Merge pull request #123 from mcode/dev

Dev

README.md

@@ -53,7 +53,7 @@ NOTE: The REMS Administrator is a work in progress.
 ## Running the REMS Adminstrator
 
 #### Initialization
-After cloning the repsistory, the submodules must be initialized. To do this you can run:
+After cloning the repository, the submodules must be initialized. To do this you can run:
 
 ```
 git submodule update --init
@@ -70,7 +70,7 @@ npm test
 ```
 npm start
 ```
-Application will be runnin on port 8090.
+Application will be running on port 8090.
 
 To reach the CDS Services discovery information:
 

package.json

@@ -42,7 +42,7 @@
     "moment": "^2.24.0",
     "moment-timezone": "^0.5.40",
     "mongodb": "^4.12.1",
-    "mongoose": "7.0.3",
+    "mongoose": "7.3.3",
     "morgan": "^1.9.1",
     "uid": "^2.0.1",
     "uuid": "^9.0.0",

src/fhir/models.ts

@@ -1,6 +1,6 @@
 import { Document, Schema, model } from 'mongoose';
 
-interface Medication extends Document {
+export interface Medication extends Document {
   name: string;
   codeSystem: string;
   code: string;

src/fhir/questionnaireUtilities.ts

@@ -1,7 +1,6 @@
 import {
   Bundle,
   BundleEntry,
-  DataRequirement,
   Extension,
   FhirResource,
   Library,
@@ -10,10 +9,8 @@ import {
   QuestionnaireItem,
   ValueSet
 } from 'fhir/r4';
-import { FhirUtilities } from './utilities';
 import container from '../lib/winston';
 import config from '../config';
-import axios from 'axios';
 import ValueSetModel from '../lib/schemas/resources/ValueSet';
 import QuestionnaireModel from '../lib/schemas/resources/Questionnaire';
 import LibraryModel from '../lib/schemas/resources/Library';
@@ -29,7 +26,6 @@ interface LibraryMap {
   [key: string]: Library;
 }
 
-const VSAC_CANONICAL_BASE = 'https://cts.nlm.nih.gov/fhir/ValueSet/';
 const CQF_LIBRARY_EXTENSION = 'http://hl7.org/fhir/StructureDefinition/cqf-library';
 
 export class QuestionnaireUtilities {
@@ -41,7 +37,6 @@ export class QuestionnaireUtilities {
     const bundle: Bundle = { resourceType: 'Bundle', type: 'collection' };
     const entries: BundleEntry[] = [];
     const extensions: Extension[] = processedQuestionnaire.extension || [];
-    const fetchedSets: ValueSetMap = {};
     const fetchedLibraries: LibraryMap = {};
     for (const extension of extensions) {
       if (extension.url === CQF_LIBRARY_EXTENSION) {
@@ -105,7 +100,7 @@ export class QuestionnaireUtilities {
   }
   // On load of new library, finds ValueSets in codefilters and
   // loads them as well
-  static async processLibraryCodeFilters(library: Library, fetchedSets: ValueSetMap) {
+  static async processLibraryCodeFilters(library: Library) {
     const returnValue = this.vsacCache.cacheLibrary(library);
     return returnValue;
   }

src/fhir/utilities.ts

@@ -84,7 +84,7 @@ export class FhirUtilities {
         switch (resource.resourceType) {
           case 'Library':
             model = LibraryModel;
-            await QuestionnaireUtilities.processLibraryCodeFilters(resource, {});
+            await QuestionnaireUtilities.processLibraryCodeFilters(resource);
             break;
           case 'Patient':
             model = PatientModel;
@@ -167,7 +167,7 @@ export class FhirUtilities {
             requiredToDispense: true
           },
           {
-            name: 'Patient Status Update Form',
+            name: 'Patient Status Update',
             description: 'Submit Patient Status Update form to the REMS Administrator',
             stakeholderType: 'patient',
             createNewCase: false,

src/hooks/hookResources.ts

@@ -1,7 +1,6 @@
-import { Coding } from 'fhir/r4';
+import { MedicationRequest, Coding } from 'fhir/r4';
 import { Link } from '../cards/Card';
-import config from '../config';
-import { Hook, TypedRequestBody } from '../rems-cds-hooks/resources/HookTypes';
+import { TypedRequestBody } from '../rems-cds-hooks/resources/HookTypes';
 import axios from 'axios';
 
 export interface CardRule {
@@ -205,3 +204,29 @@ export function getFhirResource(token: string, req: TypedRequestBody) {
     return e.data;
   });
 }
+
+/*
+ * Retrieve the coding for the medication from the medicationCodeableConcept if available.
