Add linting, testing and type checks

.github/workflows/ci.yml

@@ -3,32 +3,38 @@ name: CI
 on: [push]
 
 jobs:
-  test:
+  lint:
+    name: Lint
     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
+      - uses: actions/checkout@v4
+      - name: Set up Node
+        uses: actions/setup-node@v4
         with:
-          ruby-version: ${{ matrix.ruby }}
-          bundler-cache: true
-      - name: Test
+          node-version: 22.x
+          cache: yarn
+      - name: Install dependencies
         run: |
-          bundle exec rake test
-  lint:
-    name: Lint
+          yarn install
+      - name: Lint
+        run: |
+          yarn lint
+      - name: Type check
+        run: |
+          yarn typecheck
+  test:
+    name: Test
     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
+          node-version: 22.x
+          cache: yarn
+      - name: Install dependencies
+        run: |
+          yarn install
       - name: Test
         run: |
-          bundle exec rake test_style
+          yarn test

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 <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<string> {
-  // 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();

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/"] }
+];

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: [
+  //   "<rootDir>"
+  // ],
+
+  // 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;