Easily manage, curate, and share FAIR and AI-ready clinical and biomedical research data.

fairhub.io · User Documentation · Changelog · Report Bug or Make Suggestions

Description

As part of AI-READI, a data generation project supported by the NIH-funded Bridge2AI program, we are developing FAIRhub. This is a web platform for easily managing, curating, and sharing clinical and biomedical research data such that the data is FAIR (Findable, Accessible, Interoperable, Reusable) and ready for downstream AI-based analysis. For the duration of the project, we anticipate the platform to support the mangement, curation, and sharing of data generated by the AI-READI project where we expect to collect diabetes-related multimodal data from 4,000 study participant during 2022-2026 (more details are available on the project website aireadi.org). This repository contains the source code of FAIRhub along with instructions for using the source code as well as pointers to various documentation and resources related to the platform.

Getting started

Prerequisites/Dependencies

VSCode + Volar (and disable Vetur) + TypeScript Vue Plugin (Volar).

Type Support for .vue Imports in TS

TypeScript cannot handle type information for .vue imports by default, so we replace the tsc CLI with vue-tsc for type checking. In editors, we need TypeScript Vue Plugin (Volar) to make the TypeScript language service aware of .vue types.

If the standalone TypeScript plugin doesn't feel fast enough to you, Volar has also implemented a Take Over Mode that is more performant. You can enable it by the following steps:

1. Disable the built-in TypeScript Extension
   1. Run Extensions: Show Built-in Extensions from VSCode's command palette
   2. Find TypeScript and JavaScript Language Features, right click and select Disable (Workspace)
2. Reload the VSCode window by running Developer: Reload Window from the command palette.

Installing

See Vite Configuration Reference.

sh yarn install

Compile and Hot-Reload for Development

sh yarn dev

Type-Check, Compile, and Minify for Production

sh yarn build

Run Unit Tests with Vitest

sh yarn test:unit

Run End-to-End Tests with Cypress

sh yarn build yarn test:e2e # or `npm run test:e2e:ci` for headless testing

Lint with ESLint

sh yarn lint

Deployment

fairhub.io

This repository is automatically deployed to Azure on every push to the repository. If you need to reference a specific branch or pull request, you can do so by using the following URL pattern:

• https://brave-ground-07b6bfb10-BRANCH_NAME.centralus.2.azurestaticapps.net
• https://brave-ground-07b6bfb10-GITHUB_PR_NUMBER.centralus.2.azurestaticapps.net

The production branch is automatically deployed to the following URL: fairhub.io.

style.fairhub.io

The storybook for the FAIRhub UI library is automatically deployed to Azure on every push to the repository. If you need to reference a specific branch or pull request, you can do so by using the following URL pattern:

• https://white-ocean-00e852610--BRANCH_NAME.centralus.2.azurestaticapps.net
• https://white-ocean-00e852610--GITHUB_PR_NUMBER.centralus.2.azurestaticapps.net

The production branch is automatically deployed to the following URL: style.fairhub.io.

Documentation

User documentation

Our user documentation for FAIRhub is available at docs.fairhub.io (STATUS: not active). The source code of the user documentation is maintained from its dedicated GitHub repository.

Developer documentation

The basic instructions for running a local version of FAIRhub for development purposes are provided above in this README. Details about our high-level development best practices and standards are available at dev.aireadi.org (the source code is maintained from its dedicated GitHub repository). Details about our development practices specific to FAIRhub are available at dev.fairhub.io (the source code is maintained from its dedicated GitHub repository).

APIs documentation

The APIs of FAIRhub are documented at api.fairhub.io (STATUS: not active). The source code of the API documentation is maintained from its dedicated GitHub repository.

Style guide

We use Storybook for documenting our design system. It is available at style.fairhub.io. You can refer to that for design guidelines, component documentation, and resources for editing components locally. The source code of the storybook in included in this repository in the storybook folder. Changes between different versions of the storybook are documented in its dedicated CHANGELOG. Instructions for running the storybook locally for editing and suggesting changes are provided below:

```sh // You will need to be on node 16.13.0 or higher

yarn install

yarn storybook ```

Changelog

Changes between different versions of FAIRhub are documented in the CHANGELOG.

Inputs and Outputs

The typical inputs of FAIRhub will be clinical and biomedical research related data uploaded by the users. The typical output of FAIRhub will be FAIR and AI-ready datasets shared by the users.

Contributing

Contributions are always welcome!

If you are interested in reporting/fixing issues and contributing directly to the code base, please see CONTRIBUTING.md for more information on what we're looking for and how to get started.

We recommend to look at the documentation for more information.

Issues and Feedback

If you have any questions or suggestions, please contact us using GitHub issues.

License

This work is licensed under MIT. See LICENSE for more information.

How to cite

If you are using FAIRhub or reusing the source code from this repository for any purpose, please cite:

bash ADD Citation here

Acknowledgements

This project is supported by the NIH-funded Bridge2AI program (1OT2OD032644). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.