fixes

packages/apollo-cli/src/commands/jbrowse/set-config.ts

@@ -1,9 +1,9 @@
 import * as fs from 'node:fs'
 import {
-  ImportJBrowseConfigChange,
-  JBrowseConfig,
+  type JBrowseConfig,
+  type SerializedImportJBrowseConfigChange,
 } from '@apollo-annotation/shared'
-import { Flags } from '@oclif/core'
+import { Args } from '@oclif/core'
 import { Agent, RequestInit, fetch } from 'undici'
 import { ConfigError } from '../../ApolloConf.js'
 import { BaseCommand } from '../../baseCommand.js'
@@ -22,35 +22,34 @@ export default class SetConfig extends BaseCommand<typeof SetConfig> {
   static examples = [
     {
       description: 'Add jbrowse configuration:',
-      command: '<%= config.bin %> <%= command.id %> -i config.json',
+      command: '<%= config.bin %> <%= command.id %> config.json',
     },
   ]
 
-  static flags = {
-    'input-file': Flags.string({
-      char: 'i',
+  static args = {
+    inputFile: Args.string({
       description: 'Input jbrowse configuration file',
       required: true,
     }),
   }
 
   async run(): Promise<void> {
-    const { flags } = await this.parse(SetConfig)
+    const { args, flags } = await this.parse(SetConfig)
 
-    if (!fs.existsSync(flags['input-file'])) {
-      this.error(`File ${flags['input-file']} does not exist`)
+    if (!fs.existsSync(args.inputFile)) {
+      this.error(`File ${args.inputFile} does not exist`)
     }
 
     const access: { address: string; accessToken: string } =
       await this.getAccess(flags['config-file'], flags.profile)
-    const filehandle = await fs.promises.open(flags['input-file'])
+    const filehandle = await fs.promises.open(args.inputFile)
     const fileContent = await filehandle.readFile({ encoding: 'utf8' })
     await filehandle.close()
 
-    const change = new ImportJBrowseConfigChange({
+    const change: SerializedImportJBrowseConfigChange = {
       typeName: 'ImportJBrowseConfigChange',
       newJBrowseConfig: JSON.parse(fileContent) as JBrowseConfig,
-    })
+    }
 
     const auth: RequestInit = {
       method: 'POST',

packages/website/docs/cli/jbrowse.md

@@ -3,7 +3,7 @@
 Get Jbrowse configuration from Apollo
 
 - [`apollo jbrowse get-config`](#apollo-jbrowse-get-config)
-- [`apollo jbrowse set-config`](#apollo-jbrowse-set-config)
+- [`apollo jbrowse set-config INPUTFILE`](#apollo-jbrowse-set-config-inputfile)
 
 ## `apollo jbrowse get-config`
 
@@ -26,18 +26,20 @@ DESCRIPTION
 _See code:
 [src/commands/jbrowse/get-config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/jbrowse/get-config.ts)_
 
-## `apollo jbrowse set-config`
+## `apollo jbrowse set-config INPUTFILE`
 
 Add jbrowse configuration
 
 ```
 USAGE
-  $ apollo jbrowse set-config -i <value> [--profile <value>] [--config-file <value>]
+  $ apollo jbrowse set-config INPUTFILE [--profile <value>] [--config-file <value>]
+
+ARGUMENTS
+  INPUTFILE  Input jbrowse configuration file
 
 FLAGS
-  -i, --input-file=<value>   (required) Input jbrowse configuration file
-      --config-file=<value>  Use this config file (mostly for testing)
-      --profile=<value>      Use credentials from this profile
+  --config-file=<value>  Use this config file (mostly for testing)
+  --profile=<value>      Use credentials from this profile
 
 DESCRIPTION
   Add jbrowse configuration
@@ -47,7 +49,7 @@ DESCRIPTION
 EXAMPLES
   Add jbrowse configuration:
 
-    $ apollo jbrowse set-config -i config.json
+    $ apollo jbrowse set-config config.json
 ```
 
 _See code: