diff --git a/README.md b/README.md index e501033b..8912b131 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ Overture Docs is a centralized documentation site built with [Docusaurus](https://docusaurus.io/) that aggregates and renders Markdown content from `/docs` directories across our GitHub repositories. It transforms distributed documentation into a cohesive and easy to navigate knowledge base. -![Overture Docs](./preview.png 'Docs for developers and informaticians') +![Overture Docs](./preview.png "Docs for developers and informaticians") > [!NOTE] > This repository is documented in detail on the Overture Docs site linked here (to be linked once live) @@ -39,13 +39,12 @@ npm start - **Docusaurus**: We use Docusaurus to render the site, providing a sleek and navigable interface for our documentation. -- **Markdown Files**: All documentation content is stored as markdown files in the `/website/docs` directory. +- **Markdown Files**: All documentation content is stored as markdown files in the `/website/docs` directory. - **Git Submodules**: We use Git submodules to store and track all our GitHub repositories within one main repository. All submodules can be found in the `submodule` folder. - **Symlinks**: Only the necessary documentation files are symlinked from the submodules in the `submodule` folder to the `/website/docs` directory. This allows us to import only the required markdown content that Docusaurus needs. - ## Repository structure ``` @@ -91,8 +90,7 @@ npm start - **Robust Error Handling**: Docusaurus has excellent error catching, particularly for broken and missing links, reducing the need for manual testing. -![Pro Tip](./website/docs/03-other-software/images/proTip.png 'Use Overture Docs repo to search across all Overture repos') +![Pro Tip](./website/docs/03-other-software/images/proTip.png "Use Overture Docs repo to search across all Overture repos") > [!TIP] > The Overture Docs repo contains everything, therefore finding & tracking links and content across all our repos has never been easier. - diff --git a/bridge.sh b/libretto.sh similarity index 100% rename from bridge.sh rename to libretto.sh diff --git a/submodules/.github b/submodules/.github index 7f96a50c..d5736f30 160000 --- a/submodules/.github +++ b/submodules/.github @@ -1 +1 @@ -Subproject commit 7f96a50c5f9ac4666572b52e7df2d7a2a9230537 +Subproject commit d5736f30c43226a664e8ed934cab4ca96481cb2f diff --git a/submodules/arranger b/submodules/arranger index 544d33c0..d430dd4a 160000 --- a/submodules/arranger +++ b/submodules/arranger @@ -1 +1 @@ -Subproject commit 544d33c09edad347779bcc572af921f4fa3e71e9 +Subproject commit d430dd4aea083274f116a7e4167e29ebec737e55 diff --git a/submodules/lectern b/submodules/lectern index db7cb954..f65fb1ca 160000 --- a/submodules/lectern +++ b/submodules/lectern @@ -1 +1 @@ -Subproject commit db7cb954dd010051a7fe5cf6ba7e985c7fc09856 +Subproject commit f65fb1cab599b1ec59cbe6ad390ea57211e1b07c diff --git a/submodules/lyric b/submodules/lyric index 54ecc6b6..b1d289fe 160000 --- a/submodules/lyric +++ b/submodules/lyric @@ -1 +1 @@ -Subproject commit 54ecc6b6cab501521524cee5799e17f5b8263b7d +Subproject commit b1d289fec5c0f68f023e35fe1141677614c6242f diff --git a/submodules/maestro b/submodules/maestro index e67e09e2..b3267fab 160000 --- a/submodules/maestro +++ b/submodules/maestro @@ -1 +1 @@ -Subproject commit e67e09e2981130a7ac8c828663f39080fa3f07ba +Subproject commit b3267fabc42fab1f6250ba212b2e7e85fdbe2e37 diff --git a/submodules/score b/submodules/score index 8c70c287..26ecc754 160000 --- a/submodules/score +++ b/submodules/score @@ -1 +1 @@ -Subproject commit 8c70c28799ef10cff0116411361074768ca8e7f1 +Subproject commit 26ecc754fe7fbe71e7d2acd31b2ec066c5be3f49 diff --git a/submodules/song b/submodules/song index be2ba33d..2e01f7bc 160000 --- a/submodules/song +++ b/submodules/song @@ -1 +1 @@ -Subproject commit be2ba33d0f908318dcaf37367a7c1610ca578f0d +Subproject commit 2e01f7bcf97db303fad64932e36afedc264125be diff --git a/submodules/stage b/submodules/stage index 323580db..597d8df0 160000 --- a/submodules/stage +++ b/submodules/stage @@ -1 +1 @@ -Subproject commit 323580db1d1b04868c753f31146056a4bcb3e3c4 +Subproject commit 597d8df0838901874ac92141f1c5ed9943980ca5 diff --git a/website/docs/03-other-software/01-prelude.md b/website/docs/03-other-software/01-prelude.md new file mode 100644 index 00000000..83f8993b --- /dev/null +++ b/website/docs/03-other-software/01-prelude.md @@ -0,0 +1,118 @@ +# Prelude + +**Prelude** is a toolkit designed for the **planning and development stages** of Overture data platform implementation. It helps teams incrementally build and validate platform requirements, enabling them to: + +- Systematically verify requirements +- Minimize technical overhead +- Build a foundation for production deployment + +:::important +Prelude is **not intended for production environments**. It serves as a preparatory tool to ensure successful production deployments. We will be actively improving resources to support teams transitioning from Prelude to production. +::: + +We welcome feedback and