From 4f50dbf13a533a67fc4eb3f41efa9d8695badcd2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 29 Aug 2024 01:16:07 +0000 Subject: [PATCH 01/16] Bump fast-xml-parser from 4.3.6 to 4.4.1 in /documentation Bumps [fast-xml-parser](https://github.com/NaturalIntelligence/fast-xml-parser) from 4.3.6 to 4.4.1. - [Release notes](https://github.com/NaturalIntelligence/fast-xml-parser/releases) - [Changelog](https://github.com/NaturalIntelligence/fast-xml-parser/blob/master/CHANGELOG.md) - [Commits](https://github.com/NaturalIntelligence/fast-xml-parser/compare/v4.3.6...v4.4.1) --- updated-dependencies: - dependency-name: fast-xml-parser dependency-type: indirect ... Signed-off-by: dependabot[bot] --- documentation/package-lock.json | 2538 +++++++++++++++---------------- 1 file changed, 1209 insertions(+), 1329 deletions(-) diff --git a/documentation/package-lock.json b/documentation/package-lock.json index ef8a7dcf7..bc3059839 100644 --- a/documentation/package-lock.json +++ b/documentation/package-lock.json @@ -8,56 +8,73 @@ "name": "@aehrc/smart-forms-documentation", "version": "0.0.0", "dependencies": { - "@aehrc/smart-forms-renderer": "^0.27.3", - "@docusaurus/core": "3.3.2", - "@docusaurus/preset-classic": "3.3.2", - "@emotion/react": "^11.11.4", + "@aehrc/smart-forms-renderer": "^0.38.4", + "@docusaurus/core": "^3.4.0", + "@docusaurus/preset-classic": "^3.4.0", + "@docusaurus/theme-live-codeblock": "^3.4.0", + "@emotion/react": "^11.13.0", "@emotion/styled": "^11.11.5", "@iconify/react": "^4.1.1", "@mdx-js/react": "^3.0.0", - "@mui/material": "^5.15.17", + "@mui/material": "^5.16.6", + "@tanstack/react-query": "^4.36.1", "clsx": "^2.0.0", "prism-react-renderer": "^2.3.0", "react": "^18.0.0", "react-dom": "^18.0.0" }, "devDependencies": { - 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[Release notes](https://github.com/webpack/webpack/releases) - [Commits](https://github.com/webpack/webpack/compare/v5.91.0...v5.94.0) --- updated-dependencies: - dependency-name: webpack dependency-type: indirect ... Signed-off-by: dependabot[bot] --- documentation/package-lock.json | 2575 +++++++++++++++---------------- 1 file changed, 1218 insertions(+), 1357 deletions(-) diff --git a/documentation/package-lock.json b/documentation/package-lock.json index ef8a7dcf7..6b8edcb53 100644 --- a/documentation/package-lock.json +++ b/documentation/package-lock.json @@ -8,56 +8,73 @@ "name": "@aehrc/smart-forms-documentation", "version": "0.0.0", "dependencies": { - "@aehrc/smart-forms-renderer": "^0.27.3", - "@docusaurus/core": "3.3.2", - "@docusaurus/preset-classic": "3.3.2", - "@emotion/react": "^11.11.4", + "@aehrc/smart-forms-renderer": "^0.38.4", + "@docusaurus/core": "^3.4.0", + "@docusaurus/preset-classic": "^3.4.0", + "@docusaurus/theme-live-codeblock": "^3.4.0", + "@emotion/react": "^11.13.0", "@emotion/styled": "^11.11.5", "@iconify/react": "^4.1.1", "@mdx-js/react": "^3.0.0", - "@mui/material": "^5.15.17", + "@mui/material": "^5.16.6", + "@tanstack/react-query": "^4.36.1", "clsx": "^2.0.0", "prism-react-renderer": "^2.3.0", "react": "^18.0.0", "react-dom": "^18.0.0" }, "devDependencies": { - 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"es-module-lexer": "^1.2.1", "eslint-scope": "5.1.1", "events": "^3.2.0", @@ -25980,6 +25862,8 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/which-boxed-primitive/-/which-boxed-primitive-1.0.2.tgz", "integrity": "sha512-bwZdv0AKLpplFY2KZRX6TvyuN7ojjr7lwkg6ml0roIy9YeuSr7JS372qlNW18UQYzgYK9ziGcerWqZOmEn9VNg==", + "optional": true, + "peer": true, "dependencies": { "is-bigint": "^1.0.1", "is-boolean-object": "^1.1.0", @@ -25991,23 +25875,6 @@ "url": "https://github.com/sponsors/ljharb" } }, - "node_modules/which-collection": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/which-collection/-/which-collection-1.0.2.tgz", - "integrity": "sha512-K4jVyjnBdgvc86Y6BkaLZEN933SwYOuBFkdmBu9ZfkcAbdVbpITnDmjvZ/aQjRXQrv5EPkTnD1s39GiiqbngCw==", - "dependencies": { - "is-map": "^2.0.3", - "is-set": "^2.0.3", - "is-weakmap": "^2.0.2", - "is-weakset": "^2.0.3" - }, - "engines": { - "node": ">= 0.4" - }, - "funding": { - "url": "https://github.com/sponsors/ljharb" - } - }, "node_modules/which-module": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/which-module/-/which-module-2.0.1.tgz", @@ -26019,6 +25886,8 @@ "version": "1.1.15", "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.15.tgz", "integrity": "sha512-oV0jmFtUky6CXfkqehVvBP/LSWJ2sy4vWMioiENyJLePrBO/yKyV9OyJySfAKosh+RYkIl5zJCNZ8/4JncrpdA==", + "optional": true, + "peer": true, "dependencies": { "available-typed-arrays": "^1.0.7", "call-bind": "^1.0.7", @@ -26336,11 +26205,11 @@ } }, "node_modules/zustand": { - "version": "4.5.2", - "resolved": "https://registry.npmjs.org/zustand/-/zustand-4.5.2.tgz", - "integrity": "sha512-2cN1tPkDVkwCy5ickKrI7vijSjPksFRfqS6237NzT0vqSsztTNnQdHw9mmN7uBdk3gceVXU0a+21jFzFzAc9+g==", + "version": "4.5.5", + "resolved": "https://registry.npmjs.org/zustand/-/zustand-4.5.5.tgz", + "integrity": "sha512-+0PALYNJNgK6hldkgDq2vLrw5f6g/jCInz52n9RTpropGgeAf/ioFUCdtsjCqu4gNhW9D01rUQBROoRjdzyn2Q==", "dependencies": { - "use-sync-external-store": "1.2.0" + "use-sync-external-store": "1.2.2" }, "engines": { "node": ">=12.7.0" @@ -26362,14 +26231,6 @@ } } }, - "node_modules/zustand/node_modules/use-sync-external-store": { - "version": "1.2.0", - "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.0.tgz", - "integrity": "sha512-eEgnFxGQ1Ife9bzYs6VLi8/4X6CObHMw9Qr9tPY43iKwsPw8xE8+EFsf/2cFZ5S3esXgpWgtSCtLNS41F+sKPA==", - "peerDependencies": { - "react": "^16.8.0 || ^17.0.0 || ^18.0.0" - } - }, "node_modules/zwitch": { "version": "2.0.4", "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz", From d2893fc1ede0e2eae36e77d0144551a8cb0028ee Mon Sep 17 00:00:00 2001 From: Riza Nafis Date: Wed, 4 Sep 2024 00:26:56 +0700 Subject: [PATCH 03/16] Add extractObservationBased functionallity --- .../src/tests/extractObservation.test.ts | 62 ++++++ .../src/tests/test-data/observationSample.ts | 196 ++++++++++++++++++ .../src/utils/extractObservation.ts | 150 ++++++++++++++ .../src/utils/genericRecursive.ts | 12 +- 4 files changed, 415 insertions(+), 5 deletions(-) create mode 100644 packages/smart-forms-renderer/src/tests/extractObservation.test.ts create mode 100644 packages/smart-forms-renderer/src/tests/test-data/observationSample.ts create mode 100644 packages/smart-forms-renderer/src/utils/extractObservation.ts diff --git a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts new file mode 100644 index 000000000..3eb824143 --- /dev/null +++ b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts @@ -0,0 +1,62 @@ +import type { Questionnaire, QuestionnaireResponse } from 'fhir/r4'; + +import { extractObservationBased } from '../utils/extractObservation'; +import { + observationResults, + qObservationSample, + qrObservationSample +} from './test-data/observationSample'; + +describe('extractObservationBased', () => { + it('should correctly extract Observations from a QuestionnaireResponse', () => { + const observations = extractObservationBased(qObservationSample, qrObservationSample); + expect(observations).toHaveLength(2); + expect(observations[0]).toEqual(observationResults[0]); + }); + + it('should return an empty array if there are no items in the Questionnaire or QuestionnaireResponse', () => { + const emptyQuestionnaire: Questionnaire = { + resourceType: 'Questionnaire', + item: [], + status: 'draft' + }; + const emptyResponse: QuestionnaireResponse = { + resourceType: 'QuestionnaireResponse', + item: [], + status: 'completed' + }; + + const observations = extractObservationBased(emptyQuestionnaire, emptyResponse); + expect(observations).toHaveLength(0); + }); + + // TODO: bug readQuestionnaireResponse + // it('should return an empty array if no matching Questionnaire item is found for a QuestionnaireResponse item', () => { + // const responseWithNoMatch: QuestionnaireResponse = { + // resourceType: 'QuestionnaireResponse', + // status: 'completed', + // id: 'qr2', + // item: [ + // { + // linkId: '999', // No matching linkId in the questionnaire + // answer: [ + // { + // valueQuantity: { + // value: 100, + // unit: 'kg', + // system: 'http://unitsofmeasure.org', + // code: 'kg' + // } + // } + // ] + // } + // ], + // subject: { + // reference: 'Patient/456' + // } + // }; + // + // const observations = extractObservationBased(qObservationSample, responseWithNoMatch); + // expect(observations).toHaveLength(0); + // }); +}); diff --git a/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts b/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts new file mode 100644 index 000000000..71d7f9ae9 --- /dev/null +++ b/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts @@ -0,0 +1,196 @@ +import type { Observation, Questionnaire, QuestionnaireResponse } from 'fhir/r4'; + +export const qObservationSample: Questionnaire = { + resourceType: 'Questionnaire', + id: 'phq-2-questionnaire', + meta: { + versionId: '1', + lastUpdated: '2024-08-29T12:00:00Z' + }, + title: 'PHQ-2 Depression Screening', + status: 'active', + date: '2024-08-29T12:00:00Z', + publisher: 'Konsulin', + description: 'Patient Health Questionnaire-2 (PHQ-2) for depression screening.', + subjectType: ['Patient'], + item: [ + { + linkId: 'phq2-1', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ] + }, + { + linkId: 'phq2-2', + text: 'Over the last 2 weeks, how often have you been bothered by feeling down, depressed, or hopeless?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '307077003', + display: 'Feeling hopeless' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ] + } + ] +}; + +export const qrObservationSample: QuestionnaireResponse = { + resourceType: 'QuestionnaireResponse', + id: 'phq2-response', + questionnaire: 'https://fhir.konsulin.care/fhir/Questionnaire/phq-2-questionnaire', + status: 'completed', + subject: { + reference: 'Patient/123' + }, + authored: '2024-08-29T12:00:00Z', + item: [ + { + linkId: 'phq2-1', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + answer: [ + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + } + ] + }, + { + linkId: 'phq2-2', + text: 'Over the last 2 weeks, how often have you been bothered by feeling down, depressed, or hopeless?', + answer: [ + { + valueCoding: { + code: '1', + display: 'Several days' + } + } + ] + } + ] +}; + +export const observationResults: Observation[] = [ + { + resourceType: 'Observation', + id: 'obs-phq2-1', + status: 'final', + code: { + coding: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ] + }, + subject: { + reference: 'Patient/123' + }, + derivedFrom: [ + { + reference: 'QuestionnaireResponse/phq2-response' + } + ], + effectiveDateTime: '2024-08-29T12:00:00Z', + valueCodeableConcept: { + coding: [ + { + code: '2', + display: 'More than half the days' + } + ] + } + }, + { + resourceType: 'Observation', + id: 'obs-phq2-2', + status: 'final', + code: { + coding: [ + { + system: 'http://snomed.info/sct', + code: '307077003', + display: 'Feeling hopeless' + } + ] + }, + subject: { + reference: 'Patient/123' + }, + derivedFrom: [ + { + reference: 'QuestionnaireResponse/phq2-response' + } + ], + effectiveDateTime: '2024-08-29T12:00:00Z', + valueCodeableConcept: { + coding: [ + { + code: '1', + display: 'Several days' + } + ] + } + } +]; diff --git a/packages/smart-forms-renderer/src/utils/extractObservation.ts b/packages/smart-forms-renderer/src/utils/extractObservation.ts new file mode 100644 index 000000000..6a40d9ebc --- /dev/null +++ b/packages/smart-forms-renderer/src/utils/extractObservation.ts @@ -0,0 +1,150 @@ +import type { + CodeableConcept, + Observation, + Questionnaire, + QuestionnaireItem, + QuestionnaireResponse, + QuestionnaireResponseItem, + QuestionnaireResponseItemAnswer +} from 'fhir/r4'; +import { readQuestionnaireResponse } from './genericRecursive'; + +/** + * Extract QuestionnaireResponse into Observation. + * + * @author Riza Nafis + */ +export function extractObservationBased( + questionnaire: Questionnaire, + questionnaireResponse: QuestionnaireResponse +): Observation[] { + const observations: Observation[] = []; + + if ( + !questionnaire.item || + questionnaire.item.length === 0 || + !questionnaireResponse.item || + questionnaireResponse.item.length === 0 + ) { + return observations; + } + + return readQuestionnaireResponse( + questionnaire, + questionnaireResponse, + extractObservationBasedRecursive, + questionnaireResponse + ); +} + +function extractObservationBasedRecursive( + qItem: QuestionnaireItem, + qrItemOrItems: QuestionnaireResponseItem | QuestionnaireResponseItem[] | null, + qr?: QuestionnaireResponse +): Observation[] | null { + // Process items with child items + const observations: Observation[] = []; + if (qr) { + // Map qrItemOrItems into an array of qrItems + let qrItems: QuestionnaireResponseItem[] = []; + if (qrItemOrItems) { + if (Array.isArray(qrItemOrItems)) { + qrItems = qrItemOrItems; + } else { + qrItems = [qrItemOrItems]; + } + } + + const categories: CodeableConcept[] = []; + + for (const responseItem of qrItems) { + if (categories.length) break; + + if (responseItem.extension) { + const exts = responseItem.extension.filter( + (e) => + e.url === + 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category' + ); + + exts.forEach((e) => e.valueCodeableConcept && categories.push(e.valueCodeableConcept)); + } + } + + for (const responseItem of qrItems) { + // Check if the response item has any values or nested items + if (responseItem.answer && responseItem.answer.length > 0) { + for (const answer of responseItem.answer) { + const observation = createObservation(qItem, qr, answer, categories); + + observations.push(observation); + } + } + } + + return observations; + } + + return observations; +} + +export function createObservation( + questionnaireItem: QuestionnaireItem, + questionnaireResponse: QuestionnaireResponse, + answer: QuestionnaireResponseItemAnswer, + categories: CodeableConcept[] +): Observation { + const qrRef = `QuestionnaireResponse/${questionnaireResponse.id}`; + + const observation: Observation = { + resourceType: 'Observation', + status: 'final', + ...removeIfNull('id', questionnaireItem.linkId, `obs-${questionnaireItem.linkId}`), + code: { + coding: [ + { + ...removeIfNull('system', questionnaireItem.code?.[0]?.system), + ...removeIfNull('code', questionnaireItem.code?.[0]?.code), + ...removeIfNull('display', questionnaireItem.code?.[0]?.display) + } + ] + }, + ...removeIfNull('basedOn', questionnaireResponse.basedOn), + ...removeIfNull('partOf', questionnaireResponse.partOf), + ...removeIfNull('subject', questionnaireResponse.subject), + ...removeIfNull('encounter', questionnaireResponse.encounter), + derivedFrom: [{ reference: qrRef }], + ...removeIfNull('effectiveDateTime', questionnaireResponse.authored) + }; + + // Set the value of the Observation based on the answer type + if (answer.valueQuantity) { + observation.valueQuantity = answer.valueQuantity; + } else if (answer.valueString) { + observation.valueString = answer.valueString; + } else if (answer.valueBoolean) { + observation.valueBoolean = answer.valueBoolean; + } else if (answer.valueInteger) { + observation.valueInteger = answer.valueInteger; + } else if (answer.valueCoding) { + observation.valueCodeableConcept = { coding: [answer.valueCoding] }; + } + + if (categories.length) { + observation.category = categories; + } + + return observation; +} + +function removeIfNull( + key: string, + value?: T, + expectedValue?: U +): Record | Record | Record { + if (!value) return {}; + + if (expectedValue) return { [key]: expectedValue }; + + return { [key]: value }; +} diff --git a/packages/smart-forms-renderer/src/utils/genericRecursive.ts b/packages/smart-forms-renderer/src/utils/genericRecursive.ts index 2399e8308..a1e16ec4d 100644 --- a/packages/smart-forms-renderer/src/utils/genericRecursive.ts +++ b/packages/smart-forms-renderer/src/utils/genericRecursive.ts @@ -87,9 +87,10 @@ export function updateQuestionnaireResponse( return { ...questionnaireResponse, item: topLevelQrItems }; } -export type RecursiveReadArrayFunction = ( +export type RecursiveReadArrayFunction = ( qItem: QuestionnaireItem, - qrItemOrItems: QuestionnaireResponseItem | QuestionnaireResponseItem[] | null + qrItemOrItems: QuestionnaireResponseItem | QuestionnaireResponseItem[] | null, + extraData?: U ) => T[] | null; /** @@ -98,10 +99,11 @@ export type RecursiveReadArrayFunction = ( * * @author Sean Fong */ -export function readQuestionnaireResponse( +export function readQuestionnaireResponse( questionnaire: Questionnaire, questionnaireResponse: QuestionnaireResponse, - recursiveReadFunction: RecursiveReadArrayFunction + recursiveReadFunction: RecursiveReadArrayFunction, + extraData?: U ): T[] { if (!questionnaire.item || questionnaire.item.length === 0) { return []; @@ -122,7 +124,7 @@ export function readQuestionnaireResponse( item: [] }; - const readValue = recursiveReadFunction(topLevelQItem, topLevelQRItemOrItems); + const readValue = recursiveReadFunction(topLevelQItem, topLevelQRItemOrItems, extraData); if (readValue) { readValueArray.push(...readValue); From 2fb59603b4b2d48b3a8c33a086768d376f7bcdb2 Mon Sep 17 00:00:00 2001 From: Sean Fong Date: Fri, 6 Sep 2024 14:23:10 +0930 Subject: [PATCH 04/16] Add clearer comments and expose observation-based extract function as library function --- packages/smart-forms-renderer/src/index.ts | 3 ++- packages/smart-forms-renderer/src/utils/extractObservation.ts | 3 ++- packages/smart-forms-renderer/src/utils/genericRecursive.ts | 1 + packages/smart-forms-renderer/src/utils/index.ts | 1 + 4 files changed, 6 insertions(+), 2 deletions(-) diff --git a/packages/smart-forms-renderer/src/index.ts b/packages/smart-forms-renderer/src/index.ts index 1032197c3..7f9f8948e 100644 --- a/packages/smart-forms-renderer/src/index.ts +++ b/packages/smart-forms-renderer/src/index.ts @@ -46,7 +46,8 @@ export { isRepeatItemAndNotCheckbox, initialiseQuestionnaireResponse, generateItemsToRepopulate, - repopulateResponse + repopulateResponse, + extractObservationBased } from './utils'; // theme provider exports diff --git a/packages/smart-forms-renderer/src/utils/extractObservation.ts b/packages/smart-forms-renderer/src/utils/extractObservation.ts index 6a40d9ebc..f30f93546 100644 --- a/packages/smart-forms-renderer/src/utils/extractObservation.ts +++ b/packages/smart-forms-renderer/src/utils/extractObservation.ts @@ -10,7 +10,8 @@ import type { import { readQuestionnaireResponse } from './genericRecursive'; /** - * Extract QuestionnaireResponse into Observation. + * Extract an array of Observations from a QuestionnaireResponse and its source Questionnaire. + * @see https://build.fhir.org/ig/HL7/sdc/extraction.html#observation-based-extraction * * @author Riza Nafis */ diff --git a/packages/smart-forms-renderer/src/utils/genericRecursive.ts b/packages/smart-forms-renderer/src/utils/genericRecursive.ts index a1e16ec4d..3b880f671 100644 --- a/packages/smart-forms-renderer/src/utils/genericRecursive.ts +++ b/packages/smart-forms-renderer/src/utils/genericRecursive.ts @@ -95,6 +95,7 @@ export type RecursiveReadArrayFunction = ( /** * A generic (and safe) way to read an array of element(s) i.e. QuestionnaireResponseItem[], extracted Observation[] from a QuestionnaireResponse given a recursive function. + * It also provides an optional extraData (generic U) parameter for additional data that the recursive function may need. * This function relies heavily on mapQItemsIndex() and getQrItemsIndex() to accurately pinpoint the locations of QR items based on their positions in the Q, taking into account repeating group answers, non-filled questions, etc * * @author Sean Fong diff --git a/packages/smart-forms-renderer/src/utils/index.ts b/packages/smart-forms-renderer/src/utils/index.ts index 3c77caf0c..d69332fe2 100644 --- a/packages/smart-forms-renderer/src/utils/index.ts +++ b/packages/smart-forms-renderer/src/utils/index.ts @@ -22,3 +22,4 @@ export { isRepeatItemAndNotCheckbox } from './qItem'; export type { ItemToRepopulate } from './repopulateItems'; export { generateItemsToRepopulate } from './repopulateItems'; export { repopulateResponse } from './repopulateIntoResponse'; +export { extractObservationBased } from './extractObservation'; From bf781b69ad4f34cfb98674f05cfbc1f8cf2e9ada Mon Sep 17 00:00:00 2001 From: Sean Fong Date: Fri, 6 Sep 2024 14:24:37 +0930 Subject: [PATCH 05/16] Add observation-based extraction in Playground --- apps/smart-forms-app/src/App.tsx | 2 +- .../components/ExtractButtonForPlayground.tsx | 67 --------- .../playground/components/ExtractMenu.tsx | 130 ++++++++++++++++++ .../playground/components/Playground.tsx | 30 +++- .../components/PlaygroundRenderer.tsx | 17 ++- 5 files changed, 166 insertions(+), 80 deletions(-) delete mode 100644 apps/smart-forms-app/src/features/playground/components/ExtractButtonForPlayground.tsx create mode 100644 apps/smart-forms-app/src/features/playground/components/ExtractMenu.tsx diff --git a/apps/smart-forms-app/src/App.tsx b/apps/smart-forms-app/src/App.tsx index 72d77d35f..9faee5b1a 100644 --- a/apps/smart-forms-app/src/App.tsx +++ b/apps/smart-forms-app/src/App.tsx @@ -25,7 +25,7 @@ import DebugModeContextProvider from './contexts/DebugModeContext.tsx'; function App() { return ( - + diff --git a/apps/smart-forms-app/src/features/playground/components/ExtractButtonForPlayground.tsx b/apps/smart-forms-app/src/features/playground/components/ExtractButtonForPlayground.tsx deleted file mode 100644 index 3268afa7f..000000000 --- a/apps/smart-forms-app/src/features/playground/components/ExtractButtonForPlayground.tsx +++ /dev/null @@ -1,67 +0,0 @@ -/* - * 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. - */ - -// @ts-ignore -import React from 'react'; -import { CircularProgress, Fade, IconButton, Tooltip } from '@mui/material'; -import Typography from '@mui/material/Typography'; -import CloudUploadIcon from '@mui/icons-material/CloudUpload'; -import { FORMS_SERVER_URL } from '../../../globals.ts'; - -interface ExtractForPlaygroundProps { - extractEnabled: boolean; - isExtracting: boolean; - onExtract: () => void; -} - -function ExtractButtonForPlayground(props: ExtractForPlaygroundProps) { - const { extractEnabled, isExtracting, onExtract } = props; - - const toolTipText = extractEnabled - ? 