@apollo-annotation/cli 0.1.17 → 0.1.18

package/dist/utils.d.ts

@@ -1,6 +1,6 @@
 import EventEmitter from 'node:events';
 import { Response } from 'undici';
-import { Config } from './Config.js';
+import { ApolloConf } from './ApolloConf.js';
 export declare const CLI_SERVER_ADDRESS = "http://127.0.0.1:5657";
 export declare const CLI_SERVER_ADDRESS_CALLBACK = "http://127.0.0.1:5657/auth/callback";
 export declare class CheckError extends Error {
@@ -10,7 +10,7 @@ export interface UserCredentials {
 }
 export declare function createFetchErrorMessage(response: Response, additionalText?: string): Promise<string>;
 export declare function checkConfigfileExists(configFile: string): void;
-export declare function checkProfileExists(profileName: string, config: Config): void;
+export declare function checkProfileExists(profileName: string, config: ApolloConf): void;
 export declare function basicCheckConfig(configFile: string, profileName: string): void;
 /**
  * @deprecated Use this function while we wait to resolve the TypeError when using localhost in fetch.

package/dist/utils.js

@@ -8,7 +8,7 @@ import * as fs from 'node:fs';
 import * as os from 'node:os';
 import * as path from 'node:path';
 import { Agent, FormData, Response, fetch } from 'undici';
-import { Config, ConfigError } from './Config.js';
+import { ApolloConf, ConfigError } from './ApolloConf.js';
 const CONFIG_PATH = path.resolve(os.homedir(), '.clirc');
 export const CLI_SERVER_ADDRESS = 'http://127.0.0.1:5657';
 export const CLI_SERVER_ADDRESS_CALLBACK = `${CLI_SERVER_ADDRESS}/auth/callback`;
@@ -37,7 +37,7 @@ export function checkProfileExists(profileName, config) {
 }
 export function basicCheckConfig(configFile, profileName) {
     checkConfigfileExists(configFile);
-    const config = new Config(configFile);
+    const config = new ApolloConf(configFile);
     checkProfileExists(profileName, config);
 }
 /**
@@ -307,19 +307,13 @@ export async function uploadFile(address, accessToken, file, type) {
         }),
     };
     const url = new URL(localhostToAddress(`${address}/files`));
-    try {
-        const response = await fetch(url, auth);
-        if (!response.ok) {
-            const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
-            throw new ConfigError(errorMessage);
-        }
-        const json = (await response.json());
-        return json['_id'];
-    }
-    catch (error) {
-        console.error(error);
-        throw error;
+    const response = await fetch(url, auth);
+    if (!response.ok) {
+        const errorMessage = await createFetchErrorMessage(response, 'uploadFile failed');
+        throw new ConfigError(errorMessage);
     }
+    const json = (await response.json());
+    return json['_id'];
 }
 /* Wrap text to max `length` per line */
 export function wrapLines(s, length) {

