resolve merge conflict

.devcontainer/Dockerfile

@@ -1,5 +1,5 @@
 # [Choice] Node.js version (use -bullseye variants on local arm64/Apple Silicon): 16, 14, 12, 16-bullseye, 14-bullseye, 12-bullseye, 16-buster, 14-buster, 12-buster
-ARG VARIANT=16-buster
+ARG VARIANT=18-buster
 FROM mcr.microsoft.com/vscode/devcontainers/javascript-node:0-${VARIANT}
 
 # Install MongoDB command line tools if on buster and x86_64 (arm64 not supported)

.devcontainer/docker-compose.yml

@@ -9,7 +9,7 @@ services:
         # Update 'VARIANT' to pick an LTS version of Node.js: 16, 14, 12.
         # Append -bullseye or -buster to pin to an OS version.
         # Use -bullseye variants on local arm64/Apple Silicon.
-        VARIANT: 16-buster
+        VARIANT: 18-buster
 
     volumes:
       - ..:/workspace:cached

.eslintrc.js

@@ -3,14 +3,15 @@
 module.exports = {
   extends: [
     'eslint:recommended',
+    'plugin:unicorn/recommended',
     'plugin:cypress/recommended',
     'plugin:import/recommended',
     'plugin:import/typescript',
     'plugin:@typescript-eslint/strict',
     'plugin:@typescript-eslint/stylistic-type-checked',
     'plugin:prettier/recommended',
   ],
-  plugins: ['tsdoc'],
+  plugins: ['tsdoc', 'sort-destructure-keys'],
   parser: '@typescript-eslint/parser',
   parserOptions: {
     project: true,
@@ -70,8 +71,16 @@ module.exports = {
     'import/no-extraneous-dependencies': 'error',
     // eslint-plugin-prettier rules (override recommended)
     'prettier/prettier': 'warn',
+    // eslint-plugin-sort-destructure-keys rules
+    'sort-destructure-keys/sort-destructure-keys': 'warn',
     // eslint-plugin-tsdoc rules
     'tsdoc/syntax': 'warn',
+    // eslint-plugin-unicorn rules (override recommended)
+    'unicorn/filename-case': 'off', // Doesn't match our file naming, maybe can be configured later
+    'unicorn/no-empty-file': 'off', // False positives
+    'unicorn/no-null': 'off', // A lot of null in React and other libraries
+    'unicorn/prefer-module': 'off', // Cypress and apollo-collaboration-server need this
+    'unicorn/prevent-abbreviations': 'off', // Doesn't guess a lot of abbreviations correctly
     // Special case @typescript-eslint/eslint-plugin rule
     // Will be part of "plugin:@typescript-eslint/recommended-type-checked" when
     // that extension is enabled. Remove from here at that time.
@@ -123,6 +132,50 @@ module.exports = {
       env: { node: true },
     },
     // Don't enforce tsdoc syntax in JS files
+    {
+      files: ['./packages/jbrowse-plugin-apollo/**/*.{ts,tsx}'],
+      env: { browser: true },
+      extends: [
+        'plugin:react/recommended',
+        'plugin:react-hooks/recommended',
+        'plugin:jsx-a11y/recommended',
+      ],
+      settings: {
+        // These settings are from eslint-plugin-react
+        react: {
+          // React version. "detect" automatically picks the version you have installed.
+          // You can also use `16.0`, `16.3`, etc, if you want to override the detected value.
+          // It will default to "latest" and warn if missing, and to "detect" in the future
+          version: 'detect',
+        },
+        componentWrapperFunctions: [
+          // The name of any function used to wrap components, e.g. Mobx `observer` function. If this isn't set, components wrapped by these functions will be skipped.
+          'observer', // `property`
+          { property: 'styled' }, // `object` is optional
+          { property: 'observer', object: 'Mobx' },
+          { property: 'observer', object: '<pragma>' }, // sets `object` to whatever value `settings.react.pragma` is set to
+        ],
+      },
+    },
+    // Lint non-src files (e.g. jest.config.js) using a separate tsconfig
+    {
+      files: ['./packages/jbrowse-plugin-apollo/*.js'],
+      parserOptions: {
+        project: 'packages/jbrowse-plugin-apollo/tsconfig.eslint.json',
+      },
+      env: { node: true },
+    },
+    // Specify Node env for cypress testing files
+    {
+      files: ['./packages/jbrowse-plugin-apollo/cypress/**/*.js'],
+      env: { node: true },
+    },
+    // Specify Node env for apollo-collaboration-server/
+    {
+      files: ['./packages/apollo-collaboration-server/**/*.ts'],
+      env: { node: true },
+    },
+    // Don't enforce tsdoc syntax in JS files
     {
       files: ['**/*.js'],
       rules: {

