diff --git a/frontend/TESTING_GUIDE.md b/frontend/TESTING_GUIDE.md index 557d391..f555b6a 100644 --- a/frontend/TESTING_GUIDE.md +++ b/frontend/TESTING_GUIDE.md @@ -15,16 +15,19 @@ We use the modern Vite testing ecosystem: ## How to Run the Tests To run the entire test suite once: + ```bash npm run test ``` To run tests in **Watch Mode** (automatically re-runs tests when you save a file): + ```bash npm run test:watch ``` To enforce code style alongside your tests: + ```bash npm run lint # Checks for code issues npm run format # Auto-formats code with Prettier @@ -46,19 +49,13 @@ import userEvent from '@testing-library/user-event'; import SequenceInput from '../components/SequenceInput'; describe('SequenceInput Component', () => { - // 1. Testing simple rendering it('renders correctly', () => { // Render the component with some mock props render( - {}} - onPredict={() => {}} - status="ready" - /> + {}} onPredict={() => {}} status="ready" /> ); - + // Check if what the user sees is on screen expect(screen.getByPlaceholderText(/Paste your amino-acid sequence/i)).toBeInTheDocument(); }); @@ -69,18 +66,18 @@ describe('SequenceInput Component', () => { const user = userEvent.setup(); // Setup user interaction render( - {}} - onPredict={mockPredict} - status="ready" + {}} + onPredict={mockPredict} + status="ready" /> ); - + // Find the button and click it const btn = screen.getByRole('button', { name: /Predict/i }); await user.click(btn); - + // Assert the function was called! expect(mockPredict).toHaveBeenCalled(); }); @@ -88,5 +85,6 @@ describe('SequenceInput Component', () => { ``` ### Best Practices + - **Query by Accessibility**: Prefer `getByRole`, `getByLabelText`, and `getByText`. Avoid querying by CSS classes, as tests should test functionality, not DOM structure. - **Mock External Hooks**: If your component relies on global states (like `useAuth`), mock the hook using `vi.spyOn(AuthProvider, 'useAuth')` so you can test the component in isolation. diff --git a/frontend/package-lock.json b/frontend/package-lock.json index 32917f7..4f8beac 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -13,7 +13,8 @@ "chart.js": "^4.5.1", "react": "^19.2.0", "react-chartjs-2": "^5.3.1", - "react-dom": "^19.2.0" + "react-dom": "^19.2.0", + "recharts": "^3.8.0" }, "devDependencies": { "@eslint/js": "^9.39.1", @@ -133,6 +134,7 @@ "integrity": "sha512-CGOfOJqWjg2qW/Mb6zNsDm+u5vFQ8DxXfbM09z69p5Z6+mE1ikP2jUXw+j42Pf1XTYED2Rni5f95npYeuwMDQA==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.29.0", "@babel/generator": "^7.29.0", @@ -495,6 +497,7 @@ } ], "license": "MIT", + "peer": true, "engines": { "node": 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"sha512-ROY9fvHhwOD9ySfrF0wmvu//bKCQ6AeZZq1nJNtbDC+kk5DuSuNX/n6YWYF/SYy7bSba4D4FSz8DJeKY/S/r+g==", + "license": "MIT", + "peer": true, + "dependencies": { + "@types/use-sync-external-store": "^0.0.6", + "use-sync-external-store": "^1.4.0" + }, + "peerDependencies": { + "@types/react": "^18.2.25 || ^19", + "react": "^18.0 || ^19", + "redux": "^5.0.0" + }, + "peerDependenciesMeta": { + "@types/react": { + "optional": true + }, + "redux": { + "optional": true + } + } + }, "node_modules/react-refresh": { "version": "0.18.0", "resolved": "https://registry.npmjs.org/react-refresh/-/react-refresh-0.18.0.tgz", @@ -3616,6 +3927,36 @@ "node": ">=0.10.0" } }, + "node_modules/recharts": { + "version": "3.8.0", + "resolved": "https://registry.npmjs.org/recharts/-/recharts-3.8.0.tgz", + "integrity": "sha512-Z/m38DX3L73ExO4Tpc9/iZWHmHnlzWG4njQbxsF5aSjwqmHNDDIm0rdEBArkwsBvR8U6EirlEHiQNYWCVh9sGQ==", + "license": "MIT", + "workspaces": [ + "www" + ], + "dependencies": { + "@reduxjs/toolkit": "^1.9.0 || 2.x.x", + "clsx": "^2.1.1", + "decimal.js-light": "^2.5.1", + "es-toolkit": "^1.39.3", + "eventemitter3": "^5.0.1", + "immer": "^10.1.1", + "react-redux": "8.x.x || 9.x.x", + "reselect": "5.1.1", + "tiny-invariant": "^1.3.3", + "use-sync-external-store": "^1.2.2", + "victory-vendor": "^37.0.2" + }, + "engines": { + "node": ">=18" + }, + "peerDependencies": { + "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0", + "react-dom": "^16.0.0 || ^17.0.0 || ^18.0.0 || ^19.0.0", + "react-is": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0" + } + }, "node_modules/redent": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/redent/-/redent-3.0.0.tgz", @@ -3630,6 +3971,22 @@ "node": ">=8" } }, + "node_modules/redux": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/redux/-/redux-5.0.1.tgz", + "integrity": "sha512-M9/ELqF6fy8FwmkpnF0S3YKOqMyoWJ4+CS5Efg2ct3oY9daQvd/Pc71FpGZsVsbl3Cpb+IIcjBDUnnyBdQbq4w==", + "license": "MIT", + "peer": true + }, + "node_modules/redux-thunk": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/redux-thunk/-/redux-thunk-3.1.0.tgz", + "integrity": "sha512-NW2r5T6ksUKXCabzhL9z+h206HQw/NJkcLm1GPImRQ8IzfXwRGqjVhKJGauHirT0DAuyy6hjdnMZaRoAcy0Klw==", + "license": "MIT", + "peerDependencies": { + "redux": "^5.0.0" + } + }, "node_modules/require-from-string": { "version": "2.0.2", "resolved": "https://registry.npmjs.org/require-from-string/-/require-from-string-2.0.2.tgz", @@ -3640,6 +3997,12 @@ "node": ">=0.10.0" } }, + "node_modules/reselect": { + "version": "5.1.1", + "resolved": "https://registry.npmjs.org/reselect/-/reselect-5.1.1.tgz", + "integrity": "sha512-K/BG6eIky/SBpzfHZv/dd+9JBFiS4SWV7FIujVyJRux6e45+73RaUHXLmIR1f7WOMaQ0U1km6qwklRQxpJJY0w==", + "license": "MIT" + }, "node_modules/resolve-from": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-4.0.0.tgz", @@ -3824,6 +4187,12 @@ "dev": true, "license": "MIT" }, + "node_modules/tiny-invariant": { + "version": "1.3.3", + "resolved": "https://registry.npmjs.org/tiny-invariant/-/tiny-invariant-1.3.3.tgz", + "integrity": "sha512-+FbBPE1o9QAYvviau/qC5SE3caw21q3xkvWKBtja5vgqOWIHHJ3ioaq1VPfn/Szqctz2bU/oYeKd9/z5BL+PVg==", + "license": "MIT" + }, "node_modules/tinybench": { "version": "2.9.0", "resolved": "https://registry.npmjs.org/tinybench/-/tinybench-2.9.0.tgz", @@ -4005,12 +4374,44 @@ "punycode": "^2.1.0" } }, + "node_modules/use-sync-external-store": { + "version": "1.6.0", + "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.6.0.tgz", + "integrity": "sha512-Pp6GSwGP/NrPIrxVFAIkOQeyw8lFenOHijQWkUTrDvrF4ALqylP2C/KCkeS9dpUM3KvYRQhna5vt7IL95+ZQ9w==", + "license": "MIT", + "peerDependencies": { + "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0" + } + }, + "node_modules/victory-vendor": { + "version": "37.3.6", + "resolved": "https://registry.npmjs.org/victory-vendor/-/victory-vendor-37.3.6.tgz", + "integrity": "sha512-SbPDPdDBYp+5MJHhBCAyI7wKM3d5ivekigc2Dk2s7pgbZ9wIgIBYGVw4zGHBml/qTFbexrofXW6Gu4noGxrOwQ==", + "license": "MIT AND ISC", + "dependencies": { + "@types/d3-array": "^3.0.3", + "@types/d3-ease": "^3.0.0", + "@types/d3-interpolate": "^3.0.1", + "@types/d3-scale": "^4.0.2", + "@types/d3-shape": "^3.1.0", + "@types/d3-time": "^3.0.0", + "@types/d3-timer": "^3.0.0", + "d3-array": "^3.1.6", + "d3-ease": "^3.0.1", + "d3-interpolate": "^3.0.1", + "d3-scale": "^4.0.2", + "d3-shape": "^3.1.0", + "d3-time": "^3.0.0", + "d3-timer": "^3.0.1" + } + }, "node_modules/vite": { "version": "7.3.1", "resolved": "https://registry.npmjs.org/vite/-/vite-7.3.1.tgz", "integrity": "sha512-w+N7Hifpc3gRjZ63vYBXA56dvvRlNWRczTdmCBBa+CotUzAPf5b7YMdMR/8CQoeYE5LX3W4wj6RYTgonm1b9DA==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "esbuild": "^0.27.0", "fdir": "^6.5.0", @@ -4317,6 +4718,7 @@ "integrity": "sha512-rftlrkhHZOcjDwkGlnUtZZkvaPHCsDATp4pGpuOOMDaTdDDXF91wuVDJoWoPsKX/3YPQ5fHuF3STjcYyKr+Qhg==", "dev": true, "license": "MIT", + "peer": true, "funding": { "url": "https://github.com/sponsors/colinhacks" } diff --git a/frontend/package.json b/frontend/package.json index 754e2be..a43f208 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -19,7 +19,8 @@ "chart.js": "^4.5.1", "react": "^19.2.0", "react-chartjs-2": "^5.3.1", - "react-dom": "^19.2.0" + "react-dom": "^19.2.0", + "recharts": "^3.8.0" }, "devDependencies": { "@eslint/js": "^9.39.1", diff --git a/frontend/src/components/PldtMetrics.jsx b/frontend/src/components/PldtMetrics.jsx index 5e555ea..8322aa9 