eslint-plugin-unicorn major version updates

package.json

@@ -34,7 +34,7 @@
     "eslint-plugin-react": "^7.37.2",
     "eslint-plugin-react-hooks": "^5.0.0",
     "eslint-plugin-tsdoc": "^0.3.0",
-    "eslint-plugin-unicorn": "^48.0.1",
+    "eslint-plugin-unicorn": "^56.0.0",
     "husky": "^9.0.11",
     "lint-staged": "^15.2.2",
     "npm-run-all": "^4.1.5",

packages/apollo-cli/src/commands/assembly/add-from-fasta.ts

@@ -1,6 +1,6 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import * as fs from 'node:fs'
-import * as path from 'node:path'
+import path from 'node:path'
 import { Args, Flags } from '@oclif/core'
 import { ObjectId } from 'bson'
 

packages/apollo-cli/src/commands/assembly/add-from-gff.ts

@@ -1,5 +1,5 @@
 import * as fs from 'node:fs'
-import * as path from 'node:path'
+import path from 'node:path'
 
 import { Args, Flags } from '@oclif/core'
 import { ObjectId } from 'bson'

packages/apollo-cli/src/commands/assembly/get.test.ts

@@ -1,5 +1,5 @@
 import fs from 'node:fs'
-import { dirname } from 'node:path'
+import path from 'node:path'
 import { fileURLToPath } from 'node:url'
 
 import { expect, test } from '@oclif/test'
@@ -26,7 +26,7 @@ describe.skip('apollo assembly get: Fail without token', () => {
   const cmd = ['assembly:get']
   test
     .stderr()
-    .command(cmd, { root: dirname(dirname(__dirname)) })
+    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
     .exit(1)
     .do((output) =>
       expect(output.stderr).to.contain('Profile "default" has no access token'),
@@ -47,7 +47,7 @@ describe.skip('apollo assembly get: Get assemblies as YAML string', () => {
   const cmd = ['assembly:get']
   test
     .stdout()
-    .command(cmd, { root: dirname(dirname(__dirname)) })
+    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
     .it(cmd.join(' '), (output) => {
       JSON.parse(output.stdout)
     })
@@ -60,7 +60,7 @@ describe.skip('apollo assembly get: Test nock', () => {
     .nock('http://127.0.0.1:3999', (api) =>
       api.persist().get('/assemblies').reply(200, { stuff: 'foo' }),
     )
-    .command(cmd, { root: dirname(dirname(__dirname)) })
+    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
     .it(cmd.join(' '), (output) => {
       console.error(output.stdout)
       // const out = JSON.parse(output.stdout)

packages/apollo-cli/src/commands/change/get.test.ts

@@ -1,5 +1,5 @@
 import fs from 'node:fs'
-import { dirname } from 'node:path'
+import path from 'node:path'
 import { fileURLToPath } from 'node:url'
 
 import { test } from '@oclif/test'
@@ -25,7 +25,7 @@ describe.skip('apollo change get: Get changes as YAML string', () => {
   const cmd = ['change:get']
   test
     .stdout()
-    .command(cmd, { root: dirname(dirname(__dirname)) })
+    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
     .it(cmd.join(' '), (output) => {
       JSON.parse(output.stdout)
     })

packages/apollo-cli/src/commands/feature/add-child.ts

@@ -130,7 +130,7 @@ to retrive the parent ID of interest and to populate the child feature with attr
     }
     const change: SerializedAddFeatureChange = {
       typeName: 'AddFeatureChange',
-      // eslint-disable-next-line unicorn/consistent-destructuring
+
       changedIds: [parentFeature._id],
       assembly,
       addedFeature: {
@@ -140,7 +140,7 @@ to retrive the parent ID of interest and to populate the child feature with attr
         max,
         type,
       },
-      // eslint-disable-next-line unicorn/consistent-destructuring
+
       parentFeatureId: parentFeature._id,
     }
     const url = new URL(localhostToAddress(`${address}/changes`))

