Merge pull request #520 from GMOD/cra_rescripts

Electron build of JBrowse desktop
GMOD · Oct 30, 2019 · 37e3512 · 37e3512
2 parents 1babf91 + 8e64e7b
commit 37e3512
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Showing 166 changed files with 9,396 additions and 6,674 deletions.
diff --git a/.eslintrc.js b/.eslintrc.js
@@ -16,14 +16,15 @@ module.exports = {
   },
   rules: {
     'class-methods-use-this': 'off',
+    'global-require': 'off',
     'import/no-cycle': 'warn',
     'import/prefer-default-export': 'off',
+    'max-classes-per-file': 'off',
     'monorepo/no-internal-import': 'off',
     'no-console': ['warn', { allow: ['warn', 'error'] }],
     'no-debugger': 'warn',
     'no-param-reassign': 'off',
     'no-restricted-syntax': 'off',
-    'global-require': 'off',
     'no-underscore-dangle': 'warn',
     'no-unused-vars': 'warn',
     'no-use-before-define': 'off',
@@ -42,11 +43,13 @@ module.exports = {
     'react/prefer-stateless-function': 'warn',
     'react/prop-types': 'warn',
     'react/require-default-props': 'warn',
+    'spaced-comment': ['error', 'always', { 'markers': ['/'] }],
+    '@typescript-eslint/ban-ts-ignore': 'off',
     '@typescript-eslint/explicit-function-return-type': 'off',
     '@typescript-eslint/explicit-member-accessibility': 'off',
     '@typescript-eslint/camelcase': 'warn',
-    '@typescript-eslint/no-unused-vars': 'off',
     '@typescript-eslint/no-use-before-define': 'off',
+    '@typescript-eslint/no-var-requires': 'off',
   },
   settings: {
     'import/resolver': {
@@ -56,16 +59,12 @@ module.exports = {
     },
   },
   overrides: [
-    {
-      files: ['packages/generator-jbrowse/**/*'],
-      env: { node: true },
-      rules: { '@typescript-eslint/no-var-requires': 'off' },
-    },
-    {
-      files: ['**/*.worker.js'],
-      globals: { self: true },
-      rules: { 'no-restricted-globals': 'off' },
-    },
+    // {
+    //   "files": ["*.ts", "*.tsx"],
+    //   "rules": {
+    //     "@typescript-eslint/explicit-function-return-type": ["error"]
+    //   }
+    // },
     {
       files: ['**/*.test.[t,j]s'],
       env: { jest: true },
@@ -77,7 +76,6 @@ module.exports = {
       },
       rules: {
         'import/no-extraneous-dependencies': 'off',
-        // 'no-restricted-globals': 'off',
       },
     },
   ],