+ * Read coding from contained Medication matching the medicationReference otherwise.
+ */
+export function getDrugCodeFromMedicationRequest(medicationRequest: MedicationRequest) {
+  if (medicationRequest) {
+    if (medicationRequest?.medicationCodeableConcept) {
+      console.log('Get Medication code from CodeableConcept');
+      return medicationRequest?.medicationCodeableConcept?.coding?.[0];
+    } else if (medicationRequest?.medicationReference) {
+      const reference = medicationRequest?.medicationReference;
+      let coding = null;
+      medicationRequest?.contained?.every(e => {
+        if (e.resourceType + '/' + e.id === reference.reference) {
+          if (e.resourceType === 'Medication') {
+            console.log('Get Medication code from contained resource');
+            coding = e.code?.coding?.[0];
+          }
+        }
+      });
+      return coding;
+    }
+  }
+  return null;
+}

src/hooks/rems.orderselect.ts

@@ -10,7 +10,12 @@ import { MedicationRequest } from 'fhir/r4';
 import { Link } from '../cards/Card';
 import config from '../config';
 import { hydrate } from '../rems-cds-hooks/prefetch/PrefetchHydrator';
-import { validCodes, codeMap, CARD_DETAILS, getFhirResource } from './hookResources';
+import {
+  validCodes,
+  codeMap,
+  CARD_DETAILS,
+  getDrugCodeFromMedicationRequest
+} from './hookResources';
 import axios from 'axios';
 
 interface TypedRequestBody extends Express.Request {
@@ -86,13 +91,17 @@ const handler = (req: TypedRequestBody, res: any) => {
     const prefetchRequest = context.draftOrders?.entry?.[0].resource;
     const practitioner = hydratedPrefetch?.practitioner;
     const npi = practitioner?.identifier;
-    console.log('    Practitioner: ' + practitioner?.id + ' NPI: ' + npi);
-    console.log('    Patient: ' + patient?.id);
 
     console.log('    MedicationRequest: ' + prefetchRequest?.id);
     console.log('    Practitioner: ' + practitioner?.id + ' NPI: ' + npi);
     console.log('    Patient: ' + patient?.id);
 
+    // verify there is a contextRequest
+    if (!contextRequest) {
+      res.json(buildErrorCard('DraftOrders does not contain a request'));
+      return;
+    }
+
     // verify a MedicationRequest was sent
     if (contextRequest && contextRequest.resourceType !== 'MedicationRequest') {
       res.json(buildErrorCard('DraftOrders does not contain a MedicationRequest'));
@@ -125,7 +134,7 @@ const handler = (req: TypedRequestBody, res: any) => {
       return;
     }
 
-    const medicationCode = contextRequest?.medicationCodeableConcept?.coding?.[0];
+    const medicationCode = getDrugCodeFromMedicationRequest(contextRequest);
     if (medicationCode && medicationCode.code) {
       // find the drug in the medicationCollection to get the smart links
       const drug = await medicationCollection
@@ -192,12 +201,13 @@ const handler = (req: TypedRequestBody, res: any) => {
                     smartLinkCount++;
                   }
                 } else {
-                  // if (etasu)
-                  // add all the links if no etasu to check
-                  card.addLink(
-                    createSmartLink(requirement.name, requirement.appContext, contextRequest)
-                  );
-                  smartLinkCount++;
+                  // add all the required to dispense links if no etasu to check
+                  if (requirement.requiredToDispense) {
+                    card.addLink(
+                      createSmartLink(requirement.name, requirement.appContext, contextRequest)
+                    );
+                    smartLinkCount++;
+                  }
                 }
               }
             }
@@ -218,10 +228,12 @@ const handler = (req: TypedRequestBody, res: any) => {
       res.json(buildErrorCard('MedicationRequest does not contain a code'));
     }
   }
+
   console.log('REMS order-select hook');
   try {
     const fhirUrl = req.body.fhirServer;
-    if (fhirUrl) {
+    const fhirAuth = req.body.fhirAuthorization;
+    if (fhirUrl && fhirAuth && fhirAuth.access_token) {
       hydrate(getFhirResource, hookPrefetch, req.body).then(
         (hydratedPrefetch: OrderSelectPrefetch) => {
           handleCard(hydratedPrefetch);

src/hooks/rems.ordersign.ts

@@ -10,7 +10,12 @@ import { MedicationRequest } from 'fhir/r4';
