Merge pull request #852 from aehrc/main

Merging main to acdc-pilot

apps/smart-forms-app/package.json

@@ -28,7 +28,7 @@
   "dependencies": {
     "@aehrc/sdc-assemble": "^1.2.0",
     "@aehrc/sdc-populate": "^2.2.1",
-    "@aehrc/smart-forms-renderer": "^0.35.4",
+    "@aehrc/smart-forms-renderer": "^0.35.5",
     "@emotion/react": "^11.11.4",
     "@emotion/styled": "^11.11.5",
     "@fontsource/material-icons": "^5.0.16",

documentation/package.json

@@ -15,7 +15,7 @@
     "typecheck": "tsc"
   },
   "dependencies": {
-    "@aehrc/smart-forms-renderer": "^0.35.4",
+    "@aehrc/smart-forms-renderer": "^0.35.5",
     "@docusaurus/core": "^3.4.0",
     "@docusaurus/preset-classic": "^3.4.0",
     "@docusaurus/theme-live-codeblock": "^3.4.0",

packages/smart-forms-renderer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@aehrc/smart-forms-renderer",
-  "version": "0.35.4",
+  "version": "0.35.5",
   "description": "FHIR Structured Data Captured (SDC) rendering engine for Smart Forms",
   "main": "lib/index.js",
   "scripts": {

packages/smart-forms-renderer/src/interfaces/questionnaireStore.interface.ts

@@ -21,7 +21,7 @@ import type { LaunchContext } from './populate.interface';
 import type { EnableWhenExpressions, EnableWhenItems } from './enableWhen.interface';
 import type { CalculatedExpression } from './calculatedExpression.interface';
 import type { AnswerExpression } from './answerExpression.interface';
-import type { Coding } from 'fhir/r4';
+import type { Coding, QuestionnaireItemAnswerOption } from 'fhir/r4';
 
 export interface QuestionnaireModel {
   itemTypes: Record<string, string>;
@@ -32,6 +32,7 @@ export interface QuestionnaireModel {
   enableWhenExpressions: EnableWhenExpressions;
   calculatedExpressions: Record<string, CalculatedExpression[]>;
   answerExpressions: Record<string, AnswerExpression>;
+  answerOptions: Record<string, QuestionnaireItemAnswerOption[]>;
   processedValueSetCodings: Record<string, Coding[]>;
   processedValueSetUrls: Record<string, string>;
   fhirPathContext: Record<string, any>;

packages/smart-forms-renderer/src/stores/questionnaireStore.ts

@@ -46,6 +46,7 @@ import { createSelectors } from './selector';
 import { mutateRepeatEnableWhenExpressionInstances } from '../utils/enableWhenExpression';
 import { questionnaireResponseStore } from './questionnaireResponseStore';
 import { createQuestionnaireResponseItemMap } from '../utils/questionnaireResponseStoreUtils/updatableResponseItems';
+import { insertCompleteAnswerOptionsIntoQuestionnaire } from '../utils/questionnaireStoreUtils/insertAnswerOptions';
 
 /**
  * QuestionnaireStore properties and methods
@@ -180,6 +181,13 @@ export const questionnaireStore = createStore<QuestionnaireStoreType>()((set, ge
       terminologyServerUrl
     );
 
+    // Insert answerOptions with displays into questionnaire
+    questionnaire = insertCompleteAnswerOptionsIntoQuestionnaire(
+      questionnaire,
+      questionnaireModel.answerOptions
+    );
+
+    // Initialise form with questionnaire response and properties in questionnaire model
     const {
       initialEnableWhenItems,
       initialEnableWhenLinkedQuestions,

packages/smart-forms-renderer/src/utils/questionnaireStoreUtils/addDisplayToCodings.ts

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 
-import type { Coding } from 'fhir/r4';
+import type { Coding, QuestionnaireItemAnswerOption } from 'fhir/r4';
 import type { CodeSystemLookupPromise } from '../../interfaces/lookup.interface';
 import * as FHIR from 'fhirclient';
 
@@ -56,6 +56,45 @@ export async function addDisplayToProcessedCodings(
   return processedCodings;
 }
 
