First Apollo CLI commands: config, login, logout, and status (GMOD#354)

* Remove clientId from plugin

* Consolidate to one login endpoint

* Fix menu items not appearing

* Stub for apollo login (issue GMOD#330 and GMOD#331)

* A few mostly automatic fixes

* Temporary commit with stubs for login using name and password

* Start implementing login with username and password

* Root login should work but needs tidying up for errors

* Misc cleanups

* Fix loading of commands

* Get one test working

* Get tests working even with imported files

* Add coverage to CLI tests

* Don't lint bin/ files

* Draft for apollo config cli

* Refactor to allow multiple profiles

* Add some validation and update tests

* Update oclif so we can use flagSortOrder

* Make login subcommand aware of profiles

* Add missing file

* Refactor Profile to have address and accessType not null

* Misc. cleanup

* Address [checklist](GMOD#354 (review))

This commit should address most of the items in
GMOD#354 (review)

There are tests for most of them.

`"default.rootCredentials.password" must be a string` occurs if an entry is
expected to be string and instead is a number without quotes. The cli quotes as
appropriate.

> Make sure all commands print a sensible error message if the config file is
> not valid YAML or doesn't pass validation

Currently, the cli fails with a fairly friendly message if the yaml is
malformed, but if it is valid, it will process it anyway

* Lint and formatting fixes

* Make sure tests work if config dir doesn't exist yet

* Disable one test until server can be mocked

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>

.eslintignore

@@ -2,3 +2,4 @@ dist/
 .eslintrc.js
 esm/
 coverage/
+bin/

.eslintrc.js

@@ -121,6 +121,13 @@ module.exports = {
       },
       env: { node: true },
     },
+    {
+      files: ['./packages/apollo-cli/*.{c,}js'],
+      parserOptions: {
+        project: 'packages/apollo-cli/tsconfig.eslint.json',
+      },
+      env: { node: true },
+    },
     // Specify Node env and tsconfig for cypress testing and config files
     {
       files: [

.vscode/launch.json

@@ -76,6 +76,19 @@
         "<node_internals>/**",
         "**/.yarn/cache/**"
       ]
-    }
+    },
+    {
+      "type": "node",
+      "request": "launch",
+      "name": "Execute Command",
+      "skipFiles": [
+          "<node_internals>/**"
+      ],
+      "program": "${workspaceFolder}/bin/dev.js",
+      "args": [
+        "hello",
+        "world",
+      ],
+    },
   ],
 }

.yarnrc.yml

@@ -10,6 +10,9 @@ packageExtensions:
   cypress-mongodb@*:
     dependencies:
       bson: ^4
+  fancy-test@*:
+    dependencies:
+      chai: "*"
   material-ui-popup-state@*:
     peerDependencies:
       "@emotion/react": "*"
@@ -18,6 +21,10 @@ packageExtensions:
   mobx-react@*:
     peerDependencies:
       react-dom: "*"
+  mocha@*:
+    dependencies:
+      ts-node: "*"
+      source-map-support: "*"
   mongoose-id-validator@*:
     peerDependencies:
       mongoose: "*"

package.json

@@ -12,7 +12,7 @@
     "start:server": "yarn workspace apollo-collaboration-server run start",
     "start:plugin": "yarn workspace jbrowse-plugin-apollo run start",
     "start": "npm-run-all --print-label --parallel start:shared start:server start:plugin",
-    "test": "yarn workspace jbrowse-plugin-apollo run test:ci"
+    "test": "yarn workspaces foreach --all run test:ci"
   },
   "devDependencies": {
     "@typescript-eslint/eslint-plugin": "^6.1.0",

packages/apollo-cli/.mocharc.yml

@@ -0,0 +1,14 @@
+---
+require:
+  - ../../.pnp.cjs
+watch-extensions:
+  - ts
+recursive: true
+reporter: spec
+forbidOnly: true
+timeout: 60000
+node-option:
+  - import=tsx
+  - no-warnings=ExperimentalWarning
+  - loader=@istanbuljs/esm-loader-hook
+  - experimental-loader=../../.pnp.loader.mjs

