add basic command runner tests

lib/commands/unipept/unipept_subcommand.ts

@@ -149,6 +149,6 @@ export abstract class UnipeptSubcommand {
   }
 
   private globToRegex(glob: string): RegExp {
-    return new RegExp(glob.replace(/\*/g, ".*"));
+    return new RegExp(`^${glob.replace(/\*/g, ".*")}$`);
   }
 }

tests/commands/unipept/unipept_subcommand.test.ts

@@ -0,0 +1,58 @@
+import { Interface } from 'readline';
+import { Pept2lca } from '../../../lib/commands/unipept/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");
+});
+
+test('test correct host', () => {
+  const command = new Pept2lca();
+
+  expect(command.host).toBe("https://api.unipept.ugent.be");
+  expect(command["getHost"]()).toBe("https://api.unipept.ugent.be");
+
+  command.options.host = "https://optionshost";
+  expect(command["getHost"]()).toBe("https://optionshost");
+
+  command.options.host = "http://optionshost";
+  expect(command["getHost"]()).toBe("http://optionshost");
+
+  command.options.host = "optionshost";
+  expect(command["getHost"]()).toBe("http://optionshost");
+});
+
+test('test correct inputIterator', async () => {
+  const command = new Pept2lca();
+
+  // should be stdin
+  let input = command["getInputIterator"]([]) as Interface;
+  expect(input).toBeInstanceOf(Interface);
+  input.close();
+
+  // should be a (non-existant) file and error
+  input = command["getInputIterator"]([], "filename") as Interface;
+  input.on("error", (e) => {
+    expect(e.toString()).toMatch(/no such file/);
+  });
+
+  // should be array
+  const inputArray = command["getInputIterator"](["A", "B"]);
+  expect(inputArray).toBeInstanceOf(Array);
+});
+
+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$/]);
+});