From 15db0e6705c3defc80e286657ca66709eee815b1 Mon Sep 17 00:00:00 2001
From: Patrick LaRocque <41444457+plarocque4@users.noreply.github.com>
Date: Fri, 19 Aug 2022 13:32:31 -0400
Subject: [PATCH] Add ability to deidentify Patient and Coverage resources.
 (#70)

* DMEERX-367: IG - Add support for PHI and Hook Invocation

* Only deidentify the patient and coverage if box is checked.

* Remove the telecom key from the Patient resource. Make sure only one deidentified profile can be found in the patient meta.

* Fix issue with duplicate profile in the coverage as well.

* Fix issue with deselecting deidentify resources still sends deidentified resources. Make a deep copy of the data to not change the original when deidentifying the resources.
---
 package.json                            |  1 +
 src/components/RequestBox/RequestBox.js | 25 +++++++--
 src/containers/RequestBuilder.js        |  4 +-
 src/util/buildRequest.js                | 34 ++++++++++-
 src/util/deidentifyCoverage.js          | 39 +++++++++++++
 src/util/deidentifyPatient.js           | 75 +++++++++++++++++++++++++
 6 files changed, 170 insertions(+), 8 deletions(-)
 create mode 100644 src/util/deidentifyCoverage.js
 create mode 100644 src/util/deidentifyPatient.js

diff --git a/package.json b/package.json
index 65328ff5..8ffe2508 100644
--- a/package.json
+++ b/package.json
@@ -7,6 +7,7 @@
     "axios": "^0.18.0",
     "base64url": "^3.0.0",
     "classnames": "^2.2.6",
+    "clone": "^2.1.2",
     "fhirclient": "^2.3.1",
     "json-server": "^0.16.3",
     "jsrsasign": "^10.2.0",
diff --git a/src/components/RequestBox/RequestBox.js b/src/components/RequestBox/RequestBox.js
index 6232cd93..1c4375b2 100644
--- a/src/components/RequestBox/RequestBox.js
+++ b/src/components/RequestBox/RequestBox.js
@@ -2,6 +2,7 @@ import React, { Component } from "react";
 import FHIR from "fhirclient";
 import SMARTBox from "../SMARTBox/SMARTBox";
 import PatientBox from "../SMARTBox/PatientBox";
+import CheckBox from '../Inputs/CheckBox';
 import { defaultValues, shortNameMap } from "../../util/data";
 import { getAge } from "../../util/fhir";
 import _ from "lodash";
@@ -23,7 +24,8 @@ export default class RequestBox extends Component {
       display: null,
       request: {},
       gatherCount: 0,
-      response: {}
+      response: {},
+      deidentifyRecords: false
     };
 
     this.renderRequestResources = this.renderRequestResources.bind(this);
@@ -33,6 +35,7 @@ export default class RequestBox extends Component {
     this.renderPrefetchedResources = this.renderPrefetchedResources.bind(this);
     this.renderError = this.renderError.bind(this);
     this.buildLaunchLink = this.buildLaunchLink.bind(this);
+    this.updateDeidentifyCheckbox = this.updateDeidentifyCheckbox.bind(this);
   }
 
   // TODO - see how to submit response for alternative therapy
@@ -42,7 +45,7 @@ export default class RequestBox extends Component {
     // Prepare the prefetch.
     const prefetch = this.prepPrefetch();
     // Submit the CRD request.
-    this.props.submitInfo(prefetch, request, this.state.patient, "order-sign");
+    this.props.submitInfo(prefetch, request, this.state.patient, "order-sign", this.state.deidentifyRecords);
   }
 
   componentDidMount() {}
@@ -68,7 +71,8 @@ export default class RequestBox extends Component {
         this.prepPrefetch(),
         this.state.request,
         this.state.patient,
-        "order-sign"
+        "order-sign",
+        this.state.deidentifyRecords
       );
     }
   };
@@ -326,6 +330,10 @@ export default class RequestBox extends Component {
     return Object.keys(this.state.request).length === 0;
   }
 
