From 71823bf2758cc4794d0c5d317890c0d850e56e75 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 13:50:18 +0200 Subject: [PATCH 1/7] refactor --- bin/uniprot.ts | 71 ++------------------------------- lib/commands/base_command.ts | 31 +++++++++++++++ lib/commands/uniprot.ts | 77 ++++++++++++++++++++++++++++++++++++ tsconfig.json | 3 +- 4 files changed, 113 insertions(+), 69 deletions(-) create mode 100644 lib/commands/base_command.ts create mode 100644 lib/commands/uniprot.ts diff --git a/bin/uniprot.ts b/bin/uniprot.ts index bbe9aab0..7746fac9 100755 --- a/bin/uniprot.ts +++ b/bin/uniprot.ts @@ -1,71 +1,6 @@ #!/usr/bin/env node -import { Option, program } from 'commander'; -import { createInterface } from 'node:readline'; -import { version } from '../package.json'; +import { Uniprot } from '../lib/commands/uniprot.js'; -const VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"]; - -const description = `Command line interface to UniProt web services. - -The uniprot command fetches UniProt entries from the UniProt web services. The command expects a list of UniProt Accession Numbers that are passed - -- as separate command line arguments -- to standard input - -The command will give priority to the first way UniProt Accession Numbers are passed, in the order as listed above. The standard input should have one UniProt Accession Number per line. - -The uniprot command yields just the protein sequences as a default, but can return several formats.`; - -program - .version(version) - .summary("Command line interface to UniProt web services.") - .description(description) - .argument("[accessions...]", "UniProt Accession Numbers") - .addOption(new Option("-f, --format ", `output format`).choices(VALID_FORMATS).default("sequence")); - -program.parse(process.argv); -const format = program.opts().format; -const accessions = program.args; - -if (accessions.length !== 0) { // input from command line arguments - accessions.forEach(processUniprotEntry); -} else { // input from standard input - for await (const line of createInterface({ input: process.stdin })) { - processUniprotEntry(line.trim()); - }; -} - -/** - * Fetches a UniProt entry and writes it to standard output. - * - * @param accession UniProt Accession Number - */ -async function processUniprotEntry(accession: string) { - process.stdout.write(await getUniprotEntry(accession, format) + "\n"); -} - -/** - * Fetches a UniProt entry in the requested format. - * - * @param accession UniProt Accession Number - * @param format output format - * @returns UniProt entry in the requested format - */ -async function getUniprotEntry(accession: string, format: string): Promise { - // The UniProt REST API does not support the "sequence" format, so fetch fasta and remove the header - if (format === "sequence") { - return (await getUniprotEntry(accession, "fasta")) - .split("\n") - .slice(1) - .join(""); - } else { - const r = await fetch(`https://rest.uniprot.org/uniprotkb/${accession}.${format}`); - if (r.ok) { - return r.text(); - } else { - process.stderr.write(`Error fetching ${accession}: ${r.status} ${r.statusText}\n`); - return ""; - } - } -} +const command = new Uniprot(); +command.run(); diff --git a/lib/commands/base_command.ts b/lib/commands/base_command.ts new file mode 100644 index 00000000..e9980643 --- /dev/null +++ b/lib/commands/base_command.ts @@ -0,0 +1,31 @@ +import { Command } from "commander"; +import { version } from '../../package.json'; + +export abstract class BaseCommand { + public program: Command; + + constructor(options?: { exitOverride?: boolean, suppressOutput?: boolean }) { + this.program = this.create(options); + } + + abstract run(): void; + + create(options?: { exitOverride?: boolean, suppressOutput?: boolean }): Command { + const program = new Command(); + + // used for debugging + if (options?.exitOverride) { + program.exitOverride(); // don't exit on error + } + if (options?.suppressOutput) { + program.configureOutput({ + writeOut: () => { }, + writeErr: () => { } + }); + } + + program.version(version); + + return program; + } +} diff --git a/lib/commands/uniprot.ts b/lib/commands/uniprot.ts new file mode 100644 index 00000000..1e07a7e7 --- /dev/null +++ b/lib/commands/uniprot.ts @@ -0,0 +1,77 @@ +import { Option } from 'commander'; +import { createInterface } from 'node:readline'; +import { BaseCommand } from './base_command.js'; + +export class Uniprot extends BaseCommand { + readonly VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"]; + + readonly description = `Command line interface to UniProt web services. + +The uniprot command fetches UniProt entries from the UniProt web services. The command expects a list of UniProt Accession Numbers that are passed + +- as separate command line arguments +- to standard input + +The command will give priority to the first way UniProt Accession Numbers are passed, in the order as listed above. The standard input should have one UniProt Accession Number per line. + +The uniprot command yields just the protein sequences as a default, but can return several formats.`; + format = "sequence"; + + constructor() { + super(); + + this.program + .summary("Command line interface to UniProt web services.") + .description(this.description) + .argument("[accessions...]", "UniProt Accession Numbers") + .addOption(new Option("-f, --format ", `output format`).choices(this.VALID_FORMATS).default("sequence")); + } + + async run() { + this.program.parse(process.argv); + this.format = this.program.opts().format; + const accessions = this.program.args; + + if (accessions.length !