+// Use this for a Record<linkId, answerOption[]>
+export async function addDisplayToAnswerOptions(
+  answerOptions: Record<string, QuestionnaireItemAnswerOption[]>,
+  terminologyServerUrl: string
+): Promise<Record<string, QuestionnaireItemAnswerOption[]>> {
+  // Store code system lookup promises for codings without displays
+  const codeSystemLookupPromises: Record<string, CodeSystemLookupPromise> = {};
+  for (const key in answerOptions) {
+    const options = answerOptions[key];
+    for (const option of options) {
+      if (option.valueCoding && !option.valueCoding.display) {
+        const query = `system=${option.valueCoding.system}&code=${option.valueCoding.code}`;
+        codeSystemLookupPromises[query] = {
+          promise: getCodeSystemLookupPromise(query, terminologyServerUrl),
+          oldCoding: option.valueCoding
+        };
+      }
+    }
+  }
+
+  // Resolves lookup promises in one go and assign newCodings to processedCodings
+  const resolvedCodeSystemLookupPromises = await resolveLookupPromises(codeSystemLookupPromises);
+  for (const key in answerOptions) {
+    const options = answerOptions[key];
+
+    for (const option of options) {
+      if (option.valueCoding) {
+        const lookUpKey = `system=${option.valueCoding.system}&code=${option.valueCoding.code}`;
+        const resolvedLookup = resolvedCodeSystemLookupPromises[lookUpKey];
+        if (resolvedLookup?.newCoding?.display) {
+          option.valueCoding.display = resolvedLookup.newCoding.display;
+        }
+      }
+    }
+  }
+
+  return answerOptions;
+}
+
 // Use this for an array of codings
 export async function addDisplayToCodingArray(
   codings: Coding[],

packages/smart-forms-renderer/src/utils/questionnaireStoreUtils/createQuestionaireModel.ts

@@ -28,7 +28,7 @@ import type { Variables } from '../../interfaces/variables.interface';
 import { resolveValueSets } from './resolveValueSets';
 import { addAdditionalVariables } from './addAdditionalVariables';
 import { getLinkIdTypeTuples } from '../qItem';
-import { addDisplayToProcessedCodings } from './addDisplayToCodings';
+import { addDisplayToAnswerOptions, addDisplayToProcessedCodings } from './addDisplayToCodings';
 
 export async function createQuestionnaireModel(
   questionnaire: Questionnaire,
@@ -62,8 +62,13 @@ export async function createQuestionnaireModel(
     terminologyServerUrl
   );
 
-  const { enableWhenItems, enableWhenExpressions, calculatedExpressions, answerExpressions } =
-    extractOtherExtensionsResult;
+  const {
+    enableWhenItems,
+    enableWhenExpressions,
+    calculatedExpressions,
+    answerExpressions,
+    answerOptions
+  } = extractOtherExtensionsResult;
   variables = extractOtherExtensionsResult.variables;
   valueSetPromises = extractOtherExtensionsResult.valueSetPromises;
 
@@ -83,6 +88,12 @@ export async function createQuestionnaireModel(
     terminologyServerUrl
   );
 
+  // In answerOptions, add display values to codings lacking them
+  const completeAnswerOptions = await addDisplayToAnswerOptions(
+    answerOptions,
+    terminologyServerUrl
+  );
+
   return {
     itemTypes,
     tabs,
@@ -92,6 +103,7 @@ export async function createQuestionnaireModel(
     enableWhenExpressions,
     calculatedExpressions,
     answerExpressions,
+    answerOptions: completeAnswerOptions,
     processedValueSetCodings,
     processedValueSetUrls,
     fhirPathContext: {}
@@ -107,6 +119,7 @@ function createEmptyModel(): QuestionnaireModel {
     calculatedExpressions: {},
     enableWhenExpressions: { singleExpressions: {}, repeatExpressions: {} },
     answerExpressions: {},
+    answerOptions: {},
     enableWhenItems: { singleItems: {}, repeatItems: {} },
     processedValueSetCodings: {},
     processedValueSetUrls: {},

packages/smart-forms-renderer/src/utils/questionnaireStoreUtils/extractOtherExtensions.ts

