diff --git a/.github/workflows/PULL_REQUEST_TEMPLATE.md b/.github/workflows/PULL_REQUEST_TEMPLATE.md deleted file mode 100644 index 008f8d7..0000000 --- a/.github/workflows/PULL_REQUEST_TEMPLATE.md +++ /dev/null @@ -1,35 +0,0 @@ - - -## Description - - - -## Type of Change - - - -- [ ] โœจ New feature (non-breaking change which adds functionality) -- [ ] ๐Ÿ› ๏ธ Bug fix (non-breaking change which fixes an issue) -- [ ] โŒ Breaking change (fix or feature that would cause existing functionality to change) -- [ ] ๐Ÿงน Code refactor -- [ ] โœ… Build configuration change -- [ ] ๐Ÿ“ Documentation - - -## Changes - - - -Please which part of the project your changes affect ? - -- [ ] Frontend (Templates, CSS, JS) -- [ ] Documentation (readme files , configuration file) -- [ ] Backend (R, api, database, Dockerfile) - - diff --git a/frontend/bun.lock b/frontend/bun.lock new file mode 100644 index 0000000..2bfac05 --- /dev/null +++ b/frontend/bun.lock @@ -0,0 +1,1878 @@ +{ + "lockfileVersion": 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"sha512-VLaYcn81dtHVTjEHd8B+pbe9yHWpXKZUC87PzoFmsFrJqgFwDe/qxfp5MlfsfM1V5E/iVt0MmEbWQ7FVIXh/bg=="], + } +} diff --git a/frontend/bun.lockb b/frontend/bun.lockb deleted file mode 100755 index fe8c6c6..0000000 Binary files a/frontend/bun.lockb and /dev/null differ diff --git a/frontend/package.json b/frontend/package.json index 1986482..14ce4c8 100755 --- a/frontend/package.json +++ b/frontend/package.json @@ -15,6 +15,10 @@ }, "dependencies": { "@headlessui/react": "^2.2.0", + "@nightingale-elements/nightingale-interpro-track": "^5.2.0", + "@nightingale-elements/nightingale-manager": "^5.2.0", + "@nightingale-elements/nightingale-navigation": "^5.2.0", + "@nightingale-elements/nightingale-sequence": "^5.2.0", "@radix-ui/react-popover": "^1.1.2", "@radix-ui/react-slider": "^1.2.1", "@radix-ui/react-tabs": "^1.1.1", @@ -25,7 +29,6 @@ "clsx": "^2.1.1", "csv-parse": "^5.5.6", "csv-stringify": "^6.5.1", - "cytoscape": "^3.30.3", "cytoscape-avsdf": "^1.0.0", "cytoscape-cola": "^2.5.1", "cytoscape-d3-force": "^1.1.4", @@ -33,19 +36,20 @@ "cytoscape-fcose": "^2.2.0", "cytoscape-klay": "^3.1.4", "cytoscape-spread": "^3.0.0", + "cytoscape": "^3.30.3", "d3": "^7.9.0", "dom-to-image-more": "^3.5.0", "javascript-time-ago": "^2.5.11", "jotai": "^2.10.1", "lodash": "^4.17.21", - "react": "^18.3.1", "react-aria-components": "^1.4.1", "react-children-utilities": "^2.10.0", "react-dom": "^18.3.1", "react-icons": "^5.3.0", - "react-router": "^6.27.0", "react-router-dom": "^6.27.0", - "react-time-ago": "^7.3.3" + "react-router": "^6.27.0", + "react-time-ago": "^7.3.3", + "react": "^18.3.1" }, "devDependencies": { "@axe-core/playwright": "^4.10.0", @@ -54,17 +58,17 @@ "@eslint/js": "^9.13.0", "@ianvs/prettier-plugin-sort-imports": "^4.3.1", "@playwright/test": "^1.48.2", - "@types/cytoscape": "^3.21.8", "@types/cytoscape-avsdf": "^1.0.3", "@types/cytoscape-dagre": "^2.3.3", "@types/cytoscape-fcose": "^2.2.4", "@types/cytoscape-klay": "^3.1.4", + "@types/cytoscape": "^3.21.8", "@types/d3": "^7.4.3", "@types/dom-to-image": "^2.6.7", "@types/lodash": "^4.17.12", "@types/node": "^22.8.4", - "@types/react": "^18.3.12", "@types/react-dom": "^18.3.1", + "@types/react": "^18.3.12", "@typescript-eslint/eslint-plugin": "^8.12.2", "@typescript-eslint/parser": "^8.12.2", "@vitejs/plugin-react-swc": "^3.7.1", @@ -78,16 +82,17 @@ "msw": "^2.6.0", "playwright-lighthouse": "^4.0.0", "postcss": "^8.4.47", - "prettier": "^3.3.3", "prettier-plugin-css-order": "^2.1.2", "prettier-plugin-jsdoc": "^1.3.0", + "prettier": "^3.3.3", + "type-fest": "^4.26.1", "typescript": "^5.6.3", - "vite": "^5.4.10", - "vite-plugin-svgr": "^4.2.0" + "vite-plugin-svgr": "^4.2.0", + "vite": "^5.4.10" }, "msw": { "workerDirectory": "public" }, "name": "frontend", "module": "index.ts" -} \ No newline at end of file +} diff --git