== 0) { // input from command line arguments + accessions.forEach(this.processUniprotEntry); + } else { // input from standard input + for await (const line of createInterface({ input: process.stdin })) { + this.processUniprotEntry(line.trim()); + }; + } + } + + /** + * Fetches a UniProt entry and writes it to standard output. + * + * @param accession UniProt Accession Number + */ + async processUniprotEntry(accession: string) { + process.stdout.write(await Uniprot.getUniprotEntry(accession, this.format) + "\n"); + } + + /** + * Fetches a UniProt entry in the requested format. + * + * @param accession UniProt Accession Number + * @param format output format + * @returns UniProt entry in the requested format + */ + static async getUniprotEntry(accession: string, format: string): Promise { + // The UniProt REST API does not support the "sequence" format, so fetch fasta and remove the header + if (format === "sequence") { + return (await Uniprot.getUniprotEntry(accession, "fasta")) + .split("\n") + .slice(1) + .join(""); + } else { + const r = await fetch(`https://rest.uniprot.org/uniprotkb/${accession}.${format}`); + if (r.ok) { + return r.text(); + } else { + process.stderr.write(`Error fetching ${accession}: ${r.status} ${r.statusText}\n`); + return ""; + } + } + } +} diff --git a/tsconfig.json b/tsconfig.json index e101d71c..bfb2d08f 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,6 +1,7 @@ { "include": [ - "bin/**/*" + "bin/**/*", + "lib/**/*", ], "compilerOptions": { "outDir": "./dist", From dc6c822adb02b0f5ba0bbaa31095edaff7826db4 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 14:03:02 +0200 Subject: [PATCH 2/7] add eslint --- eslint.config.js | 11 + package.json | 9 +- yarn.lock | 809 +++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 828 insertions(+), 1 deletion(-) create mode 100644 eslint.config.js diff --git a/eslint.config.js b/eslint.config.js new file mode 100644 index 00000000..17c0f257 --- /dev/null +++ b/eslint.config.js @@ -0,0 +1,11 @@ +import globals from "globals"; +import pluginJs from "@eslint/js"; +import tseslint from "typescript-eslint"; + + +export default [ + { languageOptions: { globals: globals.node } }, + pluginJs.configs.recommended, + ...tseslint.configs.recommended, + { ignores: ["dist/"] } +]; diff --git a/package.json b/package.json index 74077291..fc3569b4 100644 --- a/package.json +++ b/package.json @@ -12,14 +12,21 @@ }, "scripts": { "build": "yarn run tsc", + "lint": "yarn run eslint", "uniprot": "yarn run tsx bin/uniprot.ts" }, "dependencies": { "commander": "^12.1.0" }, "devDependencies": { + "@eslint/js": "^9.5.0", "@types/node": "^20.14.2", + "@typescript-eslint/eslint-plugin": "^7.13.1", + "@typescript-eslint/parser": "^7.13.1", + "eslint": "9.x", + "globals": "^15.6.0", "tsx": "^4.15.6", - "typescript": "^5.4.5" + "typescript": "^5.4.5", + "typescript-eslint": "^7.13.1" } } diff --git a/yarn.lock b/yarn.lock index f6423ed5..8fa12631 100644 --- a/yarn.lock +++ b/yarn.lock @@ -117,6 +117,83 @@ resolved "https://registry.yarnpkg.com/@esbuild/win32-x64/-/win32-x64-0.21.5.tgz#acad351d582d157bb145535db2a6ff53dd514b5c" integrity sha512-tQd/1efJuzPC6rCFwEvLtci/xNFcTZknmXs98FYDfGE4wP9ClFV98nyKrzJKVPMhdDnjzLhdUyMX4PsQAPjwIw== +"@eslint-community/eslint-utils@^4.2.0", 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"https://registry.yarnpkg.com/ts-api-utils/-/ts-api-utils-1.3.0.tgz#4b490e27129f1e8e686b45cc4ab63714dc60eea1" + integrity sha512-UQMIo7pb8WRomKR1/+MFVLTroIvDVtMX3K6OUir8ynLyzB8Jeriont2bTAtmNPa1ekAgN7YPDyf6V+ygrdU+eQ== + tsx@^4.15.6: version "4.15.6" resolved "https://registry.yarnpkg.com/tsx/-/tsx-4.15.6.tgz#4522ed093f7fa54f031a7a999274e8b35dbf3165" @@ -185,6 +954,22 @@ tsx@^4.15.6: optionalDependencies: fsevents "~2.3.3" +type-check@^0.4.0, type-check@~0.4.0: + version "0.4.0" + resolved "https://registry.yarnpkg.com/type-check/-/type-check-0.4.0.tgz#07b8203bfa7056c0657050e3ccd2c37730bab8f1" + integrity sha512-XleUoc9uwGXqjWwXaUTZAmzMcFZ5858QA2vvx1Ur5xIcixXIP+8LnFDgRplU30us6teqdlskFfu+ae4K79Ooew== + dependencies: + prelude-ls "^1.2.1" + +typescript-eslint@^7.13.1: + version "7.13.1" + resolved "https://registry.yarnpkg.com/typescript-eslint/-/typescript-eslint-7.13.1.tgz#8bbcc4b59b6bb0c457505ee17a356b1868c3fcd5" + integrity sha512-pvLEuRs8iS9s3Cnp/Wt//hpK8nKc8hVa3cLljHqzaJJQYP8oys8GUyIFqtlev+2lT/fqMPcyQko+HJ6iYK3nFA== + dependencies: + "@typescript-eslint/eslint-plugin" "7.13.1" + "@typescript-eslint/parser" "7.13.1" + "@typescript-eslint/utils" "7.13.1" + typescript@^5.4.5: version "5.4.5" resolved "https://registry.yarnpkg.com/typescript/-/typescript-5.4.5.tgz#42ccef2c571fdbd0f6718b1d1f5e6e5ef006f611" @@ -194,3 +979,27 @@ undici-types@~5.26.4: version "5.26.5" resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA== + +uri-js@^4.2.2: + version "4.4.1" + resolved "https://registry.yarnpkg.com/uri-js/-/uri-js-4.4.1.tgz#9b1a52595225859e55f669d928f88c6c57f2a77e" + integrity sha512-7rKUyy33Q1yc98pQ1DAmLtwX109F7TIfWlW1Ydo8Wl1ii1SeHieeh0HHfPeL2fMXK6z0s8ecKs9frCuLJvndBg== + dependencies: + punycode "^2.1.0" + +which@^2.0.1: + version "2.0.2" + resolved "https://registry.yarnpkg.com/which/-/which-2.0.2.tgz#7c6a8dd0a636a0327e10b59c9286eee93f3f51b1" + integrity sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA== + dependencies: + isexe "^2.0.0" + +word-wrap@^1.2.5: + version "1.2.5" + resolved "https://registry.yarnpkg.com/word-wrap/-/word-wrap-1.2.5.tgz#d2c45c6dd4fbce621a66f136cbe328afd0410b34" + integrity sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA== + +yocto-queue@^0.1.0: + version "0.1.0" + resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" + integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== From 5ba8ae294a790c7dd93259588dfea8c825112e50 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 14:08:38 +0200 Subject: [PATCH 3/7] add github action --- .github/workflows/ci.yml | 36 +++++++++++++----------------------- package.json | 1 + 2 files changed, 14 insertions(+), 23 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 273acce5..ef58d4e6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -3,32 +3,22 @@ name: CI on: [push] jobs: - test: - runs-on: ubuntu-latest - strategy: - matrix: - ruby: ["2.7", "3.0", "3.1", "3.2"] - fail-fast: false - name: Test Ruby ${{ matrix.ruby }} - steps: - - uses: actions/checkout@v1 - - name: Setup Ruby - uses: ruby/setup-ruby@v1 - with: - ruby-version: ${{ matrix.ruby }} - bundler-cache: true - - name: Test - run: | - bundle exec rake test lint: name: Lint runs-on: ubuntu-latest steps: - - uses: actions/checkout@v1 - - name: Setup Ruby - uses: ruby/setup-ruby@v1 + - uses: actions/checkout@v4 + - name: Set up Node + uses: actions/setup-node@v4 with: - bundler-cache: true - - name: Test + node-version: 22.x + cache: yarn + - name: Install dependencies + run: | + yarn install + - name: Lint + run: | + yarn lint + - name: Type check run: | - bundle exec rake test_style + yarn typecheck diff --git a/package.json b/package.json index fc3569b4..dd419f31 100644 --- a/package.json +++ b/package.json @@ -13,6 +13,7 @@ "scripts": { "build": "yarn run tsc", "lint": "yarn run eslint", + "typecheck": "yarn tsc --skipLibCheck --noEmit", "uniprot": "yarn run tsx bin/uniprot.ts" }, "dependencies": { From 5077b025513e597a4b7061b46f0834848b4fd184 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 16:40:59 +0200 Subject: [PATCH 4/7] refactor --- lib/commands/base_command.ts | 13 ++++++++++++- lib/commands/uniprot.ts | 23 ++++++++++------------- tsconfig.json | 2 +- 3 files changed, 23 insertions(+), 15 deletions(-) diff --git a/lib/commands/base_command.ts b/lib/commands/base_command.ts index e9980643..14a3b934 100644 --- a/lib/commands/base_command.ts +++ b/lib/commands/base_command.ts @@ -3,9 +3,11 @@ import { version } from '../../package.json'; export abstract class BaseCommand { public program: Command; + args: string[] | undefined; - constructor(options?: { exitOverride?: boolean, suppressOutput?: boolean }) { + constructor(options?: { exitOverride?: boolean, suppressOutput?: boolean, args?: string[] }) { this.program = this.create(options); + this.args = options?.args; } abstract run(): void; @@ -28,4 +30,13 @@ export abstract class BaseCommand { return program; } + + parseArguments() { + if (this.args) { + // custom arg parsing to be able to inject args for testing + this.program.parse(this.args, { from: "user" }); + } else { + this.program.parse(); + } + } } diff --git a/lib/commands/uniprot.ts b/lib/commands/uniprot.ts index 1e07a7e7..51c32629 100644 --- a/lib/commands/uniprot.ts +++ b/lib/commands/uniprot.ts @@ -15,10 +15,9 @@ The uniprot command fetches UniProt entries from the UniProt web services. The c The command will give priority to the first way UniProt Accession Numbers are passed, in the order as listed above. The standard input should have one UniProt Accession Number per line. The uniprot command yields just the protein sequences as a default, but can return several formats.`; - format = "sequence"; - constructor() { - super(); + constructor(options?: { exitOverride?: boolean, suppressOutput?: boolean, args?: string[] }) { + super(options); this.program .summary("Command line interface to UniProt web services.") @@ -28,16 +27,14 @@ The uniprot command yields just the protein sequences as a default, but can retu } async run() { - this.program.parse(process.argv); - this.format = this.program.opts().format; + this.parseArguments(); + const format = this.program.opts().format; const accessions = this.program.args; - if (accessions.length !== 0) { // input from command line arguments - accessions.forEach(this.processUniprotEntry); - } else { // input from standard input - for await (const line of createInterface({ input: process.stdin })) { - this.processUniprotEntry(line.trim()); - }; + // alternatively, we can also wrap the array in a Readable stream with ReadableStream.from() + const input = accessions.length !