Fix error with tooltips in embedded components in vite dev mode (#4612)

GMOD · Oct 21, 2024 · 4608823 · 4608823
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diff --git a/component_tests/lgv-vite/.gitignore b/component_tests/lgv-vite/.gitignore
@@ -0,0 +1,7 @@
+packed/
+/node_modules
+/coverage
+/build
+yarn.lock
+cypress/screenshots/
+cypress/videos/
diff --git a/component_tests/lgv-vite/README.md b/component_tests/lgv-vite/README.md
@@ -0,0 +1,58 @@
+# React + TypeScript + Vite
+
+This template provides a minimal setup to get React working in Vite with HMR and
+some ESLint rules.
+
+Currently, two official plugins are available:
+
+- [@vitejs/plugin-react](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react/README.md)
+  uses [Babel](https://babeljs.io/) for Fast Refresh
+- [@vitejs/plugin-react-swc](https://github.com/vitejs/vite-plugin-react-swc)
+  uses [SWC](https://swc.rs/) for Fast Refresh
+
+## Expanding the ESLint configuration
+
+If you are developing a production application, we recommend updating the
+configuration to enable type aware lint rules:
+
+- Configure the top-level `parserOptions` property like this:
+
+```js
+export default tseslint.config({
+  languageOptions: {
+    // other options...
+    parserOptions: {
+      project: ['./tsconfig.node.json', './tsconfig.app.json'],
+      tsconfigRootDir: import.meta.dirname,
+    },
+  },
+})
+```
+
+- Replace `tseslint.configs.recommended` to
+  `tseslint.configs.recommendedTypeChecked` or
+  `tseslint.configs.strictTypeChecked`
+- Optionally add `...tseslint.configs.stylisticTypeChecked`
+- Install
+  [eslint-plugin-react](https://github.com/jsx-eslint/eslint-plugin-react) and
+  update the config:
+
+```js
+// eslint.config.js
+import react from 'eslint-plugin-react'
+
+export default tseslint.config({
+  // Set the react version
+  settings: { react: { version: '18.3' } },
+  plugins: {
+    // Add the react plugin
+    react,
+  },
+  rules: {
+    // other rules...
+    // Enable its recommended rules
+    ...react.configs.recommended.rules,
+    ...react.configs['jsx-runtime'].rules,
+  },
+})
+```
diff --git a/component_tests/lgv-vite/eslint.config.js b/component_tests/lgv-vite/eslint.config.js
@@ -0,0 +1,28 @@
+import js from '@eslint/js'
+import globals from 'globals'
+import reactHooks from 'eslint-plugin-react-hooks'
+import reactRefresh from 'eslint-plugin-react-refresh'
+import tseslint from 'typescript-eslint'
+
+export default tseslint.config(
+  { ignores: ['dist'] },
+  {
+    extends: [js.configs.recommended, ...tseslint.configs.recommended],
+    files: ['**/*.{ts,tsx}'],
+    languageOptions: {
+      ecmaVersion: 2020,
+      globals: globals.browser,
+    },
+    plugins: {
+      'react-hooks': reactHooks,
+      'react-refresh': reactRefresh,
+    },
+    rules: {
+      ...reactHooks.configs.recommended.rules,
+      'react-refresh/only-export-components': [
+        'warn',
+        { allowConstantExport: true },
+      ],
+    },
+  },
+)
diff --git a/component_tests/lgv-vite/index.html b/component_tests/lgv-vite/index.html
@@ -0,0 +1,13 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8" />
+    <link rel="icon" type="image/svg+xml" href="/vite.svg" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Vite + React + TS</title>
+  </head>
+  <body>
+    <div id="root"></div>
+    <script type="module" src="/src/main.tsx"></script>
+  </body>
+</html>
diff --git a/component_tests/lgv-vite/package.json b/component_tests/lgv-vite/package.json