 import { Link } from '../cards/Card';
 import config from '../config';
 import { hydrate } from '../rems-cds-hooks/prefetch/PrefetchHydrator';
-import { validCodes, codeMap, CARD_DETAILS, getFhirResource } from './hookResources';
+import {
+  validCodes,
+  codeMap,
+  CARD_DETAILS,
+  getDrugCodeFromMedicationRequest
+} from './hookResources';
 import axios from 'axios';
 
 interface TypedRequestBody extends Express.Request {
@@ -41,7 +46,7 @@ function buildErrorCard(reason: string) {
 }
 
 const handler = (req: TypedRequestBody, res: any) => {
-  function getFhirResource(token: string) {
+  async function getFhirResource(token: string) {
     const ehrUrl = `${req.body.fhirServer}/${token}`;
     const access_token = req.body.fhirAuthorization?.access_token;
     const options = {
@@ -50,10 +55,15 @@ const handler = (req: TypedRequestBody, res: any) => {
         Authorization: `Bearer ${access_token}`
       }
     };
-    const response = axios(ehrUrl, options);
-    return response.then(e => {
-      return e.data;
-    });
+    // application errors out here if you can't reach out to the EHR and results in server stopping and subsequent requests failing
+    let response = { data: {} };
+    try {
+      response = await axios(ehrUrl, options);
+    } catch (error: any) {
+      console.warn('Could not connect to EHR Server: ' + error);
+      response = error;
+    }
+    return response?.data;
   }
 
   function createSmartLink(
@@ -80,13 +90,17 @@ const handler = (req: TypedRequestBody, res: any) => {
     const prefetchRequest = hydratedPrefetch?.request;
     const practitioner = hydratedPrefetch?.practitioner;
     const npi = practitioner?.identifier;
-    console.log('    Practitioner: ' + practitioner?.id + ' NPI: ' + npi);
-    console.log('    Patient: ' + patient?.id);
 
     console.log('    MedicationRequest: ' + prefetchRequest?.id);
     console.log('    Practitioner: ' + practitioner?.id + ' NPI: ' + npi);
     console.log('    Patient: ' + patient?.id);
 
+    // verify there is a contextRequest
+    if (!contextRequest) {
+      res.json(buildErrorCard('DraftOrders does not contain a request'));
+      return;
+    }
+
     // verify a MedicationRequest was sent
     if (contextRequest && contextRequest.resourceType !== 'MedicationRequest') {
       res.json(buildErrorCard('DraftOrders does not contain a MedicationRequest'));
@@ -119,8 +133,11 @@ const handler = (req: TypedRequestBody, res: any) => {
       return;
     }
 
-    const medicationCode = contextRequest?.medicationCodeableConcept?.coding?.[0];
-    if (medicationCode && medicationCode.code) {
+    const medicationCode = getDrugCodeFromMedicationRequest(contextRequest);
+    if (!medicationCode) {
+      return;
+    }
+    if (medicationCode && medicationCode?.code) {
       // find the drug in the medicationCollection to get the smart links
       const drug = await medicationCollection
         .findOne({
@@ -186,12 +203,13 @@ const handler = (req: TypedRequestBody, res: any) => {
                     smartLinkCount++;
                   }
                 } else {
-                  // if (etasu)
-                  // add all the links if no etasu to check
-                  card.addLink(
-                    createSmartLink(requirement.name, requirement.appContext, contextRequest)
-                  );
-                  smartLinkCount++;
+                  // add all the required to dispense links if no etasu to check
+                  if (requirement.requiredToDispense) {
+                    card.addLink(
+                      createSmartLink(requirement.name, requirement.appContext, contextRequest)
+                    );
+                    smartLinkCount++;
+                  }
                 }
               }
             }
@@ -212,10 +230,12 @@ const handler = (req: TypedRequestBody, res: any) => {
       res.json(buildErrorCard('MedicationRequest does not contain a code'));
     }
   }
+
   console.log('REMS order-sign hook');
   try {
     const fhirUrl = req.body.fhirServer;
-    if (fhirUrl) {
+    const fhirAuth = req.body.fhirAuthorization;
+    if (fhirUrl && fhirAuth && fhirAuth.access_token) {
       hydrate(getFhirResource, hookPrefetch, req.body).then(
         (hydratedPrefetch: OrderSignPrefetch) => {
           handleCard(hydratedPrefetch);