Merge pull request #828 from aehrc/issue/827

Issue/827

README.md

@@ -82,7 +82,7 @@ The default configuration is set to:
 ```
 # Ontoserver endpoint for $expand operations
 # To run your own Ontoserver instance, contact us at https://ontoserver.csiro.au/site/contact-us/ontoserver-contact-form/
-VITE_ONTOSERVER_URL=https://r4.ontoserver.csiro.au/fhir
+VITE_ONTOSERVER_URL=https://tx.ontoserver.csiro.au/fhir
 
 # Questionnaire-hosting FHIR server
 VITE_FORMS_SERVER_URL=https://smartforms.csiro.au/api/fhir

apps/smart-forms-app/.env

@@ -5,5 +5,3 @@ VITE_LAUNCH_SCOPE=fhirUser online_access openid profile patient/Condition.rs pat
 VITE_LAUNCH_CLIENT_ID=a57d90e3-5f69-4b92-aa2e-2992180863c1
 
 VITE_IN_APP_POPULATE=true
-
-VITE_SHOW_DEBUG_MODE=true

apps/smart-forms-app/.env.production

@@ -5,5 +5,3 @@ VITE_LAUNCH_SCOPE=fhirUser online_access openid profile patient/Condition.rs pat
 VITE_LAUNCH_CLIENT_ID=a57d90e3-5f69-4b92-aa2e-2992180863c1
 
 VITE_IN_APP_POPULATE=true
-
-VITE_SHOW_DEBUG_MODE=false

apps/smart-forms-app/package.json

@@ -26,8 +26,8 @@
   "homepage": "https://github.com/aehrc/smart-forms#readme",
   "dependencies": {
     "@aehrc/sdc-assemble": "^1.2.0",
-    "@aehrc/sdc-populate": "^2.0.3",
-    "@aehrc/smart-forms-renderer": "^0.32.2",
+    "@aehrc/sdc-populate": "^2.1.0",
+    "@aehrc/smart-forms-renderer": "^0.33.0",
     "@emotion/react": "^11.11.4",
     "@emotion/styled": "^11.11.5",
     "@fontsource/material-icons": "^5.0.16",

apps/smart-forms-app/src/features/dashboard/components/DashboardDebugFooter/DashboardDebugFooter.tsx

@@ -17,8 +17,8 @@
 
 import { StyledRoot } from '../../../../components/DebugFooter/DebugFooter.styles.ts';
 import { Box, Typography } from '@mui/material';
-import { FORMS_SERVER_ENDPOINT } from '../../../../utils/env.ts';
 import useSmartClient from '../../../../hooks/useSmartClient.ts';
+import { FORMS_SERVER_URL, LAUNCH_CLIENT_ID } from '../../../../globals.ts';
 
 function DashboardDebugFooter() {
   const { smartClient } = useSmartClient();
@@ -32,13 +32,10 @@ function DashboardDebugFooter() {
           </Typography>
           <Typography variant="overline">
             {`Forms server: ${
-              FORMS_SERVER_ENDPOINT ??
