Merge branch 'main' into service-account

StanfordBDHG · Oct 3, 2024 · 2c21004 · 2c21004
2 parents 1d7326a + 9c10e94
commit 2c21004
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Showing 17 changed files with 102 additions and 39 deletions.
diff --git a/functions/src/models/medicationRequestContext.ts b/functions/src/models/medicationRequestContext.ts
@@ -14,6 +14,7 @@ import {
 } from '@stanfordbdhg/engagehf-models'
 
 export interface MedicationRequestContext {
+  lastUpdate: Date
   request: FHIRMedicationRequest
   requestReference: FHIRReference
   drug: FHIRMedication

diff --git a/functions/src/services/database/databaseService.ts b/functions/src/services/database/databaseService.ts
@@ -16,6 +16,7 @@ import { type CollectionsService } from './collections'
 export interface Document<Content> {
   id: string
   path: string
+  lastUpdate: Date
   content: Content
 }
 

diff --git a/functions/src/services/database/firestoreService.ts b/functions/src/services/database/firestoreService.ts
@@ -41,6 +41,7 @@ export class FirestoreService implements DatabaseService {
     return collection.docs.map((doc) => ({
       id: doc.id,
       path: doc.ref.path,
+      lastUpdate: doc.updateTime.toDate(),
       content: doc.data(),
     }))
   }
@@ -53,8 +54,14 @@ export class FirestoreService implements DatabaseService {
     const ref = reference(this.collectionsService.value)
     const doc = await ref.get()
     const data = doc.exists ? doc.data() : undefined
-    return doc.exists && data ?
-        { id: doc.id, path: doc.ref.path, content: data }
+    return doc.exists && data !== undefined ?
+        {
+          id: doc.id,
+          path: doc.ref.path,
+          // `lastUpdate` should not be undefined in this case
+          lastUpdate: doc.updateTime?.toDate() ?? doc.readTime.toDate(),
+          content: data,
+        }
       : undefined
   }
 

diff --git a/functions/src/services/medication/databaseMedicationService.ts b/functions/src/services/medication/databaseMedicationService.ts
@@ -33,10 +33,9 @@ export class DatabaseMedicationService implements MedicationService {
   // Methods - Medication Request Context
 
   async getContext(
-    request: FHIRMedicationRequest,
-    reference: FHIRReference,
+    request: Document<FHIRMedicationRequest>,
   ): Promise<MedicationRequestContext> {
-    const drugReference = request.medicationReference
+    const drugReference = request.content.medicationReference
     if (drugReference === undefined) throw new Error('Drug reference not found')
     const drug = (await this.getReference(drugReference))?.content
     if (drug === undefined)
@@ -61,8 +60,9 @@ export class DatabaseMedicationService implements MedicationService {
         `Medication class not found at ${medicationClassReference.reference}`,
       )
     return {
-      requestReference: reference,
-      request,
+      lastUpdate: request.lastUpdate,
+      requestReference: { reference: request.path },
+      request: request.content,
       drugReference,
       drug,
       medicationReference,

diff --git a/functions/src/services/medication/medicationService.ts b/functions/src/services/medication/medicationService.ts
@@ -19,8 +19,7 @@ export interface MedicationService {
   // Medication Request Context
 
   getContext(
-    request: FHIRMedicationRequest,
-    reference: FHIRReference,
+    request: Document<FHIRMedicationRequest>,
   ): Promise<MedicationRequestContext>
 
   // Medication Classes

diff --git a/functions/src/services/message/defaultMessageService.ts b/functions/src/services/message/defaultMessageService.ts
@@ -164,6 +164,7 @@ export class DefaultMessageService implements MessageService {
           transaction.set(newMessageRef, message)
           const document: Document<UserMessage> = {
             id: newMessageRef.id,
+            lastUpdate: new Date(),
             path: newMessageRef.path,
             content: message,
           }

diff --git a/functions/src/services/patient/patientService.mock.ts b/functions/src/services/patient/patientService.mock.ts
@@ -55,6 +55,7 @@ export class MockPatientService implements PatientService {
   ): Promise<Document<FHIRAppointment> | undefined> {
     return {
       id: '123',
+      lastUpdate: new Date(),
       path: `users/${userId}/appointments/123`,
       content: FHIRAppointment.create({
         userId,
@@ -82,6 +83,7 @@ export class MockPatientService implements PatientService {
     const values: UserMedicationRecommendation[] = []
     return values.map((value, index) => ({
       id: index.toString(),
+      lastUpdate: new Date(),
       path: `users/${userId}/medicationRecommendations/${index}`,
       content: value,
     }))
@@ -99,6 +101,7 @@ export class MockPatientService implements PatientService {
     ]
     return values.map((value, index) => ({
       id: index.toString(),
+      lastUpdate: new Date(),
       path: `users/${userId}/medicationRequests/${index}`,
       content: value,
     }))
@@ -243,6 +246,7 @@ export class MockPatientService implements PatientService {
   ): Promise<Array<Document<FHIRQuestionnaireResponse>>> {
     return [mockQuestionnaireResponse()].map((value, index) => ({
       id: index.toString(),
+      lastUpdate: new Date(),
       path: `users/${userId}/questionnaireResponses/${index}`,
       content: value,
     }))
@@ -296,6 +300,7 @@ export class MockPatientService implements PatientService {
     ]
     return values.map((value, index) => ({
       id: index.toString(),
+      lastUpdate: new Date(),
       path: `users/${userId}/symptomScores/${index}`,
       content: value,
     }))

