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Creating new mask field 'genderAndSex' which masks all related fields #161

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Merged
dmendelowitz merged 3 commits into from
Oct 27, 2021
Merged

Creating new mask field 'genderAndSex' which masks all related fields #161

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aede88d
Creating new mask field 'genderAndSex' which masks all related fields
dmendelowitz Oct 25, 2021
e11d065
README updates
dmendelowitz Oct 26, 2021
6f3ccaf
updating patient fixtures to have new genderAndSex maskable fields
dmendelowitz Oct 26, 2021
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -135,7 +135,7 @@ 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`, `race`, `telecom`, `multipleBirth`, `photo`, `contact`, `generalPractitioner`, `managingOrganization`, and `link`.
Patient properties that can be masked are: `genderAndSex`, `mrn`, `name`, `address`, `birthDate`, `language`, `ethnicity`, `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
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58 changes: 36 additions & 22 deletions src/helpers/patientUtils.js
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Expand Up @@ -78,7 +78,7 @@ 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',
* 'genderAndSex','mrn','name','address','birthDate','language','ethnicity',
* 'race', 'telecom', 'multipleBirth', 'photo', 'contact', 'generalPractitioner',
* 'managingOrganization', and 'link'
* @param {Boolean} maskAll indicates that all supported fields should be masked, defaults to false
Expand All @@ -91,14 +91,13 @@ function maskPatientData(bundle, mask, maskAll = false) {
)[0];

const validFields = [
'gender',
'genderAndSex',
'mrn',
'name',
'address',
'birthDate',
'language',
'ethnicity',
'birthsex',
'race',
'telecom',
'multipleBirth',
Expand All @@ -117,13 +116,40 @@ function maskPatientData(bundle, mask, maskAll = false) {
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 === '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;
if (field === 'genderAndSex') {
if ('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 ('_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;
}
// 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 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;
}
const legalsex = fhirpath.evaluate(
patient,
'Patient.extension.where(url=\'http://open.epic.com/FHIR/StructureDefinition/extension/legal-sex\')',
);
if (legalsex.length > 0) {
legalsex[0].valueCodeableConcept = masked;
}
const clinicaluse = fhirpath.evaluate(
patient,
'Patient.extension.where(url=\'http://open.epic.com/FHIR/StructureDefinition/extension/sex-for-clinical-use\')',
);
if (clinicaluse.length > 0) {
clinicaluse[0].valueCodeableConcept = masked;
}
} else if (field === 'mrn' && 'identifier' in patient) {
// id and fullURL still need valid values, so we use a hashed version of MRN instead of dataAbsentReason
const hash = crypto.createHash('sha256');
Expand All @@ -147,18 +173,6 @@ function maskPatientData(bundle, mask, maskAll = false) {
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 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;
}
} else if (field === 'race') {
const race = fhirpath.evaluate(
patient,
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22 changes: 22 additions & 0 deletions test/extractors/fixtures/extended-patient-bundle.json
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Expand Up @@ -154,6 +154,28 @@
],
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
},
{
"valueCodeableConcept": {
"coding": [
{
"system": "urn:oid:1.2.840.114350.1.13.0.1.7.10.698084.130.657370.19999000",
"code": "female"
}
]
},
"url": "http://open.epic.com/FHIR/StructureDefinition/extension/legal-sex"
},
{
"valueCodeableConcept": {
"coding": [
{
"system": "urn:oid:1.2.840.114350.1.13.0.1.7.10.698084.130.657370.19999000",
"code": "female"
}
]
},
"url": "http://open.epic.com/FHIR/StructureDefinition/extension/sex-for-clinical-use"
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
"valueCode": "male"
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22 changes: 22 additions & 0 deletions test/helpers/fixtures/masked-patient-bundle.json
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Expand Up @@ -104,6 +104,28 @@
],
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity"
},
{
"valueCodeableConcept": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
},
"url": "http://open.epic.com/FHIR/StructureDefinition/extension/legal-sex"
},
{
"valueCodeableConcept": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "masked"
}
]
},
"url": "http://open.epic.com/FHIR/StructureDefinition/extension/sex-for-clinical-use"
},
{
"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex",
"_valueCode": {
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6 changes: 2 additions & 4 deletions test/helpers/patientUtils.test.js
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Expand Up @@ -93,14 +93,13 @@ describe('PatientUtils', () => {
test('bundle should be modified to have dataAbsentReason for all fields specified in mask', () => {
const bundle = _.cloneDeep(examplePatient);
maskPatientData(bundle, [
'gender',
'genderAndSex',
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@jafeltra jafeltra Oct 26, 2021

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I think it might be good to include thew two new extensions that genderAndSex now mask on the examplePatient bundle, and then include the masked properties in the exampleMaskedPatient, just to ensure we don't accidentally break the masking of these fields in the future.

'mrn',
'name',
'address',
'birthDate',
'language',
'ethnicity',
'birthsex',
'race',
'telecom',
'multipleBirth',
Expand Down Expand Up @@ -132,14 +131,13 @@ describe('PatientUtils', () => {
],
};
maskPatientData(bundle, [
'gender',
'genderAndSex',
'mrn',
'name',
'address',
'birthDate',
'language',
'ethnicity',
'birthsex',
'race',
'telecom',
'multipleBirth',
Expand Down