add formatter tests

lib/formatters/formatter.ts

@@ -2,17 +2,17 @@ export abstract class Formatter {
 
   abstract header(sampleData: object, fastaMapper?: boolean): string;
   abstract footer(): string;
-  abstract convert(data: { [key: string]: string }[], first?: boolean): string;
+  abstract convert(data: object[], first?: boolean): string;
 
-  format(data: { [key: string]: string }[], fastaMapper?: boolean, first?: boolean): string {
+  format(data: object[], fastaMapper?: boolean, first?: boolean): string {
     if (fastaMapper) {
       data = this.integrateFastaHeaders(data, fastaMapper);
     }
     return this.convert(data, first);
   }
 
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  integrateFastaHeaders(data: { [key: string]: string }[], fastaMapper: boolean): { [key: string]: string }[] {
+  integrateFastaHeaders(data: object[], fastaMapper: boolean): object[] {
     return data;
   }
 }

tests/commands/unipept.test.ts

@@ -1,6 +1,6 @@
 import { Unipept } from '../../lib/commands/unipept';
 
-test('test single argument', async () => {
+test('test if all commands are available', async () => {
   const command = new Unipept();
   const commandNames = command.program.commands.map(c => c.name());
   expect(commandNames).toContain("pept2lca");

tests/formatters/csv_formatter.test.ts

@@ -0,0 +1,30 @@
+import { FormatterFactory } from "../../lib/formatters/formatter_factory";
+import { TestObject } from "./test_object";
+
+const formatter = FormatterFactory.getFormatter("csv");
+
+test('test header', () => {
+  const fasta = [["peptide", ">test"]];
+  const object = [TestObject.testObject(), TestObject.testObject()];
+  expect(formatter.header(object)).toBe(TestObject.asCsvHeader());
+  //expect(formatter.header(object, fasta)).toBe(`fasta_header,${TestObject.asCsvHeader()}`);
+});
+
+test('test footer', () => {
+  expect(formatter.footer()).toBe("");
+});
+
+test('test convert', () => {
+  const object = [TestObject.testObject(), TestObject.testObject()];
+  const csv = [TestObject.asCsv(), TestObject.asCsv(), ""].join("\n");
+
+  expect(formatter.convert(object, true)).toBe(csv);
+  expect(formatter.convert(object, false)).toBe(csv);
+});
+
+test('test format with fasta', () => {
+  const fasta = [['>test', '5']];
+  const object = [TestObject.testObject(), TestObject.testObject()];
+  const csv = [`>test,${TestObject.asCsv()}`, TestObject.asCsv(), ""].join("\n");
+  //expect(formatter.format(object, fasta, false)).toBe(csv);
+});

tests/formatters/formatter_factory.test.ts

@@ -0,0 +1,11 @@
+import { FormatterFactory } from "../../lib/formatters/formatter_factory";
+
+test('test if default formatter is csv', async () => {
+  const formatter = FormatterFactory.getFormatter("foo");
+  expect(formatter.constructor.name).toBe("CSVFormatter");
+});
+
+test('test if csv formatter is csv', async () => {
+  const formatter = FormatterFactory.getFormatter("csv");
+  expect(formatter.constructor.name).toBe("CSVFormatter");
+});

tests/formatters/test_object.ts

@@ -0,0 +1,21 @@
+export class TestObject {
+  static testObject() {
+    return { "integer": 5, "string": "string", "list": ["a", 2, false] };
+  }
+
+  static asJson() {
+    return '{"integer":5,"string":"string","list":["a",2,false]}';
+  }
+
+  static asXml() {
+    return '<integer>5</integer><string>string</string><list><item>a</item><item>2</item><item>false</item></list>';
+  }
+
+  static asCsv() {
+    return '5,string,"[""a"",2,false]"';
+  }
+
+  static asCsvHeader() {
+    return "integer,string,list\n";
+  }
+}