Upgrade oclif to v3 (#3896)

* Update create command

* Update remaining commands

* Don't use fileTransform in Jest

* Use data URL for PNGs

* Remove unneeded mocks from tests

* Add exit code cleanup to CLI tests

* Add comment to exitCode cleanup

jest.config.js

@@ -6,8 +6,6 @@ module.exports = {
   transform: {
     '^.+\\.(ts|tsx|js|jsx)$': '<rootDir>/config/jest/babelTransform.js',
     '^.+\\.css$': '<rootDir>/config/jest/cssTransform.js',
-    '^(?!.*\\.(ts|js|tsx|jsx|css|json)$)':
-      '<rootDir>/config/jest/fileTransform.js',
   },
   transformIgnorePatterns: [
     '[/\\\\]node_modules[/\\\\].+\\.(js|jsx)$',

package.json

@@ -40,8 +40,7 @@
     "@mui/system": "^5.14.4",
     "@mui/x-data-grid": "^6.0.1",
     "@node-oauth/express-oauth-server": "^3.0.0",
-    "@oclif/dev-cli": "^1.26.9",
-    "@oclif/test": "^1.2.7",
+    "@oclif/test": "^2.4.8",
     "@pmmmwh/react-refresh-webpack-plugin": "^0.5.3",
     "@storybook/addon-essentials": "^7.0.0",
     "@storybook/node-logger": "^7.0.0",
@@ -138,6 +137,7 @@
     "nock": "^13.2.1",
     "node-polyfill-webpack-plugin": "^2.0.1",
     "npm-run-all": "^4.1.5",
+    "oclif": "^3.15.0",
     "postcss": "^8.4.4",
     "postcss-flexbugs-fixes": "^5.0.2",
     "postcss-loader": "^7.3.3",

products/jbrowse-cli/bin/dev

@@ -0,0 +1,17 @@
+#!/usr/bin/env node
+
+const oclif = require('@oclif/core')
+
+const path = require('path')
+const project = path.join(__dirname, '..', 'tsconfig.json')
+
+// In dev mode -> use ts-node and dev plugins
+process.env.NODE_ENV = 'development'
+
+require('ts-node').register({ project })
+
+// In dev mode, always show stack traces
+oclif.settings.debug = true
+
+// Start the CLI
+oclif.run().then(oclif.flush).catch(oclif.Errors.handle)

products/jbrowse-cli/bin/dev.cmd

@@ -0,0 +1,3 @@
+@echo off
+
+node "%~dp0\dev" %*

products/jbrowse-cli/bin/run

@@ -1,5 +1,8 @@
 #!/usr/bin/env node
 
-require('@oclif/command').run()
-.then(require('@oclif/command/flush'))
-.catch(require('@oclif/errors/handle'))
+const oclif = require('@oclif/core')
+
+oclif
+  .run()
+  .then(require('@oclif/core/flush'))
+  .catch(require('@oclif/core/handle'))

products/jbrowse-cli/package.json

@@ -28,26 +28,23 @@
     "/oclif.manifest.json"
   ],
   "engines": {
-    "node": ">=10.4.0"
+    "node": ">=16"
   },
   "scripts": {
-    "build": "oclif-dev pack",
-    "build:typescript": "tsc --build",
+    "build": "tsc --build",
     "postpack": "rimraf oclif.manifest.json",
     "clean": "rimraf lib",
-    "prepack": "npm run clean  && npm run build:typescript && npm run manifest && npm run docs",
-    "manifest": "oclif-dev manifest",
+    "prepack": "npm run clean  && npm run build && npm run manifest && npm run docs",
+    "manifest": "oclif manifest",
     "version": "npm run docs && npm run docs:version:add",
     "docs": "npm run docs:create && npm run docs:format",
-    "docs:create": "oclif-dev readme",
+    "docs:create": "oclif readme",
     "docs:format": "prettier --write README.md",
     "docs:version:add": "git add README.md"
   },
   "dependencies": {
-    "@oclif/command": "^1.8.11",
-    "@oclif/config": "^1.18.2",
-    "@oclif/errors": "^1",
-    "@oclif/plugin-help": "3.2.14",
+    "@oclif/core": "^2.12.0",
+    "@oclif/plugin-help": "^5.2.18",
     "boxen": "^4.2.0",
     "chalk": "^4.1.0",
     "cli-progress": "^3.9.0",

products/jbrowse-cli/src/base.ts

@@ -2,7 +2,7 @@
  * By convention, exit codes in this base class are below 100
  */
 