diff --git a/package.json b/package.json
@@ -7,6 +7,7 @@
     "scripts": {
         "build": "NODE_ENV=production lerna run build",
         "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts,.jsx,.tsx .",
+        "typecheck": "tsc --noEmit",
         "test-ci": "jest --ci --coverage",
         "built-test-ci": "jest --ci packages/integration-tests",
         "test": "jest"
@@ -24,98 +25,80 @@
         "@gmod/jbrowse-plugin-linear-genome-view": "^2.0.0",
         "@material-ui/core": "^4.0.0",
         "@material-ui/styles": "^4.0.0",
+        "@rescripts/cli": "^0.0.12",
         "@svgr/webpack": "^4.1.0",
         "@testing-library/jest-dom": "^4.0.0",
         "@testing-library/react": "^9.0.0",
         "@types/base64-js": "^1.2.5",
         "@types/get-value": "^3.0.1",
         "@types/jest": "^24.0.9",
         "@types/long": "^4.0.0",
+        "@types/node": "12.7.5",
         "@types/pako": "^1.0.1",
+        "@types/react": "16.9.2",
         "@types/react-dom": "^16.9.1",
         "@types/set-value": "^2.0.0",
         "@types/shortid": "^0.0.29",
         "@types/string-template": "^1.0.2",
-        "@typescript-eslint/eslint-plugin": "^1.7.0",
-        "@typescript-eslint/parser": "^1.7.0",
-        "babel-eslint": "^10.0.1",
-        "babel-jest": "^24.7.1",
+        "@typescript-eslint/eslint-plugin": "^2.0.0",
+        "@typescript-eslint/parser": "^2.0.0",
         "babel-loader": "^8.0.4",
         "babel-plugin-named-asset-import": "^0.3.0",
         "babel-preset-mobx": "^2.0.0",
         "babel-preset-react-app": "8.0.0-next.b0cbf2ca",
         "babel-preset-typescript": "^7.0.0-alpha.19",
         "bfj": "^6.1.1",
-        "case-sensitive-paths-webpack-plugin": "^2.1.2",
         "chalk": "^2.4.1",
+        "concurrently": "^4.1.2",
         "core-js": "^3.2.1",
         "css-loader": "^2.1.0",
-        "documentation": "^9.3.1",
-        "dotenv": "^6.0.0",
-        "dotenv-expand": "^4.2.0",
-        "eslint": "^5.16.0",
-        "eslint-config-airbnb": "^17.1.0",
-        "eslint-config-airbnb-base": "^13.1.0",
-        "eslint-config-prettier": "^4.1.0",
-        "eslint-config-react-app": "^4.0.0",
+        "electron": "^6.0.0",
+        "eslint-config-airbnb": "^18.0.0",
+        "eslint-config-airbnb-base": "^14.0.0",
+        "eslint-config-prettier": "^6.0.0",
+        "eslint-config-react-app": "^5.0.0",
         "eslint-config-xo": "^0.26.0",
-        "eslint-loader": "^2.1.2",
-        "eslint-plugin-flowtype": "^3.6.1",
+        "eslint-loader": "^3.0.0",
+        "eslint-plugin-flowtype": "^4.0.0",
         "eslint-plugin-import": "^2.17.2",
         "eslint-plugin-jsx-a11y": "^6.2.1",
         "eslint-plugin-monorepo": "^0.2.1",
         "eslint-plugin-prettier": "^3.0.1",
         "eslint-plugin-react": "^7.12.4",
-        "eslint-plugin-react-hooks": "^1.6.0",
+        "eslint-plugin-react-hooks": "^2.0.0",
         "fetch-mock": "^7.3.3",
         "file-loader": "^3.0.1",
-        "fs-extra": "^7.0.0",
-        "html-webpack-plugin": "4.0.0-alpha.2",
         "identity-obj-proxy": "^3.0.0",
-        "jest": "^24.8.0",
         "jest-environment-jsdom-fourteen": "^0.1.0",
         "jest-pnp-resolver": "^1.2.0",
-        "jest-resolve": "^24.3.0",
         "lerna": "^3.4.1",
-        "mini-css-extract-plugin": "^0.5.0",
         "mobx": "^5.0.0",
         "mobx-react": "^6.0.0",
         "mobx-state-tree": "3.14.1",
         "node-sass": "^4.9.3",
         "open-cli": "^5.0.0",
-        "optimize-css-assets-webpack-plugin": "^5.0.1",
-        "pnp-webpack-plugin": "^1.1.0",
         "postcss-flexbugs-fixes": "^4.1.0",
         "postcss-loader": "^3.0.0",
         "postcss-preset-env": "^6.5.0",
-        "postcss-safe-parser": "^4.0.1",
         "prettier": "^1.18.2",
         "prop-types": "^15.0.0",
         "range-parser": "^1.2.1",
         "react": "^16.8.0",
-        "react-app-polyfill": "^0.2.0",
-        "react-dev-utils": "<8.0.0",
         "react-dom": "^16.8.0",
-        "resolve": "^1.8.1",
+        "react-scripts": "^3.2.0",
+        "rescript-worker-loader": "^1.0.3",
+        "rescripts-use-yarn-workspaces": "^1.1.0",
         "rimraf": "^2.6.3",
         "rxjs": "^6.0.0",
         "sass-loader": "^7.1.0",
         "standard-changelog": "^2.0.7",
         "style-loader": "^0.23.0",
-        "terser-webpack-plugin": "^1.1.0",
         "text-encoding-polyfill": "^0.6.7",
-        "thread-loader": "^2.1.1",
-        "ts-jest": "^24.0.2",
         "typedoc": "^0.15.0",
-        "typedoc-plugin-markdown": "^1.1.27",
         "typescript": "^3.3.4000",
-        "url-loader": "^1.1.1",
-        "webpack": "^4.19.1",
-        "webpack-cli": "^3.2.3",
-        "webpack-dev-server": "^3.1.14",
-        "webpack-manifest-plugin": "^2.0.4",
+        "wait-on": "^3.3.0",
+        "webpack-cli": "^3.3.9",
         "whatwg-fetch": "^3.0.0",
-        "workbox-webpack-plugin": "^4.0.0",
         "worker-loader": "^2.0.0",
         "yeoman-test": "^1.9.1"
     }

