql/translator",
  "active": true
}

This should replace any existing cqlToElm configuration block where active is set to false. See the Configuration section of the API README for details on configuring the API.

Once the configuration is updated and the API has been restarted the translation service can be run locally in docker via:

docker run -p 8080:8080 cqframework/cql-translation-service:v2.3.0

Running tests

The API tests can be run with

npm --prefix api test

The frontend tests can be run with

npm --prefix frontend test

Docker

This project can also be built into a Docker image and deployed as a Docker container. To do any of the commands below, Docker must be installed.

Building the docker image

To build the Docker image, execute the following command from the project's root directory (the directory containing api and frontend):

docker build -t cdsauthoringtool .

Running the docker container

For the Authoring Tool to run in a docker container, MongoDB and CQL-to-ELM docker containers must be linked. The following commands run the necessary containers, with the required links and exposed ports:

docker run --name cat-cql2elm -d cqframework/cql-translation-service:v2.3.0
docker run --name cat-mongo -d mongo:6.0
docker run --name cat \
  --link cat-cql2elm:cql2elm \
  --link cat-mongo:mongo \
  -e "CQL_TO_ELM_URL=http://cql2elm:8080/cql/translator" \
  -e "CQL_FORMATTER_URL=http://cql2elm:8080/cql/formatter" \
  -e "MONGO_URL=mongodb://mongo/cds_authoring" \
  -e "AUTH_SESSION_SECRET=secret" \
  -e "AUTH_LDAP_URL=ldap://localhost:389" \
  -e "AUTH_LDAP_BIND_DN=cn=root" \
  -e "AUTH_LDAP_BIND_CREDENTIALS={{password}}" \
  -e "AUTH_LDAP_SEARCH_BASE=ou=passport-ldapauth" \
  -e "AUTH_LDAP_SEARCH_FILTER=(uid={{username}})" \
  -e "NODE_ENV=development" \
  -p "3001:3001" \
  -p "9000:9000" \
  cdsauthoringtool

To run the CDS Authoring Tool in a detached process, add a -d to the run command (before cdsauthoringtool).

Of course you will need to modify some of the values above according to your environment (e.g., LDAP details).

Proxying the API

By default, the server on port 9000 will proxy requests on /authoring/api to the local API server using express-http-proxy. In production environments, a dedicated external proxy server may be desired. In that case, the external proxy server will be responsible for proxying /authoring/api to port 3001. To accomodate this, disable the express-http-proxy by adding this addition flag to the last command above:

  -e "API_PROXY_ACTIVE=false" \

Enabling HTTPS

By default, the API server and frontend server listen over unsecure HTTP. To listen over HTTPS, add these three flags to the docker run command above:

  -v /data/ssl:/data/ssl \
  -e "HTTPS=true" \
  -e "SSL_KEY_FILE=/data/ssl/server.key" \
  -e "SSL_CRT_FILE=/data/ssl/server.cert" \

You should substitute the volume mapping and SSL filenames as needed for your specific environment.

Using the Container

When the container is running, access the app at http://localhost:9000.

To stop the container:

docker stop cat cat-mongo cat-cql2elm

To start the containers again:

docker start cat-cql2elm cat-mongo cat

To remove the containers (usually when building new images):

docker rm cat cat-mongo cat-cql2elm

NOTE: This configuration stores data in Mongo's container. This means it is tied to the lifecycle of the mongo container and is not persisted when the container is removed.

Using Docker Compose

Alternately, use Docker Compose to build and run all of the containers. Execute:

docker compose up

The first time, it will build the cdsauthoringtoolapi_cat and cdsauthoringtool_cat images. Subsequent times it may re-use the already built images. To force it to rebuild, pass in the --build flag.

To stop and remove the containers, run:

docker compose down

LICENSE

Copyright 2016-2023 Agency for Healthcare Research and Quality

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.