packages/apollo-cli/src/commands/file/upload.ts

@@ -81,11 +81,11 @@ export default class Upload extends FileCommand {
     }
 
     let isGzip = args['input-file'].endsWith('.gz')
-    // eslint-disable-next-line unicorn/consistent-destructuring
+
     if (flags.gzip) {
       isGzip = true
     }
-    // eslint-disable-next-line unicorn/consistent-destructuring
+
     if (flags.decompressed) {
       isGzip = false
     }

packages/apollo-cli/src/commands/user/get.test.ts

@@ -1,5 +1,5 @@
 import fs from 'node:fs'
-import { dirname } from 'node:path'
+import path from 'node:path'
 import { fileURLToPath } from 'node:url'
 
 import { expect, test } from '@oclif/test'
@@ -25,7 +25,7 @@ describe.skip('apollo user get: Get users as YAML string', () => {
   const cmd = ['user:get']
   test
     .stdout()
-    .command(cmd, { root: dirname(dirname(__dirname)) })
+    .command(cmd, { root: path.dirname(path.dirname(__dirname)) })
     .it(cmd.join(' '), (output) => {
       const str: string = JSON.stringify(JSON.parse(output.stdout))
       expect(str).contain('username')

packages/apollo-cli/src/fileCommand.ts

@@ -1,5 +1,5 @@
 import * as fs from 'node:fs'
-import * as path from 'node:path'
+import path from 'node:path'
 import {
   Transform,
   TransformCallback,

packages/apollo-cli/src/utils.ts

@@ -123,7 +123,7 @@ export async function getAssembly(
   const assemblies = (await res.json()) as ApolloAssemblySnapshot[]
   for (const x of assemblies) {
     if (x._id === assemblyId[0]) {
-      return JSON.parse(JSON.stringify(x)) as ApolloAssemblySnapshot
+      return structuredClone(x)
     }
   }
   throw new Error(`Assembly "${assemblyNameOrId}" not found`)

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

@@ -1,6 +1,6 @@
 import { ReadStream, createReadStream } from 'node:fs'
 import { unlink } from 'node:fs/promises'
-import { join } from 'node:path'
+import path from 'node:path'
 import { Gunzip, createGunzip } from 'node:zlib'
 
 import { File, FileDocument } from '@apollo-annotation/schemas'
@@ -76,7 +76,9 @@ export class FilesService {
     const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', {
       infer: true,
     })
-    const fileStream = createReadStream(join(fileUploadFolder, file.checksum))
+    const fileStream = createReadStream(
+      path.join(fileUploadFolder, file.checksum),
+    )
     if (compressed) {
       return fileStream
     }
@@ -90,7 +92,7 @@ export class FilesService {
     const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', {
       infer: true,
     })
-    const fileName = join(fileUploadFolder, file.checksum)
+    const fileName = path.join(fileUploadFolder, file.checksum)
     switch (file.type) {
       case 'text/x-fai':
       case 'application/x-gzi': {
@@ -142,7 +144,7 @@ export class FilesService {
       const fileUploadFolder = this.configService.get('FILE_UPLOAD_FOLDER', {
         infer: true,
       })
-      const compressedFullFileName = join(fileUploadFolder, file.checksum)
+      const compressedFullFileName = path.join(fileUploadFolder, file.checksum)
       this.logger.debug(
         `Delete the file "${compressedFullFileName}" from server folder`,
       )

packages/apollo-collaboration-server/src/files/filesUtil.ts

@@ -8,7 +8,7 @@ import {
   rename,
   rmdir,
 } from 'node:fs/promises'
-import { join } from 'node:path'
+import path from 'node:path'
 import { Readable } from 'node:stream'
 import { pipeline } from 'node:stream/promises'
 import { promisify } from 'node:util'
@@ -41,8 +41,8 @@ export async function writeFileAndCalculateHash(
   const { contentEncoding, originalname, size, stream } = file
   await mkdir(fileUploadFolder, { recursive: true })
   logger.log(`Starting file upload: "${originalname}"`)
-  const tmpDir = await mkdtemp(join(fileUploadFolder, 'upload-tmp-'))
-  const tmpFileName = join(tmpDir, `${originalname}.gz`)
+  const tmpDir = await mkdtemp(path.join(fileUploadFolder, 'upload-tmp-'))
+  const tmpFileName = path.join(tmpDir, `${originalname}.gz`)
   logger.debug(`Uploading to temporary file "${tmpFileName}"`)
 