'Perform $extract' - : `The current questionnaire does not have a target StructureMap for $extract, or the target StructureMap cannot be found on ${FORMS_SERVER_URL}`; - - return ( - <> - - - - {isExtracting ? ( - - ) : ( - - )} - - - - {isExtracting ? ( - - - Performing extraction... - - - ) : null} - - ); -} - -export default ExtractButtonForPlayground; diff --git a/apps/smart-forms-app/src/features/playground/components/ExtractMenu.tsx b/apps/smart-forms-app/src/features/playground/components/ExtractMenu.tsx new file mode 100644 index 000000000..2affbea14 --- /dev/null +++ b/apps/smart-forms-app/src/features/playground/components/ExtractMenu.tsx @@ -0,0 +1,130 @@ +/* + * 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 Button from '@mui/material/Button'; +import Menu from '@mui/material/Menu'; +import MenuItem from '@mui/material/MenuItem'; +import KeyboardArrowDown from '@mui/icons-material/KeyboardArrowDown'; +import type { SetStateAction } from 'react'; +import { useState } from 'react'; +import { CircularProgress, Fade, ListItemIcon, ListItemText, Tooltip } from '@mui/material'; +import Typography from '@mui/material/Typography'; +import { useExtractOperationStore } from '../stores/extractOperationStore.ts'; +import { FORMS_SERVER_URL } from '../../../globals.ts'; +import Iconify from '../../../components/Iconify/Iconify.tsx'; + +interface ExtractMenuProps { + isExtracting: boolean; + onObservationExtract: () => void; + onStructureMapExtract: () => void; +} + +function ExtractMenu(props: ExtractMenuProps) { + const { isExtracting, onObservationExtract, onStructureMapExtract } = props; + + const targetStructureMap = useExtractOperationStore.use.targetStructureMap(); + + const [anchorEl, setAnchorEl] = useState(null); + const open = Boolean(anchorEl); + const handleClick = (event: { currentTarget: SetStateAction }) => { + setAnchorEl(event.currentTarget); + }; + const handleClose = () => { + setAnchorEl(null); + }; + + const structuredMapExtractEnabled = targetStructureMap !== null; + const structuredMapToolTipText = structuredMapExtractEnabled + ? '' + : `The current questionnaire does not have a target StructureMap for $extract, or the target StructureMap cannot be found on ${FORMS_SERVER_URL}`; + + return ( + <> + + + { + onObservationExtract(); + handleClose(); + }}> + + + + Observation-based $extract + + + + + + + + Definition-based $extract + + + + + + { + onStructureMapExtract(); + handleClose(); + }}> + + + + StructureMap-based $extract + + + + + + {isExtracting ? ( + + + Performing extraction... + + + ) : null} + + ); +} + +export default ExtractMenu; diff --git a/apps/smart-forms-app/src/features/playground/components/Playground.tsx b/apps/smart-forms-app/src/features/playground/components/Playground.tsx index fa2169a03..12ce17d15 100644 --- a/apps/smart-forms-app/src/features/playground/components/Playground.tsx +++ b/apps/smart-forms-app/src/features/playground/components/Playground.tsx @@ -30,6 +30,7 @@ import { isQuestionnaire } from '../typePredicates/isQuestionnaire.ts'; import type { BuildState } from '../types/buildState.interface.ts'; import { useLocalStorage } from 'usehooks-ts'; import { + extractObservationBased, removeEmptyAnswersFromResponse, useQuestionnaireResponseStore, useQuestionnaireStore @@ -152,8 +153,30 @@ function Playground() { }; } - // $extract - async function handleExtract() { + // Observation $extract + async function handleObservationExtract() { + const observations = extractObservationBased(sourceQuestionnaire, updatableResponse); + setExtractedResource(observations); + + if (observations.length > 0) { + enqueueSnackbar( + 'Observation-based extraction successful. See Advanced Properties > Extracted to view extracted resource.', + { + preventDuplicate: true, + action: , + autoHideDuration: 8000 + } + ); + } else { + enqueueSnackbar('Extraction performed but no observations are extracted.', { + preventDuplicate: true, + action: + }); + } + } + + // StructureMap $extract + async function handleStructureMapExtract() { setExtracting(true); const response = await fetch(defaultExtractEndpoint + '/QuestionnaireResponse/$extract', { @@ -209,7 +232,8 @@ function Playground() { patient={patient} user={user} isExtracting={isExtracting} - onExtract={handleExtract} + onObservationExtract={handleObservationExtract} + onStructureMapExtract={handleStructureMapExtract} /> ) : buildingState === 'building' ? ( diff --git a/apps/smart-forms-app/src/features/playground/components/PlaygroundRenderer.tsx b/apps/smart-forms-app/src/features/playground/components/PlaygroundRenderer.tsx index 0cac3f23b..65bb3ee61 100644 --- a/apps/smart-forms-app/src/features/playground/components/PlaygroundRenderer.tsx +++ b/apps/smart-forms-app/src/features/playground/components/PlaygroundRenderer.tsx @@ -24,23 +24,23 @@ import type { Patient, Practitioner } from 'fhir/r4'; import { Box, Typography } from '@mui/material'; import useLaunchContextNames from '../hooks/useLaunchContextNames.ts'; import { TERMINOLOGY_SERVER_URL } from '../../../globals.ts'; -import ExtractButtonForPlayground from './ExtractButtonForPlayground.tsx'; -import { useExtractOperationStore } from '../stores/extractOperationStore.ts'; import { buildFormWrapper } from '../../../utils/manageForm.ts'; +import ExtractMenu from './ExtractMenu.tsx'; interface PlaygroundRendererProps { endpointUrl: string | null; patient: Patient | null; user: Practitioner | null; isExtracting: boolean; - onExtract: () => void; + onObservationExtract: () => void; + onStructureMapExtract: () => void; } function PlaygroundRenderer(props: PlaygroundRendererProps) { - const { endpointUrl, patient, user, isExtracting, onExtract } = props; + const { endpointUrl, patient, user, isExtracting, onObservationExtract, onStructureMapExtract } = + props; const sourceQuestionnaire = useQuestionnaireStore.use.sourceQuestionnaire(); - const targetStructureMap = useExtractOperationStore.use.targetStructureMap(); const setPopulatedContext = useQuestionnaireStore.use.setPopulatedContext(); const [isPopulating, setIsPopulating] = useState(false); @@ -48,7 +48,6 @@ function PlaygroundRenderer(props: PlaygroundRendererProps) { const { patientName, userName } = useLaunchContextNames(patient, user); const prePopEnabled = endpointUrl !== null && patient !== null; - const extractEnabled = targetStructureMap !== null; function handlePrepopulate() { if (!prePopEnabled) { @@ -97,10 +96,10 @@ function PlaygroundRenderer(props: PlaygroundRendererProps) { isPopulating={isPopulating} onPopulate={handlePrepopulate} /> - From 081cdad385ed3bf59c0549ac8cd4925007049aaa Mon Sep 17 00:00:00 2001 From: Sean Fong Date: Fri, 6 Sep 2024 14:29:25 +0930 Subject: [PATCH 06/16] Fix failing observation-based extract test --- .../src/tests/extractObservation.test.ts | 57 +++++++++---------- .../src/utils/itemControl.ts | 2 +- .../smart-forms-renderer/src/utils/qItem.ts | 6 ++ 3 files changed, 35 insertions(+), 30 deletions(-) diff --git a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts index 3eb824143..ed280ffea 100644 --- a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts +++ b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts @@ -30,33 +30,32 @@ describe('extractObservationBased', () => { expect(observations).toHaveLength(0); }); - // TODO: bug readQuestionnaireResponse - // it('should return an empty array if no matching Questionnaire item is found for a QuestionnaireResponse item', () => { - // const responseWithNoMatch: QuestionnaireResponse = { - // resourceType: 'QuestionnaireResponse', - // status: 'completed', - // id: 'qr2', - // item: [ - // { - // linkId: '999', // No matching linkId in the questionnaire - // answer: [ - // { - // valueQuantity: { - // value: 100, - // unit: 'kg', - // system: 'http://unitsofmeasure.org', - // code: 'kg' - // } - // } - // ] - // } - // ], - // subject: { - // reference: 'Patient/456' - // } - // }; - // - // const observations = extractObservationBased(qObservationSample, responseWithNoMatch); - // expect(observations).toHaveLength(0); - // }); + it('should return an empty array if no matching Questionnaire item is found for a QuestionnaireResponse item', () => { + const responseWithNoMatch: QuestionnaireResponse = { + resourceType: 'QuestionnaireResponse', + status: 'completed', + id: 'qr2', + item: [ + { + linkId: '999', // No matching linkId in the questionnaire + answer: [ + { + valueQuantity: { + value: 100, + unit: 'kg', + system: 'http://unitsofmeasure.org', + code: 'kg' + } + } + ] + } + ], + subject: { + reference: 'Patient/456' + } + }; + + const observations = extractObservationBased(qObservationSample, responseWithNoMatch); + expect(observations).toHaveLength(0); + }); }); diff --git a/packages/smart-forms-renderer/src/utils/itemControl.ts b/packages/smart-forms-renderer/src/utils/itemControl.ts index 180ee8b8a..dc1c66169 100644 --- a/packages/smart-forms-renderer/src/utils/itemControl.ts +++ b/packages/smart-forms-renderer/src/utils/itemControl.ts @@ -47,7 +47,7 @@ export function shouldRenderNestedItems(qItem: QuestionnaireItem): boolean { * @author Sean Fong */ export function isSpecificItemControl(qItem: QuestionnaireItem, itemControlCode: string): boolean { - const itemControl = qItem.extension?.find( + const itemControl = qItem?.extension?.find( (extension: Extension) => extension.url === 'http://hl7.org/fhir/StructureDefinition/questionnaire-itemControl' ); diff --git a/packages/smart-forms-renderer/src/utils/qItem.ts b/packages/smart-forms-renderer/src/utils/qItem.ts index 33befb978..6ce13b35e 100644 --- a/packages/smart-forms-renderer/src/utils/qItem.ts +++ b/packages/smart-forms-renderer/src/utils/qItem.ts @@ -74,6 +74,12 @@ export function isHiddenByEnableWhen(params: isHiddenByEnableWhensParams): boole * @author Sean Fong */ export function isRepeatItemAndNotCheckbox(qItem: QuestionnaireItem): boolean { + // Prevents form from crashing due to mismatched Q and QR + // In reality this should never happen + if (!qItem) { + return false; + } + const isCheckbox = getChoiceControlType(qItem) === ChoiceItemControl.Checkbox || getOpenChoiceControlType(qItem) === OpenChoiceItemControl.Checkbox; From 503c7053ce9b57a57d0421121cfbe7552479ed36 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 05:25:43 +0000 Subject: [PATCH 07/16] Bump micromatch from 4.0.5 to 4.0.8 in /apps/demo-renderer-app Bumps [micromatch](https://github.com/micromatch/micromatch) from 4.0.5 to 4.0.8. - [Release notes](https://github.com/micromatch/micromatch/releases) - [Changelog](https://github.com/micromatch/micromatch/blob/master/CHANGELOG.md) - [Commits](https://github.com/micromatch/micromatch/compare/4.0.5...4.0.8) --- updated-dependencies: - dependency-name: micromatch dependency-type: indirect ... Signed-off-by: dependabot[bot] --- apps/demo-renderer-app/package-lock.json | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/apps/demo-renderer-app/package-lock.json b/apps/demo-renderer-app/package-lock.json index dc894e560..b51bd3cc3 100644 --- a/apps/demo-renderer-app/package-lock.json +++ b/apps/demo-renderer-app/package-lock.json @@ -8373,12 +8373,12 @@ } }, "node_modules/braces": { - "version": "3.0.2", - "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.2.tgz", - "integrity": "sha512-b8um+L1RzM3WDSzvhm6gIz1yfTbBt6YTlcEKAvsmqCZZFw46z626lVj9j1yEPW33H5H+lBQpZMP1k8l+78Ha0A==", + "version": "3.0.3", + "resolved": "https://registry.npmjs.org/braces/-/braces-3.0.3.tgz", + "integrity": "sha512-yQbXgO/OSZVD2IsiLlro+7Hf6Q18EJrKSEsdoMzKePKXct3gvD8oLcOQdIzGupr5Fj+EDe8gO/lxc1BzfMpxvA==", "optional": true, "dependencies": { - "fill-range": "^7.0.1" + "fill-range": "^7.1.1" }, "engines": { "node": ">=8" @@ -10496,9 +10496,9 @@ } }, "node_modules/fill-range": { - "version": "7.0.1", - "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz", - "integrity": "sha512-qOo9F+dMUmC2Lcb4BbVvnKJxTPjCm+RRpe4gDuGrzkL7mEVl/djYSu2OdQ2Pa302N4oqkSg9ir6jaLWJ2USVpQ==", + "version": "7.1.1", + "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz", + "integrity": "sha512-YsGpe3WHLK8ZYi4tWDg2Jy3ebRz2rXowDxnld4bkQB00cc/1Zw9AWnC0i9ztDJitivtQvaI9KaLyKrc+hBW0yg==", "optional": true, "dependencies": { "to-regex-range": "^5.0.1" @@ -14008,12 +14008,12 @@ } }, "node_modules/micromatch": { - "version": "4.0.5", - "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.5.tgz", - "integrity": "sha512-DMy+ERcEW2q8Z2Po+WNXuw3c5YaUSFjAO5GsJqfEl7UjvtIuFKO6ZrKvcItdy98dwFI2N1tg3zNIdKaQT+aNdA==", + "version": "4.0.8", + "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.8.tgz", + "integrity": "sha512-PXwfBhYu0hBCPw8Dn0E+WDYb7af3dSLVWKi3HGv84IdF4TyFoC0ysxFd0Goxw7nSv4T/PzEJQxsYsEiFCKo2BA==", "optional": true, "dependencies": { - "braces": "^3.0.2", + "braces": "^3.0.3", "picomatch": "^2.3.1" }, "engines": { From 7ae9be947f54a69158eb8a16c36f9eb0eb426384 Mon Sep 17 00:00:00 2001 From: Sean Fong Date: Fri, 6 Sep 2024 15:03:34 +0930 Subject: [PATCH 08/16] Update renderer package versions to 0.40.0 (not published yet) --- apps/smart-forms-app/package.json | 2 +- documentation/package.json | 2 +- packages/smart-forms-renderer/package.