== 0 ? accessions : createInterface({ input: process.stdin }); + for await (const line of input) { + await Uniprot.processUniprotEntry(line.trim(), format); } } @@ -46,8 +43,8 @@ The uniprot command yields just the protein sequences as a default, but can retu * * @param accession UniProt Accession Number */ - async processUniprotEntry(accession: string) { - process.stdout.write(await Uniprot.getUniprotEntry(accession, this.format) + "\n"); + static async processUniprotEntry(accession: string, format: string) { + process.stdout.write(await Uniprot.getUniprotEntry(accession, format) + "\n"); } /** diff --git a/tsconfig.json b/tsconfig.json index bfb2d08f..5c9bef88 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -7,6 +7,6 @@ "outDir": "./dist", "module": "NodeNext", "strict": true, - "resolveJsonModule": true + "resolveJsonModule": true, } } From d6ed622a82c0eb9bcacba6a81e4d8d4f7bc2f513 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 17:32:46 +0200 Subject: [PATCH 5/7] add tests --- jest.config.ts | 203 ++++ lib/commands/uniprot.ts | 4 +- package.json | 6 + tests/commands/uniprot.test.ts | 93 ++ yarn.lock | 2060 +++++++++++++++++++++++++++++++- 5 files changed, 2352 insertions(+), 14 deletions(-) create mode 100644 jest.config.ts create mode 100644 tests/commands/uniprot.test.ts diff --git a/jest.config.ts b/jest.config.ts new file mode 100644 index 00000000..9627c0f6 --- /dev/null +++ b/jest.config.ts @@ -0,0 +1,203 @@ +/** + * For a detailed explanation regarding each configuration property, visit: + * https://jestjs.io/docs/configuration + */ + +import type { Config } from 'jest'; + +const config: Config = { + // All imported modules in your tests should be mocked automatically + // automock: false, + + // Stop running tests after `n` failures + // bail: 0, + + // The directory where Jest should store its cached dependency information + // cacheDirectory: "/private/var/folders/j3/38fskpy159v07np8syk3p_2m0000gn/T/jest_dx", + + // Automatically clear mock calls, instances, contexts and results before every test + clearMocks: true, + + // Indicates whether the coverage information should be collected while executing the test + // collectCoverage: false, + + // An array of glob patterns indicating a set of files for which coverage information should be collected + // collectCoverageFrom: undefined, + + // The directory where Jest should output its coverage files + // coverageDirectory: undefined, + + // An array of regexp pattern strings used to skip coverage collection + // coveragePathIgnorePatterns: [ + // "/node_modules/" + // ], + + // Indicates which provider should be used to instrument code for coverage + coverageProvider: "v8", + + // A list of reporter names that Jest uses when writing coverage reports + // coverageReporters: [ + // "json", + // "text", + // "lcov", + // "clover" + // ], + + // An object that configures minimum threshold enforcement for coverage results + // coverageThreshold: undefined, + + // A path to a custom dependency extractor + // dependencyExtractor: undefined, + + // Make calling deprecated APIs throw helpful error messages + // errorOnDeprecated: false, + + // The default configuration for fake timers + // fakeTimers: { + // "enableGlobally": false + // }, + + // Force coverage collection from ignored files using an array of glob patterns + // forceCoverageMatch: [], + + // A path to a module which exports an async function that is triggered once before all test suites + // globalSetup: undefined, + + // A path to a module which exports an async function that is triggered once after all test suites + // globalTeardown: undefined, + + // A set of global variables that need to be available in all test environments + // globals: {}, + + // The maximum amount of workers used to run your tests. Can be specified as % or a number. E.g. maxWorkers: 10% will use 10% of your CPU amount + 1 as the maximum worker number. maxWorkers: 2 will use a maximum of 2 workers. + // maxWorkers: "50%", + + // An array of directory names to be searched recursively up from the requiring module's location + // moduleDirectories: [ + // "node_modules" + // ], + + // An array of file extensions your modules use + // moduleFileExtensions: [ + // "js", + // "mjs", + // "cjs", + // "jsx", + // "ts", + // "tsx", + // "json", + // "node" + // ], + + // A map from regular expressions to module names or to arrays of module names that allow to stub out resources with a single module + moduleNameMapper: { + "(.+)\\.js": "$1", + }, + + // An array of regexp pattern strings, matched against all module paths before considered 'visible' to the module loader + // modulePathIgnorePatterns: [], + + // Activates notifications for test results + // notify: false, + + // An enum that specifies notification mode. Requires { notify: true } + // notifyMode: "failure-change", + + // A preset that is used as a base for Jest's configuration + // preset: undefined, + + // Run tests from one or more projects + // projects: undefined, + + // Use this configuration option to add custom reporters to Jest + // reporters: undefined, + + // Automatically reset mock state before every test + // resetMocks: false, + + // Reset the module registry before running each individual test + // resetModules: false, + + // A path to a custom resolver + // resolver: undefined, + + // Automatically restore mock state and implementation before every test + // restoreMocks: false, + + // The root directory that Jest should scan for tests and modules within + // rootDir: undefined, + + // A list of paths to directories that Jest should use to search for files in + // roots: [ + // "" + // ], + + // Allows you to use a custom runner instead of Jest's default test runner + // runner: "jest-runner", + + // The paths to modules that run some code to configure or set up the