package/oclif.manifest.json

@@ -395,7 +395,7 @@
     "assembly:check": {
       "aliases": [],
       "args": {},
-      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible.\nThis command only sets the check to apply, to retrieve features flagged by these\nchecks use `apollo feature check`.",
+      "description": "Manage checks, i.e. the rules ensuring features in an assembly are plausible.\nThis command only sets the checks to apply, to retrieve features flagged by\nthese checks use `apollo feature check`.",
       "examples": [
         {
           "description": "View available check types:",
@@ -699,61 +699,6 @@
         "get.js"
       ]
     },
-    "refseq:get": {
-      "aliases": [],
-      "args": {},
-      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
-      "examples": [
-        {
-          "description": "All sequences in the database:",
-          "command": "<%= config.bin %> <%= command.id %>"
-        },
-        {
-          "description": "Only sequences for these assemblies:",
-          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
-        }
-      ],
-      "flags": {
-        "profile": {
-          "description": "Use credentials from this profile",
-          "name": "profile",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "config-file": {
-          "description": "Use this config file (mostly for testing)",
-          "name": "config-file",
-          "hasDynamicHelp": false,
-          "multiple": false,
-          "type": "option"
-        },
-        "assembly": {
-          "char": "a",
-          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
-          "name": "assembly",
-          "hasDynamicHelp": false,
-          "multiple": true,
-          "type": "option"
-        }
-      },
-      "hasDynamicHelp": false,
-      "hiddenAliases": [],
-      "id": "refseq:get",
-      "pluginAlias": "@apollo-annotation/cli",
-      "pluginName": "@apollo-annotation/cli",
-      "pluginType": "core",
-      "strict": true,
-      "summary": "Get reference sequences",
-      "enableJsonFlag": false,
-      "isESM": true,
-      "relativePath": [
-        "dist",
-        "commands",
-        "refseq",
-        "get.js"
-      ]
-    },
     "feature:add-child": {
       "aliases": [],
       "args": {},
@@ -1560,6 +1505,61 @@
         "search.js"
       ]
     },
+    "refseq:get": {
+      "aliases": [],
+      "args": {},
+      "description": "Output the reference sequences in one or more assemblies in json format. This\ncommand returns the sequence characteristics (e.g., name, ID, etc), not the DNA\nsequences. Use `assembly sequence` for that.",
+      "examples": [
+        {
+          "description": "All sequences in the database:",
+          "command": "<%= config.bin %> <%= command.id %>"
+        },
+        {
+          "description": "Only sequences for these assemblies:",
+          "command": "<%= config.bin %> <%= command.id %> -a mm9 mm10"
+        }
+      ],
+      "flags": {
+        "profile": {
+          "description": "Use credentials from this profile",
+          "name": "profile",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "config-file": {
+          "description": "Use this config file (mostly for testing)",
+          "name": "config-file",
+          "hasDynamicHelp": false,
+          "multiple": false,
+          "type": "option"
+        },
+        "assembly": {
+          "char": "a",
+          "description": "Get reference sequences for these assembly names or IDs; use - to read it from stdin",
+          "name": "assembly",
+          "hasDynamicHelp": false,
+          "multiple": true,
+          "type": "option"
+        }
+      },
+      "hasDynamicHelp": false,
+      "hiddenAliases": [],
+      "id": "refseq:get",
+      "pluginAlias": "@apollo-annotation/cli",
+      "pluginName": "@apollo-annotation/cli",
+      "pluginType": "core",
+      "strict": true,
+      "summary": "Get reference sequences",
+      "enableJsonFlag": false,
+      "isESM": true,
+      "relativePath": [
+        "dist",
+        "commands",
+        "refseq",
+        "get.js"
+      ]
+    },
     "user:get": {
       "aliases": [],
       "args": {},
@@ -1628,5 +1628,5 @@
       ]
     }
   },
-  "version": "0.1.17"
+  "version": "0.1.18"
 }

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@apollo-annotation/cli",
   "description": "Command line interface for the Apollo annotation server",
-  "version": "0.1.17",
+  "version": "0.1.18",
   "author": "Apollo Team",
   "repository": {
     "type": "git",
@@ -41,6 +41,7 @@
     "@oclif/core": "^3.18.2",
     "@oclif/plugin-help": "^6.0.8",
     "bson": "^6.3.0",
+    "conf": "^12.0.0",
     "joi": "^17.7.0",
     "open": "^10.1.0",
     "tslib": "^2.3.1",

package/dist/Config.d.ts

@@ -1,43 +0,0 @@
-import Joi from 'joi';
-export declare class ConfigError extends Error {
-}
-interface BaseProfile {
-    address: string;
-    accessType: 'google' | 'microsoft' | 'guest';
-    accessToken: string;
-}
-interface RootProfile extends Omit<BaseProfile, 'accessType'> {
-    accessType: 'root';
-    rootCredentials: {
-        username: string;
-        password: string;
-    };
-}
-export type Profile = BaseProfile | RootProfile;
-export declare enum KEYS {
-    address = "address",
-    accessType = "accessType",
-    accessToken = "accessToken",
-    rootCredentials_username = "rootCredentials.username",
-    rootCredentials_password = "rootCredentials.password"
-}
-export declare function optionDesc(): string[];
-export declare class Config {
-    private configFile;
-    private profiles;
-    constructor(configFile: string);
-    private index;
-    private addProps;
-    private checkKey;
-    get(key: string, profileName: string): string;
-    set(key: string, value: string, profileName: string): void;
-    writeConfigFile(): void;
-    getProfileNames(): string[];
-    validate(): Joi.ValidationResult;
-    getAccess(profileName: string): Promise<{
-        address: string;
-        accessToken: string;
-    }>;
-    toString(): string;
-}
-export {};

