fix(input check): set input defaults appropriately

Checks and sets the input to the corresponding type/format required for successful execution. Moved
the checks into its own function for handling.

src/__tests__/setInquirerDefaults.test.js

@@ -0,0 +1,24 @@
+import { describe, test, expect } from 'vitest';
+
+import { setInquirerDefaults } from '../utils/setInquirerDefaults';
+
+/**
+ * To test setInquirerDefaults()
+ * Input: configParam (Object)
+ * Output: configParam (Object)
+ */
+describe('setInquirerDefaults', () => {
+  // Dummy data
+  const testConfigParam = {
+    outputFormat: ['JSON'],
+    msLevel: '1 2',
+  };
+
+  // Tests
+  test('configure configParam appropriately', async () => {
+    const configParam = await setInquirerDefaults(testConfigParam);
+
+    expect(configParam.outputFormat).toStrictEqual('JSON');
+    expect(configParam.msLevel).toStrictEqual([1, 2]);
+  });
+});

src/__tests__/setDefaults.test.js → src/__tests__/setYargsDefaults.test.js

@@ -10,31 +10,31 @@ import { join, basename } from 'path';
 
 import { describe, test, expect, beforeAll, afterAll } from 'vitest';
 
-import { setDefaults } from '../utils/setDefaults.js';
+import { setYargsDefaults } from '../utils/setYargsDefaults.js';
 
 /**
- * To test setDefaults()
+ * To test setYargsDefaults()
  * Input: argv (Yargs)
  * Output: configParam (Object) || Error message (Error)
  */
-describe('setDefaults', () => {
+describe('setYargsDefaults', () => {
   // Dummy data
   /**
    * @type {Yargs}
    */
   const testArgv = {
     interactive: false,
-    inputDirectory: './.tmp/setDefaults/inputDirectory/',
+    inputDirectory: './.tmp/setYargsDefaults/inputDirectory/',
     fileList: ['*'],
     outputFormat: ['JSON'],
     outputDirectory: join(
       homedir(),
       '/exfilms/outputFormat/inputDirectoryName/',
     ),
-    logDirectory: './.tmp/setDefaults/logDirectory/',
+    logDirectory: './.tmp/setYargsDefaults/logDirectory/',
     decimalPlace: NaN,
     targeted: false,
-    targetFile: './.tmp/setDefaults/targetFile.tsv',
+    targetFile: './.tmp/setYargsDefaults/targetFile.tsv',
     mzTolerance: 0.005,
     ppmTolerance: 5,
     mzRange: false,
@@ -60,7 +60,7 @@ describe('setDefaults', () => {
 
   // Tests
   test('return configParam: using default values', async () => {
-    const configParam = await setDefaults(testArgv);
+    const configParam = await setYargsDefaults(testArgv);
     expect(configParam.inputDirectory).toStrictEqual(testArgv.inputDirectory);
     expect(configParam.fileList).toStrictEqual([
       'testFile1.mzML',
@@ -95,11 +95,11 @@ describe('setDefaults', () => {
 
   test('return configParam: using defined values', async () => {
     testArgv.fileList = ['testFile1.mzML'];
-    testArgv.outputDirectory = './.tmp/setDefaults/outputDirectory/';
+    testArgv.outputDirectory = './.tmp/setYargsDefaults/outputDirectory/';
     testArgv.targeted = true;
     testArgv.mzRange = true;
     testArgv.filterSpectrumData = true;
-    const configParam = await setDefaults(testArgv);
+    const configParam = await setYargsDefaults(testArgv);
     expect(configParam.fileList).toStrictEqual(testArgv.fileList);
     expect(configParam.outputDirectory).toStrictEqual(testArgv.outputDirectory);
     expect(configParam.targetFile).toStrictEqual(testArgv.targetFile);
@@ -116,13 +116,13 @@ describe('setDefaults', () => {
   test('throw error: listMZML() input type check', async () => {
     testArgv.inputDirectory = 0;
     testArgv.fileList = ['*'];
-    await expect(setDefaults(testArgv)).rejects.toThrowError(
+    await expect(setYargsDefaults(testArgv)).rejects.toThrowError(
       'listMZML(): directory must be of type string',
     );
   });
 