.github/workflows/pull_request.yml

@@ -9,10 +9,10 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v3
-      - name: Use Node.js 16.x
+      - name: Use Node.js 18.x
         uses: actions/setup-node@v3
         with:
-          node-version: 16
+          node-version: 18
           cache: yarn
       - name: Install
         run: yarn --immutable

.github/workflows/push.yml

@@ -9,10 +9,10 @@ jobs:
     steps:
       - name: Check out
         uses: actions/checkout@v3
-      - name: Use Node.js 16.x
+      - name: Use Node.js 18.x
         uses: actions/setup-node@v3
         with:
-          node-version: 16
+          node-version: 18
           cache: yarn
       - name: Install
         run: yarn --immutable

package.json

@@ -27,7 +27,9 @@
     "eslint-plugin-prettier": "^5.0.0",
     "eslint-plugin-react": "^7.32.2",
     "eslint-plugin-react-hooks": "^4.6.0",
+    "eslint-plugin-sort-destructure-keys": "^1.5.0",
     "eslint-plugin-tsdoc": "^0.2.17",
+    "eslint-plugin-unicorn": "^48.0.0",
     "import-sort-parser-typescript": "^6.0.0",
     "import-sort-style-module": "^6.0.0",
     "jest": "^29.6.1",

packages/apollo-collaboration-server/package.json

@@ -81,7 +81,7 @@
     "@types/express-session": "^1",
     "@types/jest": "^27.0.1",
     "@types/multer": "^1.4.7",
-    "@types/node": "^16.0.0",
+    "@types/node": "^18.11.9",
     "@types/node-fetch": "^2.6.2",
     "@types/passport-google-oauth20": "^2.0.11",
     "@types/passport-jwt": "^3.0.6",
@@ -96,7 +96,7 @@
     "rimraf": "^3.0.2",
     "source-map-support": "^0.5.20",
     "supertest": "^6.1.3",
-    "ts-jest": "^27.0.3",
+    "ts-jest": "^29.1.1",
     "ts-loader": "^9.2.3",
     "ts-node": "^10.3.0",
     "ts-node-dev": "^1.1.8",

packages/apollo-collaboration-server/src/app.module.ts

@@ -1,5 +1,5 @@
-import fs from 'fs/promises'
-import path from 'path'
+import fs from 'node:fs/promises'
+import path from 'node:path'
 
 import { Module } from '@nestjs/common'
 import { ConfigModule, ConfigService } from '@nestjs/config'
@@ -59,7 +59,7 @@ const validationSchema = Joi.object({
       const errorMessage =
         'LOG_LEVELS must be a comma-separated list of log levels to output, where the possible values are: error, warn, log, debug, verbose'
       if (typeof value !== 'string') {
-        throw new Error(errorMessage)
+        throw new TypeError(errorMessage)
       }
       const levels = value.split(',')
       for (const level of levels) {
@@ -85,7 +85,7 @@ const validationSchema = Joi.object({
       const errorMessage =
         'PLUGIN_URLS must be a comma-separated list of plugin URLs'
       if (typeof value !== 'string') {
-        throw new Error(errorMessage)
+        throw new TypeError(errorMessage)
       }
       const urls = value.split(',')
       for (const url of urls) {
@@ -116,15 +116,14 @@ async function mongoDBURIFactory(
   if (!uri) {
     // We can use non-null assertion since joi already checks this for us
     // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-    const uriFile = configService.get('MONGODB_URI_FILE', {
-      infer: true,
-    })!
-    uri = (await fs.readFile(uriFile, 'utf-8')).trim()
+    const uriFile = configService.get('MONGODB_URI_FILE', { infer: true })!
+    const uriFileText = await fs.readFile(uriFile, 'utf8')
+    uri = uriFileText.trim()
   }
   return {
     uri,
     connectionFactory: (connection: Connection) => {
-      connection.set('maxTimeMS', 7200000)
+      connection.set('maxTimeMS', 7_200_000)
       return connection
     },
   }

packages/apollo-collaboration-server/src/authentication/authentication.module.ts

@@ -1,4 +1,4 @@
-import fs from 'fs/promises'
+import fs from 'node:fs/promises'
 
 import { Module } from '@nestjs/common'
 import { ConfigModule, ConfigService } from '@nestjs/config'
@@ -24,10 +24,9 @@ async function jwtConfigFactory(
   if (!jwtSecret) {
     // We can use non-null assertion since joi already checks this for us
     // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-    const uriFile = configService.get('JWT_SECRET_FILE', {
-      infer: true,
-    })!
-    jwtSecret = (await fs.readFile(uriFile, 'utf-8')).trim()
+    const jwtFile = configService.get('JWT_SECRET_FILE', { infer: true })!
+    const jwtFileText = await fs.readFile(jwtFile, 'utf8')
+    jwtSecret = jwtFileText.trim()
   }
   return { secret: jwtSecret, signOptions: { expiresIn: '1d' } }
 }

packages/apollo-collaboration-server/src/authentication/authentication.service.ts

