wip: 🚧 add v1 documentation

.github/CODEOWNERS

@@ -1,6 +1,4 @@
-* @slugb0t
-/docs/ @bvhpatel @slugb0t
-/versioned_docs/ @slugb0t
-/.github/ @megasanjay @slugb0t
-package.json @megasanjay slugb0t
-yarn.lock @megasanjay slugb0t
+* @megasanjay
+/docs/ @bvhpatel @megasanjay
+/versioned_docs/ @bvhpatel
+/.github/ @megasanjay

.github/workflows/semantic-release.yml

@@ -27,7 +27,8 @@ jobs:
       - name: Lint check
         run: yarn lint
 
-      - name: Release
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: yarn semantic-release
+      # todo: disabling release for now
+      # - name: Release
+      #   env:
+      #     GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      #   run: yarn semantic-release

.prettierignore

@@ -0,0 +1 @@
+.github/CODEOWNERS

README.md

@@ -37,10 +37,119 @@
 
 content here
 
+## :toolbox: Getting Started
+
+### :bangbang: Prerequisites
+
+This project uses Yarn as package manager
+
+```bash
+npm install --global yarn
+```
+
+Additionally, a version of Node.js that is >= 14 is required for compatibility with Docusarus.
+If your Node.js version is < 14 you can download the latest Node.js version from [the Node.js download page.](https://nodejs.org/en/download/)
+
+### :key: Environment Variables
+
+To run this project, you will need to add the following environment variables to your `.env.local` file
+
+- None at the moment
+
+### :running: Run Locally
+
+Clone the project
+
+```bash
+git clone https://github.com/AI-READI/ai-readi-docs.git
+```
+
+Go to the project directory
+
+```bash
+cd ai-readi-docs
+```
+
+Install dependencies
+
+```bash
+yarn install
+```
+
+Start the server
+
+```bash
+yarn dev
+```
+
+### :stopwatch: Versioning
+
+You can use the version script to create a new documentation version based on the latest content in the `docs` directory. That specific set of documentation will then be preserved and accessible even as the documentation in the `docs` directory changes moving forward.
+
+Ideally, you should create a new branch and update the relevant pages. Then send a PR with [@megasanjay](https://github.com/megasanjay) or [@bvhpatel](https://github.com/bvhpatel) on the review page.
+
+Only do these steps after all changes to the documentation for the specific version have been completed:
+
+1. Make sure the current docs version (the `docs` directory) is ready to be frozen.
+2. Update the `version` key in package.json for this repository.
+
+```bash
+yarn run docusaurus docs:version 2
+```
+
+This will freeze the current version of the documentation. The files under the current `docs` directory will be considered to be `Upcoming 🚧` version.
+
+### :building_construction: Build locally
+
+Use this step to build a local production version of the site. Use `serve` to preview the local build.
+
+```bash
+yarn build
+yarn serve
+```
+
+### :triangular_flag_on_post: Deployment
+
+You will not need to do anything to the hosted site. Continuous Delivery has been setup with Azure Static Web Apps. All you need to do is push your commit and wait for it to deploy.
+
+## :wave: Contributing
+
+<a href="https://github.com/AI-READI/ai-readi-docs/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=AI-READI/ai-readi-docs" alt='repository contributors' />
+</a>
+
+Contributions are always welcome!
+
+See [`contributing.md`](https://github.com/AI-READI/ai-readi-docs/blob/main/CONTRIBUTING.md) for ways to get started.
+
+### :scroll: Code of Conduct
+
+Please read the [Code of Conduct](https://github.com/AI-READI/ai-readi-docs/blob/master/CODE_OF_CONDUCT.md)
+
+## :grey_question: FAQ
+
+- Can I make changes to previous versions of the documentation?
+
+  - Yes, you can make changes to previous versions of the documentation. You can do this by creating a new branch and adding your changes directly in the `versioned_docs` directory.
+
+## :warning: License
+
+Distributed under the MIT License. See [`LICENSE`](https://github.com/AI-READI/ai-readi-docs/blob/main/LICENSE) for more information.
+
+## :handshake: Contact
+
+Contact us on Twitter: [@fairdataihub](https://twitter.com/fairdataihub)
+
+Send us an E-mail: [info@fairdataihub.org](mailto:info@fairdataihub.org)
+
 ## :gem: Acknowledgements
 
-A special thank you to Vercel for hosting this documentation.
+This project is funded by the NIH under award number 1OT2OD032644. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
+
+<div align="center">
 