+  updateDeidentifyCheckbox(elementName, value) {
+    this.setState({ deidentifyRecords: value });
+  }
+
   render() {
     const params = {};
     params['serverUrl'] = this.props.ehrUrl;
@@ -379,8 +387,15 @@ export default class RequestBox extends Component {
             <div>
               {this.renderPatientInfo()}
               {this.renderPrefetchedResources()}
-            </div> 
-             
+            </div>
+            <div>
+              <b>Deidentify Records</b>
+              <CheckBox
+                toggle = {this.state.deidentifyRecords}
+                updateCB={this.updateDeidentifyCheckbox}
+                elementName = "deidentifyCheckbox" 
+                />
+            </div>
           </div>
         </div>
         <button className={"submit-btn btn btn-class "} onClick={this.relaunch} disabled={disableLaunchDTR}>
diff --git a/src/containers/RequestBuilder.js b/src/containers/RequestBuilder.js
index 7a5f26a6..68d3d797 100644
--- a/src/containers/RequestBuilder.js
+++ b/src/containers/RequestBuilder.js
@@ -109,14 +109,14 @@ export default class RequestBuilder extends Component {
 
     }
 
-    submit_info(prefetch, request, patient, hook) {
+    submit_info(prefetch, request, patient, hook, deidentifyRecords) {
         this.consoleLog("Initiating form submission", types.info);
         this.setState({patient});
         const hookConfig = {
             "includeConfig": this.state.includeConfig,
             "alternativeTherapy": this.state.alternativeTherapy
         }
-        let json_request = buildRequest(request, patient, this.state.ehrUrl, this.state.token, prefetch, this.state.sendPrefetch, hook, hookConfig);
+        let json_request = buildRequest(request, patient, this.state.ehrUrl, this.state.token, prefetch, this.state.sendPrefetch, hook, hookConfig, deidentifyRecords);
         let cdsUrl = this.state.cdsUrl;
         if (hook === "order-sign") {
             cdsUrl = cdsUrl + "/" + this.state.orderSign;
diff --git a/src/util/buildRequest.js b/src/util/buildRequest.js
index 8111db23..b6e0ded4 100644
--- a/src/util/buildRequest.js
+++ b/src/util/buildRequest.js
@@ -1,5 +1,37 @@
 