packages/apollo-cli/.nycrc.yml

@@ -0,0 +1,8 @@
+---
+extends: '@istanbuljs/nyc-config-typescript'
+all: true
+reporter:
+  - lcov
+  - text
+include:
+  - src/**

packages/apollo-cli/README.md

@@ -0,0 +1,138 @@
+# oclif-hello-world
+
+oclif example Hello World CLI
+
+[![oclif](https://img.shields.io/badge/cli-oclif-brightgreen.svg)](https://oclif.io)
+[![CircleCI](https://circleci.com/gh/oclif/hello-world/tree/main.svg?style=shield)](https://circleci.com/gh/oclif/hello-world/tree/main)
+[![GitHub license](https://img.shields.io/github/license/oclif/hello-world)](https://github.com/oclif/hello-world/blob/main/LICENSE)
+
+<!-- toc -->
+
+- [Usage](#usage)
+- [Commands](#commands)
+<!-- tocstop -->
+
+# Usage
+
+<!-- usage -->
+
+```sh-session
+$ npm install -g apollo-cli
+$ apollo COMMAND
+running command...
+$ apollo (--version)
+apollo-cli/0.0.0 linux-x64 node-v18.19.0
+$ apollo --help [COMMAND]
+USAGE
+  $ apollo COMMAND
+...
+```
+
+<!-- usagestop -->
+
+# Commands
+
+<!-- commands -->
+
+- [`apollo config [KEY] [VALUE]`](#apollo-config-key-value)
+- [`apollo help [COMMANDS]`](#apollo-help-commands)
+- [`apollo login`](#apollo-login)
+- [`apollo logout`](#apollo-logout)
+- [`apollo status`](#apollo-status)
+
+## `apollo config [KEY] [VALUE]`
+
+Get or set Apollo configuration options
+
+```
+USAGE
+  $ apollo config [KEY] [VALUE] [-p <value>]
+
+ARGUMENTS
+  KEY    Name of configuration parameter
+  VALUE  Parameter value
+
+FLAGS
+  -p, --profile=<value>  [default: default] Set or get configuration for this profile
+
+DESCRIPTION
+  Get or set Apollo configuration options
+```
+
+_See code:
+[src/commands/config.ts](https://github.com/GMOD/Apollo3/blob/v0.0.0/packages/apollo-cli/src/commands/config.ts)_
+
+## `apollo help [COMMANDS]`
+
+Display help for apollo.
+
+```
+USAGE
+  $ apollo help [COMMANDS] [-n]
+
+ARGUMENTS
+  COMMANDS  Command to show help for.
+
+FLAGS
+  -n, --nested-commands  Include all nested commands in the output.
+
+DESCRIPTION
+  Display help for apollo.
+```
+
+_See code:
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.0.8/src/commands/help.ts)_
+
+## `apollo login`
+
+Log in to Apollo
+
+```
+USAGE
+  $ apollo login [--profile <value>] [-a <value>] [-u <value>] [-p <value>] [-f]
+
+FLAGS
+  -a, --address=<value>   Address of Apollo server
+  -f, --force             Force re-authentication even if user is already logged in
+  -p, --password=<value>  Password for <username>
+  -u, --username=<value>  Username for root login
+      --profile=<value>   [default: default] Use credentials from this profile
+
+DESCRIPTION
+  Log in to Apollo
+```
+
+_See code:
+[src/commands/login.ts](https://github.com/GMOD/Apollo3/blob/v0.0.0/packages/apollo-cli/src/commands/login.ts)_
+
+## `apollo logout`
+
+Log out of Keycloak
+
+```
+USAGE
+  $ apollo logout
+
+DESCRIPTION
+  Log out of Keycloak
+```
+
+_See code:
+[src/commands/logout.ts](https://github.com/GMOD/Apollo3/blob/v0.0.0/packages/apollo-cli/src/commands/logout.ts)_
+
+## `apollo status`
+
+View authentication status
+
+```
+USAGE
+  $ apollo status
+
+DESCRIPTION
+  View authentication status
+```
+
+_See code:
+[src/commands/status.ts](https://github.com/GMOD/Apollo3/blob/v0.0.0/packages/apollo-cli/src/commands/status.ts)_
+
+<!-- commandsstop -->

