Merge pull request #39 from jembi/retain-source-id

Allow source ID ot be saved as FHIR logical ID, map between source id and interaction id
jembi · May 2, 2024 · 715186d · 715186d
2 parents 375665d + 7eea2fb
commit 715186d
Show file tree

Hide file tree

Showing 10 changed files with 204 additions and 33 deletions.
diff --git a/src/routes/index.ts b/src/routes/index.ts
@@ -8,11 +8,14 @@ import { matchAsyncHandler } from './handlers/matchPatientAsync';
 import { matchSyncHandler } from './handlers/matchPatientSync';
 import { mpiMdmQueryLinksMiddleware } from '../middlewares/mpi-mdm-query-links';
 import { validationMiddleware } from '../middlewares/validation';
-import { buildOpenhimResponseObject } from '../utils/utils';
+import { buildOpenhimResponseObject, getData } from '../utils/utils';
 import { fetchEverythingByRef } from './handlers/fetchPatientResources';
 import { mpiMdmSummaryMiddleware } from '../middlewares/mpi-mdm-summary';
 import { fetchPatientSummaryByRef } from './handlers/fetchPatientSummaries';
 import { getConfig } from '../config/config';
+import { Patient } from 'fhir/r3';
+import { getMpiAuthToken } from '../utils/mpi';
+import logger from '../logger';
 
 const routes = express.Router();
 
@@ -61,6 +64,75 @@ routes.post(
   mpiAccessProxyMiddleware
 );
 
+// swap source ID for interaction ID
+routes.get('/fhir/Patient/:patientId', async (req, res) => {
+  const requestedId = req.params.patientId;
+
+  logger.debug(`Fetching patient ${requestedId} from FHIR store`);
+
+  const {
+    fhirDatastoreProtocol: fhirProtocol,
+    fhirDatastoreHost: fhirHost,
+    fhirDatastorePort: fhirPort,
+    mpiProtocol: mpiProtocol,
+    mpiHost: mpiHost,
+    mpiPort: mpiPort,
+    mpiAuthEnabled,
+  } = getConfig();
+  const fhirResponse = await getData(
+    fhirProtocol,
+    fhirHost,
+    fhirPort,
+    `/fhir/Patient/${requestedId}`,
+    {}
+  );
+
+  let upstreamId = requestedId;
+
+  if (fhirResponse.status === 200) {
+    const patient = fhirResponse.body as Patient;
+    const interactionId =
+      patient.link && patient.link[0]?.other.reference?.match(/Patient\/([^/]+)/)?.[1];
+
+    if (interactionId) {
+      upstreamId = interactionId;
+      logger.debug(`Swapping source ID ${requestedId} for interaction ID ${upstreamId}`);
+    }
+  }
+
+  logger.debug(`Fetching patient ${upstreamId} from MPI`);
+
+  const headers: HeadersInit = {
+    'Content-Type': 'application/fhir+json',
+  };
+
+  if (mpiAuthEnabled) {
+    const token = await getMpiAuthToken();
+
+    headers['Authorization'] = `Bearer ${token.accessToken}`;
+  }
+
+  const mpiResponse = await getData(
+    mpiProtocol,
+    mpiHost,
+    mpiPort,
+    `/fhir/links/Patient/${upstreamId}`,
+    {}
+  );
+
+  // Map the upstreamId to the requestedId
+  if (mpiResponse.status === 200) {
+    const patient = mpiResponse.body as Patient;
+
+    patient.id = requestedId;
+    logger.debug(
+      `Mapped upstream ID ${upstreamId} to requested ID ${requestedId} in response body`
+    );
+  }
+
+  res.status(mpiResponse.status).send(mpiResponse.body);
+});
+
 routes.get(
   '/fhir/Patient/:patientId/\\$everything',
   mpiMdmEverythingMiddleware,

diff --git a/src/utils/mpi.ts b/src/utils/mpi.ts
@@ -1,6 +1,6 @@
 import { Patient, Resource } from 'fhir/r3';
 import { getConfig } from '../config/config';
-import { getData, isHttpStatusOk } from './utils';
+import { createNewPatientRef, getData, isHttpStatusOk } from './utils';
 import { ClientOAuth2, OAuth2Token } from './client-oauth2';
 
 // Singleton instance of MPI Token stored in memory
@@ -60,24 +60,76 @@ export const fetchMpiResourceByRef = async <T extends Resource>(
   return isHttpStatusOk(response.status) ? (response.body as T) : undefined;
 };
 