   // We calculate the md5 hash as the file is being uploaded
@@ -81,7 +81,7 @@ export async function writeFileAndCalculateHash(
   const fileChecksum = hash.digest('hex')
   logger.debug(`Uploaded file checksum: "${fileChecksum}"`)
 
-  const uploadedFileName = join(fileUploadFolder, fileChecksum)
+  const uploadedFileName = path.join(fileUploadFolder, fileChecksum)
   logger.debug(
     `File uploaded successfully, moving temporary file to final location: "${uploadedFileName}"`,
   )

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

@@ -21,6 +21,7 @@ export class RefSeqsService {
   }
 
   findAll(filter?: FindRefSeqDto) {
+    // eslint-disable-next-line unicorn/no-array-callback-reference
     return this.refSeqModel.find(filter ?? {}).exec()
   }
 

packages/apollo-shared/src/Changes/AddFeatureChange.ts

@@ -1,5 +1,5 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
@@ -143,7 +143,7 @@ export class AddFeatureChange extends FeatureChange {
             }
             attributes = {
               _id: [parentFeature._id.toString()],
-              ...JSON.parse(JSON.stringify(attributes)),
+              ...structuredClone(attributes),
             }
             parentFeature.attributes = attributes
           }

packages/apollo-shared/src/util.ts

@@ -12,6 +12,7 @@ export function makeGFF3Feature(
   // const locations = feature.discontinuousLocations?.length
   //   ? feature.discontinuousLocations
   //   : [{ start: feature.start, end: feature.end, phase: feature.phase }]
+  // eslint-disable-next-line unicorn/prefer-structured-clone
   const attributes: Record<string, string[] | undefined> = JSON.parse(
     JSON.stringify(feature.attributes),
   )

packages/jbrowse-plugin-apollo/cypress/e2e/editFeature.cy.ts

@@ -2,10 +2,10 @@ describe('Different ways of editing features', () => {
   before(() => {
     cy.deleteAssemblies()
     cy.wrap(
-      window.indexedDB.databases().then((dbs) => {
+      globalThis.indexedDB.databases().then((dbs) => {
         for (const db of dbs) {
           if (db.name) {
-            window.indexedDB.deleteDatabase(db.name)
+            globalThis.indexedDB.deleteDatabase(db.name)
           }
         }
       }),

packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts

@@ -135,7 +135,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
         ) {
           const redirectUri = isElectron
             ? 'http://localhost/auth'
-            : window.location.origin + window.location.pathname
+            : globalThis.location.origin + globalThis.location.pathname
           const url = new URL('auth/login', self.baseURL)
           const params = new URLSearchParams({
             type,
@@ -144,7 +144,7 @@ const stateModelFactory = (configSchema: ApolloInternetAccountConfigModel) => {
           url.search = params.toString()
           const eventName = `JBrowseAuthWindow-${self.internetAccountId}`
           if (isElectron) {
-            const { ipcRenderer } = window.require('electron')
+            const { ipcRenderer } = globalThis.require('electron')
             const redirectUriFromElectron = await ipcRenderer.invoke(
               'openAuthWindow',
               {

packages/jbrowse-plugin-apollo/src/ApolloSixFrameRenderer/components/ApolloRendering.tsx