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/apps/smart-forms-app/package.json b/apps/smart-forms-app/package.json index fe6aece62..fb261cc1e 100644 --- a/apps/smart-forms-app/package.json +++ b/apps/smart-forms-app/package.json @@ -28,7 +28,7 @@ "dependencies": { "@aehrc/sdc-assemble": "^1.3.1", "@aehrc/sdc-populate": "^2.3.1", - "@aehrc/smart-forms-renderer": "^0.39.0", + "@aehrc/smart-forms-renderer": "^0.40.0", "@emotion/react": "^11.13.0", "@emotion/styled": "^11.11.5", "@fontsource/material-icons": "^5.0.18", diff --git a/documentation/package.json b/documentation/package.json index 1681065f5..97705ace7 100644 --- a/documentation/package.json +++ b/documentation/package.json @@ -15,7 +15,7 @@ "typecheck": "tsc" }, "dependencies": { - "@aehrc/smart-forms-renderer": "^0.39.0", + "@aehrc/smart-forms-renderer": "^0.40.0", "@docusaurus/core": "^3.4.0", "@docusaurus/preset-classic": "^3.4.0", "@docusaurus/theme-live-codeblock": "^3.4.0", diff --git a/packages/smart-forms-renderer/package.json b/packages/smart-forms-renderer/package.json index 7644b0883..4cf6fe3d4 100644 --- a/packages/smart-forms-renderer/package.json +++ b/packages/smart-forms-renderer/package.json @@ -1,6 +1,6 @@ { "name": "@aehrc/smart-forms-renderer", - "version": "0.39.0", + "version": "0.40.0", "description": "FHIR Structured Data Captured (SDC) rendering engine for Smart Forms", "main": "lib/index.js", "scripts": { From 10b88c614da2f0b153478bf34fcbb97c1bafa039 Mon Sep 17 00:00:00 2001 From: Sean Fong Date: Fri, 6 Sep 2024 15:11:23 +0930 Subject: [PATCH 09/16] Update package-lock.json --- package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/package-lock.json b/package-lock.json index 5986cead9..17adc06e9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -26,7 +26,7 @@ "dependencies": { "@aehrc/sdc-assemble": "^1.3.1", "@aehrc/sdc-populate": "^2.3.1", - "@aehrc/smart-forms-renderer": "^0.39.0", + "@aehrc/smart-forms-renderer": "^0.40.0", "@emotion/react": "^11.13.0", "@emotion/styled": "^11.11.5", "@fontsource/material-icons": "^5.0.18", @@ -457,7 +457,7 @@ "name": "@aehrc/smart-forms-documentation", "version": "0.0.0", "dependencies": { - "@aehrc/smart-forms-renderer": "^0.39.0", + "@aehrc/smart-forms-renderer": "^0.40.0", "@docusaurus/core": "^3.4.0", "@docusaurus/preset-classic": "^3.4.0", "@docusaurus/theme-live-codeblock": "^3.4.0", @@ -40235,7 +40235,7 @@ }, "packages/smart-forms-renderer": { "name": "@aehrc/smart-forms-renderer", - "version": "0.39.0", + "version": "0.40.0", "license": "Apache-2.0", "dependencies": { "@aehrc/sdc-populate": "^2.3.1", From affd884cd9906cc67b4ae41d24fb9279022d4e73 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 17:49:29 +0000 Subject: [PATCH 10/16] Bump @emotion/styled from 11.11.5 to 11.13.0 Bumps [@emotion/styled](https://github.com/emotion-js/emotion) from 11.11.5 to 11.13.0. - [Release notes](https://github.com/emotion-js/emotion/releases) - [Changelog](https://github.com/emotion-js/emotion/blob/main/CHANGELOG.md) - [Commits](https://github.com/emotion-js/emotion/compare/@emotion/styled@11.11.5...@emotion/styled@11.13.0) --- updated-dependencies: - dependency-name: "@emotion/styled" dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- apps/smart-forms-app/package.json | 2 +- documentation/package.json | 2 +- package-lock.json | 46 ++++++++++++------------------- 3 files changed, 19 insertions(+), 31 deletions(-) diff --git a/apps/smart-forms-app/package.json b/apps/smart-forms-app/package.json index fe6aece62..b505063d9 100644 --- a/apps/smart-forms-app/package.json +++ b/apps/smart-forms-app/package.json @@ -30,7 +30,7 @@ "@aehrc/sdc-populate": "^2.3.1", "@aehrc/smart-forms-renderer": "^0.39.0", "@emotion/react": "^11.13.0", - "@emotion/styled": "^11.11.5", + "@emotion/styled": "^11.13.0", "@fontsource/material-icons": "^5.0.18", "@fontsource/roboto": "^5.0.12", "@iconify/react": "^4.1.1", diff --git a/documentation/package.json b/documentation/package.json index 1681065f5..15bcdc112 100644 --- a/documentation/package.json +++ b/documentation/package.json @@ -20,7 +20,7 @@ "@docusaurus/preset-classic": "^3.4.0", "@docusaurus/theme-live-codeblock": "^3.4.0", "@emotion/react": "^11.13.0", - "@emotion/styled": "^11.11.5", + "@emotion/styled": "^11.13.0", "@iconify/react": "^4.1.1", "@mdx-js/react": "^3.0.0", "@mui/material": "^5.16.7", diff --git a/package-lock.json b/package-lock.json index 5986cead9..42c6affb3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -28,7 +28,7 @@ "@aehrc/sdc-populate": "^2.3.1", "@aehrc/smart-forms-renderer": "^0.39.0", "@emotion/react": "^11.13.0", - "@emotion/styled": "^11.11.5", + "@emotion/styled": "^11.13.0", "@fontsource/material-icons": "^5.0.18", "@fontsource/roboto": "^5.0.12", "@iconify/react": "^4.1.1", @@ -462,7 +462,7 @@ "@docusaurus/preset-classic": "^3.4.0", "@docusaurus/theme-live-codeblock": "^3.4.0", "@emotion/react": "^11.13.0", - "@emotion/styled": "^11.11.5", + "@emotion/styled": "^11.13.0", "@iconify/react": "^4.1.1", "@mdx-js/react": "^3.0.0", "@mui/material": "^5.16.7", @@ -3769,11 +3769,6 @@ "stylis": "4.2.0" } }, - "node_modules/@emotion/babel-plugin/node_modules/@emotion/memoize": { - "version": "0.9.0", - "resolved": "https://registry.npmjs.org/@emotion/memoize/-/memoize-0.9.0.tgz", - "integrity": "sha512-30FAj7/EoJ5mwVPOWhAyCX+FPfMDrVecJAM+Iw9NRoSl4BBAQeqj4cApHHUXOVvIPgLVDsCFoz/hGD+5QQD1GQ==" - }, "node_modules/@emotion/cache": { "version": "11.13.1", "resolved": "https://registry.npmjs.org/@emotion/cache/-/cache-11.13.1.tgz", @@ -3786,26 +3781,23 @@ "stylis": "4.2.0" } }, - "node_modules/@emotion/cache/node_modules/@emotion/memoize": { - "version": "0.9.0", - "resolved": "https://registry.npmjs.org/@emotion/memoize/-/memoize-0.9.0.tgz", - "integrity": "sha512-30FAj7/EoJ5mwVPOWhAyCX+FPfMDrVecJAM+Iw9NRoSl4BBAQeqj4cApHHUXOVvIPgLVDsCFoz/hGD+5QQD1GQ==" - }, "node_modules/@emotion/hash": { "version": "0.9.2", "resolved": "https://registry.npmjs.org/@emotion/hash/-/hash-0.9.2.tgz", "integrity": "sha512-MyqliTZGuOm3+5ZRSaaBGP3USLw6+EGykkwZns2EPC5g8jJ4z9OrdZY9apkl3+UP9+sdz76YYkwCKP5gh8iY3g==" }, "node_modules/@emotion/is-prop-valid": { - "version": "1.2.2", - "license": "MIT", + "version": "1.3.0", + "resolved": "https://registry.npmjs.org/@emotion/is-prop-valid/-/is-prop-valid-1.3.0.tgz", + "integrity": "sha512-SHetuSLvJDzuNbOdtPVbq6yMMMlLoW5Q94uDqJZqy50gcmAjxFkVqmzqSGEFq9gT2iMuIeKV1PXVWmvUhuZLlQ==", "dependencies": { - "@emotion/memoize": "^0.8.1" + "@emotion/memoize": "^0.9.0" } }, "node_modules/@emotion/memoize": { - "version": "0.8.1", - "license": "MIT" + "version": "0.9.0", + "resolved": "https://registry.npmjs.org/@emotion/memoize/-/memoize-0.9.0.tgz", + "integrity": "sha512-30FAj7/EoJ5mwVPOWhAyCX+FPfMDrVecJAM+Iw9NRoSl4BBAQeqj4cApHHUXOVvIPgLVDsCFoz/hGD+5QQD1GQ==" }, "node_modules/@emotion/react": { "version": "11.13.0", @@ -3842,26 +3834,22 @@ "csstype": "^3.0.2" } }, - "node_modules/@emotion/serialize/node_modules/@emotion/memoize": { - "version": "0.9.0", - "resolved": "https://registry.npmjs.org/@emotion/memoize/-/memoize-0.9.0.tgz", - "integrity": "sha512-30FAj7/EoJ5mwVPOWhAyCX+FPfMDrVecJAM+Iw9NRoSl4BBAQeqj4cApHHUXOVvIPgLVDsCFoz/hGD+5QQD1GQ==" - }, "node_modules/@emotion/sheet": { "version": "1.4.0", "resolved": "https://registry.npmjs.org/@emotion/sheet/-/sheet-1.4.0.tgz", "integrity": "sha512-fTBW9/8r2w3dXWYM4HCB1Rdp8NLibOw2+XELH5m5+AkWiL/KqYX6dc0kKYlaYyKjrQ6ds33MCdMPEwgs2z1rqg==" }, "node_modules/@emotion/styled": { - "version": "11.11.5", - "license": "MIT", + "version": "11.13.0", + "resolved": "https://registry.npmjs.org/@emotion/styled/-/styled-11.13.0.tgz", + "integrity": "sha512-tkzkY7nQhW/zC4hztlwucpT8QEZ6eUzpXDRhww/Eej4tFfO0FxQYWRyg/c5CCXa4d/f174kqeXYjuQRnhzf6dA==", "dependencies": { "@babel/runtime": "^7.18.3", - "@emotion/babel-plugin": "^11.11.0", - "@emotion/is-prop-valid": "^1.2.2", - "@emotion/serialize": "^1.1.4", - "@emotion/use-insertion-effect-with-fallbacks": "^1.0.1", - "@emotion/utils": "^1.2.1" + "@emotion/babel-plugin": "^11.12.0", + "@emotion/is-prop-valid": "^1.3.0", + "@emotion/serialize": "^1.3.0", + "@emotion/use-insertion-effect-with-fallbacks": "^1.1.0", + "@emotion/utils": "^1.4.0" }, "peerDependencies": { "@emotion/react": "^11.0.0-rc.0", From cb3a9c4d02517e40714b23ed38c2fc472efa621c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 17:50:01 +0000 Subject: [PATCH 11/16] Bump @storybook/blocks from 7.5.2 to 8.2.9 Bumps [@storybook/blocks](https://github.com/storybookjs/storybook/tree/HEAD/code/lib/blocks) from 7.5.2 to 8.2.9. - [Release notes](https://github.com/storybookjs/storybook/releases) - [Changelog](https://github.com/storybookjs/storybook/blob/next/CHANGELOG.md) - [Commits](https://github.com/storybookjs/storybook/commits/v8.2.9/code/lib/blocks) --- updated-dependencies: - dependency-name: "@storybook/blocks" dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- apps/smart-forms-app/package.json | 2 +- package-lock.json | 418 ++---------------------------- 2 files changed, 18 insertions(+), 402 deletions(-) diff --git a/apps/smart-forms-app/package.json b/apps/smart-forms-app/package.json index fe6aece62..83c9e7135 100644 --- a/apps/smart-forms-app/package.json +++ b/apps/smart-forms-app/package.json @@ -84,7 +84,7 @@ "@storybook/addon-links": "^8.0.3", "@storybook/addon-onboarding": "^8.0.0", "@storybook/addon-styling": "^1.3.7", - "@storybook/blocks": "^7.5.2", + "@storybook/blocks": "^8.2.9", "@storybook/react": "^8.2.6", "@storybook/react-vite": "^7.4.5", "@storybook/testing-library": "^0.2.1", diff --git a/package-lock.json b/package-lock.json index 5986cead9..7059f3ca1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -82,7 +82,7 @@ "@storybook/addon-links": "^8.0.3", "@storybook/addon-onboarding": "^8.0.0", "@storybook/addon-styling": "^1.3.7", - "@storybook/blocks": "^7.5.2", + "@storybook/blocks": "^8.2.9", "@storybook/react": "^8.2.6", "@storybook/react-vite": "^7.4.5", "@storybook/testing-library": "^0.2.1", @@ -7303,45 +7303,6 @@ "storybook": "^8.2.9" } }, - 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"react": { - "optional": true - }, - "react-dom": { - "optional": true - } - } - }, "node_modules/@storybook/addon-essentials": { "version": "8.2.9", "resolved": "https://registry.npmjs.org/@storybook/addon-essentials/-/addon-essentials-8.2.9.tgz", @@ -7827,31 +7788,23 @@ } }, "node_modules/@storybook/blocks": { - "version": "7.5.2", + "version": "8.2.9", + "resolved": "https://registry.npmjs.org/@storybook/blocks/-/blocks-8.2.9.tgz", + "integrity": "sha512-5276q/s/UL8arwftuBXovUNHqYo/HPQFMGXEmjVVAMXUyFjzEAfKj3+xU897J6AuL+7XVZG32WnqA+X6LJMrcQ==", "dev": true, - "license": "MIT", "dependencies": { - "@storybook/channels": "7.5.2", - "@storybook/client-logger": "7.5.2", - "@storybook/components": "7.5.2", - "@storybook/core-events": "7.5.2", - "@storybook/csf": "^0.1.0", - "@storybook/docs-tools": "7.5.2", + "@storybook/csf": "0.1.11", "@storybook/global": "^5.0.0", - "@storybook/manager-api": "7.5.2", - "@storybook/preview-api": "7.5.2", - "@storybook/theming": "7.5.2", - "@storybook/types": "7.5.2", + "@storybook/icons": "^1.2.5", "@types/lodash": "^4.14.167", "color-convert": "^2.0.1", "dequal": "^2.0.2", "lodash": "^4.17.21", - "markdown-to-jsx": "^7.1.8", + "markdown-to-jsx": "^7.4.5", "memoizerific": "^1.11.3", "polished": "^4.2.2", "react-colorful": "^5.1.2", "telejson": "^7.2.0", - "tocbot": "^4.20.1", "ts-dedent": "^2.0.0", "util-deprecate": "^1.0.2" }, @@ -7860,188 +7813,19 @@ "url": "https://opencollective.com/storybook" }, "peerDependencies": { - "react": "^16.8.0 || ^17.0.0 || ^18.0.0", - "react-dom": "^16.8.0 || ^17.0.0 || ^18.0.0" - } - }, - "node_modules/@storybook/blocks/node_modules/@storybook/channels": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/client-logger": "7.5.2", - "@storybook/core-events": "7.5.2", - "@storybook/global": "^5.0.0", - "qs": "^6.10.0", - "telejson": "^7.2.0", - "tiny-invariant": "^1.3.1" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - } - }, - "node_modules/@storybook/blocks/node_modules/@storybook/client-logger": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - 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"version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/client-logger": "7.5.2", - "memoizerific": "^1.11.3", - "qs": "^6.10.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - }, - "peerDependencies": { - "react": "^16.8.0 || ^17.0.0 || ^18.0.0", - "react-dom": "^16.8.0 || ^17.0.0 || ^18.0.0" - } - }, - "node_modules/@storybook/blocks/node_modules/@storybook/theming": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@emotion/use-insertion-effect-with-fallbacks": "^1.0.0", - "@storybook/client-logger": "7.5.2", - "@storybook/global": "^5.0.0", - "memoizerific": "^1.11.3" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - }, - "peerDependencies": { - "react": "^16.8.0 || ^17.0.0 || ^18.0.0", - "react-dom": "^16.8.0 || ^17.0.0 || ^18.0.0" - } - }, - "node_modules/@storybook/blocks/node_modules/@storybook/types": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/channels": "7.5.2", - "@types/babel__core": "^7.0.0", - "@types/express": "^4.7.0", - "file-system-cache": "2.3.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - } - }, - "node_modules/@storybook/blocks/node_modules/lru-cache": { - "version": "6.0.0", - "dev": true, - "license": "ISC", - "dependencies": { - "yallist": "^4.0.0" - }, - "engines": { - "node": ">=10" - } - }, - "node_modules/@storybook/blocks/node_modules/semver": { - "version": "7.5.4", - "dev": true, - "license": "ISC", - "dependencies": { - "lru-cache": "^6.0.0" - }, - "bin": { - "semver": "bin/semver.js" + "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0-beta", + "react-dom": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0-beta", + "storybook": "^8.2.9" }, - "engines": { - "node": ">=10" + "peerDependenciesMeta": { + "react": { + "optional": true + }, + "react-dom": { + "optional": true + } } }, - "node_modules/@storybook/blocks/node_modules/yallist": { - "version": "4.0.0", - "dev": true, - "license": "ISC" - }, "node_modules/@storybook/builder-manager": { "version": "7.6.20", "resolved": "https://registry.npmjs.org/@storybook/builder-manager/-/builder-manager-7.6.20.tgz", @@ -9361,130 +9145,6 @@ "integrity": "sha512-JDaBR9lwVY4eSH5W8EGHrhODjygPd6QImRbwjAuJNEnY0Vw4ie3bPkeGfnacB3OBW6u/agqPv2aRlR46JcAQLg==", "dev": true }, - "node_modules/@storybook/docs-tools": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/core-common": "7.5.2", - "@storybook/preview-api": "7.5.2", - "@storybook/types": "7.5.2", - "@types/doctrine": "^0.0.3", - "doctrine": "^3.0.0", - "lodash": "^4.17.21" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - } - }, - "node_modules/@storybook/docs-tools/node_modules/@storybook/channels": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/client-logger": "7.5.2", - "@storybook/core-events": "7.5.2", - "@storybook/global": "^5.0.0", - "qs": "^6.10.0", - "telejson": "^7.2.0", - "tiny-invariant": "^1.3.1" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - } - }, - "node_modules/@storybook/docs-tools/node_modules/@storybook/client-logger": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/global": "^5.0.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - } - }, - "node_modules/@storybook/docs-tools/node_modules/@storybook/core-common": { - "version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/core-events": "7.5.2", - "@storybook/node-logger": "7.5.2", - "@storybook/types": "7.5.2", - "@types/find-cache-dir": "^3.2.1", - "@types/node": "^18.0.0", - "@types/node-fetch": "^2.6.4", - "@types/pretty-hrtime": "^1.0.0", - "chalk": "^4.1.0", - "esbuild": "^0.18.0", - "esbuild-register": "^3.5.0", - "file-system-cache": "2.3.0", - 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"version": "7.5.2", - "dev": true, - "license": "MIT", - "dependencies": { - "@storybook/channels": "7.5.2", - "@types/babel__core": "^7.0.0", - "@types/express": "^4.7.0", - "file-system-cache": "2.3.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - } - }, - "node_modules/@storybook/docs-tools/node_modules/@types/node": { - "version": "18.18.8", - "dev": true, - "license": "MIT", - "dependencies": { - "undici-types": "~5.26.4" - } - }, "node_modules/@storybook/global": { "version": "5.0.0", "dev": true, @@ -37824,11 +37484,6 @@ "node": ">=8.0" } }, - "node_modules/tocbot": { - "version": "4.21.1", - "dev": true, - "license": "MIT" - }, "node_modules/toidentifier": { "version": "1.0.1", "license": "MIT", @@ -40356,45 +40011,6 @@ "storybook": "^8.2.9" } }, - "packages/smart-forms-renderer/node_modules/@storybook/blocks": { - "version": "8.2.9", - "resolved": "https://registry.npmjs.org/@storybook/blocks/-/blocks-8.2.9.tgz", - "integrity": "sha512-5276q/s/UL8arwftuBXovUNHqYo/HPQFMGXEmjVVAMXUyFjzEAfKj3+xU897J6AuL+7XVZG32WnqA+X6LJMrcQ==", - "dev": true, - "dependencies": { - "@storybook/csf": "0.1.11", - "@storybook/global": "^5.0.0", - "@storybook/icons": "^1.2.5", - "@types/lodash": "^4.14.167", - "color-convert": "^2.0.1", - "dequal": "^2.0.2", - "lodash": "^4.17.21", - "markdown-to-jsx": "^7.4.5", - "memoizerific": "^1.11.3", - "polished": "^4.2.2", - "react-colorful": "^5.1.2", - "telejson": "^7.2.0", - "ts-dedent": "^2.0.0", - "util-deprecate": "^1.0.2" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/storybook" - }, - "peerDependencies": { - "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0-beta", - "react-dom": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0-beta", - "storybook": "^8.2.9" - }, - "peerDependenciesMeta": { - "react": { - "optional": true - }, - "react-dom": { - "optional": true - } - } - }, "packages/smart-forms-renderer/node_modules/@storybook/builder-vite": { "version": "8.2.9", "resolved": "https://registry.npmjs.org/@storybook/builder-vite/-/builder-vite-8.2.9.tgz", From 6e63c7dc05d3f0ca4d8e4adf53cfe2570ad3e44e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 17:50:31 +0000 Subject: [PATCH 12/16] Bump @docusaurus/module-type-aliases from 3.4.0 to 3.5.2 Bumps [@docusaurus/module-type-aliases](https://github.com/facebook/docusaurus/tree/HEAD/packages/docusaurus-module-type-aliases) from 3.4.0 to 3.5.2. - [Release notes](https://github.com/facebook/docusaurus/releases) - [Changelog](https://github.com/facebook/docusaurus/blob/main/CHANGELOG.md) - [Commits](https://github.com/facebook/docusaurus/commits/v3.5.2/packages/docusaurus-module-type-aliases) --- updated-dependencies: - dependency-name: "@docusaurus/module-type-aliases" dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- documentation/package.json | 2 +- package-lock.json | 94 ++++++++++++++++++++++++++++++++++++-- 2 files changed, 91 insertions(+), 5 deletions(-) diff --git a/documentation/package.json b/documentation/package.json index 1681065f5..bf031de2d 100644 --- a/documentation/package.json +++ b/documentation/package.json @@ -31,7 +31,7 @@ "react-dom": "^18.0.0" }, "devDependencies": { - "@docusaurus/module-type-aliases": "^3.4.0", + "@docusaurus/module-type-aliases": "^3.5.2", "@docusaurus/tsconfig": "^3.4.0", "@docusaurus/types": "^3.4.0", "docusaurus-plugin-typedoc": "^1.0.1", diff --git a/package-lock.json b/package-lock.json index 5986cead9..e225c2f47 100644 --- a/package-lock.json +++ b/package-lock.json @@ -473,7 +473,7 @@ "react-dom": "^18.0.0" }, "devDependencies": { - "@docusaurus/module-type-aliases": "^3.4.0", + "@docusaurus/module-type-aliases": "^3.5.2", "@docusaurus/tsconfig": "^3.4.0", "@docusaurus/types": "^3.4.0", "docusaurus-plugin-typedoc": "^1.0.1", @@ -3086,10 +3086,12 @@ } }, "node_modules/@docusaurus/module-type-aliases": { - "version": "3.4.0", - "license": "MIT", + "version": "3.5.2", + "resolved": "https://registry.npmjs.org/@docusaurus/module-type-aliases/-/module-type-aliases-3.5.2.tgz", + "integrity": "sha512-Z+Xu3+2rvKef/YKTMxZHsEXp1y92ac0ngjDiExRdqGTmEKtCUpkbNYH8v5eXo5Ls+dnW88n6WTa+Q54kLOkwPg==", + "dev": true, "dependencies": { - "@docusaurus/types": "3.4.0", + "@docusaurus/types": "3.5.2", "@types/history": "^4.7.11", "@types/react": "*", "@types/react-router-config": "*", @@ -3102,6 +3104,36 @@ "react-dom": "*" } }, + "node_modules/@docusaurus/module-type-aliases/node_modules/@docusaurus/types": { + "version": "3.5.2", + "resolved": "https://registry.npmjs.org/@docusaurus/types/-/types-3.5.2.tgz", + "integrity": "sha512-N6GntLXoLVUwkZw7zCxwy9QiuEXIcTVzA9AkmNw16oc0AP3SXLrMmDMMBIfgqwuKWa6Ox6epHol9kMtJqekACw==", + "dev": true, + "dependencies": { + "@mdx-js/mdx": "^3.0.0", + "@types/history": "^4.7.11", + "@types/react": "*", + "commander": "^5.1.0", + "joi": "^17.9.2", + "react-helmet-async": "^1.3.0", + "utility-types": "^3.10.0", + "webpack": "^5.88.1", + "webpack-merge": "^5.9.0" + }, + "peerDependencies": { + "react": "^18.0.0", + "react-dom": "^18.0.0" + } + }, + "node_modules/@docusaurus/module-type-aliases/node_modules/commander": { + "version": "5.1.0", + "resolved": "https://registry.npmjs.org/commander/-/commander-5.1.0.tgz", + "integrity": "sha512-P0CysNDQ7rtVw4QIQtm+MRxV66vKFSvlsQvGYXZWR3qFU0jlMKHZZZgw8e+8DSah4UDKMqnknRDQz+xuQXQ/Zg==", + "dev": true, + "engines": { + "node": ">= 6" + } + }, "node_modules/@docusaurus/plugin-content-blog": { "version": "3.4.0", "license": "MIT", @@ -3201,6 +3233,24 @@ "react-dom": "^18.0.0" } }, + "node_modules/@docusaurus/plugin-content-docs/node_modules/@docusaurus/module-type-aliases": { + "version": "3.4.0", + "resolved": "https://registry.npmjs.org/@docusaurus/module-type-aliases/-/module-type-aliases-3.4.0.tgz", + "integrity": "sha512-A1AyS8WF5Bkjnb8s+guTDuYmUiwJzNrtchebBHpc0gz0PyHJNMaybUlSrmJjHVcGrya0LKI4YcR3lBDQfXRYLw==", + "dependencies": { + "@docusaurus/types": "3.4.0", + "@types/history": "^4.7.11", + "@types/react": "*", + "@types/react-router-config": "*", + "@types/react-router-dom": "*", + "react-helmet-async": "*", + "react-loadable": "npm:@docusaurus/react-loadable@6.0.0" + }, + "peerDependencies": { + "react": "*", + "react-dom": "*" + } + }, "node_modules/@docusaurus/plugin-content-docs/node_modules/argparse": { "version": "2.0.1", "license": "Python-2.0" @@ -3437,6 +3487,24 @@ "react-dom": "^18.0.0" } }, + "node_modules/@docusaurus/theme-classic/node_modules/@docusaurus/module-type-aliases": { + "version": "3.4.0", + "resolved": "https://registry.npmjs.org/@docusaurus/module-type-aliases/-/module-type-aliases-3.4.0.tgz", + "integrity": "sha512-A1AyS8WF5Bkjnb8s+guTDuYmUiwJzNrtchebBHpc0gz0PyHJNMaybUlSrmJjHVcGrya0LKI4YcR3lBDQfXRYLw==", + "dependencies": { + "@docusaurus/types": "3.4.0", + "@types/history": "^4.7.11", + "@types/react": "*", + "@types/react-router-config": "*", + "@types/react-router-dom": "*", + "react-helmet-async": "*", + "react-loadable": "npm:@docusaurus/react-loadable@6.0.0" + }, + "peerDependencies": { + "react": "*", + "react-dom": "*" + } + }, "node_modules/@docusaurus/theme-classic/node_modules/isarray": { "version": "0.0.1", "license": "MIT" @@ -3514,6 +3582,24 @@ "react-dom": "^18.0.0" } }, + "node_modules/@docusaurus/theme-common/node_modules/@docusaurus/module-type-aliases": { + "version": "3.4.0", + "resolved": "https://registry.npmjs.org/@docusaurus/module-type-aliases/-/module-type-aliases-3.4.0.tgz", + "integrity": "sha512-A1AyS8WF5Bkjnb8s+guTDuYmUiwJzNrtchebBHpc0gz0PyHJNMaybUlSrmJjHVcGrya0LKI4YcR3lBDQfXRYLw==", + "dependencies": { + "@docusaurus/types": "3.4.0", + "@types/history": "^4.7.11", + "@types/react": "*", + "@types/react-router-config": "*", + "@types/react-router-dom": "*", + "react-helmet-async": "*", + "react-loadable": "npm:@docusaurus/react-loadable@6.0.0" + }, + "peerDependencies": { + "react": "*", + "react-dom": "*" + } + }, "node_modules/@docusaurus/theme-live-codeblock": { "version": "3.4.0", "license": "MIT", From 566f1d876ecdb618313369e70be81af255fc1126 Mon Sep 17 00:00:00 2001 From: Riza Nafis Date: Sat, 7 Sep 2024 14:07:17 +0700 Subject: [PATCH 13/16] add check for observation-extract extension --- .../src/tests/extractObservation.test.ts | 45 ++++- .../src/tests/test-data/observationSample.ts | 184 ++++++++++++++++++ .../src/utils/extractObservation.ts | 151 ++++++++++---- .../src/utils/genericRecursive.ts | 19 ++ 4 files changed, 357 insertions(+), 42 deletions(-) diff --git a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts index ed280ffea..715a1a07f 100644 --- a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts +++ b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts @@ -1,19 +1,43 @@ import type { Questionnaire, QuestionnaireResponse } from 'fhir/r4'; -import { extractObservationBased } from '../utils/extractObservation'; +import { extractObservationBased, mapQItemsExtractable } from '../utils/extractObservation'; import { observationResults, + qExtractSample, qObservationSample, + qObservationSampleWithExtractExtension, qrObservationSample } from './test-data/observationSample'; describe('extractObservationBased', () => { it('should correctly extract Observations from a QuestionnaireResponse', () => { - const observations = extractObservationBased(qObservationSample, qrObservationSample); + const observations = extractObservationBased( + qObservationSampleWithExtractExtension, + qrObservationSample + ); expect(observations).toHaveLength(2); expect(observations[0]).toEqual(observationResults[0]); }); + it('should return an Observations array only if there are observation-extract extensions', () => { + const singleExtractExtension: Questionnaire = { + ...qObservationSampleWithExtractExtension + }; + singleExtractExtension.item!.at(0)!.extension!.at(0)!.valueBoolean = false; + + const observations = extractObservationBased( + qObservationSampleWithExtractExtension, + qrObservationSample + ); + expect(observations).toHaveLength(1); + expect(observations[0]).toEqual(observationResults[1]); + }); + + it('should return an empty array if there are no observation-extract extensions', () => { + const observations = extractObservationBased(qObservationSample, qrObservationSample); + expect(observations).toHaveLength(0); + }); + it('should return an empty array if there are no items in the Questionnaire or QuestionnaireResponse', () => { const emptyQuestionnaire: Questionnaire = { resourceType: 'Questionnaire', @@ -59,3 +83,20 @@ describe('extractObservationBased', () => { expect(observations).toHaveLength(0); }); }); + +describe('mapQItemsExtractable', () => { + it('should correctly return extractionMap from a Questionnaire', () => { + const extractionMap = mapQItemsExtractable(qExtractSample); + expect(extractionMap).toEqual({ + 'phq-2-questionnaire': false, + 'phq2-1': true, + 'phq2-2': false, + 'phq2-3': false, + 'phq2-4': true, + 'phq2-5': true, + 'phq2-6': false, + 'phq2-7': false, + 'phq2-8': true + }); + }); +}); diff --git a/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts b/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts index 71d7f9ae9..2d1bb8f1b 100644 --- a/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts +++ b/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts @@ -93,6 +93,111 @@ export const qObservationSample: Questionnaire = { ] }; +export const qObservationSampleWithExtractExtension: Questionnaire = { + resourceType: 'Questionnaire', + id: 'phq-2-questionnaire', + meta: { + versionId: '1', + lastUpdated: '2024-09-06T15:33:00Z' + }, + title: 'PHQ-2 Depression Screening', + status: 'active', + date: '2024-08-29T12:00:00Z', + publisher: 'Konsulin', + description: 'Patient Health Questionnaire-2 (PHQ-2) for depression screening.', + subjectType: ['Patient'], + item: [ + { + linkId: 'phq2-1', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ], + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ] + }, + { + linkId: 'phq2-2', + text: 'Over the last 2 weeks, how often have you been bothered by feeling down, depressed, or hopeless?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '307077003', + display: 'Feeling hopeless' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ], + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ] + } + ] +}; + export const qrObservationSample: QuestionnaireResponse = { resourceType: 'QuestionnaireResponse', id: 'phq2-response', @@ -153,6 +258,7 @@ export const observationResults: Observation[] = [ } ], effectiveDateTime: '2024-08-29T12:00:00Z', + issued: '2024-08-29T12:00:00Z', valueCodeableConcept: { coding: [ { @@ -184,6 +290,7 @@ export const observationResults: Observation[] = [ } ], effectiveDateTime: '2024-08-29T12:00:00Z', + issued: '2024-08-29T12:00:00Z', valueCodeableConcept: { coding: [ { @@ -194,3 +301,80 @@ export const observationResults: Observation[] = [ } } ]; + +export const qExtractSample: Questionnaire = { + resourceType: 'Questionnaire', + id: 'phq-2-questionnaire', + status: 'draft', + item: [ + { + linkId: 'phq2-1', + type: 'choice', + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ], + item: [ + { + linkId: 'phq2-8', + type: 'choice' + } + ] + }, + { + linkId: 'phq2-2', + type: 'choice', + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: false + } + ], + item: [ + { + linkId: 'phq2-4', + type: 'choice', + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ] + } + ] + }, + + { + linkId: 'phq2-3', + type: 'choice', + item: [ + { + linkId: 'phq2-5', + type: 'choice', + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ] + }, + { + linkId: 'phq2-6', + type: 'choice', + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: false + } + ] + }, + { + linkId: 'phq2-7', + type: 'choice' + } + ] + } + ] +}; diff --git a/packages/smart-forms-renderer/src/utils/extractObservation.ts b/packages/smart-forms-renderer/src/utils/extractObservation.ts index f30f93546..87691ecac 100644 --- a/packages/smart-forms-renderer/src/utils/extractObservation.ts +++ b/packages/smart-forms-renderer/src/utils/extractObservation.ts @@ -7,7 +7,7 @@ import type { QuestionnaireResponseItem, QuestionnaireResponseItemAnswer } from 'fhir/r4'; -import { readQuestionnaireResponse } from './genericRecursive'; +import { readQuestionnaireResponse, transverseQuestionnaire } from './genericRecursive'; /** * Extract an array of Observations from a QuestionnaireResponse and its source Questionnaire. @@ -30,65 +30,123 @@ export function extractObservationBased( return observations; } + if (!questionnaireResponse.id) { + questionnaireResponse.id = generateUniqueId( + (questionnaireResponse.identifier && questionnaireResponse.identifier.value) || 'QR' + ); + } + + const qItemExtractableMap = mapQItemsExtractable(questionnaire); + return readQuestionnaireResponse( questionnaire, questionnaireResponse, extractObservationBasedRecursive, - questionnaireResponse + { qr: questionnaireResponse, qItemMap: qItemExtractableMap } ); } +const FHIR_OBSERVATION_EXTRACT_EXTENSION = + 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract'; + +const FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION = + 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category'; + function extractObservationBasedRecursive( qItem: QuestionnaireItem, qrItemOrItems: QuestionnaireResponseItem | QuestionnaireResponseItem[] | null, - qr?: QuestionnaireResponse + extraData?: { qr: QuestionnaireResponse; qItemMap: Record } ): Observation[] | null { // Process items with child items const observations: Observation[] = []; - if (qr) { - // Map qrItemOrItems into an array of qrItems - let qrItems: QuestionnaireResponseItem[] = []; - if (qrItemOrItems) { - if (Array.isArray(qrItemOrItems)) { - qrItems = qrItemOrItems; - } else { - qrItems = [qrItemOrItems]; - } + + if (!extraData?.qr || !extraData?.qItemMap) return observations; + + if (!extraData.qItemMap[qItem.linkId]) return observations; + + // Map qrItemOrItems into an array of qrItems + let qrItems: QuestionnaireResponseItem[] = []; + if (qrItemOrItems) { + if (Array.isArray(qrItemOrItems)) { + qrItems = qrItemOrItems; + } else { + qrItems = [qrItemOrItems]; } + } - const categories: CodeableConcept[] = []; + const categories: CodeableConcept[] = []; - for (const responseItem of qrItems) { - if (categories.length) break; + for (const responseItem of qrItems) { + if (categories.length) break; - if (responseItem.extension) { - const exts = responseItem.extension.filter( - (e) => - e.url === - 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observation-extract-category' - ); + if (responseItem.extension) { + const exts = responseItem.extension.filter( + (e) => e.url === FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION + ); - exts.forEach((e) => e.valueCodeableConcept && categories.push(e.valueCodeableConcept)); - } + exts.forEach((e) => e.valueCodeableConcept && categories.push(e.valueCodeableConcept)); } + } - for (const responseItem of qrItems) { - // Check if the response item has any values or nested items - if (responseItem.answer && responseItem.answer.length > 0) { - for (const answer of responseItem.answer) { - const observation = createObservation(qItem, qr, answer, categories); + for (const responseItem of qrItems) { + // Check if the response item has any values or nested items + if (responseItem.answer && responseItem.answer.length > 0) { + for (const answer of responseItem.answer) { + const observation = createObservation(qItem, extraData.qr, answer, categories); - observations.push(observation); - } + observations.push(observation); } } - - return observations; } return observations; } +export function mapQItemsExtractable(questionnaire: Questionnaire): Record { + if (!questionnaire.item || questionnaire.item.length === 0) { + return {}; + } + + const initialExtension = questionnaire.extension?.find( + (e) => e.url === FHIR_OBSERVATION_EXTRACT_EXTENSION + ); + + const initialExtractMap: Record = { + [questionnaire.id ?? 