-<a href="https://vercel.com/?utm_source=fairdataihub&utm_campaign=oss" target="_blank">
-  <img src="https://www.datocms-assets.com/31049/1618983297-powered-by-vercel.svg"  width="auto"/>
+<a href="https://aireadi.org">
+  <img src="https://github.com/AI-READI/AI-READI-logo/raw/main/logo/png/option2.png" height="200" alt='aireadi logo' />
 </a>
+
+</div>

docusaurus.config.js

@@ -8,7 +8,7 @@ const darkCodeTheme = themes.dracula;
 
 /** @type {import('@docusaurus/types').Config} */
 export default {
-  title: 'AI-READI Docs',
+  title: 'Documentation for the AI-READI Dataset',
   // eslint-disable-next-line max-len
   tagline:
     // eslint-disable-next-line max-len
@@ -19,7 +19,7 @@ export default {
   onBrokenMarkdownLinks: 'warn',
   favicon: '/favicon.png',
   organizationName: 'ai-readi',
-  projectName: 'AI-READI Docs',
+  projectName: 'AI-READI Dataset Docs',
 
   presets: [
     [
@@ -59,7 +59,7 @@ export default {
     /** @type {import('@docusaurus/preset-classic').ThemeConfig} */
     ({
       navbar: {
-        title: 'AI-READI Docs',
+        title: 'AI-READI Dataset Docs',
         logo: {
           alt: 'My Site Logo',
           src: 'img/logo.svg',
@@ -117,7 +117,7 @@ export default {
             ],
           },
         ],
-        copyright: `Copyright © ${new Date().getFullYear()} FAIR Data Innovations Hub.`,
+        copyright: `Copyright © ${new Date().getFullYear()} AI-READI.`,
       },
       colorMode: {
         respectPrefersColorScheme: false,

package.json

@@ -26,8 +26,8 @@
     "*.{js,jsx,css,md}": "prettier --write"
   },
   "dependencies": {
-    "@docusaurus/core": "3.0.0",
-    "@docusaurus/preset-classic": "3.0.0",
+    "@docusaurus/core": "^3.1.1",
+    "@docusaurus/preset-classic": "^3.1.1",
     "@emotion/react": "11.11.1",
     "@emotion/styled": "11.11.0",
     "@iconify/react": "4.1.1",
@@ -55,8 +55,8 @@
     "@babel/eslint-parser": "7.22.15",
     "@commitlint/cli": "17.8.0",
     "@commitlint/config-conventional": "17.8.0",
-    "@docusaurus/module-type-aliases": "3.0.0",
-    "@docusaurus/types": "3.0.0",
+    "@docusaurus/module-type-aliases": "^3.1.1",
+    "@docusaurus/types": "^3.1.1",
     "@fairdataihub/config": "2.2.3",
     "@semantic-release/changelog": "6.0.3",
     "@semantic-release/commit-analyzer": "11.0.0",

src/pages/index.jsx

@@ -24,7 +24,7 @@ function HomepageHeader() {
         <p className="hero__subtitle text-xl">{siteConfig.tagline}</p>
 
         <div className={styles.buttons}>
-          <Link className="button button--secondary button--lg" to="/docs/getting-started/intro">
+          <Link className="button button--secondary button--lg" to="/docs/about">
             View the Documentation
           </Link>
 

src/theme/NavbarItem/DocsVersionDropdownNavbarItem.js

@@ -28,7 +28,7 @@ export default function DocsVersionDropdownNavbarItem({
     const versionDoc =
       activeDocContext.alternateDocVersions[version.name] ?? getVersionMainDoc(version);
     return {
-      label: `${version.label === 'Upcoming 🚧' ? '' : 'v.'}${version.label}`,
+      label: `${version.label === 'Upcoming 🚧' ? '' : 'Dataset v'}${version.label}`,
       to: versionDoc.path,
       isActive: () => version === activeDocContext.activeVersion,
       onClick: () => savePreferredVersionName(version.name),
@@ -44,7 +44,7 @@ export default function DocsVersionDropdownNavbarItem({
           message: 'Versions',
           description: 'The label for the navbar versions dropdown on mobile view',
         })
-      : `${dropdownVersion.label === 'Upcoming 🚧' ? '' : 'v.'}${dropdownVersion.label}`;
+      : `${dropdownVersion.label === 'Upcoming 🚧' ? '' : 'Dataset v'}${dropdownVersion.label}`;
   const dropdownTo =
     mobile && items.length > 1 ? undefined : getVersionMainDoc(dropdownVersion).path;
   // We don't want to render a version dropdown with 0 or 1 item. If we build

versioned_docs/version-1/AI-readiness/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "AI-readiness",
+  "position": 6
+}

versioned_docs/version-1/AI-readiness/ethical-practices.mdx

@@ -0,0 +1,13 @@
+---
+sidebar_position: 2
+title: Ethical practices
+---
+
+AI-READI is one of the data generation projects of the National Institutes of Health (NIH) funded Bridge2AI Program.
+The AI-READI project seeks to create and share a flagship ethically-sourced dataset of type 2 diabetes.
+The data will be optimized for future artificial intelligence/machine learning (AI/ML) analysis that could provide critical insights and especially shine light on the salutogenic pathways from diabetes to return to health.
+
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/AI-readiness/fair-principles.mdx