package/dist/Config.js

@@ -1,233 +0,0 @@
-/* eslint-disable @typescript-eslint/no-redundant-type-constituents */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-enum-comparison */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import fs from 'node:fs';
-import path from 'node:path';
-import Joi from 'joi';
-import YAML, { YAMLParseError } from 'yaml';
-import { checkProfileExists, queryApollo } from './utils.js';
-export class ConfigError extends Error {
-}
-export var KEYS;
-(function (KEYS) {
-    KEYS["address"] = "address";
-    KEYS["accessType"] = "accessType";
-    KEYS["accessToken"] = "accessToken";
-    KEYS["rootCredentials_username"] = "rootCredentials.username";
-    KEYS["rootCredentials_password"] = "rootCredentials.password";
-})(KEYS || (KEYS = {}));
-function optionDocs() {
-    const docs = [];
-    for (const v of Object.values(KEYS)) {
-        switch (v) {
-            case 'address': {
-                docs.push({
-                    key: v,
-                    description: 'Address and port e.g http://localhost:3999',
-                });
-                break;
-            }
-            case 'accessType': {
-                docs.push({
-                    key: v,
-                    description: 'How to access Apollo. accessType is typically one of: google, microsoft, guest, root. Allowed types depend on your Apollo setup',
-                });
-                break;
-            }
-            case 'accessToken': {
-                docs.push({
-                    key: v,
-                    description: 'Access token. Usually inserted by `apollo login`',
-                });
-                break;
-            }
-            case 'rootCredentials.username': {
-                docs.push({
-                    key: v,
-                    description: 'Username of root account. Only set this for "root" access type',
-                });
-                break;
-            }
-            case 'rootCredentials.password': {
-                docs.push({
-                    key: v,
-                    description: 'Password for root account. Only set this for "root" access type',
-                });
-                break;
-            }
-            default: {
-                throw new ConfigError(`Unexpected key: ${v}`);
-            }
-        }
-    }
-    return docs;
-}
-export function optionDesc() {
-    const docs = [];
-    for (const x of optionDocs()) {
-        docs.push(`- ${x.key}:\n${x.description}`);
-    }
-    return docs;
-}
-function isValidAddress(address) {
-    // const port: string | undefined = address.split(':').pop()
-    // if (port === undefined || /^\d+$/.test(port) === false) {
-    //   return false
-    // }
-    let url;
-    try {
-        url = new URL(address);
-    }
-    catch {
-        return false;
-    }
-    if (url.protocol !== 'http:' && url.protocol !== 'https:') {
-        return false;
-    }
-    return true;
-}
-const profileSchema = Joi.object({
-    address: Joi.string()
-        .uri({ scheme: /https?/ })
-        .required(),
-    accessType: Joi.string()
-        .valid('google', 'microsoft', 'root', 'guest')
-        .required(),
-    accessToken: Joi.string(),
-    rootCredentials: Joi.object({
-        username: Joi.string().required(),
-        password: Joi.string().required(),
-    }).when('accessType', {
-        is: Joi.string().valid('root'),
-        // eslint-disable-next-line unicorn/no-thenable
-        then: Joi.required(),
-        otherwise: Joi.forbidden(),
-    }),
-});
-const configSchema = Joi.object().pattern(Joi.string(), profileSchema);
-export class Config {
-    configFile;
-    profiles = {};
-    constructor(configFile) {
-        this.configFile = configFile;
-        if (fs.existsSync(configFile)) {
-            const data = fs.readFileSync(configFile, 'utf8').trim();
-            if (data !== '') {
-                let config;
-                try {
-                    config = YAML.parse(data);
-                }
-                catch (error) {
-                    if (error instanceof YAMLParseError) {
-                        process.stderr.write('Error: Configuration file is probably invalid yaml format:\n');