-export default function buildRequest(request, patient, ehrUrl, token, prefetch, includePrefetch, hook, hookConfig) {
+import deidentifyPatient from "./deidentifyPatient";
+import deidentifyCoverage from "./deidentifyCoverage";
+import clone from 'clone'
+
+
+export default function buildRequest(request, patient, ehrUrl, token, prefetch, includePrefetch, hook, hookConfig, deidentifyRecords) {
+    if (deidentifyRecords) {
+        // make a copy of the resources before modifying
+        let newPrefetch = clone(prefetch);
+
+        console.log("Deidentify Patient and Coverage Resources to remove PHI");
+        // loop through the prefetch looking for the patient and the coverage
+        newPrefetch.forEach((bundle) => {
+            bundle.forEach((resource) => {
+                let resourceType = resource.resource.resourceType;
+                if (resourceType == "Patient") {
+                    // deidentify the patient
+                    let patient = deidentifyPatient(resource.resource);
+                    // replace the patient resource with the deidentified version
+                    resource.resource = patient
+                } else if (resourceType === "Coverage") {
+                    // deidentify the coverage
+                    let coverage = deidentifyCoverage(resource.resource);
+                    // replace the coverage resource with the deidentified version
+                    resource.resource = coverage
+                }
+            })
+        });
+
+        // set the prefetch reference to the modified copy
+        prefetch = newPrefetch
+    }
+
     const r4json = {
         "hookInstance": "d1577c69-dfbe-44ad-ba6d-3e05e953b2ea",
         "fhirServer": ehrUrl,
diff --git a/src/util/deidentifyCoverage.js b/src/util/deidentifyCoverage.js
new file mode 100644
index 00000000..edf1f1ee
--- /dev/null
+++ b/src/util/deidentifyCoverage.js
@@ -0,0 +1,39 @@
+
+export default function deidentifyCoverage(coverage) {
+    let newCoverage = {};
+    const profile = "http://hl7.org/fhir/us/davinci-crd/StructureDefinition/profile-coverage-deident";
+    const metaKey = "meta";
+    const profileKey = "profile";
+
+    for (const key in coverage) {
+        // remove: text, identifier, policyHolder, subscriber, subscriberId, dependent, relationship, order, network, costToBeneficiary, subrogation, contract
+        if ((key !== "text") && (key !== "identifier") && (key !== "policyHolder") && (key !== "subscriber") && (key !== "subscriberId") && (key !== "dependent") && (key !== "relationship") && (key !== "order") && (key !== "network") && (key !== "costToBeneficiary") && (key !== "subrogation") && (key !== "contract")) {
+            if (key === metaKey) {
+                // copy meta if there is one
+                let meta = coverage[key];
+
+                if (profileKey in meta) {
+                    // make sure the profile is not already in the list
+                    if (!meta[profileKey].includes(profile)) {
+                        // append to the existing profile list
+                        meta[profileKey].push(profile);
+                    }
+                } else {
+                    // add the profile to meta
+                    meta[profileKey] = [ profile ];
+                }
+                newCoverage[key] = meta
+            }
+            else {
+                newCoverage[key] = coverage[key];
+            }
+        }
+    }
+
+    // if no meta, add it with the profile
+    if (!(metaKey in newCoverage)) {
+        newCoverage[metaKey] = { [profileKey]: [ profile ] };
+    }
+
+    return newCoverage;
+}
\ No newline at end of file
diff --git a/src/util/deidentifyPatient.js b/src/util/deidentifyPatient.js
new file mode 100644
index 00000000..1b63839d
--- /dev/null
+++ b/src/util/deidentifyPatient.js
@@ -0,0 +1,75 @@
+
+export default function deidentifyPatient(patient) {
+    let newPatient = {};
+    const profile = "http://hl7.org/fhir/us/davinci-crd/StructureDefinition/profile-patient-deident";
+    const metaKey = "meta";
+    const profileKey = "profile";
+
+    for (const key in patient) {
+        // remove: text, identifier, name, telecom, deceased, multipleBirth, photo, contact, link
+        if ((key !== "text") && (key !== "identifier") && (key !== "name") && (key !== "telecom") && (key !== "deceased") && (key !== "multipleBirth") && (key !== "photo") && (key !== "contact") && (key !== "link")) {
+            // handle birthDate
+            if (key === "birthDate") {
+                newPatient[key] = processDate(patient[key]);
+            }
+            else if (key === "address") {
+                // remove the following from address: text, line, city, district, postalCode, period
+                let addresses = patient[key];
+                let newAddresses = [];
+                for (const addrIndex in addresses) {
+                    let address = addresses[addrIndex];
+                    let newAddress = {};
+                    for (const addrKey in address) {
+                        if ((addrKey !== "text") && (addrKey !== "line") && (addrKey !== "city") && (addrKey !== "district") && (addrKey !== "postalCode") && (addrKey !== "period")) {
+                            newAddress[addrKey] = address[addrKey];
+                        }
+                    }
+                    newAddresses.push(newAddress);
+                }
+                newPatient[key] = newAddresses;
+            }
+            else if (key === metaKey) {
+                // copy meta if there is one
+                let meta = patient[key];
+
+                if (profileKey in meta) {
+                    // make sure the profile is not already in the list
+                    if (!meta[profileKey].includes(profile)) {
+                        // append to the existing profile list
+                        meta[profileKey].push(profile);
+                    }
+                } else {
+                    // add the profile to meta
+                    meta[profileKey] = [ profile ];
+                }
+                newPatient[key] = meta
+            }
+            else {
+                newPatient[key] = patient[key];
+            }
+        }
+    }
+
+    // if no meta, add it with the profile
+    if (!(metaKey in newPatient)) {
+        newPatient[metaKey] = { [profileKey]: [ profile ] };
+    }
+
+    return newPatient;
+}
+
+function processDate(dateString) {
+    let date = new Date(dateString);
+    const today = new Date();
+    const diffTime = Math.abs(today - date);
+    const diffDays = Math.ceil(diffTime / (1000 * 60 * 60 * 24)); 
+
+    // just the year
+    let newDateString = date.toISOString().substring(0,4);
+
+    // if less than two years old include the month
+    if (diffDays < (2 * 365)) {
+        newDateString = date.toISOString().substring(0,7);
+    }
+    return newDateString;
+}
\ No newline at end of file