diff --git a/.ncurc.yml b/.ncurc.yml index 08eb21d..33cc7fd 100644 --- a/.ncurc.yml +++ b/.ncurc.yml @@ -1,6 +1,3 @@ -# Do not update to React 19 because some packages not compatible with React 19 reject: - - react - - react-dom - - '@types/react' - - '@types/react-dom' + # remove this when typescript-eslint supports the current TypeScript version 7. + -typescript diff --git a/babel.config.js b/babel.config.js deleted file mode 100644 index eff09bc..0000000 --- a/babel.config.js +++ /dev/null @@ -1,10 +0,0 @@ -module.exports = { - plugins: ["@babel/plugin-transform-modules-commonjs"], - presets: [ - "@babel/preset-typescript", - [ - "@babel/preset-react", - { runtime: "automatic", importSource: "@emotion/react" }, - ], - ], -}; diff --git a/eslint.config.mjs b/eslint.config.mjs index b27947a..213dce0 100644 --- a/eslint.config.mjs +++ b/eslint.config.mjs @@ -1,52 +1,89 @@ +import { defineConfig, globalIgnores } from 'eslint/config'; import react from 'eslint-config-cheminfo-react/base'; import ts from 'eslint-config-cheminfo-typescript/base'; import unicorn from 'eslint-config-cheminfo-typescript/unicorn'; -export default [ - { - ignores: [ - 'dist', - 'build', - 'releases', - 'node_modules', - 'playwright-report', - 'public', - 'vite.config.ts', - ], - }, - ...ts, - ...unicorn, - ...react, +export default defineConfig( + globalIgnores([ + 'dist', + 'lib', + 'releases', + 'node_modules', + 'playwright-report', + 'test-results', + 'public', + 'vite.config.ts' + ]), + ts, + unicorn, + react, { files: ['**/*.{ts,tsx,cts,mts}'], rules: { '@typescript-eslint/consistent-type-imports': 'error', + '@typescript-eslint/naming-convention': 'off', + '@typescript-eslint/no-deprecated': 'error', + '@typescript-eslint/no-explicit-any': 'off', + '@typescript-eslint/no-implied-eval': 'off', + '@typescript-eslint/no-misused-promises': 'off', + '@typescript-eslint/no-useless-default-assignment': 'off', + '@typescript-eslint/restrict-plus-operands': 'off', + '@typescript-eslint/switch-exhaustiveness-check': 'off', 'import/consistent-type-specifier-style': ['error', 'prefer-top-level'], }, }, { rules: { + '@eslint-react/dom-no-missing-iframe-sandbox': 'off', + '@eslint-react/naming-convention-ref-name': 'off', + '@eslint-react/no-children-count': 'off', + '@eslint-react/no-children-map': 'off', + '@eslint-react/no-children-to-array': 'off', + '@eslint-react/no-clone-element': 'off', + '@eslint-react/no-unstable-default-props': 'off', + '@eslint-react/purity': 'off', + '@eslint-react/refs': 'off', + '@eslint-react/set-state-in-effect': 'off', + '@eslint-react/static-components': 'off', + '@eslint-react/use-state': 'off', 'import/default': 'off', 'import/no-unresolved': 'off', + 'react-you-might-not-need-an-effect/no-adjust-state-on-prop-change': + 'off', + 'react-you-might-not-need-an-effect/no-chain-state-updates': 'off', + 'react-you-might-not-need-an-effect/no-derived-state': 'off', + 'react-you-might-not-need-an-effect/no-event-handler': 'off', + 'react-you-might-not-need-an-effect/no-external-store-subscription': + 'off', + 'react-you-might-not-need-an-effect/no-pass-data-to-parent': 'off', + 'prefer-named-capture-group': 'off', + 'react-hooks/preserve-manual-memoization': 'off', 'react-refresh/only-export-components': 'off', - '@typescript-eslint/no-explicit-any': 'off', - '@typescript-eslint/naming-convention': 'off', - '@typescript-eslint/no-implied-eval': 'off', - '@typescript-eslint/no-misused-promises': 'off', - '@typescript-eslint/restrict-plus-operands': 'off', - 'react/no-unstable-nested-components': 'off', + 'unicorn/consistent-boolean-name': 'off', + 'unicorn/max-nested-calls': 'off', + 'unicorn/name-replacements': 'off', + 'unicorn/no-computed-property-existence-check': 'off', + 'unicorn/no-non-function-verb-prefix': 'off', + 'unicorn/no-unreadable-for-of-expression': 'off', + 'unicorn/no-unreadable-object-destructuring': 'off', + 'unicorn/no-unsafe-string-replacement': 'off', + 'unicorn/no-useless-else': 'off', + 'unicorn/prefer-await': 'off', + 'unicorn/prefer-combined-guards': 'off', + 'unicorn/prefer-continue': 'off', + 'unicorn/prefer-early-return': 'off', 'no-restricted-imports': [ 'error', { name: 'lodash', - message: "Use a deep import instead, like for example 'lodash/get'", + message: + "Use