suggestions—please share them via our [ideas forum](https://github.com/overture-stack/docs/discussions/categories/ideas). + +## Development Phases + +Prelude is structured into four incremental phases: + +![Development Phases](./images/DevelopmentPhases.png "Prelude Development Phases") + +| **Phase** | **Focus** | **Components/Tools** | +| --------------------------------------- | --------------------------------------------------- | ----------------------------------------------- | +| **Phase 0:** Pre-Deployment Check | Making sure you have all the required prerequisites | Docker, appropriate resources for docker & Node | +| **Phase 1:** Data Exploration & Theming | Data visualization in the portal | Elasticsearch, Arranger, Stage | +| **Phase 2:** Tabular Data Management | Backend data storage and validation | Lyric, Lectern, Postgres, MongoDB | +| **Phase 3:** File Management | File storage and metadata tracking | Song, Score, Object Storage | +| **_Phase 4:_** Identity & Access | Security and user management | Keycloak integration | + +**Phase 4** is not included in Prelude v1 and will be included in a future release. + +## Supplemental Tools + +### Composer + +Transforms your data (CSV or JSON) into base Overture configurations including Elasticsearch Mappings, Arranger UI Configs, Lectern Dictionary and Schema, Song Schema. This utility greatly reduces tedious manual configurations. + +Depending on the command Composer can input CSV or JSON file(s) that represent your data and output the following: + +| Output | Purpose | +| --------------------------------- | -------------------------------------------------------------------- | +| **Elasticsearch Mappings** | Defines the structure and indexing settings for your data | +| **Arranger UI Configs** | Configures the user interface for data exploration and visualization | +| **Lectern Dictionary and Schema** | Creates data dictionaries and schemas for tabular data | +| **Song Schema** | Generates schema configurations for file metadata | + +### Conductor + +Conductor runs the automated deployments from the `/apps/conductor/scripts` directory. It can also be run as a command line client made to streamline interactions with various Overture API endpoints. + +As summary of command line client interactions is provided in the table below: + +| Feature | Description | +| ---------------------------- | ---------------------------------------------------------------------------------------------------------- | +| **CSV to Elasticsearch ETL** | Validate, transform and load CSV data to a specified elasticsearch index. | +| **Configuration Management** | Submit dictionaries to Lectern, Register Lectern dictionaries with Lyric, Update Song Schema and study Ids | +| **Data Management** | Upload tabular data to Lyric, Upload and publish file data and metadata. | + +### Additional Information + +- Relevant API swagger docs can be found from the API dropdown. These swagger APIs are only available when running phases that include the respective service + +## Getting Started + +_If you’re reading from the Prelude documentation page, this section may be redundant._ + +### 1. Clone the repository + +```sh +git clone https://github.com/overture-stack/prelude.git +cd conductor +``` + +### 2. Pre-deployment Check + +Run a pre-deployment check: + +```sh +make Phase0 +``` + +**Requirements:** + +- **Docker Desktop 4.39.0+** with: + - 8-core CPU minimum + - 8 GB memory + - 2 GB swap + - 64 GB virtual disk +- **Node.js 18+ and npm 9+** + +### 3. Build the local Stage UI image + +```sh +cd apps/stage +docker build --platform linux/arm64 -t stageimage:1.0 . +``` + +### 4. Deploy Phase 1 + +Run from the root directory: + +```sh +make phase1 +``` + +### 5. Access the Portal + +Once running, access the portal at: [http://localhost:3000](http://localhost:3000). + +All Prelude documentation is available in the **Documentation** tab here or on our [documentation site](https://docs.overture.bio/other-software/prelude). + +## Support + +For assistance, reach out via our [community support channels](https://docs.overture.bio/community/support): + +- **Public support:** Use GitHub issues +- **Private inquiries:** Contact us via OICR Slack or [contact@overture.bio](mailto:contact@overture.bio) + +We’re actively working on resources to help teams transition to production. If you have suggestions, post them on our [GitHub discussion forum](https://github.com/overture-stack/docs/discussions/categories/ideas). diff --git a/website/docs/03-other-software/02-Conductor.mdx b/website/docs/03-other-software/02-Conductor.mdx deleted file mode 100644 index 80753040..00000000 --- a/website/docs/03-other-software/02-Conductor.mdx +++ /dev/null @@ -1,96 +0,0 @@ -# Conductor - -Conductor is a flexible Docker Compose setup that simplifies the process of spinning up Overture development and deployment configurations using Docker profiles and extensible scripting events. - -## Key Features - -- **Profile-based Deployments**: Uses Docker profiles to manage different environment setups. -- **Conductor-driven Execution**: The Conductor