@@ -19,6 +19,7 @@ import type {
   Expression,
   Questionnaire,
   QuestionnaireItem,
+  QuestionnaireItemAnswerOption,
   QuestionnaireItemEnableWhen
 } from 'fhir/r4';
 import type { CalculatedExpression } from '../../interfaces/calculatedExpression.interface';
@@ -55,6 +56,7 @@ interface ReturnParamsRecursive {
   calculatedExpressions: Record<string, CalculatedExpression[]>;
   answerExpressions: Record<string, AnswerExpression>;
   valueSetPromises: Record<string, ValueSetPromise>;
+  answerOptions: Record<string, QuestionnaireItemAnswerOption[]>;
 }
 
 export function extractOtherExtensions(
@@ -70,6 +72,7 @@ export function extractOtherExtensions(
   };
   const calculatedExpressions: Record<string, CalculatedExpression[]> = {};
   const answerExpressions: Record<string, AnswerExpression> = {};
+  const answerOptions: Record<string, QuestionnaireItemAnswerOption[]> = {};
 
   if (!questionnaire.item || questionnaire.item.length === 0) {
     return {
@@ -81,6 +84,7 @@ export function extractOtherExtensions(
       },
       calculatedExpressions: {},
       answerExpressions: {},
+      answerOptions: {},
       valueSetPromises: valueSetPromises
     };
   }
@@ -95,6 +99,7 @@ export function extractOtherExtensions(
       enableWhenExpressions,
       calculatedExpressions,
       answerExpressions,
+      answerOptions,
       valueSetPromises,
       defaultTerminologyServerUrl: terminologyServerUrl,
       parentRepeatGroupLinkId: isRepeatGroup ? topLevelItem.linkId : undefined
@@ -107,6 +112,7 @@ export function extractOtherExtensions(
     enableWhenExpressions,
     calculatedExpressions,
     answerExpressions,
+    answerOptions,
     valueSetPromises
   };
 }
@@ -119,6 +125,7 @@ interface extractExtensionsFromItemRecursiveParams {
   enableWhenExpressions: EnableWhenExpressions;
   calculatedExpressions: Record<string, CalculatedExpression[]>;
   answerExpressions: Record<string, AnswerExpression>;
+  answerOptions: Record<string, QuestionnaireItemAnswerOption[]>;
   valueSetPromises: Record<string, ValueSetPromise>;
   defaultTerminologyServerUrl: string;
   parentRepeatGroupLinkId?: string;
@@ -135,6 +142,7 @@ function extractExtensionsFromItemRecursive(
     enableWhenExpressions,
     calculatedExpressions,
     answerExpressions,
+    answerOptions,
     valueSetPromises,
     defaultTerminologyServerUrl,
     parentRepeatGroupLinkId
@@ -201,6 +209,12 @@ function extractExtensionsFromItemRecursive(
     };
   }
 
+  // Get answerOptions
+  const options = item.answerOption ?? null;
+  if (options) {
+    answerOptions[item.linkId] = options;
+  }
+
   const valueSetUrl = item.answerValueSet;
   if (valueSetUrl) {
     if (!valueSetPromises[valueSetUrl] && !valueSetUrl.startsWith('#')) {
@@ -229,6 +243,7 @@ function extractExtensionsFromItemRecursive(
     enableWhenExpressions,
     calculatedExpressions,
     answerExpressions,
+    answerOptions,
     valueSetPromises
   };
 }

packages/smart-forms-renderer/src/utils/questionnaireStoreUtils/insertAnswerOptions.ts

@@ -0,0 +1,56 @@
+/*
+ * 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.
+ */
+
+import type { Questionnaire, QuestionnaireItem, QuestionnaireItemAnswerOption } from 'fhir/r4';
+
+/**
+ * Filter x-fhir-query variables from questionnaire's extensions needed for population
+ *
+ * @author Sean Fong
+ */
+export function insertCompleteAnswerOptionsIntoQuestionnaire(
+  questionnaire: Questionnaire,
+  completeAnswerOptions: Record<string, QuestionnaireItemAnswerOption[]>
+): Questionnaire {
+  if (questionnaire.item && questionnaire.item.length > 0) {
+    for (const qItem of questionnaire.item) {
+      insertCompleteAnswerOptionsRecursive(qItem, completeAnswerOptions);
+    }
+  }
+
+  return questionnaire;
+}
+
+function insertCompleteAnswerOptionsRecursive(
+  qItem: QuestionnaireItem,
+  completeAnswerOptions: Record<string, QuestionnaireItemAnswerOption[]>
+) {
+  if (qItem.item) {
+    for (const childItem of qItem.item) {
+      insertCompleteAnswerOptionsRecursive(childItem, completeAnswerOptions);
+    }
+  }
+
+  if (qItem.answerOption) {
+    const options = completeAnswerOptions[qItem.linkId];
+    if (options) {
+      qItem.answerOption = options;
+    }
+  }
+
+  return;
+}