@@ -0,0 +1,54 @@
+{
+  "name": "lgv-vite",
+  "private": true,
+  "version": "0.0.0",
+  "type": "module",
+  "scripts": {
+    "dev": "vite",
+    "build": "tsc -b && vite build",
+    "lint": "eslint .",
+    "preview": "vite preview"
+  },
+  "dependencies": {
+    "@jbrowse/react-linear-genome-view": "^2.0.0",
+    "react": "^18.3.1",
+    "react-dom": "^18.3.1"
+  },
+  "resolutions": {
+    "@jbrowse/core": "file:./packed/jbrowse-core.tgz",
+    "@jbrowse/plugin-alignments": "file:./packed/jbrowse-plugin-alignments.tgz",
+    "@jbrowse/plugin-arc": "file:./packed/jbrowse-plugin-arc.tgz",
+    "@jbrowse/plugin-authentication": "file:./packed/jbrowse-plugin-authentication.tgz",
+    "@jbrowse/plugin-bed": "file:./packed/jbrowse-plugin-bed.tgz",
+    "@jbrowse/plugin-circular-view": "file:./packed/jbrowse-plugin-circular-view.tgz",
+    "@jbrowse/plugin-config": "file:./packed/jbrowse-plugin-config.tgz",
+    "@jbrowse/plugin-data-management": "file:./packed/jbrowse-plugin-data-management.tgz",
+    "@jbrowse/plugin-gccontent": "file:./packed/jbrowse-plugin-gccontent.tgz",
+    "@jbrowse/plugin-gff3": "file:./packed/jbrowse-plugin-gff3.tgz",
+    "@jbrowse/plugin-legacy-jbrowse": "file:./packed/jbrowse-plugin-legacy-jbrowse.tgz",
+    "@jbrowse/plugin-linear-genome-view": "file:./packed/jbrowse-plugin-linear-genome-view.tgz",
+    "@jbrowse/plugin-sequence": "file:./packed/jbrowse-plugin-sequence.tgz",
+    "@jbrowse/plugin-svg": "file:./packed/jbrowse-plugin-svg.tgz",
+    "@jbrowse/plugin-trix": "file:./packed/jbrowse-plugin-trix.tgz",
+    "@jbrowse/plugin-variants": "file:./packed/jbrowse-plugin-variants.tgz",
+    "@jbrowse/plugin-wiggle": "file:./packed/jbrowse-plugin-wiggle.tgz",
+    "@jbrowse/product-core": "file:./packed/jbrowse-product-core.tgz",
+    "@jbrowse/sv-core": "file:./packed/jbrowse-sv-core.tgz",
+    "@jbrowse/embedded-core": "file:./packed/jbrowse-embedded-core.tgz",
+    "@jbrowse/react-linear-genome-view": "file:./packed/jbrowse-react-linear-genome-view.tgz",
+    "@mui/icons-material": "6.0.2"
+  },
+  "devDependencies": {
+    "@eslint/js": "^9.11.1",
+    "@types/react": "^18.3.10",
+    "@types/react-dom": "^18.3.0",
+    "@vitejs/plugin-react": "^4.3.2",
+    "eslint": "^9.11.1",
+    "eslint-plugin-react-hooks": "^5.1.0-rc.0",
+    "eslint-plugin-react-refresh": "^0.4.12",
+    "globals": "^15.9.0",
+    "typescript": "^5.5.3",
+    "typescript-eslint": "^8.7.0",
+    "vite": "^5.4.8"
+  }
+}
diff --git a/component_tests/lgv-vite/public/favicon.ico b/component_tests/lgv-vite/public/favicon.ico
diff --git a/component_tests/lgv-vite/public/index.html b/component_tests/lgv-vite/public/index.html
@@ -0,0 +1,43 @@
+<!doctype html>
+<html lang="en">
+  <head>
+    <meta charset="utf-8" />
+    <link rel="icon" href="%PUBLIC_URL%/favicon.ico" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+    <meta name="theme-color" content="#000000" />
+    <meta
+      name="description"
+      content="Web site created using create-react-app"
+    />
+    <link rel="apple-touch-icon" href="%PUBLIC_URL%/logo192.png" />
+    <!--
+      manifest.json provides metadata used when your web app is installed on a
+      user's mobile device or desktop. See https://developers.google.com/web/fundamentals/web-app-manifest/
+    -->
+    <link rel="manifest" href="%PUBLIC_URL%/manifest.json" />
+    <!--
+      Notice the use of %PUBLIC_URL% in the tags above.