service executes ordered scripts based on the `PROFILE` environment variable. - -## System Architectures - -The following diagrams illustrate the system architecture for each deployment: - - - - ![Platform](./images/platform.svg 'Overture Platform') - - - ![Song Dev](./images/songDev.svg 'Song Dev Environment') - - - ![Score Dev](./images/scoreDev.svg 'Score Dev Environment') - - - ![Maestro Dev](./images/maestroDev.svg 'Maestro Dev Environment') - - - ![Arranger Dev](./images/arrangerDev.svg 'Arranger Dev Environment') - - - ![Stage Dev](./images/stageDev.svg 'Stage Dev Environment') - - - -All components are automatically deployed and configured, with exception to the services highlighted in pink. These services in the deployment context require manual setup and configuration for local development, instructions are provided within the logs following deployment. - -## Getting Started - -**1. Clone the repo branch** - -``` -git clone https://github.com/overture-stack/conductor.git && cd conductor -``` - -**2. Run one of the following commands to spin up different environments:** - -| Environment | Unix/macOS | Windows | -|-------------|------------|---------| -| Overture Platform | `make platform` | `./make.bat platform` | -| Stage Dev | `make stageDev` | `./make.bat stageDev` | -| Arranger Dev | `make arrangerDev` | `./make.bat arrangerDev` | -| Maestro Dev | `make maestroDev` | `./make.bat maestroDev` | -| Song Dev | `make songDev` | `./make.bat songDev` | -| Score Dev | `make scoreDev` | `./make.bat scoreDev` | - -Each command spins up complementary services for the specified development environment. - -## Repository Structure - -``` -. -├── conductorScripts/ -│ ├── deployments -│ └── services -├── configurationFiles/ -│ ├── arrangerConfigs -│ ├── elasticsearchConfigs -│ └── keycloakConfigs -├── guideMaterials -├── persistentStorage/ -│ ├── data-keycloak-db -│ ├── data-minio -│ └── data-song-db -├── Makefile -└── ./make.bat -``` - -- **`conductorScripts/`** Contains scripts for orchestrating the deployment process. - - `deployments/`: Scripts that execute service scripts sequentially based on the deployment configuration. These also include custom post-deployment logs with essential next steps for the deployment scenario. - - `services/`: Modular scripts for individual service setup tasks. Each file is named according to its purpose, with inline comments documenting the code. - -- **`configurationFiles/`** Stores all required configuration files, including: - - `arrangerConfigs/`: Configuration files specific to Arranger. - - `elasticsearchConfigs/`: Configuration files for Elasticsearch, encompassing indexing mappings and documents for seeding data. - - `keycloakConfigs/`: Configuration files for Keycloak, including preconfigured realm files and Overture API key provider details. - -- **`guideMaterials/`** Supplementary folders and files for use with the [Overture guides](https://www.overture.bio/documentation/guides/). - -- **`persistentStorage/`** Directory for storing persistent data during container startups and restarts. These folders come pre-loaded with mock data. - - `data-keycloak-db/`: Persistent local storage for the Keycloak database. - - `data-minio/`: Persistent local storage for MinIO object storage. - - `data-song-db/`: Persistent local storage for the Song database. - -- **`Makefile`** Contains make commands for Unix-based systems (macOS, Linux) to streamline Docker operations. - -- **`./make.bat`** Windows equivalent of the Makefile, featuring batch commands tailored for Windows systems. diff --git a/website/docs/03-other-software/02-quickstart.mdx b/website/docs/03-other-software/02-quickstart.mdx new file mode 100644 index 00000000..675c60d0 --- /dev/null +++ b/website/docs/03-other-software/02-quickstart.mdx @@ -0,0 +1,94 @@ +# Quickstart + +Our quickstart platform is a Docker Compose setup that simplifies the process of spinning up Overture development and deployment configurations using Docker profiles and extensible scripting events. + +## System Architectures + +The following diagrams illustrate the system architecture for each deployment: + + + + ![Platform](./images/platform.svg 'Overture Platform') + + + ![Song Dev](./images/songDev.svg 'Song Dev Environment') + + + ![Score Dev](./images/scoreDev.svg 'Score Dev Environment') + + + ![Maestro Dev](./images/maestroDev.svg 'Maestro Dev Environment') + + + ![Arranger Dev](./images/arrangerDev.svg 'Arranger Dev Environment') + + + ![Stage Dev](./images/stageDev.svg 'Stage Dev Environment') + + + +All components are automatically deployed and configured, with exception to the services highlighted in pink. These services in the deployment context require manual setup and configuration for local development, instructions are provided within the logs following deployment. + +## Getting Started + +**1. Clone the repo branch** + +``` +git clone -b quickstart https://github.com/overture-stack/prelude.git && cd prelude +``` + +**2. Run one of the following commands to spin up different environments:** + +| Environment | Unix/macOS | Windows | +| ----------------- | ------------------ | ------------------------ | +| Overture Platform | `make platform` | `./make.bat platform` | +| Stage Dev | `make stageDev` | `./make.bat stageDev` | +| Arranger Dev | `make arrangerDev` | `./make.bat arrangerDev` | +| Maestro Dev | `make maestroDev` | `./make.bat maestroDev` | +| Song Dev | `make songDev` | `./make.bat songDev` | +| Score Dev | `make scoreDev` | `./make.bat scoreDev` | + +Each command spins up complementary services for the specified development environment. + +## Repository Structure + +``` +. +├── quickstartScripts/ +│ ├── deployments +│ └── services +├── configurationFiles/ +│ ├── arrangerConfigs +│ ├── elasticsearchConfigs +│ └── keycloakConfigs +├── guideMaterials +├── persistentStorage/ +│ ├── data-keycloak-db +│ ├── data-minio +│ └── data-song-db +├── Makefile +└── ./make.bat +``` + +- **`quickstartScripts/`** Contains scripts for orchestrating the deployment process. + + - `deployments/`: Scripts that execute service scripts sequentially based on the deployment configuration. These also include custom post-deployment logs with essential next steps for the deployment scenario. + - `services/`: Modular scripts for individual service setup tasks. Each file is named according to its purpose, with inline comments documenting the code. + +- **`configurationFiles/`** Stores all required configuration files, including: + + - `arrangerConfigs/`: Configuration files specific to Arranger. + - `elasticsearchConfigs/`: Configuration files for Elasticsearch, encompassing indexing mappings and documents for seeding data. + - `keycloakConfigs/`: Configuration files for Keycloak, including preconfigured realm files and Overture API key provider details. + +- **`guideMaterials/`** Supplementary folders and files for use with the [Overture guides](https://www.overture.bio/documentation/guides/). + +- **`persistentStorage/`** Directory for storing persistent data during container startups and restarts. These folders come pre-loaded with mock data. + + - `data-keycloak-db/`: Persistent local storage for the Keycloak database. + - `data-minio/`: Persistent local storage for MinIO object storage. + - `data-song-db/`: Persistent local storage for the Song database. + +- **`Makefile`** Contains make commands for Unix-based systems (macOS, Linux) to streamline Docker operations. + +- **`./make.bat`** Windows equivalent of the Makefile, featuring batch commands tailored for Windows systems. diff --git a/website/docs/03-other-software/01-Bridge.md b/website/docs/03-other-software/03-libretto.md similarity index 76% rename from website/docs/03-other-software/01-Bridge.md rename to website/docs/03-other-software/03-libretto.md index 3d6ecaa2..25e813b3 100644 --- a/website/docs/03-other-software/01-Bridge.md +++ b/website/docs/03-other-software/03-libretto.md @@ -1,11 +1,6 @@ +# Libretto -# Bridge - -Bridge is a single, easy-to-navigate hub that beautifully renders all our product documentation from the `/docs` folder of all our GitHub repositories. - -:::info -Overture Docs started under the name Bridge to reflect its ability to bridge information across multiple repositories. Bridge was also chosen in fitting with Overtures Orchestral theme. -::: +Libretto is a single, easy-to-navigate hub that beautifully renders all our product documentation from the `/docs` folder of all our GitHub repositories. ## Documentation Framework @@ -19,16 +14,16 @@ Overture has three user profiles: Our documentation is split up as follows: -| Documentation | User Profile | Description -|---|---|---| -| Product Documentation (Housed here) | Software Engineers & Developers | Technical resources for those working on or contributing to the project. | -| Platform Guides (Overture.bio) | IT Specialists & Informaticians | Instructive guides covering platform setup, maintenance and usage for end-users and administrators. | +| Documentation | User Profile | Description | +| ----------------------------------- | ------------------------------- | --------------------------------------------------------------------------------------------------- | +| Product Documentation (Housed here) | Software Engineers & Developers | Technical resources for those working on or contributing to the project. | +| Platform Guides (Overture.bio) | IT Specialists & Informaticians | Instructive guides covering platform setup, maintenance and usage for end-users and administrators. | ## How Overture Docs Works - **Docusaurus**: We use Docusaurus to render the site, providing a sleek and navigable interface for our documentation. -- **Markdown Files**: All documentation content is stored as markdown files in the `/website/docs` directory. +- **Markdown Files**: All documentation content is stored as markdown files in the `/website/docs` directory. - **Git Submodules**: We use Git submodules to store and track all our GitHub repositories within one main repository. All submodules can be found in the `submodule` folder. @@ -44,11 +39,11 @@ Our documentation is split up as follows: - **Robust Error Handling**: Docusaurus has excellent error catching, particularly for