a deep import instead, like for example 'lodash/merge.js'", }, { name: '@simbathesailor/use-what-changed', message: 'Remove use-what-changed before committing the code', } ], - 'react/no-unknown-property': ['error', { ignore: ['css'] }], }, }, -]; \ No newline at end of file +); diff --git a/package-lock.json b/package-lock.json index bf369e3..23ff34f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,50 +9,44 @@ "version": "1.2.0", "license": "MIT", "dependencies": { - "@blueprintjs/core": "^6.16.0", - "@blueprintjs/icons": "^6.11.0", - "@blueprintjs/select": "^6.3.0", + "@blueprintjs/core": "^6.21.0", + "@blueprintjs/icons": "^6.14.1", "@emotion/styled": "^11.14.1", - "@vitejs/plugin-react": "^6.0.2", - "@zakodium/nmrium-core": "^0.7.30", - "@zakodium/nmrium-core-plugins": "^0.7.39", + "@vitejs/plugin-react": "^6.1.2", + "@zakodium/nmrium-core": "^0.7.77", + "@zakodium/nmrium-core-plugins": "^0.7.109", "fifo-logger": "^2.0.1", - "filelist-utils": "^1.11.3", - "nmr-processing": "^22.13.0", - "nmrium": "^2.2.0", - "openchemlib": "^9.23.0", - "react-science": "^19.11.0" + "file-collection": "^6.7.0", + "nmrium": "^3.1.0", + "openchemlib": "^9.25.1", + "react-science": "^24.0.1" }, "devDependencies": { - 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"engines": { - "node": ">= 8" + "node": ">= 12" } }, "node_modules/workbox-cacheable-response": { @@ -15555,16 +15660,6 @@ "url": "https://github.com/chalk/wrap-ansi?sponsor=1" } }, - "node_modules/wrap-ansi-cjs/node_modules/ansi-regex": { - "version": "5.0.1", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", - "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==", - "dev": true, - "license": "MIT", - "engines": { - "node": ">=8" - } - }, "node_modules/wrap-ansi-cjs/node_modules/emoji-regex": { "version": "8.0.0", "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", @@ -15587,17 +15682,17 @@ "node": ">=8" } }, - "node_modules/wrap-ansi-cjs/node_modules/strip-ansi": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", - "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "node_modules/wrap-ansi/node_modules/ansi-regex": { + "version": "6.4.0", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.4.0.tgz", + "integrity": "sha512-KzTVk2tCWAHtYrvvvaP8bJKJq2pVinhLcGEQdtLIYPbmNGNyYe8QwNaTUYQp2J7/vIsUKt5QCqAfUkYyG9DkOw==", "dev": true, "license": "MIT", - "dependencies": { - "ansi-regex": "^5.0.1" - }, "engines": { - "node": ">=8" + "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/ansi-regex?sponsor=1" } }, "node_modules/wrap-ansi/node_modules/ansi-styles": { @@ -15613,12 +15708,21 @@ "url": "https://github.com/chalk/ansi-styles?sponsor=1" } }, - "node_modules/wrappy": { - "version": "1.0.2", - "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", + "node_modules/wrap-ansi/node_modules/strip-ansi": { + "version": "7.2.0", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.2.0.tgz", + "integrity": "sha512-yDPMNjp4WyfYBkHnjIRLfca1i6KMyGCtsVgoKe/z1+6vukgaENdgGBZt+ZmKPc4gavvEZ5OgHfHdrazhgNyG7w==", "dev": true, - "license": "ISC" + "license": "MIT", + "dependencies": { + "ansi-regex": "^6.2.2" + }, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/strip-ansi?sponsor=1" + } }, "node_modules/write-file-atomic": { "version": "5.0.1", @@ -15634,6 +15738,19 @@ "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, + "node_modules/write-file-atomic/node_modules/signal-exit": { + "version": "4.1.0", + "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-4.1.0.tgz", + "integrity": "sha512-bzyZ1e88w9O1iNJbKnOlvYTrWPDl46O1bG0D3XInv+9tkPrxrN8jUUTiFlDkkmKWgn1M6CfIA13SuGqOa9Korw==", + "dev": true, + "license": "ISC", + "engines": { + "node": ">=14" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/y18n": { "version": "5.0.8", "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", @@ -15652,10 +15769,10 @@ "license": "ISC" }, "node_modules/yaml": { - "version": "2.9.0", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.0.tgz", - "integrity": "sha512-2AvhNX3mb8zd6Zy7INTtSpl1F15HW6Wnqj0srWlkKLcpYl/gMIMJiyuGq2KeI2YFxUPjdlB+3Lc10seMLtL4cA==", - "extraneous": true, + "version": "2.9.1", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.9.1.tgz", + "integrity": "sha512-3NxN8+78OdzbT7C/WjGsyfPAtJaN3FNDsWxv7Y7mcDsT/oOmgW8BpyQQFFBnvZE3j9Y2Sdz1ULFLezL7Eb2yFw==", + "devOptional": true, "license": "ISC", "bin": { "yaml": "bin.mjs" @@ -15668,9 +15785,9 @@ } }, "node_modules/yargs": { - "version": "17.7.2", - "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz", - "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==", + "version": "17.7.3", + "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.3.tgz", + "integrity": "sha512-GZtjxm/J/4TSxuL3FNYjCmLktBTnIw/rVmKSIyKeYAZpmJB2ig9VauCC5xsa82GNKVKDAqpOn3KVzNt0zmrU0g==", "dev": true, "license": "MIT", "dependencies": { @@ -15696,16 +15813,6 @@ "node": ">=12" } }, - "node_modules/yargs/node_modules/ansi-regex": { - "version": "5.0.1", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz", - "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==", - "dev": true, - "license": "MIT", - "engines": { - "node": ">=8" - } - }, "node_modules/yargs/node_modules/emoji-regex": { "version": "8.0.0", "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", @@ -15728,19 +15835,6 @@ "node": ">=8" } }, - "node_modules/yargs/node_modules/strip-ansi": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", - "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", - "dev": true, - "license": "MIT", - "dependencies": { - "ansi-regex": "^5.0.1" - }, - "engines": { - "node": ">=8" - } - }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", @@ -15779,9 +15873,9 @@ } }, "node_modules/zod": { - "version": "4.4.3", - "resolved": "https://registry.npmjs.org/zod/-/zod-4.4.3.tgz", - "integrity": "sha512-ytENFjIJFl2UwYglde2jchW2Hwm4GJFLDiSXWdTrJQBIN9Fcyp7n4DhxJEiWNAJMV1/BqWfW/kkg71UDcHJyTQ==", + "version": "4.6.5", + "resolved": "https://registry.npmjs.org/zod/-/zod-4.6.5.tgz", + "integrity": "sha512-v5l/aFXZQeai4awLbOpSoHecE9UiMrnfx75tEXLjNonXVARxQ5mOeipTjROUchszUNCqnE+hqAMujRsRHsut2Q==", "license": "MIT", "funding": { "url": "https://github.com/sponsors/colinhacks" diff --git a/package.json b/package.json index 971ba0b..4b19939 100644 --- a/package.json +++ b/package.json @@ -10,22 +10,20 @@ "src" ], "volta": { - "node": "24.4.0" + "node": "24.19.0" }, "dependencies": { - "@blueprintjs/core": "^6.16.0", - "@blueprintjs/icons": "^6.11.0", - "@blueprintjs/select": "^6.3.0", + "@blueprintjs/core": "^6.21.0", + "@blueprintjs/icons": "^6.14.1", "@emotion/styled": "^11.14.1", - "@vitejs/plugin-react": "^6.0.2", - "@zakodium/nmrium-core": "^0.7.30", - "@zakodium/nmrium-core-plugins": "^0.7.39", + "@vitejs/plugin-react": "^6.1.2", + "@zakodium/nmrium-core": "^0.7.77", + "@zakodium/nmrium-core-plugins": "^0.7.109", + "file-collection": "^6.7.0", "fifo-logger": "^2.0.1", - "filelist-utils": "^1.11.3", - "nmr-processing": "^22.13.0", - "nmrium": "^2.2.0", - "openchemlib": "^9.23.0", - "react-science": "^19.11.0" + "nmrium": "^3.1.0", + "openchemlib": "^9.25.1", + "react-science": "^24.0.1" }, "scripts": { "start": "vite --host localhost --port 3000 --open", @@ -43,28 +41,24 @@ "test-e2e-server": "serve -l tcp://localhost:3000 dist" }, "devDependencies": { - "@babel/plugin-transform-modules-commonjs": "^7.29.7", - "@babel/preset-react": "^7.29.7", - "@babel/preset-typescript": "^7.29.7", - "@playwright/test": "^1.61.0", + "@playwright/test": "^1.64.0", "@simbathesailor/use-what-changed": "^2.0.0", "@types/jest": "^30.0.0", - "@types/node": "^25.9.3", - "@types/react": "^18.3.3", - "@types/react-dom": "^18.3.0", - "@types/react-router-dom": "^5.3.3", + "@types/node": "^26.6.4", + "@types/react": "^19.3.0", + "@types/react-dom": "^19.3.0", "cross-env": "^10.1.0", - "eslint": "^9.39.2", - "eslint-config-cheminfo-react": "^20.1.0", - "eslint-config-cheminfo-typescript": "^22.1.0", - "jest": "^30.4.2", - "prettier": "3.8.4", - "react": "^18.3.1", - "react-dom": "^18.3.1", - "react-router-dom": "^7.17.0", + "eslint": "^10.12.0", + "eslint-config-cheminfo-react": "^21.0.2", + "eslint-config-cheminfo-typescript": "^23.0.0", + "jest": "^30.5.2", + "prettier": "3.9.9", + "react": "^19.3.0", + "react-dom": "^19.3.0", + "react-router-dom": "^7.18.4", "serve": "^14.2.6", "typescript": "^6.0.3", - "vite": "^8.0.16", - "vite-plugin-pwa": "^1.3.0" + "vite": "^8.3.3", + "vite-plugin-pwa": "^2.0.0" } } \ No newline at end of file diff --git a/src/NMRiumWrapper.tsx b/src/NMRiumWrapper.tsx index 9bb85d7..9011e79 100644 --- a/src/NMRiumWrapper.tsx +++ b/src/NMRiumWrapper.tsx @@ -1,10 +1,11 @@ import type { NMRiumChangeCb, NMRiumRefAPI } from 'nmrium'; import { NMRium } from 'nmrium'; import type { CSSProperties } from 'react'; -import { useCallback, useEffect, useRef } from 'react'; +import { useCallback, useEffect, useRef, useState } from 'react'; import { RootLayout } from 'react-science/ui'; import { LoadingIndicator } from './Loadingindicator.js'; +import { loadSpectraFromSource } from './data-source/loadSpectraFromSource.js'; import events from './events/event.js'; import { useLoadSpectra } from './hooks/useLoadSpectra.js'; import { usePreferences } from './hooks/usePreferences.js'; @@ -17,11 +18,35 @@ const containerStyle: CSSProperties = { position: 'relative', }; +const ACCEPTED_ACTION_TYPES = + "'exportSpectraViewerAsBlob', 'selectTab', 'highlight', or 'clearHighlight'"; + +function reportActionError(message: string) { + const error = new Error(message); + events.trigger('error', error); + // eslint-disable-next-line no-console + console.error(error); +} + +const NO_HIGHLIGHTS: readonly string[] = []; + +function isStringArray(value: unknown): value is string[] { + return ( + Array.isArray(value) && value.every((entry) => typeof entry === 'string') + ); +} + export default function NMRiumWrapper() { const { allowedOrigins, isFetchAllowedOriginsPending } = useWhiteList(); const nmriumRef = useRef(null); - const { workspace, preferences, defaultEmptyMessage, customWorkspaces } = - usePreferences(); + const [highlightedIds, setHighlightedIds] = useState(NO_HIGHLIGHTS); + const { + workspace, + preferences, + defaultEmptyMessage, + customWorkspaces, + spectraSource, + } = usePreferences(); const { load: loadSpectra, data, isLoading, setActiveTab } = useLoadSpectra(); @@ -33,6 +58,25 @@ export default function NMRiumWrapper() { events.trigger('data-change', { state, source }); }, []); + useEffect(() => { + if (!spectraSource) return; + + const { source, id } = spectraSource; + + async function loadFromSource() { + try { + const nmrium = await loadSpectraFromSource(source, id); + void loadSpectra({ nmrium }); + } catch (error) { + events.trigger('error', error as Error); + // eslint-disable-next-line no-console + console.error(error); + } + } + + void loadFromSource(); + }, [spectraSource, loadSpectra]); + useEffect(() => { const clearActionListener = events.on( 'action-request', @@ -53,9 +97,24 @@ export default function NMRiumWrapper() { setActiveTab({ tab: tab.toUpperCase() }); break; } + case 'highlight': { + const ids: unknown = request.params?.ids; + if (!isStringArray(ids)) { + reportActionError( + "ERROR! Property 'params.ids' must be an array of strings.", + ); + break; + } + setHighlightedIds(ids); + break; + } + case 'clearHighlight': { + setHighlightedIds(NO_HIGHLIGHTS); + break; + } default: { - throw new Error( - `ERROR! Property 'type' accepts only 'exportViewerAsBlob'.`, + reportActionError( + `ERROR! Property 'type' accepts only ${ACCEPTED_ACTION_TYPES}.`, ); } } @@ -73,13 +132,13 @@ export default function NMRiumWrapper() { break; } case 'file': { - const { data: files, activeTab = '' } = loadData; - void loadSpectra({ files, activeTab }); + const { data: files, activeTab = '', fileFilter } = loadData; + void loadSpectra({ files, activeTab, fileFilter }); break; } case 'url': { - const { data: urls, activeTab = '' } = loadData; - void loadSpectra({ urls, activeTab }); + const { data: urls, activeTab = '', fileFilter } = loadData; + void loadSpectra({ urls, activeTab, fileFilter }); break; } default: { @@ -108,6 +167,7 @@ export default function NMRiumWrapper() { state={data?.state} aggregator={data?.aggregator} onChange={dataChangeHandler} + highlightedIds={highlightedIds} preferences={preferences} workspace={workspace} emptyText={defaultEmptyMessage} diff --git a/src/config/nmrxiv/index.ts b/src/config/nmrxiv/index.ts new file mode 100644 index 0000000..a723cec --- /dev/null +++ b/src/config/nmrxiv/index.ts @@ -0,0 +1,10 @@ +import development from './nmrxiv.development.json' with { type: 'json' }; +import production from './nmrxiv.production.json' with { type: 'json' }; + +interface NmrXivConfig { + baseURL: string; +} + +export const nmrXivConfig: NmrXivConfig = import.meta.env.DEV + ? development + : production; diff --git a/src/config/nmrxiv/nmrxiv.development.json b/src/config/nmrxiv/nmrxiv.development.json new file mode 100644 index 0000000..d2493bf --- /dev/null +++ b/src/config/nmrxiv/nmrxiv.development.json @@ -0,0 +1,3 @@ +{ + "baseURL": "https://dev.nmrxiv.org/api/v1/samples" +} \ No newline at end of file diff --git a/src/config/nmrxiv/nmrxiv.production.json b/src/config/nmrxiv/nmrxiv.production.json new file mode 100644 index 0000000..a0f9518 --- /dev/null +++ b/src/config/nmrxiv/nmrxiv.production.json @@ -0,0 +1,3 @@ +{ + "baseURL": "https://nmrxiv.org/api/v1/samples" +} \ No newline at end of file diff --git a/src/data-source/loadSpectraFromSource.ts b/src/data-source/loadSpectraFromSource.ts new file mode 100644 index 0000000..403c090 --- /dev/null +++ b/src/data-source/loadSpectraFromSource.ts @@ -0,0 +1,20 @@ +import { loadNmrXivSpectraById } from './nmrxiv.js'; + +export type SpectraSource = 'nmrxiv'; + +type SpectraSourceLoader = (id: string) => Promise; + +const spectraSourceLoaders: Record = { + nmrxiv: loadNmrXivSpectraById, +}; + +export async function loadSpectraFromSource( + source: string, + id: string, +): Promise { + const loader = spectraSourceLoaders[source]; + if (!loader) { + throw new Error(`Unknown spectra source: "${source}"`); + } + return loader(id); +} diff --git a/src/data-source/nmrxiv.ts b/src/data-source/nmrxiv.ts new file mode 100644 index 0000000..034f000 --- /dev/null +++ b/src/data-source/nmrxiv.ts @@ -0,0 +1,17 @@ +import { nmrXivConfig } from '../config/nmrxiv/index.js'; + +function getNmrXivSpectraJsonURL(id: string): string { + return `${nmrXivConfig.baseURL}/${id}/nmriumInfo`; +} + +export async function loadNmrXivSpectraById(id: string): Promise { + const response = await fetch(getNmrXivSpectraJsonURL(id)); + + if (!response.ok) { + throw new Error( + `Failed to fetch nmrXiv spectra "${id}" (status ${response.status})`, + ); + } + + return response.json(); +} diff --git a/src/demo/NMRiumWrapperDemo.tsx b/src/demo/NMRiumWrapperDemo.tsx index 00388e3..00615be 100644 --- a/src/demo/NMRiumWrapperDemo.tsx +++ b/src/demo/NMRiumWrapperDemo.tsx @@ -6,6 +6,7 @@ import NMRiumWrapper from '../NMRiumWrapper.js'; import events from '../events/event.js'; import { loadFilesFromURLs } from '../utilities/loadFilesFromURLs.js'; +import qmSignalsData from './data/qm-signals.json' with { type: 'json' }; import jsonData from './data/test.json' with { type: 'json' }; const Container = styled.div` @@ -105,6 +106,42 @@ export default function NMRiumWrapperDemo() { > Test Logger + + + diff --git a/src/demo/data/qm-signals.json b/src/demo/data/qm-signals.json new file mode 100644 index 0000000..55c9675 --- /dev/null +++ b/src/demo/data/qm-signals.json @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/src/events/types.ts b/src/events/types.ts index eef988a..585c380 100644 --- a/src/events/types.ts +++ b/src/events/types.ts @@ -1,3 +1,4 @@ +import type { FilterOptions } from 'file-collection'; import type { NMRiumData, NMRiumState } from 'nmrium'; interface BlobObject { @@ -6,21 +7,19 @@ interface BlobObject { height: number; } type EventType = - | 'load' - | 'data-change' - | 'error' - | 'action-request' - | 'action-response'; + 'load' | 'data-change' | 'error' | 'action-request' | 'action-response'; type LoadData = | { data: string[]; activeTab?: string; + fileFilter?: FilterOptions; type: 'url'; } | { data: File[]; activeTab?: string; + fileFilter?: FilterOptions; type: 'file'; } | { @@ -36,6 +35,17 @@ type ActionRequest = | { type: 'selectTab'; params: { tab: string }; + } + | { + type: 'highlight'; + /** + * Ids passed to NMRium's `highlightedIds`, for example peak, range or + * signal ids. Replaces the previous host highlight. + */ + params: { ids: string[] }; + } + | { + type: 'clearHighlight'; }; interface ActionResponse { diff --git a/src/hooks/useLoadSpectra.ts b/src/hooks/useLoadSpectra.ts index 830bc9f..ffa8798 100644 --- a/src/hooks/useLoadSpectra.ts +++ b/src/hooks/useLoadSpectra.ts @@ -5,8 +5,9 @@ import type { ViewState, } from '@zakodium/nmrium-core'; import { CURRENT_EXPORT_VERSION } from '@zakodium/nmrium-core'; -import init from '@zakodium/nmrium-core-plugins'; +import { init } from '@zakodium/nmrium-core-plugins'; import { FifoLogger } from 