Skip to content

New options for Patient masking #155

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Dtphelan1 merged 2 commits into from
Oct 5, 2021
Merged

New options for Patient masking #155

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
703c820
Support for new masking options on patient resource, updated readme
julianxcarter Sep 29, 2021
713e4ce
Typo addressed, weird formatting corrected
julianxcarter Oct 5, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ npm start -- --entries-filter --from-date YYYY-MM-DD --to-date YYY-MM-DD --run-l
### Masking Patient Data

Patient data can be masked within the extracted `Patient` resource. When masked, the value of the field will be replaced with a [Data Absent Reason extension](https://www.hl7.org/fhir/extension-data-absent-reason.html) with the code `masked`.
Patient properties that can be masked are: `gender`, `mrn`, `name`, `address`, `birthDate`, `language`, `ethnicity`, `birthsex`, and `race`.
Patient properties that can be masked are: `gender`, `mrn`, `name`, `address`, `birthDate`, `language`, `ethnicity`, `birthsex`, `race`, `telecom`, `multipleBirth`, `photo`, `contact`, `generalPractitioner`, `managingOrganization`, and `link`.
To mask a property, provide an array of the properties to mask in the `constructorArgs` of the Patient extractor. For example, the following configuration can be used to mask `address` and `birthDate`:

```bash
Expand Down
49 changes: 47 additions & 2 deletions src/helpers/patientUtils.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,9 @@ function getPatientName(name) {
* 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']
* 'gender','mrn','name','address','birthDate','language','ethnicity','birthsex',
* 'race', 'telecom', 'multipleBirth', 'photo', 'contact', 'generalPractitioner',
* 'managingOrganization', and 'link'
*/
function maskPatientData(bundle, mask) {
// get Patient resource from bundle
Expand All @@ -87,7 +89,24 @@ function maskPatientData(bundle, mask) {
'Bundle.entry.where(resource.resourceType=\'Patient\').resource,first()',
)[0];

const validFields = ['gender', 'mrn', 'name', 'address', 'birthDate', 'language', 'ethnicity', 'birthsex', 'race'];
const validFields = [
'gender',
'mrn',
'name',
'address',
'birthDate',
'language',
'ethnicity',
'birthsex',
'race',
'telecom',
'multipleBirth',
'photo',
'contact',
'generalPractitioner',
'managingOrganization',
'link',
];
const masked = extensionArr(dataAbsentReasonExtension('masked'));

mask.forEach((field) => {
Expand Down Expand Up @@ -157,6 +176,32 @@ function maskPatientData(bundle, mask) {
delete ethnicity[0].extension[1].valueString;
ethnicity[0].extension[1]._valueString = masked;
}
} else if (field === 'telecom' && 'telecom' in patient) {
delete patient.telecom;
patient.telecom = [masked];
} else if (field === 'multipleBirth') {
if ('multipleBirthBoolean' in patient) {
delete patient.multipleBirthBoolean;
patient._multipleBirthBoolean = masked;
} else if ('multipleBirthInteger' in patient) {
delete patient.multipleBirthInteger;
patient._multipleBirthInteger = masked;
}
} else if (field === 'photo' && 'photo' in patient) {
delete patient.photo;
patient.photo = [masked];
} else if (field === 'contact' && 'contact' in patient) {
delete patient.contact;
patient.contact = [masked];
} else if (field === 'generalPractitioner' && 'generalPractitioner' in patient) {
delete patient.generalPractitioner;
patient.generalPractitioner = [masked];
} else if (field === 'managingOrganization' && 'managingOrganization' in patient) {
delete patient.managingOrganization;
patient.managingOrganization = masked;
} else if (field === 'link' && 'link' in patient) {
delete patient.link;
patient.link = [masked];
}
});
}
Expand Down
165 changes: 165 additions & 0 deletions test/extractors/fixtures/extended-patient-bundle.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,165 @@
{
"resourceType": "Bundle",
"type": "collection",
"entry": [
{
"fullUrl": "urn:uuid:119147111821125",
"resource": {
"resourceType": "Patient",
"id": "119147111821125",
"identifier": [
{
"type": {
