Merge pull request #98 from mcode/mask-mrn-references

Mask MRN when used as the ID of a Patient resource

Author: julianxcarter

src/cli/app.js

@@ -6,6 +6,7 @@ const logger = require('../helpers/logger');
 const { RunInstanceLogger } = require('./RunInstanceLogger');
 const { sendEmailNotification, zipErrors } = require('./emailNotifications');
 const { extractDataForPatients } = require('./mcodeExtraction');
+const { maskMRN } = require('../helpers/patientUtils');
 
 function getConfig(pathToConfig) {
   // Checks pathToConfig points to valid JSON file
@@ -109,6 +110,17 @@ 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) => {
+          maskMRN(bundle);
+        });
+      }
+    }
+
     // Finally, save the data to disk
     const outputPath = './output';
     if (!fs.existsSync(outputPath)) {

src/helpers/patientUtils.js

@@ -1,5 +1,6 @@
 /* eslint-disable no-underscore-dangle */
 const fhirpath = require('fhirpath');
+const shajs = require('sha.js');
 const { extensionArr, dataAbsentReasonExtension } = require('../templates/snippets/extension.js');
 
 // Based on the OMB Ethnicity table found here:http://hl7.org/fhir/us/core/STU3.1/ValueSet-omb-ethnicity-category.html
@@ -147,10 +148,33 @@ 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

@@ -0,0 +1,30 @@
+{
+    "resourceType": "Bundle",
+    "type": "collection",
+    "entry": [
+        {
+            "fullUrl": "urn:uuid:123",
+            "resource": {
+                "resourceType": "Patient",
+                "id": "123"
+                
+            }
+        },
+        {
+            "resource": {
+                "subject": {
+                    "reference": "urn:uuid:123",
+                    "type": "Patient"
+                }
+            }
+        },
+        {
+            "resource": {
+                "individual": {
+                    "reference": "urn:uuid:123",
+                    "type": "Patient"
+                }
+            }
+        }
+    ]
+}

test/helpers/patientUtils.test.js

@@ -1,9 +1,11 @@
 const _ = require('lodash');
+const shajs = require('sha.js');
 const {
-  getEthnicityDisplay, getRaceCodesystem, getRaceDisplay, getPatientName, maskPatientData,
+  getEthnicityDisplay, getRaceCodesystem, getRaceDisplay, getPatientName, maskPatientData, maskMRN,
 } = 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', () => {
@@ -101,4 +103,18 @@ 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();
+    });
+  });
 });