packages/apollo-cli/bin/dev.cmd

@@ -0,0 +1,3 @@
+@echo off
+
+node --loader ts-node/esm --no-warnings=ExperimentalWarning "%~dp0\dev" %*

packages/apollo-cli/bin/dev.js

@@ -0,0 +1,9 @@
+#!/usr/bin/env -S node --loader ts-node/esm --no-warnings=ExperimentalWarning
+
+// eslint-disable-next-line node/shebang
+async function main() {
+  const {execute} = await import('@oclif/core')
+  await execute({development: true, dir: import.meta.url})
+}
+
+await main()

packages/apollo-cli/bin/run.cmd

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

packages/apollo-cli/bin/run.js

@@ -0,0 +1,8 @@
+#!/usr/bin/env node
+
+async function main() {
+  const {execute} = await import('@oclif/core')
+  await execute({dir: import.meta.url})
+}
+
+await main()

packages/apollo-cli/package.json

@@ -0,0 +1,78 @@
+{
+  "name": "apollo-cli",
+  "description": "CLI for managing an Apollo Collaboration Server",
+  "version": "0.0.0",
+  "author": "Apollo Team",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/Apollo3.git",
+    "directory": "packages/apollo-cli"
+  },
+  "bin": {
+    "apollo": "./bin/run.js"
+  },
+  "type": "module",
+  "main": "",
+  "types": "dist/index.d.ts",
+  "exports": "./dist/index.js",
+  "engines": {
+    "node": ">=18.0.0"
+  },
+  "files": [
+    "/bin",
+    "/dist",
+    "/oclif.manifest.json"
+  ],
+  "scripts": {
+    "build": "shx rm -rf dist && tsc -b",
+    "dev": "tsx bin/dev.js",
+    "postpack": "shx rm -f oclif.manifest.json",
+    "posttest": "yarn lint",
+    "prepack": "yarn build && oclif manifest && oclif readme",
+    "prepare": "yarn build",
+    "test": "mocha 'src/**/*.test.ts'",
+    "test:ci": "nyc mocha 'src/**/*.test.ts'",
+    "version": "oclif readme && git add README.md"
+  },
+  "dependencies": {
+    "@inquirer/input": "^1.2.14",
+    "@inquirer/password": "^1.1.14",
+    "@inquirer/select": "^1.3.1",
+    "@oclif/core": "^3.18.2",
+    "@oclif/plugin-help": "^6.0.8",
+    "joi": "^17.7.0",
+    "open": "^9.1.0",
+    "tslib": "^2.3.1",
+    "yaml": "^2.3.4"
+  },
+  "devDependencies": {
+    "@istanbuljs/esm-loader-hook": "^0.2.0",
+    "@istanbuljs/nyc-config-typescript": "^1.0.2",
+    "@oclif/test": "^3.1.3",
+    "@types/chai": "^4",
+    "@types/inquirer": "^9.0.7",
+    "@types/mocha": "^10",
+    "@types/node": "^18.14.2",
+    "babel-plugin-istanbul": "^6.1.1",
+    "mocha": "^10.2.0",
+    "nyc": "^15.1.0",
+    "oclif": "^4.4.2",
+    "shx": "^0.3.3",
+    "ts-node": "^10.3.0",
+    "tsx": "^4.6.2",
+    "typescript": "^5.1.6"
+  },
+  "oclif": {
+    "helpOptions": {
+      "flagSortOrder": "none"
+    },
+    "bin": "apollo",
+    "dirname": "apollo-cli",
+    "commands": "./dist/commands",
+    "plugins": [
+      "@oclif/plugin-help"
+    ],
+    "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/packages/apollo-cli/<%- commandPath %>",
+    "topicSeparator": " "
+  }
+}