@lifeomic/cli

# CLI This [command line interface][CLI] provides functionality offered by [LifeOmic](https://lifeomic.com)'s Precision Health Cloud APIs inside an interactive terminal or in a scripted environment. ![CLI Demo](https://raw.githubusercontent.com/lifeomic/cli/master/cli-demo.svg?sanitize=true) ## Table of Contents 1. [Project Status](#project-status) 1. [Getting Started](#getting-started) 1. [Dependencies](#dependencies) 1. [Installation](#installation) 1. [Configuration](#configuration) 1. [Authentication](#authentication) 1. [API Keys](#api-keys) 1. [SSO](#sso) 1. [Usage](#usage) 1. [Release Process](#release-process) 1. [Versioning](#versioning) 1. [Contributing](#contributing) 1. [License](#license) 1. [Authors](#authors) 1. [Acknowledgements](#acknowledgements) # Project Status [![License](https://img.shields.io/badge/license-MIT-blue.svg)](https://opensource.org/licenses/MIT) [![Build Status](https://travis-ci.org/lifeomic/cli.svg?branch=master)](https://travis-ci.org/lifeomic/cli) [![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)](https://github.com/lifeomic/cli) **[Back to top](#table-of-contents)** # Getting Started ## Dependencies * [node](https://nodejs.org) version >= 7.6.0 ## Getting the Source This project is [hosted on GitHub](https://github.com/lifeomic/cli). You can clone this project directly using this command: ``` git clone git@github.com:lifeomic/cli.git ``` ## Running Tests Run tests with `npm` or `yarn`: ```bash npm test yarn test ``` ## Installation Install via `npm` or `yarn`: ```bash npm install -g @lifeomic/cli yarn global add @lifeomic/cli ``` or you can download and install the binary from the [latest release](https://github.com/lifeomic/cli/releases). ## Configuration Run `lo setup` to configure the default environment and account you wish to use. You can later override the default account using the `-a` option for commands. ## Authentication Use `lo auth` to obtain access credentials when using username / password authentication. A browser will be opened and you can enter your credentials in the LifeOmic login view. You can also use the client credentials grant flow for obtaining access tokens. To do this, create a custom authentication client [here](https://apps.us.lifeomic.com/phc/account/accounts/clients) and be sure to select the `Client credentials` flow under the `Allowed OAuth Flows` section. Run `lo setup` again and choose `Y` to use a custom authentication client and enter the client ID and secret and then choose `Y` again to use client credentials for authentication. Note that for this option, you do not need to run `lo auth` as username and password credentials are not used for this credentials grant. ### API Keys If you wish to use an API key, then you need to create an API key [here](https://apps.us.lifeomic.com/phc/account) or from `lo api-keys-create`. Be sure to capture the value of the API key when it is created as you will not be able to retrieve the value after the first attempt. Run `lo setup` and choose 'Y' to use an API key and provide the API key value. ### SSO If you wish to use SSO, then you need to create a custom authentication client [here](https://apps.us.lifeomic.com/phc/account/accounts/clients) and configure your SAML 2.0 identity provider. For the callback URL on the authentication client, be sure to add `http://localhost:8787`. Then run `lo setup` again and choose 'Y' to use a custom authentication client and provide the client ID and secret (if a private client was created). When running `lo auth` again, a browser should open and be redirected to the identity provider being used for SSO. ## Usage ```bash lo <command> [options] ``` `lo` offers many commands and those can be displayed by using the `-h / --help` command line option. For example: ```bash ❯ lo --help Usage: lo <command> [options] Options: -V, --version output the version number -h, --help output usage information Commands: accounts [options] List accounts accounts-get [options] <account> Fetch an account ... </abbreviated> ``` Get help for a specific command: ```bash ❯ lo <command> --help ❯ lo tasks --help Usage: tasks [options] <datasetId> List tasks Options: -a, --account <account> Override the default LifeOmic account --json Print output as JSON --prefix <prefix> Filter tasks where the name begins with a prefix --state <state> Filter tasks by state --view <view> Specify MINIMAL to just get task state --page-size <pageSize> Number of items to return (default: 25) --next-page-token <nextPageToken> Next page token -h, --help output usage information ``` [cli]: https://en.wikipedia.org/wiki/Command-line_interface "Command-line interface" **[Back to top](#table-of-contents)** # Release Process [Releases](https://github.com/lifeomic/cli/releases) are generally created with each merged PR. Packages for each release are published to [npm](https://www.npmjs.com/package/@lifeomic/cli). See [CHANGELOG.md](CHANGELOG.md) for release notes. ## Versioning This project uses [Semantic Versioning](http://semver.org/). **[Back to top](#table-of-contents)** # Contributing We encourage public contributions! Please review [CONTRIBUTING.md](CONTRIBUTING.md) and [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) for details on our code of conduct and development process. **[Back to top](#table-of-contents)** # License This project is licensed under the MIT License - see [LICENSE](LICENSE) file for details. **[Back to top](#table-of-contents)** # Authors See the list of [contributors](https://github.com/lifeomic/cli/contributors) who participate in this project. **[Back to top](#table-of-contents)** # Acknowledgements This project is built with the following: * [axios](https://github.com/axios/axios) - Promise based HTTP client for the browser and node.js * [yargs](https://github.com/yargs/yargs) - CLI argument parser * [configstore](https://github.com/yeoman/configstore) - Easily load and persist config without having to think about where and how * [ava](https://github.com/avajs/ava) - Testing framework **[Back to top](#table-of-contents)**