-                        process.stderr.write(error.message);
-                    }
-                    else if (error instanceof Error) {
-                        process.stderr.write('Unexpected error:');
-                        process.stderr.write(error.message);
-                    }
-                    // eslint-disable-next-line unicorn/no-process-exit
-                    process.exit(1);
-                }
-                this.profiles = config;
-            }
-        }
-    }
-    index(obj, arr, value) {
-        if (typeof arr == 'string') {
-            return this.index(obj, arr.split('.'), value);
-        }
-        if (arr.length == 1 && value !== undefined) {
-            return (obj[arr[0]] = value);
-        }
-        if (arr.length === 0) {
-            return obj;
-        }
-        return this.index(obj[arr[0]], arr.slice(1), value);
-    }
-    addProps(obj, arr, value) {
-        // credit https://stackoverflow.com/questions/17643965/how-to-automatically-add-properties-to-an-object-that-is-undefined
-        if (typeof arr == 'string') {
-            arr = arr.split('.');
-        }
-        obj[arr[0]] = obj[arr[0]] || {};
-        const tmpObj = obj[arr[0]];
-        if (arr.length > 1) {
-            arr.shift();
-            this.addProps(tmpObj, arr, value);
-        }
-        else if (value !== undefined) {
-            obj[arr[0]] = value;
-        }
-        return obj;
-    }
-    checkKey(key) {
-        for (const x of Object.values(KEYS)) {
-            if (x === key) {
-                return;
-            }
-        }
-        throw new ConfigError(`Invalid configuration key: "${key}". Valid keys are:\n${Object.values('\n')}`);
-    }
-    get(key, profileName) {
-        this.checkKey(key);
-        const profile = this.profiles[profileName];
-        if (!profile) {
-            // throw new Error(`No profile name "${profileName}" found`)
-            return '';
-        }
-        this.addProps(profile, key);
-        const value = this.index(profile, key);
-        if (typeof value === 'object' && Object.keys(value).length === 0) {
-            // The key is valid but missing from config
-            return '';
-        }
-        return value;
-    }
-    set(key, value, profileName) {
-        this.checkKey(key);
-        if (key === KEYS[KEYS.address] && !isValidAddress(value)) {
-            throw new ConfigError(`"${value}" is not a valid value for "${key}"`);
-        }
-        const profile = this.profiles[profileName] ?? {};
-        this.profiles[profileName] = profile;
-        this.addProps(profile, key, value);
-    }
-    writeConfigFile() {
-        let APOLLO_DISABLE_CONFIG_CREATE = false;
-        if (process.env.APOLLO_DISABLE_CONFIG_CREATE !== undefined &&
-            process.env.APOLLO_DISABLE_CONFIG_CREATE !== '0') {
-            APOLLO_DISABLE_CONFIG_CREATE = true;
-        }
-        if (APOLLO_DISABLE_CONFIG_CREATE && !fs.existsSync(this.configFile)) {
-            throw new ConfigError('Configuration file does not exist yet, please create it as an empty file first.');
-        }
-        const yml = YAML.stringify(this.profiles);
-        fs.mkdirSync(path.dirname(this.configFile), { recursive: true });
-        fs.writeFileSync(this.configFile, yml);
-    }
-    getProfileNames() {
-        return Object.keys(this.profiles);
-    }
-    validate() {
-        return configSchema.validate(this.profiles);
-    }
-    async getAccess(profileName) {
-        checkProfileExists(profileName, this);
-        const address = this.get('address', profileName);
-        if (address === undefined || address.trim() === '') {
-            throw new ConfigError(`Profile "${profileName}" has no address. Please run "apollo config" to set it up.`);
-        }
-        const accessToken = this.get('accessToken', profileName);
-        if (accessToken === undefined || accessToken.trim() === '') {
-            throw new ConfigError(`Profile "${profileName}" has no access token. Please run "apollo login" to set it up.`);
-        }
-        await queryApollo(address, accessToken, 'assemblies');
-        return { address, accessToken };
-    }
-    toString() {
-        return YAML.stringify(this.profiles);
-    }
-}