broken and missing links, reducing the need for manual testing. -![Pro Tip](./images/proTip.png 'Use Overture Docs repo to search across all Overture repos') +![Pro Tip](./images/proTip.png "Use Overture Docs repo to search across all Overture repos") - :::tip Pro Tip - The Overture Docs repo contains everything, therefore finding & tracking links and content across all our repos has never been easier. - ::: +:::tip Pro Tip +The Overture Docs repo contains everything, therefore finding & tracking links and content across all our repos has never been easier. +::: ## Getting Started @@ -78,9 +73,9 @@ npm start Use the following command from the submodules directory to add a new submodule: - ```bash - git submodule add -b module_name - ``` +```bash +git submodule add -b module_name +``` This will automatically update the `.gitmodules` file located in the root directory. @@ -88,9 +83,9 @@ This will automatically update the `.gitmodules` file located in the root direct To pull the latest changes for all submodules, including any newly added ones run: - ```bash - git submodule update --remote - ``` +```bash +git submodule update --remote +``` ### Using Symlinks @@ -98,30 +93,30 @@ All documentation content is stored in markdown files located within `/website/d Symlinks are used here to link only the necessary folders containing markdown files from the submodule directories. -The script for this is in the root directory, titled `bridge.sh`: +The script for this is in the root directory, titled `Libretto.sh`: - ```bash - ln -s ../../submodules/song/docs website/docs/Song - ln -s ../../submodules/score/docs website/docs/Score - ``` +```bash +ln -s ../../submodules/song/docs website/docs/Song +ln -s ../../submodules/score/docs website/docs/Score +``` - This allows us to import only the necessary markdown files that Docusaurus needs. Changes to either directory are linked and reflected in both. +This allows us to import only the necessary markdown files that Docusaurus needs. Changes to either directory are linked and reflected in both. #### Getting it to run with Docusaurus To run this without errors, I needed to create a plugin found in `website/docsPlugin.ts`: ```typescript -module.exports = function(context, options) { +module.exports = function (context, options) { return { name: "custom-docusaurus-plugin", configureWebpack(config, isServer, utils) { return { resolve: { - symlinks: false - } + symlinks: false, + }, }; - } + }, }; }; ``` @@ -139,16 +134,15 @@ The source of this fix can be found [here](https://github.com/facebook/docusauru We can import components by default across all our mdx files reducing the head matter when using these components in mdx documents. This can be configured from the `/src/theme/MDXComponents.ts`: ```ts title="MDXComponents.ts" -import type {ComponentType} from 'react'; -import MDXComponents from '@theme-original/MDXComponents'; -import Tabs from '@theme/Tabs'; -import TabItem from '@theme/TabItem'; - +import type { ComponentType } from "react"; +import MDXComponents from "@theme-original/MDXComponents"; +import Tabs from "@theme/Tabs"; +import TabItem from "@theme/TabItem"; const components: typeof MDXComponents & { - Tabs: ComponentType; - TabItem: ComponentType; - DocCardList: ComponentType; + Tabs: ComponentType; + TabItem: ComponentType; + DocCardList: ComponentType; } = { ...MDXComponents, Tabs, @@ -159,8 +153,7 @@ const components: typeof MDXComponents & { export default components; ``` - -## Custom Components +## Custom Components There are three custom components built for this site all located in the components directory as follows: @@ -182,7 +175,7 @@ There are three custom components built for this site all located in the compone - Products are defined in `const products:` array (lines 47-61) with each product requiring: - `title`: Product name - `link`: URL path - - `description`: Brief description + - `description`: Brief description - `category`: Must match a category key - `image`: Optional icon path @@ -191,12 +184,12 @@ The layout groups products into their respective categories and automatically di This component also includes our funding statement, the copy used can be updated directly from the component on line 90. :::tip Improvement Consideration -The current implementation uses hardcoded arrays (leftColumnCategories and rightColumnCategories) for column distribution. This is not ideal however it is the simplest method to organize our site content in its ideal layout. +The current implementation uses hardcoded arrays (leftColumnCategories and rightColumnCategories) for column distribution. This is not ideal however it is the simplest method to organize our site content in its ideal layout. ::: ### Sidebar Funding Statement -A simple React component that displays funding attribution information on the bottom left of all sidebars. It uses CSS Modules for scoped styling (styles.module.css). +A simple React component that displays funding attribution information on the bottom left of all sidebars. It uses CSS Modules for scoped styling (styles.module.css). :::tip Improvement Consideration