-              'Undefined. Defaulting to https://smartforms.csiro.au/api/fhir'
+              FORMS_SERVER_URL ?? 'Undefined. Defaulting to https://smartforms.csiro.au/api/fhir'
             }`}
           </Typography>
-          <Typography variant="overline">
-            {`Client ID: ${import.meta.env.VITE_LAUNCH_CLIENT_ID}`}
-          </Typography>
+          <Typography variant="overline">{`Client ID: ${LAUNCH_CLIENT_ID}`}</Typography>
         </Box>
       </StyledRoot>
     </>

apps/smart-forms-app/src/features/dashboard/utils/dashboard.ts

@@ -30,13 +30,12 @@ import type Client from 'fhirclient/lib/Client';
 import type { QuestionnaireListItem, ResponseListItem } from '../types/list.interface.ts';
 import { HEADERS } from '../../../api/headers.ts';
 import { nanoid } from 'nanoid';
-
-const endpointUrl = import.meta.env.VITE_FORMS_SERVER_URL ?? 'https://smartforms.csiro.au/api/fhir';
+import { FORMS_SERVER_URL } from '../../../globals.ts';
 
 export function getFormsServerBundlePromise(queryUrl: string): Promise<Bundle> {
   queryUrl = queryUrl.replace('|', '&version=');
 
-  return FHIR.client(endpointUrl).request({
+  return FHIR.client(FORMS_SERVER_URL).request({
     url: queryUrl,
     headers: HEADERS
   });
@@ -45,7 +44,7 @@ export function getFormsServerBundlePromise(queryUrl: string): Promise<Bundle> {
 export function getFormsServerAssembledBundlePromise(queryUrl: string): Promise<Bundle> {
   queryUrl = queryUrl.replace('|', '&version=');
 
-  return FHIR.client(endpointUrl).request({
+  return FHIR.client(FORMS_SERVER_URL).request({
     url: queryUrl,
     headers: HEADERS
   });
@@ -68,7 +67,7 @@ export function getFormsServerBundleOrQuestionnairePromise(
     queryUrl = queryUrl.substring(0, queryUrl.lastIndexOf('-SMARTcopy')) + '';
   }
 
-  return FHIR.client(endpointUrl).request({
+  return FHIR.client(FORMS_SERVER_URL).request({
     url: queryUrl,
     headers: HEADERS
   });

apps/smart-forms-app/src/features/prepopulate/api/requestPopulate.ts

@@ -15,34 +15,44 @@
  * limitations under the License.
  */
 
-import { IS_IN_APP_POPULATE } from '../../../utils/env.ts';
 import type { InputParameters, OutputParameters } from '@aehrc/sdc-populate';
 import { isOutputParameters, populate } from '@aehrc/sdc-populate';
 import type { RequestConfig } from '../utils/callback.ts';
-import { fetchResourceCallback } from '../utils/callback.ts';
+import { fetchResourceCallback, terminologyCallback } from '../utils/callback.ts';
 import { HEADERS } from '../../../api/headers.ts';
 import type Client from 'fhirclient/lib/Client';
 import type { OperationOutcome } from 'fhir/r4';
+import { IN_APP_POPULATE, TERMINOLOGY_SERVER_URL } from '../../../globals.ts';
 
 export async function requestPopulate(
   fhirClient: Client,
   inputParameters: InputParameters
 ): Promise<OutputParameters | OperationOutcome> {
-  const requestConfig: RequestConfig = {
+  const fetchResourceRequestConfig: RequestConfig = {
     clientEndpoint: fhirClient.state.serverUrl,
     authToken: fhirClient.state.tokenResponse!.access_token!
   };
 
-  const populatePromise: Promise<any> = IS_IN_APP_POPULATE
-    ? populate(inputParameters, fetchResourceCallback, requestConfig)
+  const terminologyRequestConfig: RequestConfig = {
+    clientEndpoint: TERMINOLOGY_SERVER_URL
+  };
+
+  const populatePromise: Promise<any> = IN_APP_POPULATE
+    ? populate(
+        inputParameters,
+        fetchResourceCallback,
+        fetchResourceRequestConfig,
+        terminologyCallback,
+        terminologyRequestConfig
+      )
     : fhirClient.request({
         url: 'Questionnaire/$populate',
         method: 'POST',
         body: JSON.stringify(inputParameters),
         headers: {
           ...HEADERS,
           'Content-Type': 'application/json',
-          Authorization: `Bearer ${requestConfig.authToken}`
+          Authorization: `Bearer ${fetchResourceRequestConfig.authToken}`
         }
       });
 

apps/smart-forms-app/src/features/prepopulate/utils/callback.ts

@@ -22,7 +22,7 @@ const ABSOLUTE_URL_REGEX = /^(https?|ftp):\/\/[^\s/$.?#].[^\s]*$/;
 
 export interface RequestConfig {
   clientEndpoint: string;
-  authToken: string;
+  authToken?: string;