package/dist/commands/config.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/commands/config.test.js

@@ -1,188 +0,0 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-import fs from 'node:fs';
-import { dirname } from 'node:path';
-import { fileURLToPath } from 'node:url';
-import { expect, test } from '@oclif/test';
-import YAML from 'yaml';
-import { CONFIG_FILE, TEST_DATA_DIR, VERBOSE, copyFile, } from '../test/fixtures.js';
-const __dirname = fileURLToPath(new URL('.', import.meta.url));
-describe('apollo config: Query config file', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yaml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    let cmd = ['config', 'rootCredentials.password'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('1234');
-    });
-    cmd = ['config', 'address'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('http://localhost:3999');
-    });
-    cmd = ['config', 'someInvalidKey'];
-    test
-        .stderr()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .exit(1)
-        .do((output) => expect(output.stderr).to.contain('someInvalidKey'))
-        .it(cmd.join(' '));
-    cmd = ['config', '--profile', 'profile1', 'address'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('http://localhost:1999');
-    });
-    cmd = ['config', '--profile', 'profile1', 'rootCredentials.username'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('');
-    });
-    cmd = ['config', '--profile', 'nonExistantProfile', 'address'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('');
-    });
-});
-describe('apollo config: Missing config file', () => {
-    let cmd = ['config', 'rootCredentials.password'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('');
-    });
-    cmd = ['config', 'address'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('');
-    });
-});
-describe('apollo config: Create config directory', () => {
-    const outdir = `${TEST_DATA_DIR}/_tmp`;
-    before(() => {
-        fs.rmSync(outdir, { recursive: true, force: true });
-    });
-    after(() => {
-        fs.rmSync(outdir, { recursive: true, force: true });
-    });
-    const cmd = [
-        'config',
-        '--config-file',
-        `${outdir}/config.yaml`,
-        'address',
-        'http://localhost:3999',
-    ];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), () => {
-        expect(fs.existsSync(`${outdir}/config.yaml`));
-    });
-});
-describe('apollo config: Read & edit config file', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yaml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    let cmd = ['config', 'address', 'http://localhost:4321'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), () => {
-        const cfg = YAML.parse(fs.readFileSync(CONFIG_FILE, 'utf8'));
-        expect(cfg.default.address).to.equal('http://localhost:4321');
-        expect(cfg.default.rootCredentials.username).to.equal('root');
-    });
-    cmd = ['config', 'rootCredentials.username', 'root2'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), () => {
-        const cfg = YAML.parse(fs.readFileSync(CONFIG_FILE, 'utf8'));
-        expect(cfg.default.rootCredentials.username).to.equal('root2');
-    });
-    cmd = ['config', 'accessType', 'microsoft'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), () => {
-        const cfg = YAML.parse(fs.readFileSync(CONFIG_FILE, 'utf8'));
-        expect(cfg.default.accessType).to.equal('microsoft');
-    });
-});
-describe('Do not set invalid address', () => {
-    before(() => {
-        copyFile(`${TEST_DATA_DIR}/complete_config.yaml`, CONFIG_FILE, VERBOSE);
-    });
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    const cmd = ['config', 'address', 'http://localhost:3999xxx'];
-    test
-        .stderr()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .exit(1)
-        .do((output) => expect(output.stderr).to.contain('http://localhost:3999xxx'))
-        .it(cmd.join(' '));
-});
-describe('apollo config: Write config file from scratch', () => {
-    after(() => {
-        fs.rmSync(CONFIG_FILE);
-    });
-    let cmd = ['config', 'rootCredentials.username', 'somename'];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), () => {
-        const cfg = YAML.parse(fs.readFileSync(CONFIG_FILE, 'utf8'));
-        expect(cfg.default.rootCredentials.username).to.equal('somename');
-    });
-    cmd = [
-        'config',
-        '--profile',
-        'myProfile',
-        'rootCredentials.password',
-        'somepwd',
-    ];
-    test
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .it(cmd.join(' '), () => {
-        const cfg = YAML.parse(fs.readFileSync(CONFIG_FILE, 'utf8'));
-        expect(cfg.myProfile.rootCredentials.password).to.equal('somepwd');
-    });
-});
-describe('apollo config: Handle strings as numbers in yaml', () => {
-    const cmd = [
-        'config',
-        '--config-file',
-        'test_data/nameAsNumber.yaml',
-        'rootCredentials.username',
-    ];
-    test
-        .stderr()
-        .stdout()
-        .command(cmd, { root: dirname(dirname(__dirname)) })
-        .do((output) => expect(output.stderr).contains('must be a string'))
-        .it(cmd.join(' '), (ctx) => {
-        expect(ctx.stdout.trim()).to.equal('7890');
-    });
-});

package/dist/commands/login.test.d.ts

@@ -1 +0,0 @@
-export {};