Merge pull request #103 from mcode/loosen-required-patient-fields

Loosen required fields for Patient CSV and mark missing required fields

Author: jafeltra

src/extractors/CSVPatientExtractor.js

@@ -14,8 +14,8 @@ function joinAndReformatData(patientData) {
     mrn, familyName, givenName, gender, birthsex, dateOfBirth, race, ethnicity, language, addressLine, city, state, zip,
   } = patientData;
 
-  if (!mrn || !familyName || !givenName || !gender) {
-    throw Error('Missing required field for Patient CSV Extraction. Required values include: mrn, familyName, givenName, gender');
+  if (!mrn) {
+    throw Error('Missing required field for Patient CSV Extraction: mrn');
   }
 
   return {

src/helpers/patientUtils.js

@@ -99,6 +99,9 @@ function maskPatientData(bundle, mask) {
       delete patient.gender;
       // an underscore is added when a primitive type is being replaced by an object (extension)
       patient._gender = masked;
+    } else if (field === 'gender' && '_gender' in patient) {
+      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) {
       patient.identifier = [masked];
     } else if (field === 'name' && 'name' in patient) {
@@ -119,8 +122,8 @@ function maskPatientData(bundle, mask) {
         '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 !== []) {
+      // so checking if the result is an array with anything in it checks if the field exists to be masked
+      if (birthsex.length > 0) {
         delete birthsex[0].valueCode;
         birthsex[0]._valueCode = masked;
       }
@@ -129,7 +132,7 @@ function maskPatientData(bundle, mask) {
         patient,
         'Patient.extension.where(url=\'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race\')',
       );
-      if (race !== []) {
+      if (race.length > 0) {
         race[0].extension[0].valueCoding = masked;
         delete race[0].extension[1].valueString;
         race[0].extension[1]._valueString = masked;
@@ -139,7 +142,7 @@ function maskPatientData(bundle, mask) {
         patient,
         'Patient.extension.where(url=\'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity\')',
       );
-      if (ethnicity !== []) {
+      if (ethnicity.length > 0) {
         ethnicity[0].extension[0].valueCoding = masked;
         delete ethnicity[0].extension[1].valueString;
         ethnicity[0].extension[1]._valueString = masked;

src/helpers/schemas/csv.js

@@ -31,9 +31,9 @@ const CSVConditionSchema = {
 const CSVPatientSchema = {
   headers: [
     { name: 'mrn', required: true },
-    { name: 'familyName', required: true },
-    { name: 'givenName', required: true },
-    { name: 'gender', required: true },
+    { name: 'familyName' },
+    { name: 'givenName' },
+    { name: 'gender' },
     { name: 'birthsex' },
     { name: 'dateOfBirth' },
     { name: 'race' },

src/templates/PatientTemplate.js

@@ -1,4 +1,4 @@
-const { extensionArr, coding, valueX } = require('./snippets');
+const { dataAbsentReasonExtension, extensionArr, coding, valueX } = require('./snippets');
 const { ifAllArgsObj, ifSomeArgsObj } = require('../helpers/templateUtils');
 
 function mrnIdentifierTemplate({ mrn }) {
@@ -73,13 +73,35 @@ function birthDateTemplate({ dateOfBirth }) {
   };
 }
 
+function genderTemplate({ gender }) {
+  if (!gender) {
+    // gender is 1..1 in mCODE
+    return {
+      _gender: extensionArr(dataAbsentReasonExtension('unknown')),
+    };
+  }
+
+  return {
+    gender,
+  };
+}
+
 function nameTemplate({ familyName, givenName }) {
+  if (!familyName && !givenName) {
+    // name is 1..* in mCODE
+    return {
+      name: [
+        extensionArr(dataAbsentReasonExtension('unknown')),
+      ],
+    };
+  }
+
   return {
     name: [
       {
         text: `${givenName} ${familyName}`,
-        family: familyName,
-        given: givenName.split(' '),
+        ...(familyName && { family: familyName }),
+        ...(givenName && { given: givenName.split(' ') }),
       },
     ],
   };
@@ -125,13 +147,13 @@ function languageTemplate({ language }) {
 function patientTemplate({
   id, mrn, familyName, givenName, gender, birthsex, dateOfBirth, language, addressLine, city, state, zip, raceCodesystem, raceCode, raceText, ethnicityCode, ethnicityText,
 }) {
-  if (!(id && mrn && familyName && givenName && gender)) {
-    throw Error('Trying to render a PatientTemplate, but a required argument is missing; ensure that id, mrn, familyName, givenName, and gender are all present');
+  if (!(id && mrn)) {
+    throw Error('Trying to render a PatientTemplate, but a required argument is missing; ensure that id and mrn are both present');
   }
   return {
     resourceType: 'Patient',
     id,
-    gender,
+    ...genderTemplate({ gender }),
     ...mrnIdentifierTemplate({ mrn }),
     ...nameTemplate({ familyName, givenName }),
     ...ifSomeArgsObj(addressTemplate)({ addressLine, city, state, zip }),

test/helpers/patientUtils.test.js

@@ -98,6 +98,22 @@ describe('PatientUtils', () => {
       expect(bundle).toEqual(exampleMaskedPatient);
     });
 
+    test('should mask gender even if it only had an extension', () => {
+      const bundle = _.cloneDeep(examplePatient);
+      delete bundle.entry[0].resource.gender;
+      // eslint-disable-next-line no-underscore-dangle
+      bundle.entry[0].resource._gender = {
+        extension: [
+          {
+            url: 'http://hl7.org/fhir/StructureDefinition/data-absent-reason',
+            valueCode: 'unknown',
+          },
+        ],
+      };
+      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();

test/templates/fixtures/patient-resource.json

@@ -18,11 +18,21 @@
     }
   ],
   "name": [
+    {
+      "extension": [
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+          "valueCode": "unknown"
+        }
+      ]
+    }
+  ],
+  "_gender": {
+    "extension": [
       {
-          "text": "Test Patient",
-          "family": "Patient",
-          "given": [ "Test" ]
+        "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+        "valueCode": "unknown"
       }
-  ],
-  "gender": "female"
+    ]
+  }
 }

test/templates/patient.test.js

@@ -9,9 +9,9 @@ describe('JavaScript Render Patient', () => {
     const PATIENT_VALID_DATA = {
       id: 'SomeId',
       mrn: '1234',
-      familyName: 'Patient',
-      givenName: 'Test',
-      gender: 'female',
+      familyName: null,
+      givenName: null,
+      gender: null,
       birthsex: null,
       dateOfBirth: null,
       language: null,