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 API provides a RESTful backend for the CDS Authoring Tool React web frontend.
The CDS Authoring Tool is part of the CDS Connect project, sponsored by the Agency for Healthcare Research and Quality (AHRQ), and developed under contract with AHRQ by MITRE's CAMH FFRDC.
For information about contributing to this project, please see CONTRIBUTING.
This project represents the M, E, and N in the MERN application architecture, using MongoDB, Express, and Node.
To develop and run this project, your must install mongodb, node, and yarn. On Mac OS X, this can be done through brew:
brew install mongodb # install mongodb on host system
brew services start mongodb # start mongo
brew install node # install node
brew install yarn # install yarnFor other operating systems, use the instructions provided in each tool's online documentation.
Once the prerequisite tools are installed, use yarn to install the dependency libraries:
yarn # e.g. yarn install. installs this app's dependencies based on this project's yarn.lock / package.jsonBy default, the project will attempt to convert CQL to ELM on download or publish. To disable this in development, see the configuration section below. If enabled, you will need the CQL-to-ELM translation service, a Java application that can be run locally via Maven or Docker.
- To run locally with Maven: https://github.com/cqframework/cql-translation-service
- To run locally with Docker, install Docker and run:
docker run -p 8080:8080 cqframework/cql-translation-service:v1.3.19
yarn add <thing> # add a package. add --dev if this is a development dependency.
yarn add <thing>@<version> # will adjust version
yarn remove <thing> # remove a package.This project uses the popular convict module to manage configuration. The configuration schema and default values can be found at config.js, and an example config file can be found at config/example.json.
The API server will uses the NODE_ENV environment variable to detect the active environment: production, development, or test (defaulting to development when no environment is supplied). If a corresponding configuration file (config/${NODE_ENV}.json) is present, it will merge its values into the default configuration.
For local development, a config/local.json file can also be used to override configuration settings. It has precedence over the environment-based configuration and default configuration.
Lastly, most aspects of config can also be overridden via specific environment variables. See the config.js configuration schema for the relevant environment variable names.
As the project evolves over time, the database schema may change in ways that require existing data to be transformed. This project uses the mongodb-migrations to support database migrations. Migration scripts are stored in the migrations folder.
Migrations are automatically applied on application startup. This may be disabled via configuration (migrations.active in your local config file or the MIGRATIONS_ACTIVE environment variable). Migrations should only be disabled during development.
To run migrations from the commandline, simply execute the following command from the root of the api project:
./node_modules/.bin/mmThis project uses Passport to authenticate users. By default, the project uses the LDAP Authentication Strategy.
For development purposes, the Local Authentication Strategy can be enabled via configuration. In order to do so, a config/local-users.json file must be created. For an example of the structure of this file, see config/example-local-users.json.
yarn start will run the api server:
yarn start # run the api serveryarn start-dev will run the api server in development mode, reloading the server when changes are detected.
yarn run start-dev # run the api server with hot-reloading for developmentJavaScript linting is done using ESLint.
yarn run lint # runs eslint using the configuration in .eslintrc.
yarn run lint:fix # runs eslint --fix using the configuration in .eslintrc. The --fix flag will autocorrect minor errorsAPI server testing uses Chai with Mocha as the test runner.
yarn test # runs all api testsFor information on running the CDS Authoring Tool in Docker, see the main README.
CDS_Connect_Conversions provides a list of available functions to convert units. When updating or adding to these functions, update the file in data/library_helpers/CQLFiles/CDS_Connect_Conversions.cql with the functions needed. After, regenerate the ELM file for this CQL file and update it in data/library_helpers/ELMFiles/CDS_Connect_Conversions.json. If a function requires a more understandable description to be displayed in the user interface, such as the start and target units for the function, update the list of descriptions in data/handlers/configHandler.js.
Copyright 2016-2018 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.