diff --git a/functions/src/services/recommendation/recommendationService.test.ts b/functions/src/services/recommendation/recommendationService.test.ts
@@ -81,9 +81,12 @@ describe('RecommendationService', () => {
         ].flatMap((x) => (x ? [x] : []))
 
         const requestContexts = await Promise.all(
-          medicationRequests.map(async (medicationRequest) =>
-            medicationService.getContext(medicationRequest, {
-              reference: '',
+          medicationRequests.map(async (medicationRequest, index) =>
+            medicationService.getContext({
+              id: index.toString(),
+              path: `users/0/medicationRequests/${index}`,
+              lastUpdate: new Date(),
+              content: medicationRequest,
             }),
           ),
         )

diff --git a/functions/src/services/recommendation/recommenders/betaBlockerRecommender.test.ts b/functions/src/services/recommendation/recommenders/betaBlockerRecommender.test.ts
@@ -199,8 +199,11 @@ describe('BetaBlockerRecommender', () => {
         frequencyPerDay: 1,
         quantity: 1,
       })
-      contextBelowTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      contextBelowTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
     })
 
@@ -210,8 +213,11 @@ describe('BetaBlockerRecommender', () => {
         frequencyPerDay: 1,
         quantity: 2,
       })
-      const contextAtTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      const contextAtTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
       const result = recommender.compute({
         requests: [contextAtTarget],

diff --git a/functions/src/services/recommendation/recommenders/diureticRecommender.test.ts b/functions/src/services/recommendation/recommenders/diureticRecommender.test.ts
@@ -52,6 +52,7 @@ describe('DiureticRecommender', () => {
   describe('On furosemide', () => {
     it('correctly keeps existing medication request', async () => {
       const existingMedication: MedicationRequestContext = {
+        lastUpdate: new Date(),
         requestReference: {
           reference:
             'users/mockPatient/medicationRequests/mockMedicationRequest',

diff --git a/functions/src/services/recommendation/recommenders/mraRecommender.test.ts b/functions/src/services/recommendation/recommenders/mraRecommender.test.ts
@@ -167,8 +167,11 @@ describe('MraRecommender', () => {
         frequencyPerDay: 1,
         quantity: 1,
       })
-      contextBelowTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      contextBelowTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
     })
 
@@ -178,8 +181,11 @@ describe('MraRecommender', () => {
         frequencyPerDay: 2,
         quantity: 1,
       })
-      const contextAtTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      const contextAtTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
       const result = recommender.compute({
         requests: [contextAtTarget],

diff --git a/functions/src/services/recommendation/recommenders/rasiRecommender.test.ts b/functions/src/services/recommendation/recommenders/rasiRecommender.test.ts
@@ -266,8 +266,11 @@ describe('RasiRecommender', () => {
         frequencyPerDay: 1,
         quantity: 1,
       })
-      contextBelowTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      contextBelowTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
     })
 
@@ -288,8 +291,11 @@ describe('RasiRecommender', () => {
           frequencyPerDay: 2,
           quantity: 2,
         })
-        const contextAtTarget = await medicationService.getContext(request, {
-          reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+        const contextAtTarget = await medicationService.getContext({
+          id: 'someMedicationRequest',
+          path: 'users/mockUser/medicationRequests/someMedicationRequest',
+          lastUpdate: new Date(),
+          content: request,
         })
         const result = recommender.compute({
           requests: [contextAtTarget],
@@ -525,8 +531,11 @@ describe('RasiRecommender', () => {
         frequencyPerDay: 1,
         quantity: 1,
       })
-      contextBelowTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      contextBelowTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
     })
 
@@ -536,8 +545,11 @@ describe('RasiRecommender', () => {
         frequencyPerDay: 2,
         quantity: 2,
       })
-      const contextAtTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      const contextAtTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
       const result = recommender.compute({
         requests: [contextAtTarget],

diff --git a/functions/src/services/recommendation/recommenders/recommender.ts b/functions/src/services/recommendation/recommenders/recommender.ts
@@ -55,7 +55,6 @@ export abstract class Recommender {
   protected isTargetDailyDoseReached(
     currentMedication: MedicationRequestContext[],
   ): boolean {
-    // TODO: Make sure that there is only one medication involved!
     const medication = currentMedication.at(0)?.medication
     if (!medication) throw new Error('Medication is missing')
 
