Merge pull request #124 from mcode/patient-csv-util

Add helper for parsing patient CSV ids with BOMs

Author: mgramigna

src/cli/app.js

@@ -1,4 +1,3 @@
-const parse = require('csv-parse/lib/sync');
 const fs = require('fs');
 const path = require('path');
 const moment = require('moment');
@@ -7,6 +6,7 @@ const { RunInstanceLogger } = require('./RunInstanceLogger');
 const { sendEmailNotification, zipErrors } = require('./emailNotifications');
 const { extractDataForPatients } = require('./mcodeExtraction');
 const { maskMRN } = require('../helpers/patientUtils');
+const { parsePatientIds } = require('../helpers/appUtils');
 
 function getConfig(pathToConfig) {
   // Checks pathToConfig points to valid JSON file
@@ -82,8 +82,7 @@ async function mcodeApp(Client, fromDate, toDate, pathToConfig, pathToRunLogs, d
   await mcodeClient.init();
 
   // Parse CSV for list of patient mrns
-  const patientIdsCsvPath = path.resolve(config.patientIdCsvPath);
-  const patientIds = parse(fs.readFileSync(patientIdsCsvPath, 'utf8'), { columns: true }).map((row) => row.mrn);
+  const patientIds = parsePatientIds(config.patientIdCsvPath);
 
   // Get RunInstanceLogger for recording new runs and inferring dates from previous runs
   const runLogger = allEntries ? null : new RunInstanceLogger(pathToRunLogs);

src/helpers/appUtils.js

@@ -0,0 +1,30 @@
+const fs = require('fs');
+const path = require('path');
+const parse = require('csv-parse/lib/sync');
+
+/**
+ * Parses a provided CSV with MRN column into string array of IDs
+ *
+ * @param {string} pathToCSV filePath to the CSV content to be parsed to get IDs
+ * @returns array of parsed IDs from the CSV
+ */
+function parsePatientIds(pathToCSV) {
+  // Parse CSV for list of patient IDs
+  const patientIdsCsvPath = path.resolve(pathToCSV);
+  const patientIds = parse(fs.readFileSync(patientIdsCsvPath, 'utf8'), {
+    columns: (header) => header.map((column) => column.toLowerCase()),
+    bom: true,
+  }).map((row) => {
+    if (!row.mrn) {
+      throw new Error(`${pathToCSV} has no "mrn" column`);
+    }
+
+    return row.mrn;
+  });
+
+  return patientIds;
+}
+
+module.exports = {
+  parsePatientIds,
+};

src/index.js

@@ -66,12 +66,14 @@ const { getDiseaseStatusCode, getDiseaseStatusEvidenceCode, mEpochToDate } = req
 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');
 
 module.exports = {
   // CLI Related utilities
-  mcodeApp,
   RunInstanceLogger,
   extractDataForPatients,
+  mcodeApp,
+  parsePatientIds,
   sendEmailNotification,
   zipErrors,
   // Extractors and Clients

test/helpers/appUtils.test.js

@@ -0,0 +1,24 @@
+const path = require('path');
+const { parsePatientIds } = require('../../src/helpers/appUtils');
+
+const MOCK_VALID_ID_CSV = path.join(__dirname, './fixtures/valid-mrns.csv');
+
+// Has no MRN column
+const MOCK_INVALID_ID_CSV = path.join(__dirname, './fixtures/invalid-mrns.csv');
+
+describe('appUtils', () => {
+  describe('parsePatientIds', () => {
+    test('valid path should parse content', () => {
+      const expectedIds = ['123', '456', '789'];
+      const ids = parsePatientIds(MOCK_VALID_ID_CSV);
+
+      // Should get every MRN
+      expect(ids).toHaveLength(expectedIds.length);
+      expect(ids).toEqual(expectedIds);
+    });
+
+    test('invalid path should throw error', () => {
+      expect(() => parsePatientIds(MOCK_INVALID_ID_CSV)).toThrowError();
+    });
+  });
+});

test/helpers/fixtures/invalid-mrns.csv

@@ -0,0 +1,4 @@
+not-mrn
+123
+456
+789

test/helpers/fixtures/valid-mrns.csv

@@ -0,0 +1,4 @@
+mrn
+123
+456
+789