-/**
- * Recursively fetch linked patient refs from the MPI
- */
 export const fetchMpiPatientLinks = async (patientRef: string, patientLinks: string[]) => {
-  patientLinks.push(patientRef);
-
-  const patient = await fetchMpiResourceByRef<Patient>(patientRef);
+  const patientLinksSet: Set<string> = new Set();
+  patientLinksSet.add(patientRef);
+
+  const {
+    mpiProtocol: protocol,
+    mpiHost: host,
+    mpiPort: port,
+    mpiAuthEnabled,
+    fhirDatastoreHost,
+    fhirDatastorePort,
+    fhirDatastoreProtocol,
+  } = getConfig();
+  const headers: HeadersInit = {
+    'Content-Type': 'application/fhir+json',
+  };
 
-  if (patient?.link) {
-    const linkedRefs = patient.link.map(({ other }) => other.reference);
-    const refsToFetch = linkedRefs.filter((ref) => {
-      return ref && !patientLinks.includes(ref);
-    }) as string[];
+  if (mpiAuthEnabled) {
+    const token = await getMpiAuthToken();
 
-    if (refsToFetch.length > 0) {
-      const promises = refsToFetch.map((ref) => fetchMpiPatientLinks(ref, patientLinks));
+    headers['Authorization'] = `Bearer ${token.accessToken}`;
+  }
 
-      await Promise.all(promises);
-    }
+  const guttedPatient = await getData(
+    fhirDatastoreProtocol,
+    fhirDatastoreHost,
+    fhirDatastorePort,
+    `/fhir/${patientRef}`,
+    headers
+  );
+
+  // Fetch patient links from MPI
+  let mpiPatient = await getData(
+    protocol,
+    host,
+    port,
+    `/fhir/links/Patient/${Object.assign(guttedPatient.body)
+      .link[0].other.reference.split('/')
+      .pop()}`,
+    headers
+  );
+
+  // Cater for SanteMpi client registry
+  if (!isHttpStatusOk(mpiPatient.status)) {
+    mpiPatient = await getData(
+      protocol,
+      host,
+      port,
+      `/fhir/Patient/${Object.assign(guttedPatient.body)
+        .link[0].other.reference.split('/')
+        .pop()}`,
+      headers
+    );
   }
+
+  const links: string[] = Object.assign(mpiPatient.body).link.map(
+    (element: { other: { reference: string } }) =>
+      createNewPatientRef(element.other.reference.split('/').pop() || '')
+  );
+
+  const guttedPatients = await getData(
+    fhirDatastoreProtocol,
+    fhirDatastoreHost,
+    fhirDatastorePort,
+    `/fhir/Patient?link=${encodeURIComponent(links.join(','))}`,
+    headers
+  );
+
+  Object.assign(guttedPatients.body).entry?.forEach((patient: { fullUrl: string }) => {
+    patientLinksSet.add(patient.fullUrl);
+  });
+  patientLinks.push(...patientLinksSet);
 };
diff --git a/src/utils/utils.ts b/src/utils/utils.ts
@@ -163,6 +163,7 @@ export const modifyBundle = (
         fullUrl: entry.fullUrl,
         resource: {
           resourceType: 'Patient',
+          id: entry.resource.id,
           link: [
             {
               other: {
@@ -174,7 +175,7 @@ export const modifyBundle = (
         },
         request: {
           method: 'PUT',
-          url: `Patient/${newPatientId}`,
+          url: `Patient/${entry.resource.id}`,
         },
       };
 

diff --git a/tests/cucumber/features/fhirAccessProxy.feature b/tests/cucumber/features/fhirAccessProxy.feature
@@ -3,7 +3,8 @@ Feature: FHIR Access Proxy
 
   Scenario: Valid $everything Request
     Given MPI and FHIR services are up and running
-    When an $everything search request is sent
+    When there is data
+    And an $everything search request is sent
     Then a successful response containing a bundle of related patient resources is sent back
 
   Scenario: Valid $everything Request without MDM

diff --git a/tests/cucumber/step-definitions/fhirAccessProxy.ts b/tests/cucumber/step-definitions/fhirAccessProxy.ts
@@ -29,9 +29,19 @@ Given('MPI and FHIR services are up and running', async (): Promise<void> => {
   request = supertest(server);
 });
 
+When('there is data', async (): Promise<void> => {
+  const response = await request
+    .post('/fhir')
+    .send(bundle)
+    .set('content-type', 'application/fhir+json')
+    .expect(200);
+
+  responseBody = response.body;
+});
+
 When('an $everything search request is sent', async (): Promise<void> => {
   const response = await request
-    .get('/fhir/Patient/1/$everything?_mdm=true')
+    .get('/fhir/Patient/testPatient/$everything?_mdm=true')
     .set('Content-Type', 'application/fhir+json')
     .expect(200);
   responseBody = response.body;
@@ -77,7 +87,7 @@ Then('a successful response containing a bundle is sent back', (): void => {
 