+      It will be replaced with the URL of the `public` folder during the build.
+      Only files inside the `public` folder can be referenced from the HTML.
+
+      Unlike "/favicon.ico" or "favicon.ico", "%PUBLIC_URL%/favicon.ico" will
+      work correctly both with client-side routing and a non-root public URL.
+      Learn how to configure a non-root public URL by running `npm run build`.
+    -->
+    <title>React App</title>
+  </head>
+  <body>
+    <noscript>You need to enable JavaScript to run this app.</noscript>
+    <div id="root"></div>
+    <!--
+      This HTML file is a template.
+      If you open it directly in the browser, you will see an empty page.
+
+      You can add webfonts, meta tags, or analytics to this file.
+      The build step will place the bundled scripts into the <body> tag.
+
+      To begin the development, run `npm start` or `yarn start`.
+      To create a production bundle, use `npm run build` or `yarn build`.
+    -->
+  </body>
+</html>
diff --git a/component_tests/lgv-vite/public/robots.txt b/component_tests/lgv-vite/public/robots.txt
@@ -0,0 +1,3 @@
+# https://www.robotstxt.org/robotstxt.html
+User-agent: *
+Disallow:
diff --git a/component_tests/lgv-vite/public/vite.svg b/component_tests/lgv-vite/public/vite.svg
diff --git a/component_tests/lgv-vite/public/volvox-sorted.cram b/component_tests/lgv-vite/public/volvox-sorted.cram
diff --git a/component_tests/lgv-vite/public/volvox-sorted.cram.crai b/component_tests/lgv-vite/public/volvox-sorted.cram.crai
diff --git a/component_tests/lgv-vite/public/volvox.2bit b/component_tests/lgv-vite/public/volvox.2bit
diff --git a/component_tests/lgv-vite/src/App.tsx b/component_tests/lgv-vite/src/App.tsx
@@ -0,0 +1,30 @@
+import React, { useEffect, useState } from 'react'
+import {
+  createViewState,
+  JBrowseLinearGenomeView,
+} from '@jbrowse/react-linear-genome-view'
+
+import assembly from './assembly'
+import tracks from './tracks'
+
+type ViewModel = ReturnType<typeof createViewState>
+
+export default function View() {
+  const [viewState, setViewState] = useState<ViewModel>()
+
+  useEffect(() => {
+    const state = createViewState({
+      assembly,
+      tracks,
+      location: 'ctgA:1-100',
+    })
+    state.session.view.showTrack('volvox_cram')
+    setViewState(state)
+  }, [])
+
+  if (!viewState) {
+    return null
+  }
+
+  return <JBrowseLinearGenomeView viewState={viewState} />
+}
diff --git a/component_tests/lgv-vite/src/assembly.ts b/component_tests/lgv-vite/src/assembly.ts
@@ -0,0 +1,42 @@
+const assembly = {
+  name: 'volvox',
+  aliases: ['vvx'],
+  sequence: {
+    type: 'ReferenceSequenceTrack',
+    trackId: 'volvox_refseq',
+    metadata: {
+      date: '2020-08-20',
+    },
+    formatAbout: {
+      hideUris: true,
+      config: "jexl:{extraField:'important data'}",
+    },
+    adapter: {
+      type: 'TwoBitAdapter',
+      twoBitLocation: {
+        uri: 'volvox.2bit',
+        locationType: 'UriLocation',
+      },
+    },
+  },
+  refNameAliases: {
+    adapter: {
+      type: 'FromConfigAdapter',
+      adapterId: 'W6DyPGJ0UU',
+      features: [
+        {
+          refName: 'ctgA',
+          uniqueId: 'alias1',
+          aliases: ['A', 'contigA'],