Consider making the content configurable by accepting props rather than hardcoding the grant information, allowing reuse for different funding sources. @@ -215,6 +208,7 @@ The `SwaggerAPIDoc` component renders API documentation completely client-side b - Specifications can be version controlled alongside the code Usage example with local JSON: + ```jsx // Your JSON spec file (e.g., songAPI.json) { diff --git a/website/docs/03-other-software/images/DevelopmentPhases.png b/website/docs/03-other-software/images/DevelopmentPhases.png new file mode 100644 index 00000000..e1dc16dc Binary files /dev/null and b/website/docs/03-other-software/images/DevelopmentPhases.png differ diff --git a/website/guides/00-getting-started.mdx b/website/guides/00-getting-started.mdx index c4dc416f..2b2c7568 100644 --- a/website/guides/00-getting-started.mdx +++ b/website/guides/00-getting-started.mdx @@ -57,7 +57,7 @@ For a rapid, hassle-free setup of the Overture data platform on your local machi 2. **Clone the Repository** ```bash - git clone https://github.com/overture-stack/conductor.git + git clone -b quickstart https://github.com/overture-stack/prelude.git ``` 3. **Launch the Platform:** Run the appropriate command for your operating system: diff --git a/website/guides/02-administration-guides/02-administration-guides.md b/website/guides/02-administration-guides/02-administration-guides.md index 13a65d72..f830614e 100644 --- a/website/guides/02-administration-guides/02-administration-guides.md +++ b/website/guides/02-administration-guides/02-administration-guides.md @@ -40,7 +40,7 @@ For a rapid, hassle-free setup of an Overture data platform on your local machin 2. **Clone the Repository** ```bash - git clone https://github.com/overture-stack/conductor.git + git clone -b quickstart https://github.com/overture-stack/prelude.git ``` 3. **Launch the Platform:** Run the appropriate command for your operating system: diff --git a/website/package-lock.json b/website/package-lock.json index 73c97501..0ad1624c 100644 --- a/website/package-lock.json +++ b/website/package-lock.json @@ -17,7 +17,7 @@ "prism-react-renderer": "^2.3.0", "react": "^18.0.0", "react-dom": "^18.0.0", - "swagger-ui-react": "^5.17.14" + "swagger-ui-react": "^5.20.7" }, "devDependencies": { "@docusaurus/module-type-aliases": "^3.6.2", @@ -273,6 +273,28 @@ "node": ">=6.0.0" } }, + "node_modules/@antfu/install-pkg": { + "version": "1.0.0", + "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-1.0.0.tgz", + "integrity": "sha512-xvX6P/lo1B3ej0OsaErAjqgFYzYVcJpamjLAFLYh9vRJngBrMoUG7aVnrGTeqM7yxbyTD5p3F2+0/QUEh8Vzhw==", + "license": "MIT", + "dependencies": { + "package-manager-detector": "^0.2.8", + "tinyexec": "^0.3.2" + }, + "funding": { + "url": "https://github.com/sponsors/antfu" + } + }, + "node_modules/@antfu/utils": { + "version": "8.1.1", + "resolved": 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"MIT" + }, "node_modules/undici-types": { "version": "6.19.8", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.19.8.tgz", @@ -19086,7 +19335,8 @@ "node_modules/unraw": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/unraw/-/unraw-3.0.0.tgz", - "integrity": "sha512-08/DA66UF65OlpUDIQtbJyrqTR0jTAlJ+jsnkQ4jxR7+K5g5YG1APZKQSMCE1vqqmD+2pv6+IdEjmopFatacvg==" + "integrity": "sha512-08/DA66UF65OlpUDIQtbJyrqTR0jTAlJ+jsnkQ4jxR7+K5g5YG1APZKQSMCE1vqqmD+2pv6+IdEjmopFatacvg==", + "license": "MIT" }, "node_modules/update-browserslist-db": { "version": "1.1.3", @@ -19311,11 +19561,12 @@ } }, "node_modules/use-sync-external-store": { - "version": "1.2.2", - "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.2.tgz", - "integrity": "sha512-PElTlVMwpblvbNqQ82d2n6RjStvdSoNe9FG28kNfz3WiXilJm4DdNkEzRhCZuIDwY8U08WVihhGR5iRqAwfDiw==", + "version": "1.5.0", + "resolved": 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"vscode-languageserver-protocol": "3.17.5" + }, + "bin": { + "installServerIntoExtension": "bin/installServerIntoExtension" + } + }, + "node_modules/vscode-languageserver-protocol": { + "version": "3.17.5", + "resolved": "https://registry.npmjs.org/vscode-languageserver-protocol/-/vscode-languageserver-protocol-3.17.5.tgz", + "integrity": "sha512-mb1bvRJN8SVznADSGWM9u/b07H7Ecg0I3OgXDuLdn307rl/J3A9YD6/eYOssqhecL27hK1IPZAsaqh00i/Jljg==", + "license": "MIT", + "dependencies": { + "vscode-jsonrpc": "8.2.0", + "vscode-languageserver-types": "3.17.5" + } + }, + "node_modules/vscode-languageserver-textdocument": { + "version": "1.0.12", + "resolved": "https://registry.npmjs.org/vscode-languageserver-textdocument/-/vscode-languageserver-textdocument-1.0.12.tgz", + "integrity": "sha512-cxWNPesCnQCcMPeenjKKsOCKQZ/L6Tv19DTRIGuLWe32lyzWhihGVJ/rcckZXJxfdKCFvRLS3fpBIsV/ZGX4zA==", + "license": "MIT" + }, + "node_modules/vscode-languageserver-types": { + "version": "3.17.5", + "resolved": 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"sha512-huCv9IH9Tcf95zuYCsQraZtWnJvBtLVE0QHMOs8bWyZAFZNDcYjsPq1nEx8jKA9y+Beo9v+7OBPRisQTjinQMw==" + "integrity": "sha512-huCv9IH9Tcf95zuYCsQraZtWnJvBtLVE0QHMOs8bWyZAFZNDcYjsPq1nEx8jKA9y+Beo9v+7OBPRisQTjinQMw==", + "license": "MIT" }, "node_modules/xml-but-prettier": { "version": "1.0.1", @@ -19984,6 +20257,7 @@ "version": "4.0.2", "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", + "license": "MIT", "engines": { "node": ">=0.4" } diff --git a/website/package.json b/website/package.json index fd851038..4f801bfa 100644 --- a/website/package.json +++ b/website/package.json @@ -24,7 +24,7 @@ "prism-react-renderer": "^2.3.0", "react": "^18.0.0", "react-dom": "^18.0.0", - "swagger-ui-react": "^5.17.14" + "swagger-ui-react": "^5.20.7" }, "devDependencies": { "@docusaurus/module-type-aliases": "^3.6.2", diff --git a/website/src/components/SiteMap/index.tsx b/website/src/components/SiteMap/index.tsx index ca511d2a..0b7e3554 100644 --- a/website/src/components/SiteMap/index.tsx +++ b/website/src/components/SiteMap/index.tsx @@ -1,14 +1,14 @@ -import React from 'react'; -import Heading from '@theme/Heading'; -import styles from './styles.module.css'; +import React from "react"; +import Heading from "@theme/Heading"; +import styles from "./styles.module.css"; -import iconSong from './icons/icon-song.png'; -import iconScore from './icons/icon-score.png'; -import iconMaestro from './icons/icon-maestro.png'; -import iconArranger from './icons/icon-arranger.png'; -import iconStage from './icons/icon-stage.png'; -import iconLyric from './icons/icon-lyric.png'; -import iconLectern from './icons/icon-lectern.png'; +import iconSong from "./icons/icon-song.png"; +import iconScore from "./icons/icon-score.png"; +import iconMaestro from "./icons/icon-maestro.png"; +import iconArranger from "./icons/icon-arranger.png"; +import iconStage from "./icons/icon-stage.png"; +import iconLyric from "./icons/icon-lyric.png"; +import iconLectern from "./icons/icon-lectern.png"; interface Product { title: string; @@ -25,57 +25,154 @@ interface Category { const categories: Record = { platform: { - title: 'Platform Guides', - description: 'Bringing it all together with platform focused guides' + title: "Platform Guides", + description: "Bringing it all together with platform focused guides", }, core: { - title: 'Developer Documentation', - description: 'Using our software in a development context' + title: "Developer Documentation", + description: "Using our software in a development context", }, development: { - title: 'Under Development', - description: 'New components not quite ready for production' + title: "Under Development", + description: "New components not quite ready for production", }, supporting: { - title: 'Supporting Software', - description: 'Supporting tools within the Overture project' + title: "Supporting Software", + description: "Supporting tools within the Overture project", }, standards: { - title: 'Documentation Standards', - description: 'Forming the foundation of documentation and development practice' + title: "Documentation Standards", + description: + "Forming the foundation of documentation and development practice", }, }; const products: Product[] = [ - { title: 'Deployment Guides', link: '/guides/deployment-guide/', description: 'Deploying to Production', category: 'platform' }, - { title: 'Administration Guides', link: '/guides/administration-guides/', description: 'Management and Customization', category: 'platform' }, - { title: 'User Guides', link: '/guides/user-guides/', description: 'Interacting with the platform', category: 'platform' }, - { title: 'API Reference', link: '/guides/api-reference', description: 'Interacting with the platform\'s APIs', category: 'platform' }, - { title: 'Song', link: 'docs/core-software/song/overview', image: iconSong, description: 'Metadata Management Service', category: 'core' }, - { title: 'Score', link: '/docs/core-software/score/overview', image: iconScore, description: 'File Transfer Service', category: 'core' }, - { title: 'Maestro', link: '/docs/core-software/maestro/overview', image: iconMaestro, description: 'Metadata Indexing Service', category: 'core' }, - { title: 'Arranger', link: '/docs/core-software/arranger/overview', image: iconArranger, description: 'Search API', category: 'core' }, - { title: 'Stage', link: '/docs/core-software/stage/overview', image: iconStage, description: 'Web Portal Scaffolding', category: 'core' }, - { title: 'Lectern', link: '/docs/under-development/lectern/', image: iconLectern ,description: 'Schema Management Service', category: 'development' }, - { title: 'Lyric', link: '/docs/under-development/lyric/', image: iconLyric, description: 'Tabular Data Submission Service', category: 'development' }, - { title: 'Bridge', link: '/docs/other-software/Bridge', description: 'Documentation Site', category: 'supporting' }, - { title: 'Conductor', link: 'https://docs.overture.bio/docs/other-software/Conductor', description: 'Software Setup Automation', category: 'supporting' }, - { title: 'Documenting Projects', link: '/docs/Standards/github', description: 'Organization Standards', category: 'standards' }, - { title: 'Documenting Software', link: '/docs/Standards/Software/', description: 'Software Standards', category: 'standards' }, + { + title: "Deployment Guides", + link: "/guides/deployment-guide/", + description: "Deploying to Production", + category: "platform", + }, + { + title: "Administration Guides", + link: "/guides/administration-guides/", + description: "Management and Customization", + category: "platform", + }, + { + title: "User Guides", + link: "/guides/user-guides/", + description: "Interacting with the platform", + category: "platform", + }, + { + title: "API Reference", + link: "/guides/api-reference", + description: "Interacting with the platform's APIs", + category: "platform", + }, + { + title: "Song", + link: "docs/core-software/song/overview", + image: iconSong, + description: "Metadata Management Service", + category: "core", + }, + { + title: "Score", + link: "/docs/core-software/score/overview", + image: iconScore, + description: "File Transfer Service", + category: "core", + }, + { + title: "Maestro", + link: "/docs/core-software/maestro/overview", + image: iconMaestro, + description: "Metadata Indexing Service", + category: "core", + }, + { + title: "Arranger", + link: "/docs/core-software/arranger/overview", + image: iconArranger, + description: "Search API", + category: "core", + }, + { + title: "Stage", + link: "/docs/core-software/stage/overview", + image: iconStage, + description: "Web Portal Scaffolding", + category: "core", + }, + { + title: "Lectern", + link: "/docs/under-development/lectern/", + image: iconLectern, + description: "Schema Management Service", + category: "development", + }, + { + title: "Lyric", + link: "/docs/under-development/lyric/", + image: iconLyric, + description: "Tabular Data Submission Service", + category: "development", + }, + { + title: "Quickstart", + link: "https://docs.overture.bio/docs/other-software/Quickstart", + description: "Locally Deployed Demo Portal", + category: "supporting", + }, + { + title: "Libretto", + link: "/docs/other-software/Libretto", + description: "Documentation Site", + category: "supporting", + }, + { + title: "Prelude", + link: "https://docs.overture.bio/docs/other-software/Prelude", + description: "Platform planning & development toolkit.", + category: "supporting", + }, + { + title: "Documenting Projects", + link: "/docs/Standards/github", + description: "Organization Standards", + category: "standards", + }, + { + title: "Documenting Software", + link: "/docs/Standards/Software/", + description: "Software Standards", + category: "standards", + }, ]; const Card = ({ title, description, link, image }) => ( - {image && {`${title}} - {title} + {image && ( + {`${title} + )} + + {title} +

{description}

 ); const CategorySection = ({ category, items }) => (
- {categories[category].title} -

{categories[category].description}

+ + {categories[category].title} + +

+ {categories[category].description} +

{items.map((props, idx) => ( @@ -87,11 +184,19 @@ const CategorySection = ({ category, items }) => ( const FundingBadge = () => (
- Funding Contributors + + Funding Contributors +

- Overture is supported by grant #U24CA253529 from the National Cancer Institute at the US National Institutes of Health, and additional funding from Genome Canada, the Canada Foundation for Innovation, the Canadian Institutes of Health Research, Canarie, and the Ontario Institute for Cancer Research. + Overture is supported by grant #U24CA253529 from the National Cancer + Institute at the US National Institutes of Health, and additional + funding from Genome Canada, the Canada Foundation for Innovation, the + Canadian Institutes of Health Research, Canarie, and the Ontario + Institute for Cancer Research.

- Learn More + + Learn More +
); @@ -102,21 +207,29 @@ const SiteMap = () => { return acc; }, {}); - const rightColumnCategories = ['platform', 'supporting', 'standards']; - const leftColumnCategories = ['core', 'development']; + const rightColumnCategories = ["platform", "supporting", "standards"]; + const leftColumnCategories = ["core", "development"]; return (
- {leftColumnCategories.map(category => ( - + {leftColumnCategories.map((category) => ( + ))}
- {rightColumnCategories.map(category => ( - + {rightColumnCategories.map((category) => ( + ))}
@@ -126,4 +239,4 @@ const SiteMap = () => { ); }; -export default SiteMap; \ No newline at end of file +export default SiteMap; diff --git a/website/yarn.lock b/website/yarn.lock index 2a8ce52e..e49abdc8 100644 --- a/website/yarn.lock +++ b/website/yarn.lock @@ -158,6 +158,19 @@ "@jridgewell/gen-mapping" "^0.3.5" "@jridgewell/trace-mapping" "^0.3.24" +"@antfu/install-pkg@^1.0.0": + version "1.0.0" + resolved "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-1.0.0.tgz" + integrity sha512-xvX6P/lo1B3ej0OsaErAjqgFYzYVcJpamjLAFLYh9vRJngBrMoUG7aVnrGTeqM7yxbyTD5p3F2+0/QUEh8Vzhw== + dependencies: + package-manager-detector "^0.2.8" + tinyexec "^0.3.2" + +"@antfu/utils@^8.1.0": + version "8.1.1" + resolved "https://registry.npmjs.org/@antfu/utils/-/utils-8.1.1.tgz" + integrity sha512-Mex9nXf9vR6AhcXmMrlz/HVgYYZpVGJ6YlPgwl7UnaFpnshXs6EK/oa5Gpf3CzENMjkvEx2tQtntGnb7UtSTOQ== + "@babel/code-frame@^7.0.0", "@babel/code-frame@^7.16.0", "@babel/code-frame@^7.26.2", 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