@@ -551,7 +551,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
       }
       await changeManager.submit(change)
     }
-    // eslint-disable-next-line unicorn/no-useless-undefined
+
     setDragging(undefined)
     setMovedDuringLastMouseDown(false)
   }
@@ -575,7 +575,6 @@ function ApolloRendering(props: ApolloRenderingProps) {
         }
         data-testid="base_linear_display_context_menu"
         onClose={() => {
-          // eslint-disable-next-line unicorn/no-useless-undefined
           setContextMenuFeature(undefined)
         }}
       >
@@ -595,7 +594,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
                   session,
                   handleClose: () => {
                     doneCallback()
-                    // eslint-disable-next-line unicorn/no-useless-undefined
+
                     setContextMenuFeature(undefined)
                   },
                   changeManager,
@@ -625,7 +624,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
                   session,
                   handleClose: () => {
                     doneCallback()
-                    // eslint-disable-next-line unicorn/no-useless-undefined
+
                     setContextMenuFeature(undefined)
                   },
                   changeManager,
@@ -654,7 +653,7 @@ function ApolloRendering(props: ApolloRenderingProps) {
                   session,
                   handleClose: () => {
                     doneCallback()
-                    // eslint-disable-next-line unicorn/no-useless-undefined
+
                     setContextMenuFeature(undefined)
                   },
                   changeManager,

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts

@@ -17,7 +17,7 @@ let forwardFillLight: CanvasPattern | null = null
 let backwardFillLight: CanvasPattern | null = null
 let forwardFillDark: CanvasPattern | null = null
 let backwardFillDark: CanvasPattern | null = null
-if ('document' in window) {
+if ('document' in globalThis) {
   for (const direction of ['forward', 'backward']) {
     for (const themeMode of ['light', 'dark']) {
       const canvas = document.createElement('canvas')

packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/fulltext.ts

@@ -170,7 +170,10 @@ export function elaborateMatch(
   const sortedWordIndexes = [...queryWordIndexes].sort()
   const matchedQueryWords = sortedWordIndexes.map((i) => queryWords[i])
   const queryWordRegexps = matchedQueryWords.map((queryWord) => {
-    const escaped = queryWord.replaceAll(/[$()*+./?[\\\]^{|}-]/g, '\\$&')
+    const escaped = queryWord.replaceAll(
+      /[$()*+./?[\\\]^{|}-]/g,
+      String.raw`\$&`,
+    )
     return new RegExp(`\\b${escaped}`, 'gi')
   })
   // const needle = matchedQueryWords.join(' ')

packages/jbrowse-plugin-apollo/src/OntologyManager/OntologyStore/index.test.ts

@@ -24,8 +24,7 @@ jest.mock('jsonpath', () => {
     ...original,
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     query: jest.fn((obj: any, pathExpression: string, count?: number) => {
-      const newObj =
-        obj instanceof Object ? obj : JSON.parse(JSON.stringify(obj))
+      const newObj = obj instanceof Object ? obj : structuredClone(obj)
       return original.query(newObj, pathExpression, count)
     }),
   }

packages/jbrowse-plugin-apollo/src/components/AddFeature.tsx

@@ -102,7 +102,6 @@ export function AddFeature({
         break
       }
       default: {
-        // eslint-disable-next-line unicorn/no-useless-undefined
         setStrand(undefined)
       }
     }

packages/jbrowse-plugin-apollo/src/components/LogOut.tsx

@@ -50,7 +50,7 @@ export function LogOut({ handleClose, session }: DeleteAssemblyProps) {
     event.preventDefault()
     setErrorMessage('')
     selectedInternetAccount.removeToken()
-    window.location.reload()
+    globalThis.location.reload()
   }
 
   return (

packages/jbrowse-plugin-apollo/src/components/ManageChecks.tsx

@@ -182,7 +182,7 @@ export function ManageChecks({ handleClose, session }: ManageChecksProps) {
       }
     } else {
       const index = checks.indexOf(_id, 0)
-      if (index > -1) {
+      if (index !== -1) {
         checks.splice(index, 1)
       }
       setSelectedChecks(checks)

packages/jbrowse-plugin-apollo/src/components/ManageUsers.tsx

@@ -155,7 +155,7 @@ export function ManageUsers({
           key={`delete-${params.id}`}
           icon={<DeleteIcon />}
           onClick={async () => {
-            if (window.confirm('Delete this user?')) {
+            if (globalThis.confirm('Delete this user?')) {
               await deleteUser(params.id)
             }
           }}