Merge pull request #137 from mcode/update-mrn-masking

Moving MRN masking to maskPatientData

Author: dmendelowitz

src/application/app.js

@@ -5,7 +5,6 @@ const logger = require('../helpers/logger');
 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');
 const { validateConfig } = require('../helpers/configValidator');
 
@@ -74,23 +73,6 @@ async function mcodeApp(Client, fromDate, toDate, pathToConfig, pathToRunLogs, d
     }
   }
 
-  // check if config specifies that MRN needs to be masked
-  // if it does need to be masked, mask all references to MRN outside of the patient resource
-  const patientConfig = config.extractors.find((e) => e.type === 'CSVPatientExtractor');
-  if (patientConfig && ('constructorArgs' in patientConfig && 'mask' in patientConfig.constructorArgs)) {
-    if (patientConfig.constructorArgs.mask.includes('mrn')) {
-      extractedData.forEach((bundle, i) => {
-        // NOTE: This may fail to mask MRN-related properties on non-patient resources
-        //       Need to investigate further.
-        try {
-          maskMRN(bundle);
-        } catch (e) {
-          logger.error(`Bundle ${i + 1}: ${e.message}`);
-        }
-      });
-    }
-  }
-
   return extractedData;
 }
 

src/helpers/patientUtils.js

@@ -103,6 +103,14 @@ function maskPatientData(bundle, mask) {
       delete patient._gender; // gender may have a dataAbsentReason on it for 'unknown' data, but we'll still want to mask it
       patient._gender = masked;
     } else if (field === 'mrn' && 'identifier' in patient) {
+      // id and fullURL still need valid values, so we use a hashed version of MRN instead of dataAbsentReason
+      const maskedMRN = shajs('sha256').update(patient.id).digest('hex');
+      patient.id = maskedMRN;
+      const patientEntry = fhirpath.evaluate(
+        bundle,
+        'Bundle.entry.where(resource.resourceType=\'Patient\')',
+      )[0];
+      patientEntry.fullUrl = `urn:uuid:${maskedMRN}`;
       patient.identifier = [masked];
     } else if (field === 'name' && 'name' in patient) {
       patient.name = [masked];
@@ -151,33 +159,10 @@ function maskPatientData(bundle, mask) {
   });
 }
 
-/**
- * Mask all references to the MRN used as an id
- * Currently, the MRN appears as an id in 'subject' and 'individual' objects in other resources
- * and in the 'id' and 'fullUrl' fields of the Patient resource.
- * Replaces the MRN with a hash of the MRN
- * @param {Object} bundle a FHIR bundle with a Patient resource and other resources
- */
-function maskMRN(bundle) {
-  const patient = fhirpath.evaluate(bundle, 'Bundle.entry.where(resource.resourceType=\'Patient\')')[0];
-  if (patient === undefined) throw Error('No Patient resource in bundle. Could not mask MRN.');
-  const mrn = patient.resource.id;
-  const masked = shajs('sha256').update(mrn).digest('hex');
-  patient.fullUrl = `urn:uuid:${masked}`;
-  patient.resource.id = masked;
-  const subjects = fhirpath.evaluate(bundle, `Bundle.entry.resource.subject.where(reference='urn:uuid:${mrn}')`);
-  const individuals = fhirpath.evaluate(bundle, `Bundle.entry.resource.individual.where(reference='urn:uuid:${mrn}')`);
-  const mrnOccurrences = subjects.concat(individuals);
-  for (let i = 0; i < mrnOccurrences.length; i += 1) {
-    mrnOccurrences[i].reference = `urn:uuid:${masked}`;
-  }
-}
-
 module.exports = {
   getEthnicityDisplay,
   getRaceCodesystem,
   getRaceDisplay,
   getPatientName,
   maskPatientData,
-  maskMRN,
 };

test/helpers/fixtures/bundle-with-mrn-id.json

@@ -3,10 +3,10 @@
     "type": "collection",
     "entry": [
         {
-            "fullUrl": "urn:uuid:119147111821125",
+            "fullUrl": "urn:uuid:be7e757c18743bf94cee7764b960eb69867b430232f759e706d080604fe416ad",
             "resource": {
                 "resourceType": "Patient",
-                "id": "119147111821125",
+                "id": "be7e757c18743bf94cee7764b960eb69867b430232f759e706d080604fe416ad",
                 "identifier": [
                     {
                         "extension": [

test/helpers/fixtures/masked-patient-bundle.json

@@ -1,11 +1,9 @@
 const _ = require('lodash');
-const shajs = require('sha.js');
 const {
-  getEthnicityDisplay, getRaceCodesystem, getRaceDisplay, getPatientName, maskPatientData, maskMRN,
+  getEthnicityDisplay, getRaceCodesystem, getRaceDisplay, getPatientName, maskPatientData,
 } = require('../../src/helpers/patientUtils');
 const examplePatient = require('../extractors/fixtures/csv-patient-bundle.json');
 const exampleMaskedPatient = require('./fixtures/masked-patient-bundle.json');
-const exampleBundleWithMRN = require('./fixtures/bundle-with-mrn-id.json');
 
 describe('PatientUtils', () => {
   describe('getEthnicityDisplay', () => {
@@ -119,18 +117,4 @@ describe('PatientUtils', () => {
       expect(() => maskPatientData(bundle, ['this is an invalid field', 'mrn'])).toThrowError();
     });
   });
-  describe('maskMRN', () => {
-    test('all occurances of the MRN as an id should be masked by a hashed version', () => {
-      const bundle = _.cloneDeep(exampleBundleWithMRN);
-      const hashedMRN = shajs('sha256').update(bundle.entry[0].resource.id).digest('hex');
-      maskMRN(bundle);
-      expect(bundle.entry[0].resource.id).toEqual(hashedMRN);
-      expect(bundle.entry[0].fullUrl).toEqual(`urn:uuid:${hashedMRN}`);
-      expect(bundle.entry[1].resource.subject.reference).toEqual(`urn:uuid:${hashedMRN}`);
-      expect(bundle.entry[2].resource.individual.reference).toEqual(`urn:uuid:${hashedMRN}`);
-    });
-    test('should throw error when there is no Patient resource in bundle', () => {
-      expect(() => maskMRN({})).toThrowError();
-    });
-  });
 });