Created the application folder

README.md

@@ -189,11 +189,11 @@ This framework consists of three key components: Extractors, Modules and Templat
 
 ### Glossary
 
-![Image detailing exact definitions of what is meant by Client, Extractor, Module and Template](./docs/diagrams/20_11_23_steam-terminology-breakdown.png)
+![Image detailing exact definitions of what is meant by Client, Extractor, Module and Template](./docs/diagrams/steam-terminology-breakdown.png)
 
 ### High Level Diagram
 
-![High-level architecture diagram, detailing exactly how Clients, Extractors, Modules, Templates and various web services communicate with one another](./docs/diagrams/20_11_23_steam-high-level-arch.png)
+![High-level architecture diagram, detailing exactly how Clients, Extractors, Modules, Templates and various web services communicate with one another](./docs/diagrams/steam-high-level-arch.png)
 
 These diagrams can be modified by updating the XML files in the `/docs/diagrams/` directory using draw.io or a company licensed equivalent.
 

docs/diagrams/archive/21_06_11_steam-high-level-arch.xml

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docs/diagrams/steam-high-level-arch.xml

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docs/diagrams/steam-terminology-breakdown.xml

@@ -0,0 +1 @@
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src/cli/app.js → src/application/app.js

@@ -2,9 +2,9 @@ const fs = require('fs');
 const path = require('path');
 const moment = require('moment');
 const logger = require('../helpers/logger');
-const { RunInstanceLogger } = require('./RunInstanceLogger');
-const { sendEmailNotification, zipErrors } = require('./emailNotifications');
-const { extractDataForPatients } = require('./mcodeExtraction');
+const { RunInstanceLogger } = require('./tools/RunInstanceLogger');
+const { sendEmailNotification, zipErrors } = require('./tools/emailNotifications');
+const { extractDataForPatients } = require('./tools/mcodeExtraction');
 const { maskMRN } = require('../helpers/patientUtils');
 const { parsePatientIds } = require('../helpers/appUtils');
 

src/application/index.js

@@ -0,0 +1,12 @@
+const { mcodeApp } = require('./app');
+const { RunInstanceLogger } = require('./tools/RunInstanceLogger');
+const { sendEmailNotification, zipErrors } = require('./tools/emailNotifications');
+const { extractDataForPatients } = require('./tools/mcodeExtraction');
+
+module.exports = {
+  mcodeApp,
+  RunInstanceLogger,
+  extractDataForPatients,
+  sendEmailNotification,
+  zipErrors,
+};

src/cli/RunInstanceLogger.js → src/application/tools/RunInstanceLogger.js

@@ -1,7 +1,7 @@
 const path = require('path');
 const moment = require('moment');
 const fs = require('fs');
-const logger = require('../helpers/logger');
+const logger = require('../../helpers/logger');
 
 // Sort Log records by `dateRun`, more recent (larger) dates to least recent (smaller)
 function logSorter(a, b) {

src/cli/emailNotifications.js → src/application/tools/emailNotifications.js

@@ -1,5 +1,5 @@
 const nodemailer = require('nodemailer');
-const logger = require('../helpers/logger');
+const logger = require('../../helpers/logger');
 
 function zipErrors(...allErrorSources) {
   // NOTE: assumes each error object is a k-v pair: k is the MRN-id CSV row of the patient, v is an [errors] for that patient at some pipeline step

src/cli/mcodeExtraction.js → src/application/tools/mcodeExtraction.js

@@ -1,5 +1,5 @@
-const logger = require('../helpers/logger');
-const { getResourceCountInBundle } = require('../helpers/fhirUtils');
+const logger = require('../../helpers/logger');
+const { getResourceCountInBundle } = require('../../helpers/fhirUtils');
 
 async function extractDataForPatients(patientIds, mcodeClient, fromDate, toDate) {
   // Using an initialized mcodeClient, extract data for patient ids in the appropriate toDate-fromDate range

src/cli/cli.js

@@ -3,7 +3,7 @@ const path = require('path');
 const program = require('commander');
 const { MCODEClient } = require('../client/MCODEClient');
 const logger = require('../helpers/logger');
-const { mcodeApp } = require('./app');
+const { mcodeApp } = require('../application');
 
 const defaultPathToConfig = path.join('config', 'csv.config.json');
 const defaultPathToRunLogs = path.join('logs', 'run-logs.json');

src/index.js

@@ -7,7 +7,7 @@ const {
   extractDataForPatients,
   sendEmailNotification,
   zipErrors,
-} = require('./cli');
+} = require('./application');
 const {
   BaseFHIRExtractor,
   CSVAdverseEventExtractor,

test/cli/app.test.js → test/application/app.test.js

@@ -2,15 +2,15 @@ const fs = require('fs');
 const rewire = require('rewire');
 const testConfig = require('./fixtures/test-config.json');
 
-const app = rewire('../../src/cli/app.js');
+const app = rewire('../../src/application/app.js');
 const getConfig = app.__get__('getConfig');
 const checkInputAndConfig = app.__get__('checkInputAndConfig');
 const checkLogFile = app.__get__('checkLogFile');
 const getEffectiveFromDate = app.__get__('getEffectiveFromDate');
 
 describe('App Tests', () => {
   describe('getConfig', () => {
-    const pathToConfig = 'test/cli/fixtures/test-config.json';
+    const pathToConfig = 'test/application/fixtures/test-config.json';
 
     it('should throw error when pathToConfig does not point to valid JSON file.', () => {
       expect(() => getConfig()).toThrowError();

test/cli/emailNotifications.test.js → test/application/emailNotifications.test.js

@@ -1,5 +1,5 @@
 const nodemailer = require('nodemailer');
-const { sendEmailNotification } = require('../../src/cli/emailNotifications');
+const { sendEmailNotification } = require('../../src/application/tools/emailNotifications');
 
 const createTransportSpy = jest.spyOn(nodemailer, 'createTransport');