Merge pull request #142 from mcode/config-as-object

Moving config file parsing from app to CLI

Author: Dtphelan1

src/application/app.js

@@ -1,22 +1,10 @@
-const fs = require('fs');
-const path = require('path');
 const moment = require('moment');
 const logger = require('../helpers/logger');
 const { RunInstanceLogger } = require('./tools/RunInstanceLogger');
 const { sendEmailNotification, zipErrors } = require('./tools/emailNotifications');
 const { extractDataForPatients } = require('./tools/mcodeExtraction');
 const { parsePatientIds } = require('../helpers/appUtils');
-const { validateConfig } = require('../helpers/configValidator');
-
-function getConfig(pathToConfig) {
-  // Checks pathToConfig points to valid JSON file
-  const fullPath = path.resolve(pathToConfig);
-  try {
-    return JSON.parse(fs.readFileSync(fullPath));
-  } catch (err) {
-    throw new Error(`The provided filepath to a configuration file ${pathToConfig}, full path ${fullPath} did not point to a valid JSON file.`);
-  }
-}
+const { validateConfig } = require('../helpers/configUtils');
 
 function checkInputAndConfig(config, fromDate, toDate) {
   // Check input args and needed config variables based on client being used
@@ -33,9 +21,8 @@ function checkInputAndConfig(config, fromDate, toDate) {
   }
 }
 
-async function mcodeApp(Client, fromDate, toDate, pathToConfig, pathToRunLogs, debug, allEntries) {
+async function mcodeApp(Client, fromDate, toDate, config, pathToRunLogs, debug, allEntries) {
   logger.level = debug ? 'debug' : 'info';
-  const config = getConfig(pathToConfig);
   checkInputAndConfig(config, fromDate, toDate);
 
   // Create and initialize client

src/cli/cli.js

@@ -4,6 +4,7 @@ const program = require('commander');
 const { MCODEClient } = require('../client/MCODEClient');
 const logger = require('../helpers/logger');
 const { mcodeApp } = require('../application');
+const { getConfig } = require('../helpers/configUtils');
 
 const defaultPathToConfig = path.join('config', 'csv.config.json');
 const defaultPathToRunLogs = path.join('logs', 'run-logs.json');
@@ -27,7 +28,8 @@ const allEntries = !entriesFilter;
 
 async function runApp() {
   try {
-    const extractedData = await mcodeApp(MCODEClient, fromDate, toDate, configFilepath, runLogFilepath, debug, allEntries);
+    const config = getConfig(configFilepath);
+    const extractedData = await mcodeApp(MCODEClient, fromDate, toDate, config, runLogFilepath, debug, allEntries);
 
     // Finally, save the data to disk
     const outputPath = './output';

src/helpers/configValidator.js renamed to src/helpers/configUtils.js

@@ -1,8 +1,20 @@
+const fs = require('fs');
+const path = require('path');
 const Ajv = require('ajv');
 const metaSchema = require('ajv/lib/refs/json-schema-draft-06.json');
 const logger = require('./logger');
 const configSchema = require('./schemas/config.schema.json');
 
+function getConfig(pathToConfig) {
+  // Checks pathToConfig points to valid JSON file
+  const fullPath = path.resolve(pathToConfig);
+  try {
+    return JSON.parse(fs.readFileSync(fullPath));
+  } catch (err) {
+    throw new Error(`The provided filepath to a configuration file ${pathToConfig}, full path ${fullPath} did not point to a valid JSON file.`);
+  }
+}
+
 const ajv = new Ajv({ logger: false, allErrors: true });
 ajv.addMetaSchema(metaSchema);
 
@@ -34,5 +46,6 @@ function validateConfig(config) {
 }
 
 module.exports = {
+  getConfig,
   validateConfig,
 };

src/index.js

@@ -67,6 +67,7 @@ const { formatDate, formatDateTime } = require('./helpers/dateUtils');
 const { lowercaseLookupQuery, createLowercaseLookup, createInvertedLookup } = require('./helpers/lookupUtils');
 const { getConditionEntriesFromContext, getConditionsFromContext, getEncountersFromContext, getPatientFromContext } = require('./helpers/contextUtils');
 const { parsePatientIds } = require('./helpers/appUtils');
+const { getConfig, validateConfig } = require('./helpers/configUtils');
 
 module.exports = {
   // CLI Related utilities
@@ -76,6 +77,8 @@ module.exports = {
   parsePatientIds,
   sendEmailNotification,
   zipErrors,
+  getConfig,
+  validateConfig,
   // Extractors and Clients
   BaseClient,
   BaseFHIRExtractor,

test/application/app.test.js

@@ -1,24 +1,9 @@
 const rewire = require('rewire');
-const testConfig = require('./fixtures/test-config.json');
 
 const app = rewire('../../src/application/app.js');
-const getConfig = app.__get__('getConfig');
 const checkInputAndConfig = app.__get__('checkInputAndConfig');
 
 describe('App Tests', () => {
-  describe('getConfig', () => {
-    const pathToConfig = 'test/application/fixtures/test-config.json';
-
-    it('should throw error when pathToConfig does not point to valid JSON file.', () => {
-      expect(() => getConfig()).toThrowError();
-    });
-
-    it('should return test config', () => {
-      const config = getConfig(pathToConfig);
-      expect(config).toEqual(testConfig);
-    });
-  });
-
   describe('checkInputAndConfig', () => {
     const config = { patientIdCsvPath: '', extractors: [] };
     it('should throw error when fromDate is invalid.', () => {

test/helpers/configValidator.test.js renamed to test/helpers/configUtils.test.js

@@ -1,4 +1,18 @@
-const { validateConfig } = require('../../src/helpers/configValidator.js');
+const { validateConfig, getConfig } = require('../../src/helpers/configUtils.js');
+const testConfig = require('./fixtures/test-config.json');
+
+describe('getConfig', () => {
+  const pathToConfig = 'test/helpers/fixtures/test-config.json';
+
+  it('should throw error when pathToConfig does not point to valid JSON file.', () => {
+    expect(() => getConfig()).toThrowError();
+  });
+
+  it('should return test config', () => {
+    const config = getConfig(pathToConfig);
+    expect(config).toEqual(testConfig);
+  });
+});
 
 describe('validateConfig', () => {
   const missingPropertyConfig = { patientIdCsvPath: '' };