'root']: initialExtension?.valueBoolean ?? false + }; + + transverseQuestionnaire(questionnaire, mapQItemsExtractableRecursive, initialExtractMap); + + return initialExtractMap; +} + +function mapQItemsExtractableRecursive( + qItem: QuestionnaireItem, + root?: Questionnaire, + parent?: QuestionnaireItem, + qItemExtrableMap?: Record +): void { + if (!qItemExtrableMap) return; + + const extension = qItem.extension?.find((e) => e.url === FHIR_OBSERVATION_EXTRACT_EXTENSION); + + if (extension?.valueBoolean) { + qItemExtrableMap[qItem.linkId] = true; + } else if (parent && qItemExtrableMap[parent.linkId]) { + qItemExtrableMap[qItem.linkId] = qItemExtrableMap[parent.linkId]; + } else if (root && qItemExtrableMap[root.id ?? 'root']) { + qItemExtrableMap[qItem.linkId] = qItemExtrableMap[root?.id ?? 'root']; + } else { + qItemExtrableMap[qItem.linkId] = false; + } + + if (qItem.item && qItem.item.length !== 0) { + for (const qChildItem of qItem.item) { + mapQItemsExtractableRecursive(qChildItem, root, qItem, qItemExtrableMap); + } + } +} + export function createObservation( questionnaireItem: QuestionnaireItem, questionnaireResponse: QuestionnaireResponse, @@ -102,20 +160,21 @@ export function createObservation( status: 'final', ...removeIfNull('id', questionnaireItem.linkId, `obs-${questionnaireItem.linkId}`), code: { - coding: [ - { - ...removeIfNull('system', questionnaireItem.code?.[0]?.system), - ...removeIfNull('code', questionnaireItem.code?.[0]?.code), - ...removeIfNull('display', questionnaireItem.code?.[0]?.display) - } - ] + coding: + questionnaireItem.code?.map((c) => ({ + ...removeIfNull('system', c.system), + ...removeIfNull('code', c.code), + ...removeIfNull('display', c.display) + })) ?? [] }, ...removeIfNull('basedOn', questionnaireResponse.basedOn), ...removeIfNull('partOf', questionnaireResponse.partOf), ...removeIfNull('subject', questionnaireResponse.subject), ...removeIfNull('encounter', questionnaireResponse.encounter), derivedFrom: [{ reference: qrRef }], - ...removeIfNull('effectiveDateTime', questionnaireResponse.authored) + ...removeIfNull('effectiveDateTime', questionnaireResponse.authored), + ...removeIfNull('issued', questionnaireResponse.authored), + ...removeIfNull('author', questionnaireResponse.author) }; // Set the value of the Observation based on the answer type @@ -138,6 +197,18 @@ export function createObservation( return observation; } +let ID_COUNTER = 0; + +function generateUniqueId(prefix: string) { + if (ID_COUNTER) { + ID_COUNTER = 0; + } + + return ( + prefix + '-' + Date.now() + '-' + ++ID_COUNTER + '-' + Math.random().toString(16).substring(2) + ); +} + function removeIfNull( key: string, value?: T, diff --git a/packages/smart-forms-renderer/src/utils/genericRecursive.ts b/packages/smart-forms-renderer/src/utils/genericRecursive.ts index 3b880f671..a82271434 100644 --- a/packages/smart-forms-renderer/src/utils/genericRecursive.ts +++ b/packages/smart-forms-renderer/src/utils/genericRecursive.ts @@ -134,3 +134,22 @@ export function readQuestionnaireResponse( return readValueArray; } + +export type RecursiveTranverseFunction = ( + qItem: QuestionnaireItem, + root?: Questionnaire, + parent?: QuestionnaireItem, + extraData?: U +) => void; + +export function transverseQuestionnaire( + questionnaire: Questionnaire, + recursiveTranverseFunction: RecursiveTranverseFunction, + extraData?: U +): void { + if (!questionnaire.item || questionnaire.item.length === 0) return; + + for (const topLevelQItem of questionnaire.item) { + recursiveTranverseFunction(topLevelQItem, questionnaire, undefined, extraData); + } +} From fb69d87031a3f46a09eec23409bc05a2fecaa63d Mon Sep 17 00:00:00 2001 From: Riza Nafis Date: Sat, 7 Sep 2024 16:13:45 +0700 Subject: [PATCH 14/16] add recursion on extractObservation --- .../src/tests/extractObservation.test.ts | 44 ++- .../src/tests/test-data/observationSample.ts | 345 +++++++++++++++++- .../src/utils/extractObservation.ts | 49 ++- 3 files changed, 420 insertions(+), 18 deletions(-) diff --git a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts index 715a1a07f..d17f3d8e5 100644 --- a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts +++ b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts @@ -15,22 +15,29 @@ describe('extractObservationBased', () => { qObservationSampleWithExtractExtension, qrObservationSample ); - expect(observations).toHaveLength(2); + expect(observations).toHaveLength(4); expect(observations[0]).toEqual(observationResults[0]); }); it('should return an Observations array only if there are observation-extract extensions', () => { - const singleExtractExtension: Questionnaire = { - ...qObservationSampleWithExtractExtension - }; + const singleExtractExtension: Questionnaire = JSON.parse( + JSON.stringify(qObservationSampleWithExtractExtension) + ); singleExtractExtension.item!.at(0)!.extension!.at(0)!.valueBoolean = false; - const observations = extractObservationBased( - qObservationSampleWithExtractExtension, - qrObservationSample + const observations = extractObservationBased(singleExtractExtension, qrObservationSample); + expect(observations).toHaveLength(2); + expect(observations[0].id).toContain('phq2-4'); + }); + + it('should return all Observations expect for observation-extract extensions false', () => { + const topLevelExtract: Questionnaire = JSON.parse( + JSON.stringify(qObservationSampleWithExtractExtension) ); - expect(observations).toHaveLength(1); - expect(observations[0]).toEqual(observationResults[1]); + topLevelExtract.extension!.at(0)!.valueBoolean = true; + + const observations = extractObservationBased(topLevelExtract, qrObservationSample); + expect(observations).toHaveLength(6); }); it('should return an empty array if there are no observation-extract extensions', () => { @@ -99,4 +106,23 @@ describe('mapQItemsExtractable', () => { 'phq2-8': true }); }); + + it('should correctly return extractionMap even with topLevel observation-extract extensions true', () => { + const topLevelExtract: Questionnaire = JSON.parse(JSON.stringify(qExtractSample)); + topLevelExtract.extension!.at(0)!.valueBoolean = true; + + const extractionMap = mapQItemsExtractable(topLevelExtract); + + expect(extractionMap).toEqual({ + 'phq-2-questionnaire': true, + 'phq2-1': true, + 'phq2-2': false, + 'phq2-3': true, + 'phq2-4': true, + 'phq2-5': true, + 'phq2-6': false, + 'phq2-7': true, + 'phq2-8': true + }); + }); }); diff --git a/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts b/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts index 2d1bb8f1b..62d302123 100644 --- a/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts +++ b/packages/smart-forms-renderer/src/tests/test-data/observationSample.ts @@ -106,6 +106,12 @@ export const qObservationSampleWithExtractExtension: Questionnaire = { publisher: 'Konsulin', description: 'Patient Health Questionnaire-2 (PHQ-2) for depression screening.', subjectType: ['Patient'], + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: false + } + ], item: [ { linkId: 'phq2-1', @@ -149,6 +155,46 @@ export const qObservationSampleWithExtractExtension: Questionnaire = { url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', valueBoolean: true } + ], + item: [ + { + linkId: 'phq2-8', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ] + } ] }, { @@ -191,7 +237,219 @@ export const qObservationSampleWithExtractExtension: Questionnaire = { extension: [ { url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', - valueBoolean: true + valueBoolean: false + } + ], + item: [ + { + linkId: 'phq2-4', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ], + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ] + } + ] + }, + { + linkId: 'phq2-3', + text: 'Over the last 2 weeks, how often have you been bothered by feeling down, depressed, or hopeless?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '307077003', + display: 'Feeling hopeless' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ], + item: [ + { + linkId: 'phq2-5', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ], + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: true + } + ] + }, + { + linkId: 'phq2-6', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ], + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: false + } + ] + }, + { + linkId: 'phq2-7', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + type: 'choice', + code: [ + { + system: 'http://snomed.info/sct', + code: '28669007', + display: 'Anhedonia' + } + ], + answerOption: [ + { + valueCoding: { + code: '0', + display: 'Not at all' + } + }, + { + valueCoding: { + code: '1', + display: 'Several days' + } + }, + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + }, + { + valueCoding: { + code: '3', + display: 'Nearly every day' + } + } + ] } ] } @@ -218,6 +476,20 @@ export const qrObservationSample: QuestionnaireResponse = { display: 'More than half the days' } } + ], + item: [ + { + linkId: 'phq2-8', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + answer: [ + { + valueCoding: { + code: '2', + display: 'More than half the days' + } + } + ] + } ] }, { @@ -230,6 +502,70 @@ export const qrObservationSample: QuestionnaireResponse = { display: 'Several days' } } + ], + item: [ + { + linkId: 'phq2-4', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + answer: [ + { + valueCoding: { + code: '1', + display: 'Several days' + } + } + ] + } + ] + }, + { + linkId: 'phq2-3', + text: 'Over the last 2 weeks, how often have you been bothered by feeling down, depressed, or hopeless?', + answer: [ + { + valueCoding: { + code: '1', + display: 'Several days' + } + } + ], + item: [ + { + linkId: 'phq2-5', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + answer: [ + { + valueCoding: { + code: '1', + display: 'Several days' + } + } + ] + }, + { + linkId: 'phq2-6', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + answer: [ + { + valueCoding: { + code: '1', + display: 'Several days' + } + } + ] + }, + { + linkId: 'phq2-7', + text: 'Over the last 2 weeks, how often have you been bothered by little interest or pleasure in doing things?', + answer: [ + { + valueCoding: { + code: '1', + display: 'Several days' + } + } + ] + } ] } ] @@ -306,6 +642,12 @@ export const qExtractSample: Questionnaire = { resourceType: 'Questionnaire', id: 'phq-2-questionnaire', status: 'draft', + extension: [ + { + url: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-observationExtract', + valueBoolean: false + } + ], item: [ { linkId: 'phq2-1', @@ -345,7 +687,6 @@ export const qExtractSample: Questionnaire = { } ] }, - { linkId: 'phq2-3', type: 'choice', diff --git a/packages/smart-forms-renderer/src/utils/extractObservation.ts b/packages/smart-forms-renderer/src/utils/extractObservation.ts index 87691ecac..95c0502ce 100644 --- a/packages/smart-forms-renderer/src/utils/extractObservation.ts +++ b/packages/smart-forms-renderer/src/utils/extractObservation.ts @@ -8,6 +8,7 @@ import type { QuestionnaireResponseItemAnswer } from 'fhir/r4'; import { readQuestionnaireResponse, transverseQuestionnaire } from './genericRecursive'; +import { getQrItemsIndex, mapQItemsIndex } from './mapItem'; /** * Extract an array of Observations from a QuestionnaireResponse and its source Questionnaire. @@ -62,8 +63,6 @@ function extractObservationBasedRecursive( if (!extraData?.qr || !extraData?.qItemMap) return observations; - if (!extraData.qItemMap[qItem.linkId]) return observations; - // Map qrItemOrItems into an array of qrItems let qrItems: QuestionnaireResponseItem[] = []; if (qrItemOrItems) { @@ -84,7 +83,11 @@ function extractObservationBasedRecursive( (e) => e.url === FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION ); - exts.forEach((e) => e.valueCodeableConcept && categories.push(e.valueCodeableConcept)); + for (const ext of exts) { + if (ext.valueCodeableConcept) { + categories.push(ext.valueCodeableConcept); + } + } } } @@ -92,13 +95,45 @@ function extractObservationBasedRecursive( // Check if the response item has any values or nested items if (responseItem.answer && responseItem.answer.length > 0) { for (const answer of responseItem.answer) { - const observation = createObservation(qItem, extraData.qr, answer, categories); + if (extraData.qItemMap[qItem.linkId]) { + const observation = createObservation(qItem, extraData.qr, answer, categories); - observations.push(observation); + observations.push(observation); + } } } } + const childQItems = qItem.item; + if (!childQItems || childQItems.length === 0) return observations; + + // Map qrItemOrItems into an array of qrItems + let childQrItems: QuestionnaireResponseItem[] = []; + if (qrItemOrItems) { + if (Array.isArray(qrItemOrItems)) { + childQrItems = qrItemOrItems; + } else { + childQrItems = qrItemOrItems.item ?? []; + } + } + + const indexMap = mapQItemsIndex(qItem); + const qrItemsByIndex = getQrItemsIndex(childQItems, childQrItems, indexMap); + + for (const [index, childQItem] of childQItems.entries()) { + const childQRItemOrItems = qrItemsByIndex[index]; + + const childObservations = extractObservationBasedRecursive( + childQItem, + childQRItemOrItems ?? null, + extraData + ); + + if (childObservations) { + observations.push(...childObservations); + } + } + return observations; } @@ -130,8 +165,8 @@ function mapQItemsExtractableRecursive( const extension = qItem.extension?.find((e) => e.url === FHIR_OBSERVATION_EXTRACT_EXTENSION); - if (extension?.valueBoolean) { - qItemExtrableMap[qItem.linkId] = true; + if (extension?.valueBoolean || extension?.valueBoolean === false) { + qItemExtrableMap[qItem.linkId] = extension?.valueBoolean ?? false; } else if (parent && qItemExtrableMap[parent.linkId]) { qItemExtrableMap[qItem.linkId] = qItemExtrableMap[parent.linkId]; } else if (root && qItemExtrableMap[root.id ?? 'root']) { From 250284bc5cece15fa89c8c6848786b83364e2476 Mon Sep 17 00:00:00 2001 From: Riza Nafis Date: Mon, 9 Sep 2024 09:30:11 +0700 Subject: [PATCH 15/16] Remove async keyword from handleObservationExtract button click --- .../src/features/playground/components/Playground.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/apps/smart-forms-app/src/features/playground/components/Playground.tsx b/apps/smart-forms-app/src/features/playground/components/Playground.tsx index 12ce17d15..4c4cf69ac 100644 --- a/apps/smart-forms-app/src/features/playground/components/Playground.tsx +++ b/apps/smart-forms-app/src/features/playground/components/Playground.tsx @@ -154,7 +154,7 @@ function Playground() { } // Observation $extract - async function handleObservationExtract() { + function handleObservationExtract() { const observations = extractObservationBased(sourceQuestionnaire, updatableResponse); setExtractedResource(observations); From d0fdceb0cc83248fc4b8e6e993794b396a762980 Mon Sep 17 00:00:00 2001 From: Riza Nafis Date: Mon, 9 Sep 2024 15:57:13 +0700 Subject: [PATCH 16/16] fix extract categories extension logic --- .../src/tests/extractObservation.test.ts | 46 +++++----- .../src/utils/extractObservation.ts | 85 ++++++++++++------- 2 files changed, 81 insertions(+), 50 deletions(-) diff --git a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts index d17f3d8e5..4dd0b6fcb 100644 --- a/packages/smart-forms-renderer/src/tests/extractObservation.test.ts +++ b/packages/smart-forms-renderer/src/tests/extractObservation.test.ts @@ -1,6 +1,10 @@ import type { Questionnaire, QuestionnaireResponse } from 'fhir/r4'; -import { extractObservationBased, mapQItemsExtractable } from '../utils/extractObservation'; +import { + Extractable, + extractObservationBased, + mapQItemsExtractable +} from '../utils/extractObservation'; import { observationResults, qExtractSample, @@ -95,16 +99,16 @@ describe('mapQItemsExtractable', () => { it('should correctly return extractionMap from a Questionnaire', () => { const extractionMap = mapQItemsExtractable(qExtractSample); expect(extractionMap).toEqual({ - 'phq-2-questionnaire': false, - 'phq2-1': true, - 'phq2-2': false, - 'phq2-3': false, - 'phq2-4': true, - 'phq2-5': true, - 'phq2-6': false, - 'phq2-7': false, - 'phq2-8': true - }); + 'phq-2-questionnaire': { extractable: false, extractCategories: [] }, + 'phq2-1': { extractable: true, extractCategories: [] }, + 'phq2-2': { extractable: false, extractCategories: [] }, + 'phq2-3': { extractable: false, extractCategories: [] }, + 'phq2-4': { extractable: true, extractCategories: [] }, + 'phq2-5': { extractable: true, extractCategories: [] }, + 'phq2-6': { extractable: false, extractCategories: [] }, + 'phq2-7': { extractable: false, extractCategories: [] }, + 'phq2-8': { extractable: true, extractCategories: [] } + } satisfies Record); }); it('should correctly return extractionMap even with topLevel observation-extract extensions true', () => { @@ -114,15 +118,15 @@ describe('mapQItemsExtractable', () => { const extractionMap = mapQItemsExtractable(topLevelExtract); expect(extractionMap).toEqual({ - 'phq-2-questionnaire': true, - 'phq2-1': true, - 'phq2-2': false, - 'phq2-3': true, - 'phq2-4': true, - 'phq2-5': true, - 'phq2-6': false, - 'phq2-7': true, - 'phq2-8': true - }); + 'phq-2-questionnaire': { extractable: true, extractCategories: [] }, + 'phq2-1': { extractable: true, extractCategories: [] }, + 'phq2-2': { extractable: false, extractCategories: [] }, + 'phq2-3': { extractable: true, extractCategories: [] }, + 'phq2-4': { extractable: true, extractCategories: [] }, + 'phq2-5': { extractable: true, extractCategories: [] }, + 'phq2-6': { extractable: false, extractCategories: [] }, + 'phq2-7': { extractable: true, extractCategories: [] }, + 'phq2-8': { extractable: true, extractCategories: [] } + } satisfies Record); }); }); diff --git a/packages/smart-forms-renderer/src/utils/extractObservation.ts b/packages/smart-forms-renderer/src/utils/extractObservation.ts index 95c0502ce..2f149fb49 100644 --- a/packages/smart-forms-renderer/src/utils/extractObservation.ts +++ b/packages/smart-forms-renderer/src/utils/extractObservation.ts @@ -56,7 +56,7 @@ const FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION = function extractObservationBasedRecursive( qItem: QuestionnaireItem, qrItemOrItems: QuestionnaireResponseItem | QuestionnaireResponseItem[] | null, - extraData?: { qr: QuestionnaireResponse; qItemMap: Record } + extraData?: { qr: QuestionnaireResponse; qItemMap: Record } ): Observation[] | null { // Process items with child items const observations: Observation[] = []; @@ -73,30 +73,19 @@ function extractObservationBasedRecursive( } } - const categories: CodeableConcept[] = []; - - for (const responseItem of qrItems) { - if (categories.length) break; - - if (responseItem.extension) { - const exts = responseItem.extension.filter( - (e) => e.url === FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION - ); - - for (const ext of exts) { - if (ext.valueCodeableConcept) { - categories.push(ext.valueCodeableConcept); - } - } - } - } - for (const responseItem of qrItems) { // Check if the response item has any values or nested items if (responseItem.answer && responseItem.answer.length > 0) { for (const answer of responseItem.answer) { - if (extraData.qItemMap[qItem.linkId]) { - const observation = createObservation(qItem, extraData.qr, answer, categories); + const currentQItemExtractable = extraData.qItemMap[qItem.linkId]; + + if (currentQItemExtractable.extractable) { + const observation = createObservation( + qItem, + extraData.qr, + answer, + currentQItemExtractable.extractCategories + ); observations.push(observation); } @@ -137,7 +126,12 @@ function extractObservationBasedRecursive( return observations; } -export function mapQItemsExtractable(questionnaire: Questionnaire): Record { +export type Extractable = { + extractable: boolean; + extractCategories: CodeableConcept[]; +}; + +export function mapQItemsExtractable(questionnaire: Questionnaire): Record { if (!questionnaire.item || questionnaire.item.length === 0) { return {}; } @@ -146,8 +140,15 @@ export function mapQItemsExtractable(questionnaire: Questionnaire): Record e.url === FHIR_OBSERVATION_EXTRACT_EXTENSION ); - const initialExtractMap: Record = { - [questionnaire.id ?? 'root']: initialExtension?.valueBoolean ?? false + const extractCategoryExts = questionnaire.extension + ?.filter((e) => e.url === FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION && e.valueCodeableConcept) + ?.map((e) => e.valueCodeableConcept) as CodeableConcept[] | undefined; + + const initialExtractMap: Record = { + [questionnaire.id ?? 'root']: { + extractable: initialExtension?.valueBoolean ?? false, + extractCategories: extractCategoryExts ?? [] + } }; transverseQuestionnaire(questionnaire, mapQItemsExtractableRecursive, initialExtractMap); @@ -159,20 +160,46 @@ function mapQItemsExtractableRecursive( qItem: QuestionnaireItem, root?: Questionnaire, parent?: QuestionnaireItem, - qItemExtrableMap?: Record + qItemExtrableMap?: Record ): void { if (!qItemExtrableMap) return; + if (!qItemExtrableMap[qItem.linkId]) { + qItemExtrableMap[qItem.linkId] = { extractable: false, extractCategories: [] }; + } + + // Check if questionnaire extractable const extension = qItem.extension?.find((e) => e.url === FHIR_OBSERVATION_EXTRACT_EXTENSION); if (extension?.valueBoolean || extension?.valueBoolean === false) { - qItemExtrableMap[qItem.linkId] = extension?.valueBoolean ?? false; + qItemExtrableMap[qItem.linkId].extractable = extension?.valueBoolean ?? false; } else if (parent && qItemExtrableMap[parent.linkId]) { - qItemExtrableMap[qItem.linkId] = qItemExtrableMap[parent.linkId]; + qItemExtrableMap[qItem.linkId].extractable = qItemExtrableMap[parent.linkId].extractable; } else if (root && qItemExtrableMap[root.id ?? 'root']) { - qItemExtrableMap[qItem.linkId] = qItemExtrableMap[root?.id ?? 'root']; + qItemExtrableMap[qItem.linkId].extractable = qItemExtrableMap[root?.id ?? 'root'].extractable; } else { - qItemExtrableMap[qItem.linkId] = false; + qItemExtrableMap[qItem.linkId].extractable = false; + } + + // if questionnaire extractable, check for extract category + if (qItemExtrableMap[qItem.linkId].extractable) { + const extractCategoryExts = qItem.extension + ?.filter( + (e) => e.url === FHIR_OBSERVATION_EXTRACT_CATEGORY_EXTENSION && e.valueCodeableConcept + ) + ?.map((e) => e.valueCodeableConcept) as CodeableConcept[] | undefined; + + if (extractCategoryExts) { + qItemExtrableMap[qItem.linkId].extractCategories = extractCategoryExts; + } else if (parent && qItemExtrableMap[parent.linkId].extractCategories.length) { + qItemExtrableMap[qItem.linkId].extractCategories = + qItemExtrableMap[parent.linkId].extractCategories; + } else if (root && qItemExtrableMap[root.id ?? 'root'].extractCategories.length) { + qItemExtrableMap[qItem.linkId].extractCategories = + qItemExtrableMap[root?.id ?? 'root'].extractCategories; + } else { + qItemExtrableMap[qItem.linkId].extractCategories = []; + } } if (qItem.item && qItem.item.length !== 0) {