 When('an MDM search request is sent', async (): Promise<void> => {
   const response = await request
-    .get('/fhir/Observation?subject:mdm=Patient/1')
+    .get('/fhir/Observation?subject:mdm=Patient/testPatient')
     .set('Content-Type', 'application/fhir+json')
     .expect(200);
 

diff --git a/tests/cucumber/step-definitions/patientSyncMatching.ts b/tests/cucumber/step-definitions/patientSyncMatching.ts
@@ -103,8 +103,20 @@ Then('a patient should be created on the client registry', async (): Promise<voi
 
   const patientId = response.location.split('/')[1];
 
+  const fhirPatient = await fetch(
+    `${config.fhirDatastoreProtocol}://${config.fhirDatastoreHost}:${config.fhirDatastorePort}/fhir/Patient/${patientId}`,
+    {
+      headers: {
+        Authorization: `Bearer ${auth.accessToken}`,
+      },
+      method: 'GET',
+    }
+  );
+
+  const jsonPatient = await fhirPatient.json()
+
   const res = await fetch(
-    `${config.mpiProtocol}://${config.mpiHost}:${config.mpiPort}/fhir/Patient/${patientId}`,
+    jsonPatient.link[0].other.reference,
     {
       headers: {
         Authorization: `Bearer ${auth.accessToken}`,

diff --git a/tests/unit/matchPatientSync.ts b/tests/unit/matchPatientSync.ts
@@ -343,9 +343,10 @@ describe('Match Patient Synchronously', (): void => {
             fullUrl: 'Patient/12333',
             request: {
               method: 'PUT',
-              url: 'Patient/testPatient',
+              url: 'Patient/12333',
             },
             resource: {
+              id: '12333',
               link: [
                 {
                   other: {

diff --git a/tests/unit/middlewares.ts b/tests/unit/middlewares.ts
@@ -9,6 +9,7 @@ import { mpiMdmQueryLinksMiddleware } from '../../src/middlewares/mpi-mdm-query-
 import { validationMiddleware } from '../../src/middlewares/validation';
 import { mpiAuthMiddleware } from '../../src/middlewares/mpi-auth';
 import { mpiMdmSummaryMiddleware } from '../../src/middlewares/mpi-mdm-summary';
+import { createNewPatientRef } from '../../src/utils/utils';
 
 const config = getConfig();
 
@@ -31,7 +32,7 @@ const patientFhirResource1: Patient = {
   link: [
     {
       other: {
-        reference: 'Patient/2',
+        reference: 'Patient/0x4',
       },
       type: 'refer',
     },
@@ -44,7 +45,7 @@ const patientFhirResource2: Patient = {
   link: [
     {
       other: {
-        reference: 'Patient/1',
+        reference: 'Patient/0x7',
       },
       type: 'seealso',
     },
@@ -324,8 +325,11 @@ describe('Middlewares', (): void => {
 
     it('should perform MDM expansion when mdm param is supplied', async () => {
       nock(mpiUrl).persist().post('/auth/oauth2_token').reply(200, newOauth2TokenGenerated);
-      nock(mpiUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
+      nock(mpiUrl).get('/fhir/links/Patient/0x4').reply(200, {...patientFhirResource1, link: [{other: {reference: 'Patient/0x4'}}, {other: {reference: 'Patient/0x7'}}]});
       nock(mpiUrl).get('/fhir/Patient/2').reply(200, patientFhirResource2);
+      const links = encodeURIComponent([createNewPatientRef('0x4'),createNewPatientRef('0x7')].join(','))
+      nock(fhirDatastoreUrl).get(`/fhir/Patient?link=${links}`).reply(200, {entry: [{fullUrl: 'Patient/1'}, {fullUrl: 'Patient/2'}]});
+      nock(fhirDatastoreUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
       nock(fhirDatastoreUrl)
         .get(`/fhir/Encounter?subject=${encodeURIComponent('Patient/1,Patient/2')}`)
         .reply(200, Encounters);
@@ -383,8 +387,11 @@ describe('Middlewares', (): void => {
 
