feat: add CLI feedback when waiting for stdin input

- Detects interactive TTY sessions and prints a helpful message to stderr when the command is waiting for input.
- Prevents user confusion when running commands without arguments or pipes.
- Adds test case to verify the behavior (mocking isTTY).

Author: google-labs-jules[bot]

lib/commands/unipept/unipept_subcommand.ts

@@ -303,6 +303,9 @@ export abstract class UnipeptSubcommand {
       this.streamInterface = createInterface({ input: createReadStream(input) });
       return this.streamInterface[Symbol.asyncIterator]();
     } else {
+      if (process.stdin.isTTY) {
+        process.stderr.write("Reading from standard input... (Press Ctrl+D to finish)\n");
+      }
       this.streamInterface = createInterface({ input: process.stdin });
       return this.streamInterface[Symbol.asyncIterator]();
     }

tests/commands/unipept/unipept_subcommand.test.ts

@@ -1,56 +1,103 @@
 import { Pept2lca } from '../../../lib/commands/unipept/pept2lca.js';
+import { vi, describe, test, expect, afterEach } from 'vitest';
 
-test('test command setup', () => {
-  const command = new Pept2lca();
-  expect(command.name).toBe("pept2lca");
-  expect(command.user_agent).toMatch(/^unipept-cli/);
-  expect(command.command.name()).toBe("pept2lca");
-});
+describe('UnipeptSubcommand', () => {
+  afterEach(() => {
+    vi.restoreAllMocks();
+  });
 
-test('test correct host', () => {
-  const command = new Pept2lca();
+  test('test command setup', () => {
+    const command = new Pept2lca();
+    expect(command.name).toBe("pept2lca");
+    expect(command.user_agent).toMatch(/^unipept-cli/);
+    expect(command.command.name()).toBe("pept2lca");
+  });
 
-  expect(command.host).toBe("https://api.unipept.ugent.be");
-  expect(command["getHost"]()).toBe("https://api.unipept.ugent.be");
+  test('test correct host', () => {
+    const command = new Pept2lca();
 
-  command.options.host = "https://optionshost";
-  expect(command["getHost"]()).toBe("https://optionshost");
+    expect(command.host).toBe("https://api.unipept.ugent.be");
+    expect(command["getHost"]()).toBe("https://api.unipept.ugent.be");
 
-  command.options.host = "http://optionshost";
-  expect(command["getHost"]()).toBe("http://optionshost");
+    command.options.host = "https://optionshost";
+    expect(command["getHost"]()).toBe("https://optionshost");
 
-  command.options.host = "optionshost";
-  expect(command["getHost"]()).toBe("http://optionshost");
-});
+    command.options.host = "http://optionshost";
+    expect(command["getHost"]()).toBe("http://optionshost");
 
-test('test correct inputIterator', async () => {
-  const command = new Pept2lca();
+    command.options.host = "optionshost";
+    expect(command["getHost"]()).toBe("http://optionshost");
+  });
 
-  // should be stdin
-  let input = command["getInputIterator"]([]) as AsyncIterableIterator<string>;
-  expect(typeof input[Symbol.asyncIterator]).toBe("function");
-  command['streamInterface']?.close();
+  test('test correct inputIterator', async () => {
+    const command = new Pept2lca();
 
-  // should be a (non-existant) file and error
-  input = command["getInputIterator"]([], "filename") as AsyncIterableIterator<string>;
-  expect(typeof input[Symbol.asyncIterator]).toBe("function");
-  await expect(async () => { await input.next() }).rejects.toThrow(/no such file/);
+    // should be stdin
+    let input = command["getInputIterator"]([]) as AsyncIterableIterator<string>;
+    expect(typeof input[Symbol.asyncIterator]).toBe("function");
+    command['streamInterface']?.close();
 
-  // should be array
-  const inputArray = command["getInputIterator"](["A", "B"]) as IterableIterator<string>;
-  expect(typeof inputArray[Symbol.iterator]).toBe("function");
-});
+    // should be a (non-existant) file and error
+    input = command["getInputIterator"]([], "filename") as AsyncIterableIterator<string>;
+    expect(typeof input[Symbol.asyncIterator]).toBe("function");
+    await expect(async () => { await input.next() }).rejects.toThrow(/no such file/);
 
-test('test selected fields parsing', () => {
-  const command = new Pept2lca();
+    // should be array
+    const inputArray = command["getInputIterator"](["A", "B"]) as IterableIterator<string>;
+    expect(typeof inputArray[Symbol.iterator]).toBe("function");
+  });
 
-  command.options.select = ["a,b,c"];
-  expect(command["getSelectedFields"]()).toStrictEqual([/^a$/, /^b$/, /^c$/]);
-});
+  test('test selected fields parsing', () => {
+    const command = new Pept2lca();
+
+    command.options.select = ["a,b,c"];
+    expect(command["getSelectedFields"]()).toStrictEqual([/^a$/, /^b$/, /^c$/]);
+  });
+
+  test('test selected fields with wildcards', () => {
+    const command = new Pept2lca();
+
+    command.options.select = ["taxon*,name"];
+    expect(command["getSelectedFields"]()).toStrictEqual([/^taxon.*$/, /^name$/]);
+  });
+
+  test('test inputIterator prints warning when reading from TTY stdin', async () => {
+    const command = new Pept2lca();
+
+    // Mock process.stdin.isTTY
+    const originalIsTTY = process.stdin.isTTY;
+    Object.defineProperty(process.stdin, 'isTTY', { value: true, configurable: true });
+
+    // Mock process.stderr.write
+    const stderrSpy = vi.spyOn(process.stderr, 'write').mockImplementation(() => true);
+
+    const input = command["getInputIterator"]([]) as AsyncIterableIterator<string>;
+
+    expect(stderrSpy).toHaveBeenCalledWith(expect.stringContaining("Reading from standard input..."));
+
+    command['streamInterface']?.close();
+
+    // Restore
+    Object.defineProperty(process.stdin, 'isTTY', { value: originalIsTTY });
+  });
+
+  test('test inputIterator does NOT print warning when reading from piped stdin (not TTY)', async () => {
+    const command = new Pept2lca();
+
+    // Mock process.stdin.isTTY
+    const originalIsTTY = process.stdin.isTTY;
+    Object.defineProperty(process.stdin, 'isTTY', { value: false, configurable: true });
+
+    // Mock process.stderr.write
+    const stderrSpy = vi.spyOn(process.stderr, 'write').mockImplementation(() => true);
+
+    const input = command["getInputIterator"]([]) as AsyncIterableIterator<string>;
+
+    expect(stderrSpy).not.toHaveBeenCalled();
 
-test('test selected fields with wildcards', () => {
-  const command = new Pept2lca();
+    command['streamInterface']?.close();
 
-  command.options.select = ["taxon*,name"];
-  expect(command["getSelectedFields"]()).toStrictEqual([/^taxon.*$/, /^name$/]);
+    // Restore
+    Object.defineProperty(process.stdin, 'isTTY', { value: originalIsTTY });
+  });
 });