@@ -19,10 +19,7 @@ export class AuthenticationService {
     private readonly usersService: UsersService,
     private readonly jwtService: JwtService,
     private readonly configService: ConfigService<
-      {
-        DEFAULT_NEW_USER_ROLE: Role | 'none'
-        ALLOW_GUEST_USER: boolean
-      },
+      { DEFAULT_NEW_USER_ROLE: Role | 'none'; ALLOW_GUEST_USER: boolean },
       true
     >,
   ) {
@@ -40,7 +37,7 @@ export class AuthenticationService {
     if (!profile._json.email) {
       throw new UnauthorizedException('No email provided')
     }
-    const { name, email } = profile._json
+    const { email, name } = profile._json
     return this.logIn(name ?? 'N/A', email)
   }
 
@@ -87,10 +84,7 @@ export class AuthenticationService {
       const hasAdmin = userCount > 1 || (userCount === 1 && !guestUser)
       // If there is not a non-guest user yet, the 1st user role will be admin
       const newUserRole = hasAdmin ? this.defaultNewUserRole : Role.Admin
-      const newUser: CreateUserDto = {
-        email,
-        username: name,
-      }
+      const newUser: CreateUserDto = { email, username: name }
       if (newUserRole !== 'none') {
         newUser.role = newUserRole
       }

packages/apollo-collaboration-server/src/changes/changes.service.ts

@@ -116,7 +116,7 @@ export class ChangesService {
           pluginsService: this.pluginsService,
           user: uniqUserId,
         })
-      } catch (e) {
+      } catch (error) {
         // Clean up old "temporary document" -documents
         // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
         this.logger.debug(
@@ -134,16 +134,12 @@ export class ChangesService {
         await this.refSeqChunkModel.deleteMany({
           $and: [{ status: -1, user: uniqUserId }],
         })
-        throw new UnprocessableEntityException(String(e))
+        throw new UnprocessableEntityException(String(error))
       }
 
       // Add entry to change collection
       const [savedChangedLogDoc] = await this.changeModel.create([
-        {
-          ...change,
-          user: user.email,
-          sequence,
-        },
+        { ...change, user: user.email, sequence },
       ])
       changeDoc = savedChangedLogDoc
       const validationResult2 = await validationRegistry.backendPostValidate(
@@ -181,7 +177,7 @@ export class ChangesService {
           { $and: [{ status: -1, user: uniqUserId }] },
           { $set: { status: 0 } },
         )
-      } catch (e) {
+      } catch (error) {
         // Clean up old "temporary document" -documents
         this.logger.debug(
           '*** UPDATE STATUS EXCEPTION - Start to clean up old temporary documents...',
@@ -199,7 +195,7 @@ export class ChangesService {
         await this.refSeqChunkModel.deleteMany({
           $and: [{ status: -1, user: uniqUserId }],
         })
-        throw new UnprocessableEntityException(String(e))
+        throw new UnprocessableEntityException(String(error))
       }
     })
 
@@ -240,10 +236,7 @@ export class ChangesService {
   async findAll(changeFilter: FindChangeDto) {
     const queryCond: FilterQuery<ChangeDocument> = { ...changeFilter }
     if (changeFilter.user) {
-      queryCond.user = {
-        $regex: `${changeFilter.user}`,
-        $options: 'i',
-      }
+      queryCond.user = { $regex: `${changeFilter.user}`, $options: 'i' }
     }
     if (changeFilter.since) {
       queryCond.sequence = { $gt: Number(changeFilter.since) }
@@ -252,12 +245,12 @@ export class ChangesService {
     this.logger.debug(`Search criteria: "${JSON.stringify(queryCond)}"`)
 
     let sortOrder: 1 | -1 = -1
-    if (changeFilter.sort) {
-      if (changeFilter.sort === '1') {
-        sortOrder = 1
-      }
+    if (changeFilter.sort && changeFilter.sort === '1') {
+      sortOrder = 1
     }
     let changeCursor = this.changeModel
+      // unicorn thinks this is an Array.prototype.find, so we ignore it
+      // eslint-disable-next-line unicorn/no-array-callback-reference
       .find(queryCond)
       .sort({ sequence: sortOrder })
 

packages/apollo-collaboration-server/src/features/features.module.ts

@@ -25,10 +25,7 @@ import { FeaturesService } from './features.service'
         },
         inject: [getConnectionToken()],
       },
-      {
-        name: Export.name,
-        useFactory: () => ExportSchema,
-      },
+      { name: Export.name, useFactory: () => ExportSchema },
     ]),
   ],
   exports: [MongooseModule],