 }
 
 export const fetchResourceCallback: FetchResourceCallback = (
@@ -47,3 +47,24 @@ export const fetchResourceCallback: FetchResourceCallback = (
     headers: headers
   });
 };
+
+export const terminologyCallback: FetchResourceCallback = (
+  query: string,
+  requestConfig: RequestConfig
+) => {
+  let { clientEndpoint } = requestConfig;
+
+  const headers = {
+    Accept: 'application/json;charset=utf-8'
+  };
+
+  if (!clientEndpoint.endsWith('/')) {
+    clientEndpoint += '/';
+  }
+
+  const queryUrl = ABSOLUTE_URL_REGEX.test(query) ? query : clientEndpoint + query;
+
+  return axios.get(queryUrl, {
+    headers: headers
+  });
+};

apps/smart-forms-app/src/features/renderer/components/RendererDebugFooter/DebugPanel.tsx

@@ -25,8 +25,7 @@ import AccountTreeIcon from '@mui/icons-material/AccountTree';
 import NotesIcon from '@mui/icons-material/Notes';
 import DebugResponseView from './DebugResponseView.tsx';
 import OpenInNewIcon from '@mui/icons-material/OpenInNew';
-
-const endpointUrl = import.meta.env.VITE_FORMS_SERVER_URL ?? 'https://smartforms.csiro.au/api/fhir';
+import { FORMS_SERVER_URL } from '../../../../globals.ts';
 
 interface Props {
   questionnaire: Questionnaire;
@@ -96,7 +95,7 @@ function DebugPanel(props: Props) {
           {questionnaireSelected ? (
             <Tooltip title="Open Questionnaire in new tab">
               <a
-                href={endpointUrl + '/Questionnaire/' + questionnaire.id}
+                href={FORMS_SERVER_URL + '/Questionnaire/' + questionnaire.id}
                 target="_blank"
                 rel="noreferrer">
                 <IconButton>

apps/smart-forms-app/src/features/smartAppLaunch/components/Launch.tsx

@@ -19,6 +19,7 @@ import { useSearchParams } from 'react-router-dom';
 import { oauth2 } from 'fhirclient';
 import { useState } from 'react';
 import LaunchView from './LaunchView.tsx';
+import { LAUNCH_CLIENT_ID, LAUNCH_SCOPE } from '../../../globals.ts';
 
 export type LaunchState = 'loading' | 'error' | 'success';
 
@@ -29,8 +30,8 @@ function Launch() {
   const iss = searchParams.get('iss');
   const launch = searchParams.get('launch');
 
-  const clientId = import.meta.env.VITE_LAUNCH_CLIENT_ID;
-  const scope = import.meta.env.VITE_LAUNCH_SCOPE;
+  const clientId = LAUNCH_CLIENT_ID;
+  const scope = LAUNCH_SCOPE;
 
   if (iss && launch) {
     // oauth2.authorize triggers a redirect to EHR

apps/smart-forms-app/src/features/smartAppLaunch/utils/launch.ts

@@ -28,8 +28,7 @@ import type {
 import type { fhirclient } from 'fhirclient/lib/types';
 import * as FHIR from 'fhirclient';
 import { HEADERS } from '../../../api/headers.ts';
-
-const endpointUrl = import.meta.env.VITE_FORMS_SERVER_URL ?? 'https://smartforms.csiro.au/api/fhir';
+import { FORMS_SERVER_URL } from '../../../globals.ts';
 
 export async function readCommonLaunchContexts(
   client: Client
@@ -117,7 +116,7 @@ export function readQuestionnaireContext(
 
     canonical = canonical.replace('|', '&version=');
 
-    return FHIR.client(endpointUrl).request({
+    return FHIR.client(FORMS_SERVER_URL).request({
       url: 'Questionnaire?url=' + canonical + '&_sort=_lastUpdated',
       method: 'GET',
       headers: HEADERS

apps/smart-forms-app/src/features/standalone/components/StandaloneResourceViewer.tsx

@@ -99,7 +99,7 @@ function ResourceViewSwitcher(props: ResourceViewSwitcherProps) {
     return (
       <>
         <Typography variant="subtitle2">
-          Defaults to https://r4.ontoserver.csiro.au if null
+          Defaults to https://tx.ontoserver.csiro.au if null
         </Typography>
         <pre>{JSON.stringify(state.terminologyServerUrl, null, 2)}</pre>
       </>

apps/smart-forms-app/src/globals.ts

@@ -0,0 +1,26 @@
+/*
+ * Copyright 2024 Commonwealth Scientific and Industrial Research
+ * Organisation (CSIRO) ABN 41 687 119 230.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+export const TERMINOLOGY_SERVER_URL =
+  import.meta.env.VITE_ONTOSERVER_URL ?? 'https://tx.ontoserver.csiro.au/fhir';
+export const FORMS_SERVER_URL =
+  import.meta.env.VITE_FORMS_SERVER_URL ?? 'https://smartforms.csiro.au/api/fhir';
+export const LAUNCH_SCOPE =
+  import.meta.env.VITE_LAUNCH_SCOPE ??
