Add CLI command to get and put JBrowse config files in collaboration server

packages/apollo-cli/README.md

@@ -17,7 +17,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.1.19 linux-x64 node-v18.20.3
+@apollo-annotation/cli/0.1.19 linux-x64 node-v20.17.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND
@@ -41,6 +41,8 @@ USAGE
 - [`apollo feature`](../website/docs/cli//feature.md) - Commands to handle
   features
 - [`apollo help`](../website/docs/cli//help.md) - Display help for apollo.
+- [`apollo jbrowse`](../website/docs/cli//jbrowse.md) - Commands to manage the
+  JBrowse configuration
 - [`apollo login`](../website/docs/cli//login.md) - Login to Apollo
 - [`apollo logout`](../website/docs/cli//logout.md) - Logout of Apollo
 - [`apollo refseq`](../website/docs/cli//refseq.md) - Commands to handle

packages/apollo-cli/package.json

@@ -53,6 +53,9 @@
       "feature": {
         "description": "Commands to handle features"
       },
+      "jbrowse": {
+        "description": "Commands to manage the JBrowse configuration"
+      },
       "refseq": {
         "description": "Commands to handle reference sequences"
       },

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

@@ -0,0 +1,36 @@
+import { BaseCommand } from '../../baseCommand.js'
+import { wrapLines, queryApollo } from '../../utils.js'
+
+export default class GetConfig extends BaseCommand<typeof GetConfig> {
+  static summary = 'Get JBrowse configuration from Apollo'
+  static description = wrapLines(
+    'Print to stdout the JBrowse configuration from Apollo in JSON format',
+  )
+
+  static examples = [
+    {
+      description: 'Get JBrowse configuration:',
+      command: '<%= config.bin %> <%= command.id %> > config.json',
+    },
+  ]
+
+  public async run(): Promise<void> {
+    const { flags } = await this.parse(GetConfig)
+
+    const access: { address: string; accessToken: string } =
+      await this.getAccess(flags['config-file'], flags.profile)
+
+    const response = await queryApollo(
+      access.address,
+      access.accessToken,
+      'jbrowse/config.json',
+    )
+
+    if (!response.ok) {
+      throw new Error('Failed to fetch JBrowse configuration')
+    }
+
+    const json = (await response.json()) as object
+    this.log(JSON.stringify(json, null, 2))
+  }
+}

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

@@ -0,0 +1,73 @@
+import * as fs from 'node:fs'
+import {
+  type JBrowseConfig,
+  type SerializedImportJBrowseConfigChange,
+} from '@apollo-annotation/shared'
+import { Args } from '@oclif/core'
+import { Agent, RequestInit, fetch } from 'undici'
+import { ConfigError } from '../../ApolloConf.js'
+import { BaseCommand } from '../../baseCommand.js'
+import {
+  wrapLines,
+  localhostToAddress,
+  createFetchErrorMessage,
+} from '../../utils.js'
+
+export default class SetConfig extends BaseCommand<typeof SetConfig> {
+  static summary = 'Set JBrowse configuration'
+  static description = wrapLines(
+    'Set JBrowse configuration in Apollo collaboration server',
+  )
+
+  static examples = [
+    {
+      description: 'Add JBrowse configuration:',
+      command: '<%= config.bin %> <%= command.id %> config.json',
+    },
+  ]
+
+  static args = {
+    inputFile: Args.string({
+      description: 'JBrowse configuration file',
+      required: true,
+    }),
+  }
+
+  async run(): Promise<void> {
+    const { args, flags } = await this.parse(SetConfig)
+
+    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(args.inputFile)
+    const fileContent = await filehandle.readFile({ encoding: 'utf8' })
+    await filehandle.close()
+
+    const change: SerializedImportJBrowseConfigChange = {
+      typeName: 'ImportJBrowseConfigChange',
+      newJBrowseConfig: JSON.parse(fileContent) as JBrowseConfig,
+    }
+
+    const auth: RequestInit = {
+      method: 'POST',
+      body: JSON.stringify(change),
+      headers: {
+        Authorization: `Bearer ${access.accessToken}`,
+        'Content-Type': 'application/json',
+      },
+      dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }),
+    }
+    const url = new URL(localhostToAddress(`${access.address}/changes`))
+    const response = await fetch(url, auth)
+    if (!response.ok) {
+      const errorMessage = await createFetchErrorMessage(
+        response,
+        'Failed to add JBrowse configuration',
+      )
+      throw new ConfigError(errorMessage)
+    }
+  }
+}

packages/website/docs/cli/jbrowse.md

@@ -0,0 +1,61 @@
+# `apollo jbrowse`
+
+Commands to manage the JBrowse configuration
+
+- [`apollo jbrowse get-config`](#apollo-jbrowse-get-config)
+- [`apollo jbrowse set-config INPUTFILE`](#apollo-jbrowse-set-config-inputfile)
+
+## `apollo jbrowse get-config`
+
+Get JBrowse configuration from Apollo
+
+```
+USAGE
+  $ apollo jbrowse get-config [--profile <value>] [--config-file <value>]
+
+FLAGS
+  --config-file=<value>  Use this config file (mostly for testing)
+  --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Get JBrowse configuration from Apollo
+
+  Print to stdout the JBrowse configuration from Apollo in JSON format
+
+EXAMPLES
+  Get JBrowse configuration:
+
+    $ apollo jbrowse get-config > config.json
+```
+
+_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 INPUTFILE`
+
+Set JBrowse configuration
+
+```
+USAGE
+  $ apollo jbrowse set-config INPUTFILE [--profile <value>] [--config-file <value>]
+
+ARGUMENTS
+  INPUTFILE  JBrowse configuration file
+
+FLAGS
+  --config-file=<value>  Use this config file (mostly for testing)
+  --profile=<value>      Use credentials from this profile
+
+DESCRIPTION
+  Set JBrowse configuration
+
+  Set JBrowse configuration in Apollo collaboration server
+
+EXAMPLES
+  Add JBrowse configuration:
+
+    $ apollo jbrowse set-config config.json
+```
+
+_See code:
+[src/commands/jbrowse/set-config.ts](https://github.com/GMOD/Apollo3/blob/v0.1.19/packages/apollo-cli/src/commands/jbrowse/set-config.ts)_