-import Command from '@oclif/command'
+import { Command } from '@oclif/core'
 import { promises as fsPromises } from 'fs'
 import path from 'path'
 import parseJSON from 'json-parse-better-errors'

products/jbrowse-cli/src/commands/add-assembly.test.ts

@@ -26,6 +26,9 @@ const baseSequence = {
   adapter: {},
 }
 
+// Cleaning up exitCode in Node.js 20, xref https://github.com/jestjs/jest/issues/14501
+afterAll(() => (process.exitCode = 0))
+
 describe('add-assembly', () => {
   setup
     .command(['add-assembly', '{}'])
@@ -443,6 +446,7 @@ describe('add-assembly', () => {
     })
 
   setup
+    .only()
     .command([
       'add-assembly',
       '{"type":"CustomAdapter"}',
@@ -454,7 +458,7 @@ describe('add-assembly', () => {
       'copy',
     ])
     .it('can specify a custom name and alias', async ctx => {
-      expect(ctx.stdoutWrite).toHaveBeenCalledWith(
+      expect(ctx.stdout).toContain(
         'Added assembly "customName" to config.json\n',
       )
       expect(readConf(ctx)).toEqual({

products/jbrowse-cli/src/commands/add-assembly.ts

@@ -1,4 +1,4 @@
-import { flags } from '@oclif/command'
+import { Args, Flags } from '@oclif/core'
 import fs from 'fs'
 import path from 'path'
 import JBrowseCommand, { Assembly, Sequence, Config } from '../base'
@@ -46,21 +46,20 @@ export default class AddAssembly extends JBrowseCommand {
     '$ jbrowse add-assembly myfile.fa.gz --load copy',
   ]
 
-  static args = [
-    {
-      name: 'sequence',
+  static args = {
+    sequence: Args.string({
       required: true,
       description: `sequence file or URL
 
 If TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai
 and can be optionally specified with --faiLocation
 If TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be
 optionally specified with --gziLocation`,
-    },
-  ]
+    }),
+  }
 
   static flags = {
-    type: flags.string({
+    type: Flags.string({
       char: 't',
       description: `type of sequence, by default inferred from sequence file
 
@@ -79,73 +78,73 @@ custom         Either a JSON file location or inline JSON that defines a custom
 
       options: ['indexedFasta', 'bgzipFasta', 'twoBit', 'chromSizes', 'custom'],
     }),
-    name: flags.string({
+    name: Flags.string({
       char: 'n',
       description:
         'Name of the assembly; if not specified, will be guessed using the sequence file name',
     }),
-    alias: flags.string({
+    alias: Flags.string({
       char: 'a',
       description:
         'An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38");\ncan be specified multiple times',
       multiple: true,
     }),
-    displayName: flags.string({
+    displayName: Flags.string({
       description:
         'The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"',
     }),
-    faiLocation: flags.string({
+    faiLocation: Flags.string({
       description: '[default: <fastaLocation>.fai] FASTA index file or URL',
     }),
-    gziLocation: flags.string({
+    gziLocation: Flags.string({
       description:
         '[default: <fastaLocation>.gzi] FASTA gzip index file or URL',
     }),
-    refNameAliases: flags.string({
+    refNameAliases: Flags.string({
       description:
         'Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified',
     }),
-    refNameAliasesType: flags.string({
+    refNameAliasesType: Flags.string({
       description:
         'Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter',
       options: ['aliases', 'custom'],
       dependsOn: ['refNameAliases'],
     }),
-    refNameColors: flags.string({
+    refNameColors: Flags.string({
       description:
         'A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences',
     }),
-    target: flags.string({
+    target: Flags.string({
       description:
         'path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent',
     }),
-    out: flags.string({
+    out: Flags.string({
       description: 'synonym for target',
     }),
-    help: flags.help({ char: 'h' }),
-    load: flags.string({
+    help: Flags.help({ char: 'h' }),
+    load: Flags.string({
       char: 'l',
       description:
         'Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations',
       options: ['copy', 'symlink', 'move', 'inPlace'],
     }),
-    skipCheck: flags.boolean({
+    skipCheck: Flags.boolean({
       description:
         "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory",
     }),
-    overwrite: flags.boolean({
+    overwrite: Flags.boolean({
       description:
         'Overwrite existing assembly if one with the same name exists',
     }),
-    force: flags.boolean({
+    force: Flags.boolean({
       char: 'f',
       description: 'Equivalent to `--skipCheck --overwrite`',
     }),
   }
 