   // Clean up test environment after tests
   afterAll(() => {
-    rmSync('./.tmp/setDefaults/', { recursive: true });
+    rmSync('./.tmp/setYargsDefaults/', { recursive: true });
   });
 });

src/exfilms.js

@@ -15,6 +15,7 @@ import { createDefaultDirectories } from './utils/createDefaultDirectories.js';
 import { prompts } from './utils/inquirerPrompts.js';
 import { parseMZML } from './utils/parseMZML.js';
 import { setForSpectraFiltering } from './utils/setForSpectraFiltering.js';
+import { setInquirerDefaults } from './utils/setInquirerDefaults.js';
 import { writeLog } from './utils/writeLog.js';
 import { yargsCheck } from './utils/yargsCheck.js';
 import { argv } from './utils/yargsConfig.js';
@@ -52,11 +53,8 @@ figlet('ExfilMS', async (err, data) => {
       // If interactive mode
       configParam = await inquirer.prompt(prompts);
 
-      // Configure some parameters to match argv setDefault() settings format
-      configParam.outputFormat = configParam.outputFormat[0];
-      if (configParam.msLevel) {
-        configParam.msLevel = configParam.msLevel.split(' ').map(Number);
-      }
+      // Set up configuration parameters appropriately
+      configParam = await setInquirerDefaults(configParam);
       console.log('');
     } else {
       // Check yargs arguments and set up appropriately

src/utils/setInquirerDefaults.js

@@ -0,0 +1,15 @@
+/**
+ * Set the configuration parameters based on Inquirer input.
+ * @param {Object} configParam Configuration parameters received from the Inquirer prompts
+ * @returns {Promise<Object>} A promise that resolves with an object containing the configuration parameters in the required format for execution.
+ */
+export async function setInquirerDefaults(configParam) {
+  // Set output format as a string instead on an array
+  configParam.outputFormat = configParam.outputFormat[0];
+
+  // Set MS level as a number array instead of a string
+  if (configParam.msLevel) {
+    configParam.msLevel = configParam.msLevel.split(' ').map(Number);
+  }
+  return configParam;
+}

src/utils/setDefaults.js → src/utils/setYargsDefaults.js

@@ -10,12 +10,12 @@ import { join, basename } from 'path';
 import { listMZML } from './listMZML.js';
 
 /**
- * Set the default values for configuration parameters.
+ * Set the configuration parameters based on Yargs input.
  * @param {Yargs} argv Yargs command line arguments.
- * @returns {Promise<Object>} A promise that resolves with an object containing the default values for the configuration parameters.
- * @throws {Error} Throws error if setDefaults() encounters issues in its process.
+ * @returns {Promise<Object>} A promise that resolves with an object containing the configuration parameters in the required format for execution.
+ * @throws {Error} Throws error if setYargsDefaults() encounters issues in its process.
  */
-export async function setDefaults(argv) {
+export async function setYargsDefaults(argv) {
   let configParam = {};
 
   // General config

src/utils/yargsCheck.js

@@ -2,7 +2,7 @@
  * @typedef {import('../typedef/index.mjs').Yargs} Yargs
  */
 
-import { setDefaults } from './setDefaults.js';
+import { setYargsDefaults } from './setYargsDefaults.js';
 
 /**
  * Check if CLI arguments are used correctly
@@ -60,7 +60,7 @@ export async function yargsCheck(argv) {
     );
   } else {
     // Set default values (where required)
-    configParam = await setDefaults(argv);
+    configParam = await setYargsDefaults(argv);
   }
 
   return configParam;