Adding ability to mask fields in Patient resource

src/extractors/CSVPatientExtractor.js

@@ -2,7 +2,8 @@ const { generateMcodeResources } = require('../templates');
 const { BaseCSVExtractor } = require('./BaseCSVExtractor');
 const { getEthnicityDisplay,
   getRaceCodesystem,
-  getRaceDisplay } = require('../helpers/patientUtils');
+  getRaceDisplay,
+  maskPatientData } = require('../helpers/patientUtils');
 const logger = require('../helpers/logger');
 const { CSVPatientSchema } = require('../helpers/schemas/csv');
 
@@ -39,8 +40,9 @@ function joinAndReformatData(patientData) {
 }
 
 class CSVPatientExtractor extends BaseCSVExtractor {
-  constructor({ filePath }) {
+  constructor({ filePath, mask = [] }) {
     super({ filePath, csvSchema: CSVPatientSchema });
+    this.mask = mask;
   }
 
   async getPatientData(mrn) {
@@ -58,7 +60,11 @@ class CSVPatientExtractor extends BaseCSVExtractor {
     const packagedPatientData = joinAndReformatData(patientData);
 
     // 3. Generate FHIR Resources
-    return generateMcodeResources('Patient', packagedPatientData);
+    const bundle = generateMcodeResources('Patient', packagedPatientData);
+
+    // mask fields in the patient data if specified in mask array
+    if (this.mask.length > 0) maskPatientData(bundle, this.mask);
+    return bundle;
   }
 }
 

src/extractors/FHIRPatientExtractor.js

@@ -1,9 +1,11 @@
 const { BaseFHIRExtractor } = require('./BaseFHIRExtractor');
+const { maskPatientData } = require('../helpers/patientUtils.js');
 
 class FHIRPatientExtractor extends BaseFHIRExtractor {
-  constructor({ baseFhirUrl, requestHeaders, version }) {
+  constructor({ baseFhirUrl, requestHeaders, version, mask = [] }) {
     super({ baseFhirUrl, requestHeaders, version });
     this.resourceType = 'Patient';
+    this.mask = mask;
   }
 
   // Override default behavior for PatientExtractor; just use MRN directly
@@ -13,6 +15,12 @@ class FHIRPatientExtractor extends BaseFHIRExtractor {
       identifier: `MRN|${mrn}`,
     };
   }
+
+  async get(argumentObject) {
+    const bundle = await super.get(argumentObject);
+    if (this.mask.length > 0) maskPatientData(bundle, this.mask);
+    return bundle;
+  }
 }
 
 module.exports = {

src/helpers/patientUtils.js

@@ -1,3 +1,7 @@
+/* eslint-disable no-underscore-dangle */
+const fhirpath = require('fhirpath');
+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
 const ethnicityCodeToDisplay = {
   '2135-2': 'Hispanic or Latino',
@@ -65,12 +69,88 @@ function getRaceDisplay(code) {
  * @return {string} concatenated string of name values
  */
 function getPatientName(name) {
-  return `${name[0].given.join(' ')} ${name[0].family}`;
+  return ('extension' in name[0]) ? 'masked' : `${name[0].given.join(' ')} ${name[0].family}`;
+}
+
+/**
+ * Mask fields in a Patient resource with
+ * dataAbsentReason extension with value 'masked'
+ * @param {Object} bundle a FHIR bundle with a Patient resource
+ * @param {Array} mask an array of fields to mask. Values can be:
+ * ['gender','mrn','name','address','birthDate','language','ethnicity','birthsex','race']
+ */
+function maskPatientData(bundle, mask) {
+  // get Patient resource from bundle
+  const patient = fhirpath.evaluate(
+    bundle,
+    'Bundle.entry.where(resource.resourceType=\'Patient\').resource,first()',
+  )[0];
+
+  const validFields = ['gender', 'mrn', 'name', 'address', 'birthDate', 'language', 'ethnicity', 'birthsex', 'race'];
+  const masked = extensionArr(dataAbsentReasonExtension('masked'));
+
+  mask.forEach((field) => {
+    if (!validFields.includes(field)) {
+      throw Error(`'${field}' is not a field that can be masked. Patient will only be extracted if all mask fields are valid. Valid fields include: Valid fields include: ${validFields.join(', ')}`);
+    }
+    // must check if the field exists in the patient resource, so we don't add unnecessary dataAbsent extensions
+    if (field === 'gender' && 'gender' in patient) {
+      delete patient.gender;
+      // an underscore is added when a primitive type is being replaced by an object (extension)
+      patient._gender = masked;
+    } else if (field === 'mrn' && 'identifier' in patient) {
+      patient.identifier = [masked];
+    } else if (field === 'name' && 'name' in patient) {
+      patient.name = [masked];
+    } else if (field === 'address' && 'address' in patient) {
+      patient.address = [masked];
+    } else if (field === 'birthDate' && 'birthDate' in patient) {
+      delete patient.birthDate;
+      patient._birthDate = masked;
+    } else if (field === 'language') {
+      if ('communication' in patient && 'language' in patient.communication[0]) {
+        patient.communication[0].language = masked;
+      }
+    } else if (field === 'birthsex') {
+      // fields that are extensions need to be differentiated by URL using fhirpath
+      const birthsex = fhirpath.evaluate(
+        patient,
+        'Patient.extension.where(url=\'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex\')',
+      );
+      // fhirpath.evaluate will return [] if there is no extension with the given URL
+      // so checking if the result is [] checks if the field exists to be masked
+      if (birthsex !== []) {
+        delete birthsex[0].valueCode;
+        birthsex[0]._valueCode = masked;
+      }
+    } else if (field === 'race') {
+      const race = fhirpath.evaluate(
+        patient,
+        'Patient.extension.where(url=\'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race\')',
+      );
+      if (race !== []) {
+        race[0].extension[0].valueCoding = masked;
+        delete race[0].extension[1].valueString;
+        race[0].extension[1]._valueString = masked;
+      }
+    } else if (field === 'ethnicity') {
+      const ethnicity = fhirpath.evaluate(
+        patient,
+        'Patient.extension.where(url=\'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity\')',
+      );
+      if (ethnicity !== []) {
+        ethnicity[0].extension[0].valueCoding = masked;
+        delete ethnicity[0].extension[1].valueString;
+        ethnicity[0].extension[1]._valueString = masked;
+      }
+    }
+  });
 }
 