diff --git a/packages/alignments/src/BamAdapter/BamAdapter.ts b/packages/alignments/src/BamAdapter/BamAdapter.ts
@@ -13,12 +13,14 @@ interface HeaderLine {
   tag: string
   value: string
 }
+interface SamHeader {
+  idToName?: string[]
+  nameToId?: Record<string, number>
+}
 export default class extends BaseAdapter {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private bam: any
+  private bam: BamFile
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  private samHeader: any
+  private samHeader?: SamHeader
 
   public static capabilities = ['getFeatures', 'getRefNames']
 
@@ -48,9 +50,9 @@ export default class extends BaseAdapter {
     this.bam = new BamFile(bamOpts)
   }
 
-  async setup(): Promise<void> {
+  async setup(opts: BaseOptions = {}): Promise<void> {
     if (!this.samHeader) {
-      const samHeader = await this.bam.getHeader()
+      const samHeader = await this.bam.getHeader(opts.signal)
       this.samHeader = {}
 
       // use the @SQ lines in the header to figure out the
@@ -68,16 +70,14 @@ export default class extends BaseAdapter {
           }
         })
       })
-      if (idToName.length) {
-        this.samHeader.idToName = idToName
-        this.samHeader.nameToId = nameToId
-      }
+      this.samHeader.idToName = idToName
+      this.samHeader.nameToId = nameToId
     }
   }
 
-  async getRefNames(): Promise<string[]> {
-    await this.setup()
-    return this.samHeader.idToName
+  async getRefNames(opts: BaseOptions = {}): Promise<string[]> {
+    await this.setup(opts)
+    return (this.samHeader && this.samHeader.idToName) || []
   }
 
   /**
@@ -94,7 +94,7 @@ export default class extends BaseAdapter {
   ): Observable<Feature> {
     return ObservableCreate(
       async (observer: Observer<Feature>): Promise<void> => {
-        await this.setup()
+        await this.setup(opts)
         const records = await this.bam.getRecordsForRange(
           refName,
           start,
@@ -116,6 +116,7 @@ export default class extends BaseAdapter {
    * will not be needed for the forseeable future and can be purged
    * from caches, etc
    */
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   freeResources(/* { region } */): void {}
 
   // eslint-disable-next-line @typescript-eslint/no-explicit-any
@@ -126,7 +127,7 @@ export default class extends BaseAdapter {
   refIdToName(refId: number): string | undefined {
     // use info from the SAM header if possible, but fall back to using
     // the ref name order from when the browser's ref names were loaded
-    if (this.samHeader.idToName) {
+    if (this.samHeader && this.samHeader.idToName) {
       return this.samHeader.idToName[refId]
     }
     return undefined

diff --git a/packages/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts b/packages/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
@@ -148,6 +148,7 @@ export default class implements Feature {
     return this.record._get('md')
   }
 
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   set(): void {}
 
   tags(): string[] {

diff --git a/packages/alignments/src/BamAdapter/declare.d.ts b/packages/alignments/src/BamAdapter/declare.d.ts
diff --git a/packages/alignments/src/CramAdapter/CramAdapter.ts b/packages/alignments/src/CramAdapter/CramAdapter.ts
@@ -194,6 +194,7 @@ export default class CramAdapter extends BaseAdapter {
    * will not be needed for the forseeable future and can be purged
    * from caches, etc
    */
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   freeResources(/* { region } */): void {}
 
   // eslint-disable-next-line @typescript-eslint/no-explicit-any

diff --git a/packages/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts b/packages/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts
@@ -208,6 +208,7 @@ export default class CramSlightlyLazyFeature implements Feature {
     return undefined
   }
 
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   set(): void {}
 
   pairedFeature() {

diff --git a/packages/alignments/src/PileupRenderer/PileupRenderer.ts b/packages/alignments/src/PileupRenderer/PileupRenderer.ts
@@ -43,7 +43,7 @@ export default class extends BoxRendererType {
     config: any, // eslint-disable-line @typescript-eslint/no-explicit-any
     bpPerPx: number,
     region: IRegion,
-    horizontallyFlipped: boolean = false,
+    horizontallyFlipped = false,
   ): LayoutRecord | null {
     const startPx = bpToPx(
       feature.get('start'),

diff --git a/packages/alignments/src/PileupRenderer/components/PileupRendering.js b/packages/alignments/src/PileupRenderer/components/PileupRendering.js
@@ -9,15 +9,15 @@ import PrerenderedCanvas from '@gmod/jbrowse-core/components/PrerenderedCanvas'
 import runner from 'mobx-run-in-reactive-context'
 import useTimeout from 'use-timeout'
 