     it('should preform MDM expansion when mdm param is supplied', async () => {
       nock(mpiUrl).persist().post('/auth/oauth2_token').reply(200, newOauth2TokenGenerated);
-      nock(mpiUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
+      nock(mpiUrl).get('/fhir/links/Patient/0x4').reply(200, {...patientFhirResource1, link: [{other: {reference: 'Patient/0x4'}}, {other: {reference: 'Patient/0x7'}}]});
       nock(mpiUrl).get('/fhir/Patient/2').reply(200, patientFhirResource2);
+      const links = encodeURIComponent([createNewPatientRef('0x4'),createNewPatientRef('0x7')].join(','))
+      nock(fhirDatastoreUrl).get(`/fhir/Patient?link=${links}`).reply(200, {entry: [{fullUrl: 'Patient/1'}, {fullUrl: 'Patient/2'}]});
+      nock(fhirDatastoreUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
       nock(fhirDatastoreUrl)
         .get(`/fhir/${patientRefSummary1}/$summary`)
         .reply(200, patientSummary1);
@@ -435,8 +442,12 @@ describe('Middlewares', (): void => {
 
     it('should perform MDM expansion when mdm param is supplied', async () => {
       nock(mpiUrl).persist().post('/auth/oauth2_token').reply(200, {});
-      nock(mpiUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
+      nock(mpiUrl).get('/fhir/links/Patient/0x4').reply(200, {...patientFhirResource1, link: [{other: {reference: 'Patient/0x4'}}, {other: {reference: 'Patient/0x7'}}]});
       nock(mpiUrl).get('/fhir/Patient/2').reply(200, patientFhirResource2);
+      const links = encodeURIComponent([createNewPatientRef('0x4'),createNewPatientRef('0x7')].join(','))
+      nock(fhirDatastoreUrl).get(`/fhir/Patient?link=${links}`).reply(200, {entry: [{fullUrl: 'Patient/1'}, {fullUrl: 'Patient/2'}]});
+      nock(fhirDatastoreUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
+
       const request = {
         body: {},
         headers: {},

diff --git a/tests/unit/mpi.ts b/tests/unit/mpi.ts
@@ -9,13 +9,17 @@ import {
   fetchMpiResourceByRef,
   fetchMpiPatientLinks,
 } from '../../src/utils/mpi';
+import { createNewPatientRef } from '../../src/utils/utils';
 
 const config = getConfig();
 
 const { mpiProtocol, mpiHost, mpiPort, mpiClientId, mpiClientSecret } = config;
 
 const mpiUrl = `${mpiProtocol}://${mpiHost}:${mpiPort}`;
 
+const { fhirDatastoreProtocol, fhirDatastoreHost, fhirDatastorePort } = config;
+const fhirDatastoreUrl = `${fhirDatastoreProtocol}://${fhirDatastoreHost}:${fhirDatastorePort}`;
+
 const newOauth2TokenGenerated = {
   token_type: 'bearer',
   access_token: 'accessToken',
@@ -51,7 +55,7 @@ const patientFhirResource1: Patient = {
   link: [
     {
       other: {
-        reference: 'Patient/2',
+        reference: 'Patient/0x4',
       },
       type: 'refer',
     },
@@ -64,7 +68,7 @@ const patientFhirResource2: Patient = {
   link: [
     {
       other: {
-        reference: 'Patient/1',
+        reference: 'Patient/0x7',
       },
       type: 'seealso',
     },
@@ -140,8 +144,13 @@ describe('MPI', (): void => {
 
   describe('*fetchMpiPatientLinks', async (): Promise<void> => {
     it('should fetch patient links from MPI fhir', async (): Promise<void> => {
-      nock(mpiUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
+      nock(mpiUrl).persist().post('/auth/oauth2_token').reply(200, newOauth2TokenGenerated);
+      nock(mpiUrl).get('/fhir/links/Patient/0x4').reply(200, {...patientFhirResource1, link: [{other: {reference: 'Patient/0x4'}}, {other: {reference: 'Patient/0x7'}}]});
       nock(mpiUrl).get('/fhir/Patient/2').reply(200, patientFhirResource2);
+      const links = encodeURIComponent([createNewPatientRef('0x4'),createNewPatientRef('0x7')].join(','))
+      nock(fhirDatastoreUrl).get(`/fhir/Patient?link=${links}`).reply(200, {entry: [{fullUrl: 'Patient/1'}, {fullUrl: 'Patient/2'}]});
+      nock(fhirDatastoreUrl).get('/fhir/Patient/1').reply(200, patientFhirResource1);
+
       const refs: string[] = [];
       await fetchMpiPatientLinks(`Patient/1`, refs);
       expect(refs).to.deep.equal(['Patient/1', 'Patient/2']);