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0203",
"code": "MR",
"display": "Medical Record Number"
}
],
"text": "Medical Record Number"
},
"system": "http://example.com/system/mrn",
"value": "119147111821125"
}
],
"name": [
{
"text": "Archy Marshall",
"family": "Marshall",
"given": [
"Archy"
]
}
],
"gender": "male",
"birthDate": "1994-08-24",
"address": [
{
"line": [
"57 Adams St"
],
"city": "New Rochelle",
"state": "NY",
"postalCode": "10801",
"country": "US"
}
],
"telecom": [
{
"system" : "phone",
"value" : "555-555-5555",
"use" : "home"
},
{
"system" : "email",
"value" : "[email protected]"
}
],
"managingOrganization": {
"reference": "Organization/2.16.840.1.113883.19.5",
"display": "Good Health Clinic"
},
"generalPractitioner": [
{
"reference": "Practitioner/example",
"display": "Dr Adam Careful"
}
],
"contact": [
{
"relationship": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0131",
"code": "C"
}
]
}
],
"name": {
"family": "Chalmers",
"given": [
"Peter",
"James"
]
},
"telecom": [
{
"system": "phone",
"value": "(03) 5555 6473",
"use": "work"
}
]
}
],
"photo": [
{
"contentType": "image/gif",
"data": "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"
}
],
"link": [
{
"other": {
"reference": "Patient/pat2"
},
"type": "seealso"
}
],
"multipleBirthInteger": 2,
"communication": [
{
"language": {
"coding": [
{
"system": "urn:ietf:bcp:47",
"code": "en"
}
]
}
}
],
"extension": [
{
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"code": "1002-5",
"system": "urn:oid:2.16.840.1.113883.6.238"
}
},
{
"url": "text",
"valueString": "American Indian or Alaska Native"
}
],
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
},
{
"extension": [
{
"url": "ombCategory",
"valueCoding": {
"code": "2186-5",
"system": "urn:oid:2.16.840.1.113883.6.238"
}
},
{
"url": "text",
"valueString": "Non Hispanic or Latino"
}
],
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
"valueCode": "male"
}
]
}
}
]
}
70 changes: 68 additions & 2 deletions test/helpers/fixtures/masked-patient-bundle.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -131,8 +131,74 @@
"valueCode": "masked"
}
]
}
},
"telecom": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
}
],
"_multipleBirthInteger": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
},
"contact": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
}
],
"generalPractitioner": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
}
],
"managingOrganization": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
},
"link": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
}
],
"photo": [
{
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
}
]
}
}
]
}
}
40 changes: 37 additions & 3 deletions test/helpers/patientUtils.test.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ const _ = require('lodash');
const {
getEthnicityDisplay, getRaceCodesystem, getRaceDisplay, getPatientName, maskPatientData,
} = require('../../src/helpers/patientUtils');
const examplePatient = require('../extractors/fixtures/csv-patient-bundle.json');
const examplePatient = require('../extractors/fixtures/extended-patient-bundle.json');
const exampleMaskedPatient = require('./fixtures/masked-patient-bundle.json');

describe('PatientUtils', () => {
Expand Down Expand Up @@ -92,7 +92,24 @@ describe('PatientUtils', () => {

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']);
maskPatientData(bundle, [
'gender',
'mrn',
'name',
'address',
'birthDate',
'language',
'ethnicity',
'birthsex',
'race',
'telecom',
'multipleBirth',
'photo',
'contact',
'generalPractitioner',
'managingOrganization',
'link',
]);
expect(bundle).toEqual(exampleMaskedPatient);
});

Expand All @@ -108,7 +125,24 @@ describe('PatientUtils', () => {
},
],
};
maskPatientData(bundle, ['gender', 'mrn', 'name', 'address', 'birthDate', 'language', 'ethnicity', 'birthsex', 'race']);
maskPatientData(bundle, [
'gender',
'mrn',
'name',
'address',
'birthDate',
'language',
'ethnicity',
'birthsex',
'race',
'telecom',
'multipleBirth',
'photo',
'contact',
'generalPractitioner',
'managingOrganization',
'link',
]);
expect(bundle).toEqual(exampleMaskedPatient);
});

Expand Down