testing environment before each test + // setupFiles: [], + + // A list of paths to modules that run some code to configure or set up the testing framework before each test + // setupFilesAfterEnv: [], + + // The number of seconds after which a test is considered as slow and reported as such in the results. + // slowTestThreshold: 5, + + // A list of paths to snapshot serializer modules Jest should use for snapshot testing + // snapshotSerializers: [], + + // The test environment that will be used for testing + // testEnvironment: "jest-environment-node", + + // Options that will be passed to the testEnvironment + // testEnvironmentOptions: {}, + + // Adds a location field to test results + // testLocationInResults: false, + + // The glob patterns Jest uses to detect test files + // testMatch: [ + // "**/__tests__/**/*.[jt]s?(x)", + // "**/?(*.)+(spec|test).[tj]s?(x)" + // ], + + // An array of regexp pattern strings that are matched against all test paths, matched tests are skipped + // testPathIgnorePatterns: [ + // "/node_modules/" + // ], + + // The regexp pattern or array of patterns that Jest uses to detect test files + // testRegex: [], + + // This option allows the use of a custom results processor + // testResultsProcessor: undefined, + + // This option allows use of a custom test runner + // testRunner: "jest-circus/runner", + + // A map from regular expressions to paths to transformers + transform: { + "^.+\\.tsx?$": ["ts-jest", { "useESM": true, "diagnostics": { "ignoreCodes": ["TS151001"] } }], + }, + + // An array of regexp pattern strings that are matched against all source file paths, matched files will skip transformation + // transformIgnorePatterns: [ + // "/node_modules/", + // "\\.pnp\\.[^\\/]+$" + // ], + + // An array of regexp pattern strings that are matched against all modules before the module loader will automatically return a mock for them + // unmockedModulePathPatterns: undefined, + + // Indicates whether each individual test should be reported during the run + // verbose: true, + + // An array of regexp patterns that are matched against all source file paths before re-running tests in watch mode + // watchPathIgnorePatterns: [], + + // Whether to use watchman for file crawling + // watchman: true, +}; + +export default config; diff --git a/lib/commands/uniprot.ts b/lib/commands/uniprot.ts index 51c32629..11f5e57b 100644 --- a/lib/commands/uniprot.ts +++ b/lib/commands/uniprot.ts @@ -3,7 +3,7 @@ import { createInterface } from 'node:readline'; import { BaseCommand } from './base_command.js'; export class Uniprot extends BaseCommand { - readonly VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"]; + static readonly VALID_FORMATS = ["fasta", "gff", "json", "rdf", "sequence", "xml"]; readonly description = `Command line interface to UniProt web services. @@ -23,7 +23,7 @@ The uniprot command yields just the protein sequences as a default, but can retu .summary("Command line interface to UniProt web services.") .description(this.description) .argument("[accessions...]", "UniProt Accession Numbers") - .addOption(new Option("-f, --format ", `output format`).choices(this.VALID_FORMATS).default("sequence")); + .addOption(new Option("-f, --format ", `output format`).choices(Uniprot.VALID_FORMATS).default("sequence")); } async run() { diff --git a/package.json b/package.json index dd419f31..71171b87 100644 --- a/package.json +++ b/package.json @@ -13,6 +13,7 @@ "scripts": { "build": "yarn run tsc", "lint": "yarn run eslint", + "test": "yarn run jest", "typecheck": "yarn tsc --skipLibCheck --noEmit", "uniprot": "yarn run tsx bin/uniprot.ts" }, @@ -21,11 +22,16 @@ }, "devDependencies": { "@eslint/js": "^9.5.0", + "@types/jest": "^29.5.12", "@types/node": "^20.14.2", "@typescript-eslint/eslint-plugin": "^7.13.1", "@typescript-eslint/parser": "^7.13.1", "eslint": "9.x", "globals": "^15.6.0", + "jest": "^29.7.0", + "mock-stdin": "^1.0.0", + "ts-jest": "^29.1.5", + "ts-node": "^10.9.2", "tsx": "^4.15.6", "typescript": "^5.4.5", "typescript-eslint": "^7.13.1" diff --git a/tests/commands/uniprot.test.ts b/tests/commands/uniprot.test.ts new file mode 100644 index 00000000..ca72837b --- /dev/null +++ b/tests/commands/uniprot.test.ts @@ -0,0 +1,93 @@ +import { Uniprot } from '../../lib/commands/uniprot'; +import * as mock from 'mock-stdin'; + +let output: string[]; +let error: string[]; +const writeSpy = jest + .spyOn(process.stdout, "write") + .mockImplementation((data: unknown) => { output.push(data as string); return true; }); +const errorSpy = jest + .spyOn(process.stderr, "write") + .mockImplementation((data: unknown) => { error.push(data as string); return true; }); + +beforeEach(() => { + output = []; + error = []; +}); + +test('test single argument', async () => { + const command = new Uniprot({ args: ["Q6GZX3"] }); + await command.run(); + + expect(writeSpy).toHaveBeenCalledTimes(1); + expect(errorSpy).toHaveBeenCalledTimes(0); + expect(output.length).toBe(1); +}); + +test('test two arguments', async () => { + const command = new Uniprot({ args: ["Q6GZX3", "Q6GZX4"] }); + await command.run(); + + expect(writeSpy).toHaveBeenCalledTimes(2); + expect(errorSpy).toHaveBeenCalledTimes(0); + expect(output.length).toBe(2); +}); + +test('test fasta output', async () => { + const command = new Uniprot({ args: ["--format", "fasta", "Q6GZX3", "Q6GZX4"] }); + await command.run(); + + expect(writeSpy).toHaveBeenCalledTimes(2); + expect(errorSpy).toHaveBeenCalledTimes(0); + expect(output.length).toBe(2); + expect(output[0].startsWith(">")).toBe(true); +}); + +test('test single line stdin', async () => { + const stdin = mock.stdin(); + + const command = new Uniprot(); + const run = command.run(); + + stdin.send("Q6GZX3\n"); + stdin.end(); + + await run; + + expect(writeSpy).toHaveBeenCalledTimes(1); + expect(errorSpy).toHaveBeenCalledTimes(0); + expect(output.length).toBe(1); +}); + +test('test double line stdin', async () => { + const stdin = mock.stdin(); + + const command = new Uniprot(); + const run = command.run(); + + stdin.send("Q6GZX3\n"); + stdin.send("Q6GZX4\n"); + stdin.end(); + + await run; + + expect(writeSpy).toHaveBeenCalledTimes(2); + expect(errorSpy).toHaveBeenCalledTimes(0); + expect(output.length).toBe(2); +}); + +test('test on invalid id', async () => { + const command = new Uniprot({ args: ["Bart"] }); + await command.run(); + + expect(errorSpy).toHaveBeenCalledTimes(1); +}); + +test('test all valid formats', async () => { + for (const format of Uniprot.VALID_FORMATS) { + const command = new Uniprot({ args: ["--format", format, "Q6GZX3"] }); + await command.run(); + + expect(errorSpy).toHaveBeenCalledTimes(0); + } +}); diff --git a/yarn.lock b/yarn.lock index 8fa12631..bb0cd995 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2,6 +2,312 @@ # yarn lockfile v1 +"@ampproject/remapping@^2.2.0": + version "2.3.0" + resolved 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color-convert@^2.0.1: dependencies: color-name "~1.1.4" +color-name@1.1.3: + version "1.1.3" + resolved "https://registry.yarnpkg.com/color-name/-/color-name-1.1.3.tgz#a7d0558bd89c42f795dd42328f740831ca53bc25" + integrity sha512-72fSenhMw2HZMTVHeCA9KCmpEIbzWiQsjN+BHcBbS9vr1mtt+vJjPdksIBNUmKAW8TFUDPJK5SUU3QhE9NEXDw== + color-name@~1.1.4: version "1.1.4" resolved "https://registry.yarnpkg.com/color-name/-/color-name-1.1.4.tgz#c2a09a87acbde69543de6f63fa3995c826c536a2" @@ -386,7 +1275,30 @@ concat-map@0.0.1: resolved "https://registry.yarnpkg.com/concat-map/-/concat-map-0.0.1.tgz#d8a96bd77fd68df7793a73036a3ba0d5405d477b" integrity sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg== -cross-spawn@^7.0.2: +convert-source-map@^2.0.0: + version "2.0.0" + resolved "https://registry.yarnpkg.com/convert-source-map/-/convert-source-map-2.0.0.tgz#4b560f649fc4e918dd0ab75cf4961e8bc882d82a" + integrity 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+emoji-regex@^8.0.0: + version "8.0.0" + resolved "https://registry.yarnpkg.com/emoji-regex/-/emoji-regex-8.0.0.tgz#e818fd69ce5ccfcb404594f842963bf53164cc37" + integrity sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A== + +error-ex@^1.3.1: + version "1.3.2" + resolved "https://registry.yarnpkg.com/error-ex/-/error-ex-1.3.2.tgz#b4ac40648107fdcdcfae242f428bea8a14d4f1bf" + integrity sha512-7dFHNmqeFSEt2ZBsCriorKnn3Z2pj+fd9kmI6QoWw4//DL+icEBfc0U7qJCisqrTsKTjw4fNFy2pW9OqStD84g== + dependencies: + is-arrayish "^0.2.1" + esbuild@~0.21.4: version "0.21.5" resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.21.5.tgz#9ca301b120922959b766360d8ac830da0d02997d" @@ -443,6 +1402,21 @@ esbuild@~0.21.4: "@esbuild/win32-ia32" "0.21.5" "@esbuild/win32-x64" "0.21.5" +escalade@^3.1.1, escalade@^3.1.2: + version "3.1.2" + resolved "https://registry.yarnpkg.com/escalade/-/escalade-3.1.2.tgz#54076e9ab29ea5bf3d8f1ed62acffbb88272df27" + integrity 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"^1.3.0" micromatch "^4.0.4" -fast-json-stable-stringify@^2.0.0: +fast-json-stable-stringify@2.x, fast-json-stable-stringify@^2.0.0, fast-json-stable-stringify@^2.1.0: version "2.1.0" resolved "https://registry.yarnpkg.com/fast-json-stable-stringify/-/fast-json-stable-stringify-2.1.0.tgz#874bf69c6f404c2b5d99c481341399fd55892633" integrity sha512-lhd/wF+Lk98HZoTCtlVraHtfh5XYijIjalXck7saUtuanSDyLMxnHhSXEDJqHxD7msR8D0uCmqlkwjCV8xvwHw== @@ -572,6 +1582,13 @@ fastq@^1.6.0: dependencies: reusify "^1.0.4" +fb-watchman@^2.0.0: + version "2.0.2" + resolved "https://registry.yarnpkg.com/fb-watchman/-/fb-watchman-2.0.2.tgz#e9524ee6b5c77e9e5001af0f85f3adbb8623255c" + integrity sha512-p5161BqbuCaSnB8jIbzQHOlpgsPmK5rJVDfDKO91Axs5NC1uu3HRQm6wt9cd9/+GtQQIO53JdGXXoyDpTAsgYA== + dependencies: + bser "2.1.1" + file-entry-cache@^8.0.0: version "8.0.0" resolved "https://registry.yarnpkg.com/file-entry-cache/-/file-entry-cache-8.0.0.tgz#7787bddcf1131bffb92636c69457bbc0edd6d81f" @@ -586,6 +1603,14 @@ fill-range@^7.1.1: dependencies: to-regex-range "^5.0.1" +find-up@^4.0.0, find-up@^4.1.0: + version "4.1.0" + resolved "https://registry.yarnpkg.com/find-up/-/find-up-4.1.0.tgz#97afe7d6cdc0bc5928584b7c8d7b16e8a9aa5d19" + integrity sha512-PpOwAdQ/YlXQ2vj8a3h8IipDuYRi3wceVQQGYWxNINccq40Anw7BlsEXCMbt1Zt+OLA6Fq9suIpIWD0OsnISlw== + dependencies: + locate-path "^5.0.0" + path-exists "^4.0.0" + find-up@^5.0.0: version "5.0.0" resolved "https://registry.yarnpkg.com/find-up/-/find-up-5.0.0.tgz#4c92819ecb7083561e4f4a240a86be5198f536fc" @@ -607,11 +1632,41 @@ flatted@^3.2.9: resolved "https://registry.yarnpkg.com/flatted/-/flatted-3.3.1.tgz#21db470729a6734d4997002f439cb308987f567a" integrity sha512-X8cqMLLie7KsNUDSdzeN8FYK9rEt4Dt67OsG/DNGnYTSDBG4uFAJFBnUeiV+zCVAvwFy56IjM9sH51jVaEhNxw== -fsevents@~2.3.3: +fs.realpath@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/fs.realpath/-/fs.realpath-1.0.0.tgz#1504ad2523158caa40db4a2787cb01411994ea4f" + integrity 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"^4.0.3" +glob@^7.1.3, glob@^7.1.4: + version "7.2.3" + resolved "https://registry.yarnpkg.com/glob/-/glob-7.2.3.tgz#b8df0fb802bbfa8e89bd1d938b4e16578ed44f2b" + integrity sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q== + dependencies: + fs.realpath "^1.0.0" + inflight "^1.0.4" + inherits "2" + minimatch "^3.1.1" + once "^1.3.0" + path-is-absolute "^1.0.0" + +globals@^11.1.0: + version "11.12.0" + resolved "https://registry.yarnpkg.com/globals/-/globals-11.12.0.tgz#ab8795338868a0babd8525758018c2a7eb95c42e" + integrity sha512-WOBp/EEGUiIsJSp7wcv/y6MO+lV9UoncWqxuFfm8eBwzWNgyfBd6Gz+IeKQ9jCmyhoH99g15M3T+QaVHFjizVA== + globals@^14.0.0: version "14.0.0" resolved "https://registry.yarnpkg.com/globals/-/globals-14.0.0.tgz#898d7413c29babcf6bafe56fcadded858ada724e" @@ -655,16 +1727,43 @@ globby@^11.1.0: merge2 "^1.4.1" slash "^3.0.0" +graceful-fs@^4.2.9: + version "4.2.11" + resolved 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+ +merge-stream@^2.0.0: + version "2.0.0" + resolved "https://registry.yarnpkg.com/merge-stream/-/merge-stream-2.0.0.tgz#52823629a14dd00c9770fb6ad47dc6310f2c1f60" + integrity sha512-abv/qOcuPfk3URPfDzmZU1LKmuw8kT+0nIHvKrKgFrwifol/doWcdA4ZqsWQ8ENrFKkd67Mfpo/LovbIUsbt3w== + merge2@^1.3.0, merge2@^1.4.1: version "1.4.1" resolved "https://registry.yarnpkg.com/merge2/-/merge2-1.4.1.tgz#4368892f885e907455a6fd7dc55c0c9d404990ae" @@ -772,7 +2416,12 @@ micromatch@^4.0.4: braces "^3.0.3" picomatch "^2.3.1" -minimatch@^3.0.5, minimatch@^3.1.2: +mimic-fn@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/mimic-fn/-/mimic-fn-2.1.0.tgz#7ed2c2ccccaf84d3ffcb7a69b57711fc2083401b" + integrity sha512-OqbOk5oEQeAZ8WXWydlu9HJjz9WVdEIvamMCcXmuqUYjTknH/sqsWvhQ3vgwKFRR1HpjvNBKQ37nbJgYzGqGcg== + +minimatch@^3.0.4, minimatch@^3.0.5, minimatch@^3.1.1, minimatch@^3.1.2: version "3.1.2" resolved "https://registry.yarnpkg.com/minimatch/-/minimatch-3.1.2.tgz#19cd194bfd3e428f049a70817c038d89ab4be35b" 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"https://registry.yarnpkg.com/tmpl/-/tmpl-1.0.5.tgz#8683e0b902bb9c20c4f726e3c0b69f36518c07cc" + integrity sha512-3f0uOEAQwIqGuWW2MVzYg8fV/QNnc/IpuJNG837rLuczAaLVHslWHZQj4IGiEl5Hs3kkbhwL9Ab7Hrsmuj+Smw== + +to-fast-properties@^2.0.0: + version "2.0.0" + resolved "https://registry.yarnpkg.com/to-fast-properties/-/to-fast-properties-2.0.0.tgz#dc5e698cbd079265bc73e0377681a4e4e83f616e" + integrity sha512-/OaKK0xYrs3DmxRYqL/yDc+FxFUVYhDlXMhRmv3z915w2HF1tnN1omB354j8VUGO/hbRzyD6Y3sA7v7GS/ceog== + to-regex-range@^5.0.1: version "5.0.1" resolved "https://registry.yarnpkg.com/to-regex-range/-/to-regex-range-5.0.1.tgz#1648c44aae7c8d988a326018ed72f5b4dd0392e4" @@ -944,6 +2853,39 @@ ts-api-utils@^1.3.0: resolved "https://registry.yarnpkg.com/ts-api-utils/-/ts-api-utils-1.3.0.tgz#4b490e27129f1e8e686b45cc4ab63714dc60eea1" integrity sha512-UQMIo7pb8WRomKR1/+MFVLTroIvDVtMX3K6OUir8ynLyzB8Jeriont2bTAtmNPa1ekAgN7YPDyf6V+ygrdU+eQ== +ts-jest@^29.1.5: + version "29.1.5" + resolved "https://registry.yarnpkg.com/ts-jest/-/ts-jest-29.1.5.tgz#d6c0471cc78bffa2cb4664a0a6741ef36cfe8f69" + integrity sha512-UuClSYxM7byvvYfyWdFI+/2UxMmwNyJb0NPkZPQE2hew3RurV7l7zURgOHAd/1I1ZdPpe3GUsXNXAcN8TFKSIg== + dependencies: + bs-logger "0.x" + fast-json-stable-stringify "2.x" + jest-util "^29.0.0" + json5 "^2.2.3" + lodash.memoize "4.x" + make-error "1.x" + semver "^7.5.3" + yargs-parser "^21.0.1" + +ts-node@^10.9.2: + version "10.9.2" + resolved "https://registry.yarnpkg.com/ts-node/-/ts-node-10.9.2.tgz#70f021c9e185bccdca820e26dc413805c101c71f" + integrity sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ== + dependencies: + "@cspotcode/source-map-support" "^0.8.0" + "@tsconfig/node10" "^1.0.7" + "@tsconfig/node12" "^1.0.7" + "@tsconfig/node14" "^1.0.0" + "@tsconfig/node16" "^1.0.2" + acorn "^8.4.1" + acorn-walk "^8.1.1" + arg "^4.1.0" + create-require "^1.1.0" + diff "^4.0.1" + make-error "^1.1.1" + v8-compile-cache-lib "^3.0.1" + yn "3.1.1" + tsx@^4.15.6: version "4.15.6" resolved "https://registry.yarnpkg.com/tsx/-/tsx-4.15.6.tgz#4522ed093f7fa54f031a7a999274e8b35dbf3165" @@ -961,6 +2903,16 @@ type-check@^0.4.0, type-check@~0.4.0: dependencies: prelude-ls "^1.2.1" +type-detect@4.0.8: + version "4.0.8" + resolved "https://registry.yarnpkg.com/type-detect/-/type-detect-4.0.8.tgz#7646fb5f18871cfbb7749e69bd39a6388eb7450c" + integrity sha512-0fr/mIH1dlO+x7TlcMy+bIDqKPsw/70tVyeHW787goQjhmqaZe10uwLujubK9q9Lg6Fiho1KUKDYz0Z7k7g5/g== + +type-fest@^0.21.3: + version "0.21.3" + resolved "https://registry.yarnpkg.com/type-fest/-/type-fest-0.21.3.tgz#d260a24b0198436e133fa26a524a6d65fa3b2e37" + integrity sha512-t0rzBq87m3fVcduHDUFhKmyyX+9eo6WQjZvf51Ea/M0Q7+T374Jp1aUiyUl0GKxp8M/OETVHSDvmkyPgvX+X2w== + typescript-eslint@^7.13.1: version "7.13.1" resolved "https://registry.yarnpkg.com/typescript-eslint/-/typescript-eslint-7.13.1.tgz#8bbcc4b59b6bb0c457505ee17a356b1868c3fcd5" @@ -980,6 +2932,14 @@ undici-types@~5.26.4: resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA== +update-browserslist-db@^1.0.16: + version "1.0.16" + resolved "https://registry.yarnpkg.com/update-browserslist-db/-/update-browserslist-db-1.0.16.tgz#f6d489ed90fb2f07d67784eb3f53d7891f736356" + integrity