@@ -77,12 +76,24 @@ export abstract class Recommender {
     requests: MedicationRequestContext[],
     references: MedicationClassReference[],
   ): MedicationRequestContext[] {
-    return requests.filter((request) =>
+    const validContexts = requests.filter((request) =>
       references.some(
         (reference) =>
           request.medicationClassReference.reference === reference.toString(),
       ),
     )
+    const latestContext =
+      validContexts.length > 0 ?
+        validContexts.reduce(
+          (acc, context) =>
+            acc.lastUpdate < context.lastUpdate ? context : acc,
+          validContexts[0],
+        )
+      : undefined
+    return validContexts.filter(
+      (context) =>
+        context.medicationReference === latestContext?.medicationReference,
+    )
   }
 
   protected medianValue(observations: Observation[]): number | undefined {

diff --git a/functions/src/services/recommendation/recommenders/sglt2iRecommender.test.ts b/functions/src/services/recommendation/recommenders/sglt2iRecommender.test.ts
@@ -186,8 +186,11 @@ describe('Sglt2iRecommender', () => {
         frequencyPerDay: 1,
         quantity: 1,
       })
-      contextBelowTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      contextBelowTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
     })
 
@@ -197,8 +200,11 @@ describe('Sglt2iRecommender', () => {
         frequencyPerDay: 2,
         quantity: 1,
       })
-      const contextAtTarget = await medicationService.getContext(request, {
-        reference: 'users/mockUser/medicationRequests/someMedicationRequest',
+      const contextAtTarget = await medicationService.getContext({
+        id: 'someMedicationRequest',
+        path: 'users/mockUser/medicationRequests/someMedicationRequest',
+        lastUpdate: new Date(),
+        content: request,
       })
       const result = recommender.compute({
         requests: [contextAtTarget],

diff --git a/functions/src/services/trigger/triggerService.ts b/functions/src/services/trigger/triggerService.ts
@@ -550,11 +550,7 @@ export class TriggerService {
     )
 
     const requestContexts = await Promise.all(
-      requests.map(async (document) =>
-        medicationService.getContext(document.content, {
-          reference: `users/${userId}/medicationRequests/${document.id}`,
-        }),
-      ),
+      requests.map(async (document) => medicationService.getContext(document)),
     )
 
     logger.debug(

diff --git a/functions/src/services/user/userService.mock.ts b/functions/src/services/user/userService.mock.ts
@@ -60,6 +60,7 @@ export class MockUserService implements UserService {
     return {
       id: '1',
       path: 'invitations/1',
+      lastUpdate: new Date(),
       content: new Invitation({
         user: new UserRegistration({
           type: UserType.patient,
@@ -105,6 +106,7 @@ export class MockUserService implements UserService {
     return {
       id: organizationId,
       path: 'organizations/' + organizationId,
+      lastUpdate: new Date(),
       content: new Organization({
         name: 'Stanford University',
         contactName: 'Alex Sandhu, MD',
@@ -129,6 +131,7 @@ export class MockUserService implements UserService {
     return {
       id: userId,
       path: 'users/' + userId,
+      lastUpdate: new Date(),
       content: new User({
         type: UserType.clinician,
         dateOfBirth: new Date('1970-01-02'),

diff --git a/functions/src/tests/mocks/firestore.ts b/functions/src/tests/mocks/firestore.ts
@@ -7,6 +7,7 @@
 //
 
 import {
+  Timestamp,
   type FirestoreDataConverter,
   type QueryDocumentSnapshot,
 } from 'firebase-admin/firestore'
@@ -130,6 +131,7 @@ class MockFirestoreCollectionRef extends MockFirestoreRef {
         id: key,
         exists: true,
         ref: this.doc(key as string) as any,
+        updateTime: Timestamp.now(),
         data: () => value,
       })
     })
@@ -181,6 +183,7 @@ class MockFirestoreConvertedCollectionRef<
         exists: doc.exists,
         id: doc.id,
         ref: doc.ref,
+        updateTime: doc.updateTime,
         data: () => newData,
       }
     })
@@ -292,6 +295,7 @@ class MockFirestoreDocRef extends MockFirestoreRef {
       exists: result !== undefined,
       id: pathComponents[pathComponents.length - 1],
       ref: this as any,
+      updateTime: Timestamp.now(),
       data: () => result as any,
     }
   }
@@ -369,6 +373,7 @@ class MockFirestoreConvertedDocRef<T> extends MockFirestoreDocRef {
       exists: result.exists,
       id: result.id,
       ref: result.ref,
+      updateTime: result.updateTime,
       data: () => data,
     }
     result.data = () =>