+        },
+        {
+          refName: 'ctgB',
+          uniqueId: 'alias2',
+          aliases: ['B', 'contigB'],
+        },
+      ],
+    },
+  },
+}
+
+export default assembly
diff --git a/component_tests/lgv-vite/src/index.css b/component_tests/lgv-vite/src/index.css
@@ -0,0 +1,13 @@
+body {
+  margin: 0;
+  font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Roboto', 'Oxygen',
+    'Ubuntu', 'Cantarell', 'Fira Sans', 'Droid Sans', 'Helvetica Neue',
+    sans-serif;
+  -webkit-font-smoothing: antialiased;
+  -moz-osx-font-smoothing: grayscale;
+}
+
+code {
+  font-family: source-code-pro, Menlo, Monaco, Consolas, 'Courier New',
+    monospace;
+}
diff --git a/component_tests/lgv-vite/src/main.tsx b/component_tests/lgv-vite/src/main.tsx
@@ -0,0 +1,11 @@
+import React from 'react'
+import ReactDOM from 'react-dom'
+import './index.css'
+import App from './App'
+
+ReactDOM.render(
+  <React.StrictMode>
+    <App />
+  </React.StrictMode>,
+  document.getElementById('root'),
+)
diff --git a/component_tests/lgv-vite/src/react-app-env.d.ts b/component_tests/lgv-vite/src/react-app-env.d.ts
@@ -0,0 +1 @@
+/// <reference types="react-scripts" />
diff --git a/component_tests/lgv-vite/src/setupTests.ts b/component_tests/lgv-vite/src/setupTests.ts
@@ -0,0 +1,5 @@
+// jest-dom adds custom jest matchers for asserting on DOM nodes.
+// allows you to do things like:
+// expect(element).toHaveTextContent(/react/i)
+// learn more: https://github.com/testing-library/jest-dom
+import '@testing-library/jest-dom'
diff --git a/component_tests/lgv-vite/src/tracks.ts b/component_tests/lgv-vite/src/tracks.ts
@@ -0,0 +1,29 @@
+const tracks = [
+  {
+    type: 'AlignmentsTrack',
+    trackId: 'volvox_cram',
+    name: 'volvox-sorted.cram',
+    assemblyNames: ['volvox'],
+    category: ['Alignments'],
+    adapter: {
+      type: 'CramAdapter',
+      cramLocation: {
+        uri: 'volvox-sorted.cram',
+        locationType: 'UriLocation',
+      },
+      craiLocation: {
+        uri: 'volvox-sorted.cram.crai',
+        locationType: 'UriLocation',
+      },
+      sequenceAdapter: {
+        type: 'TwoBitAdapter',
+        twoBitLocation: {
+          uri: 'volvox.2bit',
+          locationType: 'UriLocation',
+        },
+      },
+    },
+  },
+]
+
+export default tracks
diff --git a/component_tests/lgv-vite/tsconfig.app.json b/component_tests/lgv-vite/tsconfig.app.json
@@ -0,0 +1,24 @@
+{
+  "compilerOptions": {
+    "target": "ES2020",
+    "useDefineForClassFields": true,
+    "lib": ["ES2020", "DOM", "DOM.Iterable"],
+    "module": "ESNext",
+    "skipLibCheck": true,
+
+    /* Bundler mode */
+    "moduleResolution": "bundler",
+    "allowImportingTsExtensions": true,
+    "isolatedModules": true,
+    "moduleDetection": "force",
+    "noEmit": true,
+    "jsx": "react-jsx",
+
+    /* Linting */
+    "strict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "noFallthroughCasesInSwitch": true
+  },
+  "include": ["src"]
+}
diff --git a/component_tests/lgv-vite/tsconfig.json b/component_tests/lgv-vite/tsconfig.json
@@ -0,0 +1,7 @@
+{
+  "files": [],
+  "references": [
+    { "path": "./tsconfig.app.json" },
+    { "path": "./tsconfig.node.json" }
+  ]
+}