 module.exports = {
   getEthnicityDisplay,
   getRaceCodesystem,
   getRaceDisplay,
   getPatientName,
+  maskPatientData,
 };

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

@@ -0,0 +1,138 @@
+{
+    "resourceType": "Bundle",
+    "type": "collection",
+    "entry": [
+        {
+            "fullUrl": "urn:uuid:119147111821125",
+            "resource": {
+                "resourceType": "Patient",
+                "id": "119147111821125",
+                "identifier": [
+                    {
+                        "extension": [
+                            {
+                                "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                "valueCode": "masked"
+                            }
+                        ]
+                    }
+                ],
+                "name": [
+                    {
+                        "extension": [
+                            {
+                                "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                "valueCode": "masked"
+                            }
+                        ]
+                    }
+                ],
+                "address": [
+                    {
+                        "extension": [
+                            {
+                                "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                "valueCode": "masked"
+                            }
+                        ]
+                    }
+                ],
+                "communication": [
+                    {
+                        "language": {
+                            "extension": [
+                                {
+                                    "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                    "valueCode": "masked"
+                                }
+                            ]
+                        }
+                    }
+                ],
+                "extension": [
+                    {
+                        "extension": [
+                            {
+                                "url": "ombCategory",
+                                "valueCoding": {
+                                    "extension": [
+                                        {
+                                            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                            "valueCode": "masked"
+                                        }
+                                    ]
+                                }
+                            },
+                            {
+                                "url": "text",
+                                "_valueString": {
+                                    "extension": [
+                                        {
+                                            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                            "valueCode": "masked"
+                                        }
+                                    ]
+                                }
+                            }
+                        ],
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
+                    },
+                    {
+                        "extension": [
+                            {
+                                "url": "ombCategory",
+                                "valueCoding": {
+                                    "extension": [
+                                        {
+                                            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                            "valueCode": "masked"
+                                        }
+                                    ]
+                                }
+                            },
+                            {
+                                "url": "text",
+                                "_valueString": {
+                                    "extension": [
+                                        {
+                                            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                            "valueCode": "masked"
+                                        }
+                                    ]
+                                }
+                            }
+                        ],
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
+                    },
+                    {
+                        "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
+                        "_valueCode": {
+                            "extension": [
+                                {
+                                    "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                                    "valueCode": "masked"
+                                }
+                            ]
+                        }
+                    }
+                ],
+                "_gender": {
+                    "extension": [
+                        {
+                            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                            "valueCode": "masked"
+                        }
+                    ]
+                },
+                "_birthDate": {
+                    "extension": [
+                        {
+                            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+                            "valueCode": "masked"
+                        }
+                    ]
+                }
+            }
+        }
+    ]
+}

test/helpers/patientUtils.test.js

@@ -1,5 +1,9 @@
-const { getEthnicityDisplay, getRaceCodesystem, getRaceDisplay, getPatientName } = require('../../src/helpers/patientUtils');
-
+const _ = require('lodash');
+const {
+  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');
 
 describe('PatientUtils', () => {
   describe('getEthnicityDisplay', () => {
@@ -79,4 +83,22 @@ describe('PatientUtils', () => {
       expect(getPatientName(name)).toBe(expectedConcatenatedName);
     });
   });
+  describe('maskPatientData', () => {
+    test('bundle should remain the same if no fields are specified to be masked', () => {
+      const bundle = _.cloneDeep(examplePatient);
+      maskPatientData(bundle, []);
+      expect(bundle).toEqual(examplePatient);
+    });
+
+    test('bundle should be modified to have dataAbsentReason for all fields specified in mask', () => {
+      const bundle = _.cloneDeep(examplePatient);
+      maskPatientData(bundle, ['gender', 'mrn', 'name', 'address', 'birthDate', 'language', 'ethnicity', 'birthsex', 'race']);
+      expect(bundle).toEqual(exampleMaskedPatient);
+    });
+
+    test('should throw error when provided an invalid field to mask', () => {
+      const bundle = _.cloneDeep(examplePatient);
+      expect(() => maskPatientData(bundle, ['this is an invalid field', 'mrn'])).toThrowError();
+    });
+  });
 });