From c24382a1d725103d8bc3615b6c1f8630b3efcbc9 Mon Sep 17 00:00:00 2001
From: Bart Mesuere <Bart.Mesuere@UGent.be>
Date: Fri, 21 Jun 2024 14:30:08 +0200
Subject: [PATCH] add tests

---
 lib/commands/prot2pept.ts        |   9 ++-
 tests/commands/prot2pept.test.ts | 124 +++++++++++++++++++++++++++++++
 tsconfig.json                    |   1 +
 3 files changed, 133 insertions(+), 1 deletion(-)
 create mode 100644 tests/commands/prot2pept.test.ts

diff --git a/lib/commands/prot2pept.ts b/lib/commands/prot2pept.ts
index ac7c8fb7..3b3a6b01 100644
--- a/lib/commands/prot2pept.ts
+++ b/lib/commands/prot2pept.ts
@@ -23,7 +23,14 @@ The input should have either one protein sequence per line or contain a FASTA fo
    */
   async run() {
     this.parseArguments();
-    const pattern = new RegExp(this.program.opts().pattern, "g");
+
+    let pattern;
+    try {
+      pattern = new RegExp(this.program.opts().pattern, "g");
+    } catch (e) {
+      this.program.error(`Your pattern was invalid: ${(e as Error).message}`);
+      //process.exit(1);
+    }
 
     let fasta = false;
     let protein = [];
diff --git a/tests/commands/prot2pept.test.ts b/tests/commands/prot2pept.test.ts
new file mode 100644
index 00000000..ca01533a
--- /dev/null
+++ b/tests/commands/prot2pept.test.ts
@@ -0,0 +1,124 @@
+import { Prot2pept } from '../../lib/commands/prot2pept';
+import { jest } from '@jest/globals';
+import * as mock from 'mock-stdin';
+
+let output: string[];
+let error: string[];
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
+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 line input 1', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept();
+  const run = command.run();
+
+  stdin.send("AALTERAALTERPAALTER\n");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe("AALTER\nAALTERPAALTER");
+});
+
+test('test single line input 2', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept();
+  const run = command.run();
+
+  stdin.send("KRKPR\n");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe("K\nR\nKPR");
+});
+
+test('test multi line input', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept();
+  const run = command.run();
+
+  stdin.send("AALTERAALTERPAALTER\n");
+  stdin.send("AALTERAA\n");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe("AALTER\nAALTERPAALTER\nAALTER\nAA");
+});
+
+test('test fasta input 1', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept();
+  const run = command.run();
+
+  stdin.send(">AKA\nAALTERAALTERPAALTER\n");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe(">AKA\nAALTER\nAALTERPAALTER");
+});
+
+test('test fasta input 2', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept();
+  const run = command.run();
+
+  stdin.send(">AKA\nAAL\nT\nERAALTER\nP\nAALTER\n");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe(">AKA\nAALTER\nAALTERPAALTER");
+});
+
+test('test fasta input 3', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept();
+  const run = command.run();
+
+  stdin.send(">AKA\nAAL\nT\n>\nERAALTER\nP\nAALTER");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe(">AKA\nAALT\n>\nER\nAALTERPAALTER");
+});
+
+test('test custom pattern', async () => {
+  const stdin = mock.stdin();
+
+  const command = new Prot2pept({ args: ["--pattern", "([KR])([^A])"] });
+  const run = command.run();
+
+  stdin.send("AALTERAALTERPAALTER\n");
+  stdin.end();
+
+  await run;
+
+  expect(errorSpy).toHaveBeenCalledTimes(0);
+  expect(output.join("").trimEnd()).toBe("AALTERAALTER\nPAALTER");
+});
diff --git a/tsconfig.json b/tsconfig.json
index 5c9bef88..23047235 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -8,5 +8,6 @@
     "module": "NodeNext",
     "strict": true,
     "resolveJsonModule": true,
+    "target": "esnext"
   }
 }