100644 --- a/frontend/src/components/PldtMetrics.jsx +++ b/frontend/src/components/PldtMetrics.jsx @@ -1,84 +1,83 @@ import { useMemo } from 'react'; -import { Line } from 'react-chartjs-2'; import { - Chart as ChartJS, - CategoryScale, - LinearScale, - PointElement, - LineElement, - Filler, - Tooltip, -} from 'chart.js'; + ResponsiveContainer, + AreaChart, + Area, + XAxis, + YAxis, + CartesianGrid, + Tooltip as RechartsTooltip, +} from 'recharts'; -ChartJS.register(CategoryScale, LinearScale, PointElement, LineElement, Filler, Tooltip); +const CustomTooltip = ({ active, payload }) => { + if (active && payload && payload.length) { + const data = payload[0].payload; + return ( +
+
Residue {data.residueIndex}
+
+ Amino Acid: {data.aminoAcid} +
+
+ pLDDT:{' '} + {typeof data.plddt === 'number' ? data.plddt.toFixed(2) : data.plddt} +
+
90 + ? '#05cd99' + : data.plddt > 70 + ? '#4318FF' + : data.plddt > 50 + ? '#FFCE20' + : '#EE5D50', + fontWeight: 500, + marginTop: 4, + }} + > + {data.confidence} +
+
+ ); + } + return null; +}; export default function PldtMetrics({ plddtData, sequence }) { const mean = plddtData?.mean ?? null; + const perResidue = useMemo(() => plddtData?.per_residue || [], [plddtData?.per_residue]); + const sequenceLength = sequence?.length || 0; - const chartData = useMemo(() => { - const perResidue = plddtData?.per_residue || []; - if (!perResidue.length) return null; - - // Down-sample if too many residues for readability - const step = Math.max(1, Math.floor(perResidue.length / 80)); - const sampled = perResidue.filter((_, i) => i % step === 0); - const labels = sampled.map((_, i) => (i * step + 1).toString()); + const isValidated = perResidue.length > 0 && perResidue.length === sequenceLength; - return { - labels, - datasets: [ - { - data: sampled, - borderColor: '#1B2559', - backgroundColor: 'rgba(27, 37, 89, 0.06)', - borderWidth: 1.5, - pointRadius: 0, - fill: true, - tension: 0.3, - }, - ], - }; - }, [plddtData?.per_residue]); + const chartData = useMemo(() => { + if (!perResidue.length) return []; + return perResidue.map((val, i) => { + let conf = 'Very Low'; + if (val > 90) conf = 'Very High'; + else if (val > 70) conf = 'Confident'; + else if (val > 50) conf = 'Low'; - const chartOptions = { - responsive: true, - maintainAspectRatio: false, - plugins: { - tooltip: { - callbacks: { - label: (ctx) => { - const val = ctx.parsed.y; - const residueIdx = parseInt(ctx.label) - 1; - const aa = sequence?.[residueIdx] || ''; - const conf = - val > 90 ? 'Very High' : val > 70 ? 'Confident' : val > 50 ? 'Low' : 'Very Low'; - return [`pLDDT: ${val.toFixed(1)} (${conf})`, aa ? `Amino Acid: ${aa}` : ''].filter( - Boolean - ); - }, - title: (items) => `Residue ${items[0]?.label}`, - }, - }, - }, - scales: { - x: { - display: false, - }, - y: { - display: true, - min: 0, - max: 100, - ticks: { - font: { size: 10, family: 'Inter' }, - color: '#A3AED0', - stepSize: 25, - }, - grid: { - color: '#E9EDF722', - }, - }, - }, - }; + return { + residueIndex: i + 1, + plddt: val, + aminoAcid: sequence?.[i] || '?', + confidence: conf, + }; + }); + }, [perResidue, sequence]); return (
@@ -91,7 +90,11 @@ export default function PldtMetrics({ plddtData, sequence }) { ❤️ pLDDT Score - ⓘ + + ⓘ +
-

- pLDDT Analysis -

-
+ {/* Validation Check */} + {perResidue.length > 0 && ( +
+ {isValidated ? '✓' : '⚠️'} + + {isValidated + ? `Validation Passed: PDB array size (${perResidue.length}) matches sequence length (${sequenceLength}).` + : `Validation Failed: PDB array size (${perResidue.length}) does not match sequence length (${sequenceLength}).`} + +
+ )} + +
The average confidence score is @@ -127,10 +150,47 @@ export default function PldtMetrics({ plddtData, sequence }) {
- {/* Sparkline chart */} - {chartData ? ( -
- + {/* Recharts Area Chart */} + {chartData.length > 0 ? ( +
+ + + + + + + + + + + + } /> + + +
) : (
No data yet
)} -

+

pLDDT is a per-residue confidence estimate (0-100). Scores above 90 indicate very high confidence; 70-90 suggests a generally reliable backbone prediction.