Bio web components (Biowc)

This monorepo contains several plotting components that can easily be integrated in your web tools. This can either be done directly in the HTML, or through a JavaScript framework such as Vue, React, or Angular.

How to get started

Clone the repository and cd into it. Then run:
npm i
This will install the dependencies for the monorepo as well as for all subpackages specified in package.json. So whenever you add a new package, you'll need to add its location to this file (see below).
Next, run:
npm run storybook
This will first build all existing components (using lerna run build) and then start the 'Storybook' where their features are demonstrated.
If you get an error message at this time, it is probably related to your node version. Try this to solve it: https://github.com/wilhelm-lab/biowc-core/wiki/Storybook#troubleshooting.

How to view the deprecated Vue components

They are in the same monorepo, but are managed independently. Therefore you need to install dependencies separately. Run:

cd deprecated-vue-components
npm i

Then you can run

npm run storybook

from there to check out demos of the deprecated components.

How to add components

On Github

Please start by adding an Issue where you describe what kind of plot you'll implement. Make sure that this issue does not exist yet. Then, create a Branch from the issue and check it out to your local machine.

On your local machine

From within the packages directory run:

npm init @open-wc
✔ What would you like to do today? › Scaffold a new project                                                                                                                                                                                                                               
✔ What would you like to scaffold? › Web Component                                                                                                                                                                                                                                        
✔ What would you like to add? › Linting (eslint & prettier), Testing (web-test-runner)                                                                                                                                                                            
✔ Would you like to use typescript? › Yes      
✔ What is the tag name of your web component? … biowc-xyz
✔ Do you want to write this file structure to disk? › Yes                                                                                    
✔ Do you want to install dependencies? › Yes, with npm

Do not check Demoing (storybook) when asked What would you like to add?. Storybook is already managed on the root level of the monorepo, you don't need to set it up individually.

When the initial setup is done, first open the root package.json file (the one directly in biowc-core, not the one in the package you just created!) and extend the "dependencies" by the path to your package. For example, if your new package is called biowc-mycomponent, add the following line:

"biowc-mycomponent": "file:packages/biowc-mycomponent",

As mentioned above, this will allow the monorepo manager lerna to install all dependencies at once when the repository is cloned again.

Next, enter the directory of the component and edit the package.json file there:

Add the following line to the "scripts" section:
"precommit": "lint-staged && npm test"
Modify the "test" script inside the "scripts" section:
"test": "tsc && wtr --coverage --node-resolve --playwright --browsers chromium firefox"
Remove the "husky" section (we do use husky, but we control it at the repository root):
```
"husky": {
  "hooks": {
    "pre-commit": "lint-staged"
  }
},
```

Install d3.js, the package we use to create visualizations:
npm i d3@6.2.0

Install playwrightfor development. Playwright will simulate your tests in different browsers to make sure your component runs on all of them (https://playwright.dev/):
npm i -D playwright @playwright/test

Delete the file .editorconfig. There is an identical file at the monorepo root which controls this.

Replace the contents of the file tsconfig.json by the following:

{
  "extends": "../../tsconfig.json",
  "compilerOptions": {
    "outDir": "dist",
    "rootDir": "./"
  },
  "include": [
    "**/*.ts"
  ]
}

That's it! Commit your initialized package using git commit -m "Initial commit".

Happy hacking :-)
Here are some tutorials to get you started:

Javascript: https://learnxinyminutes.com/docs/javascript/
Typescript: https://learnxinyminutes.com/docs/typescript/ (focuses only on the specialties of TS, so read the JS tutorial first!)
Web Components & Lit: https://open-wc.org/guides/developing-components/codelabs/
D3.js: https://www.tutorialsteacher.com/d3js
Testing Web Components: https://open-wc.org/docs/testing/testing-package/
Storybook: https://storybook.js.org/docs/web-components/get-started/introduction

However, we recommend that as soon as you have a vague idea of the concepts, you start playing around with the example biowc-scatter component. That should get you up to speed quickly.

How to use web components

See here:
https://www.webcomponents.org/introduction
https://github.com/WICG/webcomponents#web-components
Vue.js: https://vuejs.org/guide/extras/web-components.html#using-custom-elements-in-vue
React: https://reactjs.org/docs/web-components.html
Angular: https://angular.io/guide/elements

How to publish

Make sure you have an account on npmjs.com and are listed as a maintainer for the biowc packages, then run:

npm login
npx lerna publish [major|minor|patch]

How this repo was initialized

npx lerna@latest init

How to port Vue.js components to Web Components

All existing components in ProteomicsDB are embedded into Vue.js (they live in deprecated-vue-components).
We wrote down a summary of the main steps when translating a Vue component into a framework-independent web component: https://github.com/wilhelm-lab/biowc-core/wiki/Porting-Vue.js-component-to-Web-Components