+  'fhirUser online_access openid profile patient/Condition.rs patient/Observation.rs launch patient/Encounter.rs patient/QuestionnaireResponse.cruds patient/Patient.rs';
+export const LAUNCH_CLIENT_ID = import.meta.env.VITE_LAUNCH_CLIENT_ID ?? 'smart-forms-client-id';
+export const IN_APP_POPULATE = import.meta.env.VITE_IN_APP_POPULATE ?? true;

apps/smart-forms-app/src/utils/assemble.ts

@@ -20,8 +20,7 @@ import { isInputParameters } from '@aehrc/sdc-assemble';
 import * as FHIR from 'fhirclient';
 import { HEADERS } from '../api/headers.ts';
 import { getFormsServerAssembledBundlePromise } from '../features/dashboard/utils/dashboard.ts';
-
-const endpointUrl = import.meta.env.VITE_FORMS_SERVER_URL ?? 'https://smartforms.csiro.au/api/fhir';
+import { FORMS_SERVER_URL } from '../globals.ts';
 
 export function assemblyIsRequired(questionnaire: Questionnaire): boolean {
   return !!questionnaire.extension?.find(
@@ -49,7 +48,7 @@ export async function assembleQuestionnaire(
 ): Promise<Questionnaire | OperationOutcome> {
   const parameters = defineAssembleParameters(questionnaire);
   if (isInputParameters(parameters)) {
-    const outputAssembleParams = await FHIR.client(endpointUrl).request({
+    const outputAssembleParams = await FHIR.client(FORMS_SERVER_URL).request({
       url: 'Questionnaire/$assemble',
       method: 'POST',
       body: JSON.stringify(parameters),
@@ -67,7 +66,7 @@ export async function assembleQuestionnaire(
 }
 
 export function updateAssembledQuestionnaire(questionnaire: Questionnaire) {
-  return FHIR.client(endpointUrl).request({
+  return FHIR.client(FORMS_SERVER_URL).request({
     url: `Questionnaire/${questionnaire.id}`,
     method: 'PUT',
     body: JSON.stringify(questionnaire),

documentation/docs/api/smart-forms-renderer/variables/terminologyServerStore.md

@@ -3,7 +3,7 @@
 > `const` **terminologyServerStore**: `StoreApi` \<[`TerminologyServerStoreType`](../interfaces/TerminologyServerStoreType.md)\>
 
 Terminology server state management store. This is used for resolving valueSets externally.
-Defaults to use https://r4.ontoserver.csiro.au/fhir.
+Defaults to use https://tx.ontoserver.csiro.au/fhir.
 This is the vanilla version of the store which can be used in non-React environments.
 
 ## See

documentation/docs/api/smart-forms-renderer/variables/useTerminologyServerStore.md

@@ -3,7 +3,7 @@
 > `const` **useTerminologyServerStore**: `StoreApi` \<[`TerminologyServerStoreType`](../interfaces/TerminologyServerStoreType.md)\> & `object`
 
 Terminology server state management store. This is used for resolving valueSets externally.
-Defaults to use https://r4.ontoserver.csiro.au/fhir.
+Defaults to use https://tx.ontoserver.csiro.au/fhir.
 This is the React version of the store which can be used as React hooks in React functional components.
 
 ## See

documentation/package.json

@@ -15,7 +15,7 @@
     "typecheck": "tsc"
   },
   "dependencies": {
-    "@aehrc/smart-forms-renderer": "^0.32.2",
+    "@aehrc/smart-forms-renderer": "^0.33.0",
     "@docusaurus/core": "3.3.2",
     "@docusaurus/preset-classic": "3.3.2",
     "@docusaurus/theme-live-codeblock": "^3.3.2",

packages/sdc-populate/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aehrc/sdc-populate",
-  "version": "2.0.3",
+  "version": "2.1.0",
   "description": "Performs the $populate operation from the HL7 FHIR SDC (Structured Data Capture) specification: http://hl7.org/fhir/uv/sdc",
   "main": "lib/index.js",
   "scripts": {