sha512-KVbTxlBYlckhF5wgfyZXTWnMn7MMZjMu9XG8bPlliUOP9ThaF4QnhP8qrjrH7DRzHfSk0oQv1wToW+iA5GajEQ== + dependencies: + escalade "^3.1.2" + picocolors "^1.0.1" + uri-js@^4.2.2: version "4.4.1" resolved "https://registry.yarnpkg.com/uri-js/-/uri-js-4.4.1.tgz#9b1a52595225859e55f669d928f88c6c57f2a77e" @@ -987,6 +2947,27 @@ uri-js@^4.2.2: dependencies: punycode "^2.1.0" +v8-compile-cache-lib@^3.0.1: + version "3.0.1" + resolved "https://registry.yarnpkg.com/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz#6336e8d71965cb3d35a1bbb7868445a7c05264bf" + integrity sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg== + +v8-to-istanbul@^9.0.1: + version "9.2.0" + resolved "https://registry.yarnpkg.com/v8-to-istanbul/-/v8-to-istanbul-9.2.0.tgz#2ed7644a245cddd83d4e087b9b33b3e62dfd10ad" + integrity sha512-/EH/sDgxU2eGxajKdwLCDmQ4FWq+kpi3uCmBGpw1xJtnAxEjlD8j8PEiGWpCIMIs3ciNAgH0d3TTJiUkYzyZjA== + dependencies: + "@jridgewell/trace-mapping" "^0.3.12" + "@types/istanbul-lib-coverage" "^2.0.1" + convert-source-map "^2.0.0" + +walker@^1.0.8: + version "1.0.8" + resolved "https://registry.yarnpkg.com/walker/-/walker-1.0.8.tgz#bd498db477afe573dc04185f011d3ab8a8d7653f" + integrity sha512-ts/8E8l5b7kY0vlWLewOkDXMmPdLcVV4GmOQLyxuSswIJsweeFZtAsMF7k1Nszz+TYBQrlYRmzOnr398y1JemQ== + dependencies: + makeerror "1.0.12" + which@^2.0.1: version "2.0.2" resolved "https://registry.yarnpkg.com/which/-/which-2.0.2.tgz#7c6a8dd0a636a0327e10b59c9286eee93f3f51b1" @@ -999,6 +2980,61 @@ word-wrap@^1.2.5: resolved "https://registry.yarnpkg.com/word-wrap/-/word-wrap-1.2.5.tgz#d2c45c6dd4fbce621a66f136cbe328afd0410b34" integrity sha512-BN22B5eaMMI9UMtjrGd5g5eCYPpCPDUy0FJXbYsaT5zYxjFOckS53SQDE3pWkVoWpHXVb3BrYcEN4Twa55B5cA== +wrap-ansi@^7.0.0: + version "7.0.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" + integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== + dependencies: + ansi-styles "^4.0.0" + string-width "^4.1.0" + strip-ansi "^6.0.0" + +wrappy@1: + version "1.0.2" + resolved "https://registry.yarnpkg.com/wrappy/-/wrappy-1.0.2.tgz#b5243d8f3ec1aa35f1364605bc0d1036e30ab69f" + integrity sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ== + +write-file-atomic@^4.0.2: + version "4.0.2" + resolved "https://registry.yarnpkg.com/write-file-atomic/-/write-file-atomic-4.0.2.tgz#a9df01ae5b77858a027fd2e80768ee433555fcfd" + integrity 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resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" + integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== + dependencies: + cliui "^8.0.1" + escalade "^3.1.1" + get-caller-file "^2.0.5" + require-directory "^2.1.1" + string-width "^4.2.3" + y18n "^5.0.5" + yargs-parser "^21.1.1" + +yn@3.1.1: + version "3.1.1" + resolved "https://registry.yarnpkg.com/yn/-/yn-3.1.1.tgz#1e87401a09d767c1d5eab26a6e4c185182d2eb50" + integrity sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q== + yocto-queue@^0.1.0: version "0.1.0" resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" From e09cc6d6796f6f2320c06724ae5ad57d2bb7ffb1 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 17:33:58 +0200 Subject: [PATCH 6/7] add CI --- .github/workflows/ci.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ef58d4e6..2cb4ced5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -22,3 +22,19 @@ jobs: - name: Type check run: | yarn typecheck + test: + name: Test + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: Set up Node + uses: actions/setup-node@v4 + with: + node-version: 22.x + cache: yarn + - name: Install dependencies + run: | + yarn install + - name: Test + run: | + yarn test From e8b6773dfc6f10a97ccf5299353d569bb46e75b2 Mon Sep 17 00:00:00 2001 From: Bart Mesuere Date: Tue, 18 Jun 2024 18:14:07 +0200 Subject: [PATCH 7/7] add a bit more comments --- lib/commands/base_command.ts | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/lib/commands/base_command.ts b/lib/commands/base_command.ts index 14a3b934..90897abe 100644 --- a/lib/commands/base_command.ts +++ b/lib/commands/base_command.ts @@ -1,6 +1,13 @@ import { Command } from "commander"; import { version } from '../../package.json'; +/** + * This is a base class which provides a common interface for all commands. + * This is mostly used for testing purposes. + * + * Commands implementing this class should override the run method and call parseArguments + * at the beginning of the run method. + */ export abstract class BaseCommand { public program: Command; args: string[] | undefined; @@ -12,6 +19,10 @@ export abstract class BaseCommand { abstract run(): void; + /** + * Create sets up the command line program. Implementing classes can add additional options. + * to this.program. + */ create(options?: { exitOverride?: boolean, suppressOutput?: boolean }): Command { const program = new Command(); @@ -20,6 +31,7 @@ export abstract class BaseCommand { program.exitOverride(); // don't exit on error } if (options?.suppressOutput) { + // don't write anything to the console program.configureOutput({ writeOut: () => { }, writeErr: () => { } @@ -31,6 +43,9 @@ export abstract class BaseCommand { return program; } + /** + * This allows us to pass a custom list of strings as arguments to the command during testing. + */ parseArguments() { if (this.args) { // custom arg parsing to be able to inject args for testing