Merge pull request #158 from mcode/masking-all-option

"all" option for Patient masking now supported in the config

Author: jafeltra

README.md

@@ -148,6 +148,18 @@ To mask a property, provide an array of the properties to mask in the `construct
 }
 ```
 
+Alternatively, providing a string with a value of `all` in the `constructorArgs` of the Patient extractor will mask all of the supported properties listed above. The following configuration can be used to mask all properties of the `Patient` resource, rather than listing each individual property:
+
+```bash
+{
+  "label": "patient",
+  "type": "CSVPatientExtractor",
+  "constructorArgs": {
+    "filePath": "./data/patient-information.csv"
+    "mask": "all"
+  }
+}
+```
 ### Extraction Date Range
 
 The mCODE Extraction Client will extract all data that is provided in the CSV files by default, regardless of any dates associated with each row of data. It is recommended that any required date filtering is performed outside of the scope of this client.

src/extractors/CSVPatientExtractor.js

@@ -87,8 +87,10 @@ class CSVPatientExtractor extends BaseCSVExtractor {
     // 3. Generate FHIR Resources
     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);
+    // mask specified fields in the patient data
+    if (typeof this.mask === 'string' && this.mask === 'all') {
+      maskPatientData(bundle, [], true);
+    } else if (this.mask.length > 0) maskPatientData(bundle, this.mask);
     return bundle;
   }
 }

src/extractors/FHIRPatientExtractor.js

@@ -18,7 +18,10 @@ class FHIRPatientExtractor extends BaseFHIRExtractor {
 
   async get(argumentObject) {
     const bundle = await super.get(argumentObject);
-    if (this.mask.length > 0) maskPatientData(bundle, this.mask);
+    // mask specified fields in the patient data
+    if (typeof this.mask === 'string' && this.mask === 'all') {
+      maskPatientData(bundle, [], true);
+    } else if (this.mask.length > 0) maskPatientData(bundle, this.mask);
     return bundle;
   }
 }

src/helpers/configUtils.js

@@ -34,6 +34,10 @@ ajv.addFormat('email-with-name', {
     return emailRegex.test(email.trim().split(' ').pop());
   },
 });
+ajv.addFormat('mask-all', {
+  type: 'string',
+  validate: (string) => string === 'all',
+});
 
 const validator = ajv.addSchema(configSchema, 'config');
 

src/helpers/patientUtils.js

@@ -81,8 +81,9 @@ function getPatientName(name) {
  * 'gender','mrn','name','address','birthDate','language','ethnicity','birthsex',
  * 'race', 'telecom', 'multipleBirth', 'photo', 'contact', 'generalPractitioner',
  * 'managingOrganization', and 'link'
+ * @param {Boolean} maskAll indicates that all supported fields should be masked, defaults to false
  */
-function maskPatientData(bundle, mask) {
+function maskPatientData(bundle, mask, maskAll = false) {
   // get Patient resource from bundle
   const patient = fhirpath.evaluate(
     bundle,
@@ -109,7 +110,9 @@ function maskPatientData(bundle, mask) {
   ];
   const masked = extensionArr(dataAbsentReasonExtension('masked'));
 
-  mask.forEach((field) => {
+  const maskingFields = maskAll ? validFields : mask;
+
+  maskingFields.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(', ')}`);
     }

src/helpers/schemas/config.schema.json

@@ -128,10 +128,18 @@
         },
         "mask": {
           "title": "Masked Fields",
-          "type": "array",
-          "items": {
-            "type": "string"
-          }
+          "oneOf": [
+            {
+              "type": "string",
+              "format": "mask-all"
+            },
+            {
+              "type": "array",
+              "items": {
+                "type": "string"
+              }
+            }
+          ]
         }
       }
     }

test/helpers/patientUtils.test.js

@@ -113,6 +113,12 @@ describe('PatientUtils', () => {
       expect(bundle).toEqual(exampleMaskedPatient);
     });
 
+    test('bundle should be modified to have dataAbsentReason for all fields when the maskAll flag is provided', () => {
+      const bundle = _.cloneDeep(examplePatient);
+      maskPatientData(bundle, [], true);
+      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;