@@ -0,0 +1,13 @@
+---
+sidebar_position: 1
+title: FAIR Principles
+---
+
+AI-READI is one of the data generation projects of the National Institutes of Health (NIH) funded Bridge2AI Program.
+The AI-READI project seeks to create and share a flagship ethically-sourced dataset of type 2 diabetes.
+The data will be optimized for future artificial intelligence/machine learning (AI/ML) analysis that could provide critical insights and especially shine light on the salutogenic pathways from diabetes to return to health.
+
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/about.mdx

@@ -0,0 +1,31 @@
+---
+sidebar_position: 1
+title: About 
+---
+
+## About this documentation
+This is the documentation for the AI-READI dataset called "Flagship Dataset of Type 2 Diabetes from the AI-READI Project". It is intended to complement the information provided on the dataset landing page on the FAIRhub data portal. It is highly suggested to read this documentation first before accessing the dataset.
+
+## About the AI-READI dataset
+*Brief intro to the AI-READI project and the AI-READI dataset.*
+
+## About the structure of this documentation
+There is one version of this documentation associated with each version of the AI-READI dataset. You can navigate between the different versions from the dropdown in the upper right corner. 
+
+This documentation is associated with v1.0 of the dataset, which contains data from the participants of the pilot study phase. This version of the documentation is structured as follows
+
+- The "Citation" section explains how the dataset needs to be cited if used.
+
+- The "Preliminary Information" section contains information about accessing and using the dataset so you can understand what is expected from users of the dataset.
+
+- The "Overview of the Dataset" section points to high-level information about the dataset that is contained on the dataset landing page such as a summary of the AI-READI study, a description of the dataset, etc. and also provide details about each of the data types included in the dataset.
+
+- The "Dataset Structure" section starts with a high-level description of how the dataset is organized before diving into details about the structure of each of the data types contained is this dataset (how they are organized, what standards were followed, etc.).
+
+- The "Example Use Cases" section provides some examples of how the dataset can be used.
+
+- The "Resources" section provides a list of additional resources related to the dataset that could be useful for understanding and using the dataset.
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/additional-resources.mdx

@@ -0,0 +1,14 @@
+---
+sidebar_position: 8
+title: Additional Resources
+---
+
+## Marker Paper
+
+## Other publications from the project
+
+## Resources citing the dataset
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/changelog.md

@@ -0,0 +1,15 @@
+---
+sidebar_position: 99
+title: Changelog
+image: https://kalai.fairdataihub.org/api/generate?title=Changelog&description=&app=ai-readi-docs&org=ai-readi
+---
+
+## 0.0.1 (2021-10-01)
+
+### Added
+
+- Some info about the dataset
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/citation.mdx

@@ -0,0 +1,13 @@
+---
+sidebar_position: 2
+title: Citation
+---
+
+As per the [license terms](preliminary/license), if you use the AI-READI dataset or any subset of it, you must cite the following references:
+
+*Coming soon (marker paper and dataset citation)*
+
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/dataset-overview/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "Dataset Overview",
+  "position": 4
+}

versioned_docs/version-1/dataset-overview/data_types/_category_.json

@@ -0,0 +1,4 @@
+{
+  "label": "Data types",
+  "position": 2
+}

versioned_docs/version-1/dataset-overview/data_types/clinical_data.mdx

@@ -0,0 +1,10 @@
+---
+sidebar_position: 1
+title: Clinical data
+---
+
+
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/dataset-overview/data_types/retinal_oct.mdx

@@ -0,0 +1,10 @@
+---
+sidebar_position: 2
+title: Retinal OCT
+---
+
+
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />

versioned_docs/version-1/dataset-overview/overall.mdx

@@ -0,0 +1,20 @@
+---
+sidebar_position: 1
+title: Overall Description
+---
+
+## General information
+204 participants, 3 sites, etc.
+
+## Dataset information on FAIRHub
+The landing page of the dataset on FAIRhub contains a wealth of information to learn about the provenance of the dataset. The different tabs on that page provide various information:
+
+- The "About" tab provides an overview of the dataset including a descripton of the AI-READI study, a description of the dataset
+
+## Data types available in the dataset
+
+
+import PageFeedback from '@site/src/components/PageFeedback';
+
+<PageFeedback />
+