   async getAssembly(): Promise<Assembly> {
     let sequence: Sequence
-    const { args: runArgs, flags: runFlags } = this.parse(AddAssembly)
+    const { args: runArgs, flags: runFlags } = await this.parse(AddAssembly)
     const { sequence: argsSequence } = runArgs as { sequence: string }
 
     if (this.needLoadData(argsSequence) && !runFlags.load) {
@@ -379,7 +378,7 @@ custom         Either a JSON file location or inline JSON that defines a custom
     const exists = (s: string) =>
       new Promise(r => fs.access(s, fs.constants.F_OK, e => r(!e)))
 
-    const { args: runArgs, flags: runFlags } = this.parse(AddAssembly)
+    const { args: runArgs, flags: runFlags } = await this.parse(AddAssembly)
 
     const output = runFlags.target || runFlags.out || '.'
 

products/jbrowse-cli/src/commands/add-connection.test.ts

@@ -61,6 +61,9 @@ const setupWithDateMock = setup
     Date.now = originalDateNow
   })
 
+// Cleaning up exitCode in Node.js 20, xref https://github.com/jestjs/jest/issues/14501
+afterAll(() => (process.exitCode = 0))
+
 describe('add-connection', () => {
   setup
     .nock('https://example.com', site => site.head('/hub.txt').reply(200))

products/jbrowse-cli/src/commands/add-connection.ts

@@ -1,4 +1,4 @@
-import { flags } from '@oclif/command'
+import { Args, Flags } from '@oclif/core'
 import fs from 'fs'
 import path from 'path'
 import parseJSON from 'json-parse-better-errors'
@@ -37,60 +37,59 @@ export default class AddConnection extends JBrowseCommand {
     '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
   ]
 
-  static args = [
-    {
-      name: 'connectionUrlOrPath',
+  static args = {
+    connectionUrlOrPath: Args.string({
       required: true,
       description: `URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ `,
-    },
-  ]
+    }),
+  }
 
   static flags = {
-    type: flags.string({
+    type: Flags.string({
       char: 't',
       description:
         'type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom',
     }),
-    assemblyNames: flags.string({
+    assemblyNames: Flags.string({
       char: 'a',
       description:
         'For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name',
     }),
-    config: flags.string({
+    config: Flags.string({
       char: 'c',
       description: `Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'`,
     }),
-    connectionId: flags.string({
+    connectionId: Flags.string({
       description: `Id for the connection that must be unique to JBrowse.  Defaults to 'connectionType-assemblyName-currentTime'`,
     }),
-    name: flags.string({
+    name: Flags.string({
       char: 'n',
       description:
         'Name of the connection. Defaults to connectionId if not provided',
     }),
-    target: flags.string({
+    target: Flags.string({
       description:
         'path to config file in JB2 installation directory to write out to.',
     }),
-    out: flags.string({
+    out: Flags.string({
       description: 'synonym for target',
     }),
-    help: flags.help({ char: 'h' }),
-    skipCheck: flags.boolean({
+    help: Flags.help({ char: 'h' }),
+    skipCheck: Flags.boolean({
       description:
         "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory",
     }),
-    overwrite: flags.boolean({
+    overwrite: Flags.boolean({
       description: 'Overwrites any existing connections if same connection id',
     }),
-    force: flags.boolean({
+    force: Flags.boolean({
       char: 'f',
       description: 'Equivalent to `--skipCheck --overwrite`',
     }),
   }
 
   async run() {
-    const { args: runArgs, flags: runFlags } = this.parse(AddConnection)
+    const { args: runArgs, flags: runFlags } = await this.parse(AddConnection)
 
     const output = runFlags.target || runFlags.out || '.'
     const isDir = fs.lstatSync(output).isDirectory()