'fifo-logger'; +import type { FilterOptions } from 'file-collection'; import { FileCollection } from 'file-collection'; import { useCallback, useMemo, useState } from 'react'; @@ -14,10 +15,27 @@ import events from '../events/event.js'; import { getFileNameFromURL } from '../utilities/getFileNameFromURL.js'; import { isArrayOfString } from '../utilities/isArrayOfString.js'; -type LoadOptions = - | { nmrium: object; activeTab?: string } - | { urls: string[]; activeTab?: string } - | { files: File[]; activeTab?: string }; +interface BaseLoadOptions { + activeTab?: string; +} + +interface FileLoadOptions extends BaseLoadOptions { + fileFilter?: FilterOptions; +} + +interface NMRiumLoadOptions extends BaseLoadOptions { + nmrium: object; +} + +interface URLsLoadOptions extends FileLoadOptions { + urls: string[]; +} + +interface FilesLoadOptions extends FileLoadOptions { + files: File[]; +} + +type LoadOptions = NMRiumLoadOptions | URLsLoadOptions | FilesLoadOptions; // CoreReadReturn with `state.view` made optional to allow partial injection. export type NMRiumData = Omit & { @@ -51,54 +69,68 @@ const PARSING_OPTIONS: Partial = { logger, }; -async function loadSpectraFromNMRium(nmrium: object): Promise { +async function loadSpectraFromNMRium({ + nmrium, +}: NMRiumLoadOptions): Promise { return core.readNMRiumObject(nmrium, PARSING_OPTIONS); } -async function loadSpectraFromFiles(files: File[]): Promise { - const fileCollection = await new FileCollection().appendFileList(files); +async function loadSpectraFromFiles( + options: FilesLoadOptions, +): Promise { + const { files, fileFilter } = options; + const fileCollection = await new FileCollection({ + filter: fileFilter, + }).appendFileList(files); + return core.read(fileCollection, PARSING_OPTIONS); } -async function loadSpectraFromURLs(urls: string[]): Promise { +async function loadSpectraFromURLs( + options: URLsLoadOptions, +): Promise { + const { urls, fileFilter } = options; const entries = urls.map((url) => { const refURL = new URL(url); const name = getFileNameFromURL(url); let path = refURL.pathname; if (!name?.includes('.')) { - path = `${path}.zip`; + path += '.zip'; } return { relativePath: path, baseURL: refURL.origin }; }); - return core.readFromWebSource({ entries }, PARSING_OPTIONS); + return core.readFromWebSource( + { entries }, + { ...PARSING_OPTIONS, fileFilter }, + ); } export function useLoadSpectra(): UseLoadSpectraResult { const [result, setResult] = useState(null); const [activeTab, setActiveTab] = useState<{ tab: string } | undefined>(); - const [isLoading, setLoading] = useState(false); + const [isLoading, setIsLoading] = useState(false); const load = useCallback(async (options: LoadOptions) => { - setLoading(true); + setIsLoading(true); try { let loadedResult: CoreReadReturn; let resolvedActiveTab: string | undefined; if ('nmrium' in options) { - loadedResult = await loadSpectraFromNMRium(options.nmrium); + loadedResult = await loadSpectraFromNMRium(options); resolvedActiveTab = options.activeTab ?? loadedResult.state.view?.spectra?.activeTab; } else if ('urls' in options) { if (!isArrayOfString(options.urls)) { throw new Error('The input must be a valid urls array of string[]'); } - loadedResult = await loadSpectraFromURLs(options.urls); + loadedResult = await loadSpectraFromURLs(options); resolvedActiveTab = options.activeTab; } else { - loadedResult = await loadSpectraFromFiles(options.files); + loadedResult = await loadSpectraFromFiles(options); resolvedActiveTab = options.activeTab; } @@ -123,7 +155,7 @@ export function useLoadSpectra(): UseLoadSpectraResult { // eslint-disable-next-line no-console console.log(error); } finally { - setLoading(false); + setIsLoading(false); } }, []); diff --git a/src/hooks/usePreferences.ts b/src/hooks/usePreferences.ts index 567aebc..9d7280b 100644 --- a/src/hooks/usePreferences.ts +++ b/src/hooks/usePreferences.ts @@ -3,7 +3,9 @@ import type { WorkspacePreferences, } from '@zakodium/nmrium-core'; import type { NMRiumWorkspace } from 'nmrium'; +import { useMemo } from 'react'; +import { parseSpectraSource } from '../utilities/parseSpectraSource.js'; import type { WorkspaceOptions } from '../workspaces/integration.js'; import { getIntegrationWorkspace } from '../workspaces/integration.js'; import { getNmrXivWorkspace } from '../workspaces/nmrxiv.js'; @@ -58,11 +60,18 @@ export function usePreferences() { parameters.get('hidePanelOnLoad')?.toLowerCase() === 'true'; } + const rawSpectra = parameters.get('spectra'); + const spectraSource = useMemo( + () => parseSpectraSource(rawSpectra), + [rawSpectra], + ); + return { preferences, workspace, defaultEmptyMessage, customWorkspaces, + spectraSource, }; } diff --git a/src/modal/AboutUsModal.tsx b/src/modal/AboutUsModal.tsx index 46683cc..ce73a4f 100644 --- a/src/modal/AboutUsModal.tsx +++ b/src/modal/AboutUsModal.tsx @@ -24,7 +24,7 @@ const Link = styled.a` } `; -function AboutUsModal() { +export default function AboutUsModal() { const [isOpenDialog, openDialog, closeDialog] = useOnOff(false); return ( <> @@ -55,8 +55,6 @@ function AboutUsModal() { ); } -export default AboutUsModal; - function VersionInfo() { const { version } = versionInfo; if (version === 'HEAD') { diff --git a/src/utilities/loadFilesFromURLs.ts b/src/utilities/loadFilesFromURLs.ts index ab75024..9188fb3 100644 --- a/src/utilities/loadFilesFromURLs.ts +++ b/src/utilities/loadFilesFromURLs.ts @@ -8,7 +8,7 @@ export function loadFilesFromURLs(urls: string[]): Promise { let name = getFileNameFromURL(url); const hasExtension = name?.includes('.'); if (!hasExtension) { - name = `${name}.zip`; + name += '.zip'; } return new File([data], name); }), diff --git a/src/utilities/parseSpectraSource.ts b/src/utilities/parseSpectraSource.ts new file mode 100644 index 0000000..274bea7 --- /dev/null +++ b/src/utilities/parseSpectraSource.ts @@ -0,0 +1,25 @@ +export interface SpectraSource { + source: string; + id: string; +} + +/** + * Parses a `spectra` query parameter in the format `:` and returns an object with `source` and `id` properties. + * + * Example: + * `nmrxiv:S2173` => { source: 'nmrxiv', id: 'S2173' } + */ +export function parseSpectraSource( + value: string | null, +): SpectraSource | undefined { + if (!value) return undefined; + + const separatorIndex = value.indexOf(':'); + if (separatorIndex === -1) return undefined; + + const source = value.slice(0, separatorIndex).trim(); + const id = value.slice(separatorIndex + 1).trim(); + if (!source || !id) return undefined; + + return { source, id }; +} diff --git a/test-e2e/NmriumWrapperPage.ts b/test-e2e/NmriumWrapperPage.ts index 1b30617..8f294e8 100644 --- a/test-e2e/NmriumWrapperPage.ts +++ b/test-e2e/NmriumWrapperPage.ts @@ -2,22 +2,19 @@ import type { Page } from '@playwright/test'; import { expect } from '@playwright/test'; export default class NmriumPage { + public static async create(page: Page): Promise { + await page.goto('http://localhost:3000/#/demo'); + return new NmriumPage(page); + } + public readonly page: Page; public constructor(page: Page) { this.page = page; } - public static async create(page: Page): Promise { - await page.goto('http://localhost:3000/#/demo'); - return new NmriumPage(page); - } - public async checkSpectraTabsIsVisible(tabs: string[]) { - const promises: Array> = []; - for (const tab of tabs) { - promises.push(expect(this.page.locator('.tab-list-item').getByText(tab, { exact: true })).toBeVisible()); - } + const promises: Array> = Array.from(tabs, tab => expect(this.page.locator('.tab-list-item').getByText(tab, { exact: true })).toBeVisible()); await Promise.all(promises); diff --git a/test-e2e/core.test.ts b/test-e2e/core.test.ts index 12ff66f..e4b985f 100644 --- a/test-e2e/core.test.ts +++ b/test-e2e/core.test.ts @@ -3,6 +3,8 @@ import { expect, test } from '@playwright/test'; import NmriumWrapperPage from './NmriumWrapperPage.js'; import triplinineData from './data/Triplinine.json' with { type: 'json' }; +const HIGHLIGHTED_FILL = '#ff6f0057'; + async function testLoadStructure(nmrium: NmriumWrapperPage) { // Open the "Chemical structures" panel. await nmrium.page.click('div >> text=Chemical structures'); @@ -10,7 +12,6 @@ async function testLoadStructure(nmrium: NmriumWrapperPage) { // The molecule SVG rendering should now be visible in the panel. await expect( nmrium.page.locator('.mol-svg-container #molSVG0'), - // eslint-disable-next-line unicorn/prefer-https ).toHaveAttribute('xmlns', 'http://www.w3.org/2000/svg'); // The molecular formula should now be visible in the panel. @@ -125,3 +126,136 @@ test('should load test-data.nmrium file', async ({ await nmrium.checkSpectraTabsIsVisible(['1H', '13C', '1H,1H', '1H,13C']) }); + +async function postActionRequest( + nmrium: NmriumWrapperPage, + data: Record, +) { + await nmrium.page.evaluate((data) => { + window.postMessage({ type: 'nmr-wrapper:action-request', data }, '*'); + }, data); +} + +async function loadQmSignals(nmrium: NmriumWrapperPage) { + await nmrium.page.click('text=Test load QM signals'); + await nmrium.checkSpectraTabsIsVisible(['1H', '13C']); + await expect(nmrium.page.getByTestId('range').first()).toBeVisible(); +} + +// The tab that opens after loading differs between browsers. +async function show1HTab(nmrium: NmriumWrapperPage) { + await postActionRequest(nmrium, { + type: 'selectTab', + params: { tab: '1H' }, + }); + await expect( + nmrium.page.locator('.tab-list-active').getByText('1H', { exact: true }), + ).toBeVisible(); +} + +function highlightedRanges(nmrium: NmriumWrapperPage) { + return nmrium.page.locator( + `[data-testid="range"] rect[fill="${HIGHLIGHTED_FILL}"]`, + ); +} + +function highlightedPeaks(nmrium: NmriumWrapperPage) { + return nmrium.page.locator('g.peaks path[stroke-width="3px"]'); +} + +test('should highlight a peak by id via nmr-wrapper:action-request', async ({ + page, +}) => { + const nmrium = await NmriumWrapperPage.create(page); + await loadQmSignals(nmrium); + await show1HTab(nmrium); + + await postActionRequest(nmrium, { + type: 'highlight', + params: { ids: ['qm-1H-9'] }, + }); + + await expect(highlightedPeaks(nmrium)).toHaveCount(1); + await expect(highlightedRanges(nmrium)).toHaveCount(0); + + await postActionRequest(nmrium, { type: 'clearHighlight' }); + + await expect(highlightedPeaks(nmrium)).toHaveCount(0); +}); + +test('should highlight a signal with its range and peak by ids', async ({ + page, +}) => { + const nmrium = await NmriumWrapperPage.create(page); + await loadQmSignals(nmrium); + await show1HTab(nmrium); + + await postActionRequest(nmrium, { + type: 'highlight', + params: { ids: ['qm-signal-1H-7-8', 'qm-range-1H-7-8', 'qm-1H-7-8'] }, + }); + + await expect(highlightedRanges(nmrium)).toHaveCount(1); + await expect(highlightedPeaks(nmrium)).toHaveCount(1); + + await postActionRequest(nmrium, { type: 'clearHighlight' }); + + await expect(highlightedRanges(nmrium)).toHaveCount(0); + await expect(highlightedPeaks(nmrium)).toHaveCount(0); +}); + +test('should keep the highlight when selectTab is sent right before it', async ({ + page, +}) => { + const nmrium = await NmriumWrapperPage.create(page); + await loadQmSignals(nmrium); + await show1HTab(nmrium); + + await postActionRequest(nmrium, { + type: 'selectTab', + params: { tab: '13C' }, + }); + await postActionRequest(nmrium, { + type: 'highlight', + params: { ids: ['qm-signal-13C-2', 'qm-range-13C-2', 'qm-13C-2'] }, + }); + + await expect( + nmrium.page.locator('.tab-list-active').getByText('13C'), + ).toBeVisible(); + await expect(highlightedRanges(nmrium)).toHaveCount(1); + await expect(highlightedPeaks(nmrium)).toHaveCount(1); +}); + +test('should emit nmr-wrapper:error when highlight ids are invalid', async ({ + page, +}) => { + const nmrium = await NmriumWrapperPage.create(page); + await loadQmSignals(nmrium); + await show1HTab(nmrium); + + const errorMessage = page.evaluate( + () => + new Promise((resolve) => { + window.addEventListener('message', (event) => { + if (event.data?.type === 'nmr-wrapper:error') { + resolve(String(event.data.data?.message ?? event.data.data)); + } + }); + }), + ); + + await postActionRequest(nmrium, { + type: 'highlight', + params: { ids: 'qm-1H-9' }, + }); + + expect(await errorMessage).toContain('params.ids'); + + await postActionRequest(nmrium, { + type: 'highlight', + params: { ids: ['qm-1H-9'] }, + }); + + await expect(highlightedPeaks(nmrium)).toHaveCount(1); +}); diff --git a/vite.config.ts b/vite.config.ts index 3f58be6..339d983 100644 --- a/vite.config.ts +++ b/vite.config.ts @@ -1,6 +1,7 @@ import react from '@vitejs/plugin-react'; import { defineConfig } from 'vite'; -import { VitePWA, type Options } from 'vite-plugin-pwa'; +import type { Options } from 'vite-plugin-pwa'; +import { VitePWA } from 'vite-plugin-pwa'; const pwaSettings: Partial = { // cache all the imports