-const useStyles = makeStyles(theme => ({
+const useStyles = makeStyles({
   hoverLabel: {
     border: '1px solid black',
     backgroundColor: '#fffa',
     position: 'absolute',
     pointerEvents: 'none',
     zIndex: 10000,
   },
-}))
+})
 
 function Tooltip({ offsetX, offsetY, feature, timeout = 300 }) {
   const classes = useStyles()

diff --git a/packages/bed/src/BigBedAdapter/BigBedAdapter.ts b/packages/bed/src/BigBedAdapter/BigBedAdapter.ts
@@ -130,6 +130,7 @@ export default class extends BaseAdapter {
     })
   }
 
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   public freeResources(): void {}
 }
 

diff --git a/packages/circular-view/src/ChordTrack/components/ChordTrack.js b/packages/circular-view/src/ChordTrack/components/ChordTrack.js
@@ -1,3 +1,4 @@
-export default ({ jbrequire }) => {
+export default () => {
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   return function ChordTrack() {}
 }
diff --git a/packages/circular-view/src/ChordTrack/models/ChordTrack.js b/packages/circular-view/src/ChordTrack/models/ChordTrack.js
@@ -45,7 +45,7 @@ export default pluginManager => {
       configuration: ConfigurationReference(configSchema),
       bezierRadiusRatio: 0.1,
     })
-    .volatile(self => ({
+    .volatile((/* self */) => ({
       refNameMap: undefined,
     }))
     .views(self => ({

diff --git a/packages/circular-view/src/StructuralVariantChordRenderer/ReactComponent.js b/packages/circular-view/src/StructuralVariantChordRenderer/ReactComponent.js
@@ -17,7 +17,6 @@ export default ({ jbrequire }) => {
   }
 
   const Chord = observer(function Chord({
-    trackModel,
     feature,
     blocksForRefs,
     radius,

diff --git a/packages/circular-view/src/StructuralVariantChordTrack/models/index.js b/packages/circular-view/src/StructuralVariantChordTrack/models/index.js
@@ -41,7 +41,7 @@ export default pluginManager => {
         configuration: ConfigurationReference(configSchema),
       }),
     )
-    .volatile(self => ({
+    .volatile((/* self */) => ({
       ReactComponent: mainReactComponent,
 
       // NOTE: all this volatile stuff has to be filled in at once

diff --git a/packages/circular-view/src/StructuralVariantChordTrack/models/refNameMapKeeper.js b/packages/circular-view/src/StructuralVariantChordTrack/models/refNameMapKeeper.js
@@ -10,7 +10,7 @@ export default pluginManager => {
 
   const model = types
     .model('RefNameMap', {})
-    .volatile(self => ({
+    .volatile((/* self */) => ({
       refNameMap: undefined,
     }))
     .actions(self => ({
@@ -35,6 +35,7 @@ export default pluginManager => {
         )
       },
 
+      // eslint-disable-next-line @typescript-eslint/no-empty-function
       loadAssemblyRefNameMapStarted() {},
       loadAssemblyRefNameMapSuccess(result) {
         // console.log('loaded refname map', result)

diff --git a/packages/circular-view/src/StructuralVariantChordTrack/models/renderReaction.js b/packages/circular-view/src/StructuralVariantChordTrack/models/renderReaction.js
@@ -31,12 +31,7 @@ export default ({ jbrequire }) => {
     return data
   }
 
-  async function renderReactionEffect(
-    props,
-    signal,
-    self,
-    allowRefetch = true,
-  ) {
+  async function renderReactionEffect(props, signal, self) {
     if (!props) {
       throw new Error('cannot render with no props')
     }

diff --git a/packages/circular-view/src/index.js b/packages/circular-view/src/index.js
@@ -13,6 +13,7 @@ export default class CircularViewPlugin {
     )
   }
 
+  // eslint-disable-next-line @typescript-eslint/no-empty-function
   configure() {}
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -130,6 +130,7 @@ export default class extends BaseAdapter { @@
         })
       }
+      // eslint-disable-next-line @typescript-eslint/no-empty-function
       public freeResources(): void {}
     }
@@ Expand Down @@