a/frontend/public/mockServiceWorker.js b/frontend/public/mockServiceWorker.js index 6eb8052..ec47a9a 100644 --- a/frontend/public/mockServiceWorker.js +++ b/frontend/public/mockServiceWorker.js @@ -8,8 +8,8 @@ * - Please do NOT serve this file on production. */ -const PACKAGE_VERSION = '2.6.0' -const INTEGRITY_CHECKSUM = '07a8241b182f8a246a7cd39894799a9e' +const PACKAGE_VERSION = '2.7.0' +const INTEGRITY_CHECKSUM = '00729d72e3b82faf54ca8b9621dbb96f' const IS_MOCKED_RESPONSE = Symbol('isMockedResponse') const activeClientIds = new Set() @@ -192,12 +192,26 @@ async function getResponse(event, client, requestId) { const requestClone = request.clone() function passthrough() { - const headers = Object.fromEntries(requestClone.headers.entries()) + // Cast the request headers to a new Headers instance + // so the headers can be manipulated with. + const headers = new Headers(requestClone.headers) + + // Remove the "accept" header value that marked this request as passthrough. + // This prevents request alteration and also keeps it compliant with the + // user-defined CORS policies. + const acceptHeader = headers.get('accept') + if (acceptHeader) { + const values = acceptHeader.split(',').map((value) => value.trim()) + const filteredValues = values.filter( + (value) => value !== 'msw/passthrough', + ) - // Remove internal MSW request header so the passthrough request - // complies with any potential CORS preflight checks on the server. - // Some servers forbid unknown request headers. - delete headers['x-msw-intention'] + if (filteredValues.length > 0) { + headers.set('accept', filteredValues.join(', ')) + } else { + headers.delete('accept') + } + } return fetch(requestClone, { headers }) } diff --git a/frontend/src/components/IPR.module.css b/frontend/src/components/IPR.module.css new file mode 100644 index 0000000..e3022f7 --- /dev/null +++ b/frontend/src/components/IPR.module.css @@ -0,0 +1,44 @@ +.manager { + width: 100%; +} + +.grid { + display: grid !important; + grid-template-columns: auto 1fr; + align-items: center; + gap: 5px 20px; + line-height: unset !important; +} + +.grid > *:nth-child(1), +.grid > *:nth-child(3) { + font-weight: var(--bold); +} + +.grid > *:nth-child(odd) { + line-height: var(--compact); + text-align: right; +} + +.grid > *:nth-child(even) { + width: 0; + min-width: 100%; +} + +.legend { + display: grid; + grid-template-columns: repeat(auto-fit, minmax(auto, 50px)); + justify-content: center; + width: 100%; + gap: 20px; +} + +.legend-entry { + flex-shrink: 0; + width: 10px; + height: 10px; +} + +:global(.zoom-polygon) { + fill: currentColor; +} diff --git a/frontend/src/components/IPR.tsx b/frontend/src/components/IPR.tsx new file mode 100644 index 0000000..f49052a --- /dev/null +++ b/frontend/src/components/IPR.tsx @@ -0,0 +1,128 @@ +import { Fragment, useMemo } from "react"; +import type NightingaleInterproTrack from "@nightingale-elements/nightingale-interpro-track"; +import type NightingaleManager from "@nightingale-elements/nightingale-manager"; +import type NightingaleNavigation from "@nightingale-elements/nightingale-navigation"; +import type NightingaleSequence from "@nightingale-elements/nightingale-sequence"; +import Flex from "@/components/Flex"; +import { getColorMap } from "@/util/color"; +import classes from "./IPR.module.css"; +import "@nightingale-elements/nightingale-manager"; +import "@nightingale-elements/nightingale-navigation"; +import "@nightingale-elements/nightingale-sequence"; +import "@nightingale-elements/nightingale-interpro-track"; + +/** track of features */ +type Track = { + label: string; + features: Feature[]; +}; + +type Feature = { + /** unique id */ + id: string; + /** human-readable label */ + label?: string; + /** arbitrary type/category */ + type?: string; + /** starting position of feature in sequence (1-indexed) */ + start: number; + /** ending position of feature in sequence (1-indexed) */ + end: number; +}; + +type Props = { sequence: string; tracks: Track[] }; + +const IPR = ({ sequence, tracks }: Props) => { + /** props for all nightingale components */ + const commonProps = { + length: sequence.length, + height: 50, + "display-start": 1, + "display-end": -1, + "margin-top": 0, + "margin-bottom": 0, + "margin-left": 0, + "margin-right": 0, + }; + + const managerProps: Partial = {}; + + const navigationProps: Partial = { + ...commonProps, + }; + + const sequenceProps: Partial = { + sequence, + ...commonProps, + }; + + const interproProps: Partial = { + ...commonProps, + label: ".feature.label", + "show-label": true, + expanded: true, + }; + + /** map of feature types to colors */ + const featureColors = useMemo( + () => + getColorMap( + tracks + .map((track) => track.features.map((feature) => feature.type ?? "")) + .flat(), + ), + [tracks], + ); + + return ( + <> + +
+
Navigator
+ +
Sequence
+ + {tracks.map((track, index) => ( + +
{track.label}
+ | null) => { + if (!ref) return; + + ref.data = track.features.map( + ({ id, label, type, start, end }) => ({ + accession: id, + label: label ?? id, + locations: [{ fragments: [{ start, end }] }], + residues: [], + color: featureColors[type ?? ""], + }), + ); + + return ref; + }} + {...interproProps} + height={50} + /> + + ))} +
+ + + {/* legend */} +
+ {Object.entries(featureColors).map(([type, color]) => ( + + + {type || "-"} + + ))} +
+ + ); +}; + +export default IPR; diff --git a/frontend/src/pages/Testbed.tsx b/frontend/src/pages/Testbed.tsx index 3c58467..5c70084 100755 --- a/frontend/src/pages/Testbed.tsx +++ b/frontend/src/pages/Testbed.tsx @@ -1,6 +1,7 @@ import { FaArrowRight, FaArrowsUpDown, + FaBarcode, FaBars, FaBeerMugEmpty, FaBrush, @@ -26,7 +27,7 @@ import { FaStop, FaTableCells, } from "react-icons/fa6"; -import { sample, uniqueId } from "lodash"; +import { random, sample, uniqueId } from "lodash"; import CustomIcon from "@/assets/custom-icon.svg?react"; import Ago from "@/components/Ago"; import Alert from "@/components/Alert"; @@ -36,6 +37,7 @@ import Collapsible from "@/components/Collapsible"; import Flex from "@/components/Flex"; import Form from "@/components/Form"; import Heading from "@/components/Heading"; +import IPR from "@/components/IPR"; import Link from "@/components/Link"; import Meta from "@/components/Meta"; import Network from "@/components/Network"; @@ -126,6 +128,41 @@ for (let times = 0; times < 10; times++) { edges.push({ ...edge, id: uniqueId(), source: id, target: id }); } +/** generate fake sequence data */ +const sequence = Array(random(10, 100)) + .fill(null) + .map(() => sample(["G", "A", "T", "C"])) + .join(""); + +/** generate fake interproscan track data */ +const tracks = Array(10) + .fill(null) + .map(() => ({ + label: sample(["Lbl.", "Label", "Long Label", "Really Long Label"]), + features: Array(random(1, 3)) + .fill(null) + .map(() => { + const start = random(1, Math.floor(sequence.length / 2)); + const end = random( + start + Math.floor(sequence.length / 4), + sequence.length, + ); + return { + id: uniqueId(), + label: sample([ + "Lbl.", + "Label", + "Long Label", + "Really Long Label", + undefined, + ]), + type: sample(["cat", "dog", "bird", undefined]), + start, + end, + }; + }), + })); + /** test and example usage of formatting, elements, components, etc. */ const TestbedPage = () => { return ( @@ -136,6 +173,15 @@ const TestbedPage = () => { Testbed + {/* IPR */} +
+ }> + IPR + + + +
+
}> Network diff --git a/frontend/src/vite-env.d.ts b/frontend/src/vite-env.d.ts index 3c8a474..49f0507 100755 --- a/frontend/src/vite-env.d.ts +++ b/frontend/src/vite-env.d.ts @@ -1,10 +1,20 @@ /// /// -/** no type def libraries for these libraries */ +/** no type defs for these libraries */ declare module "cytoscape-cola"; declare module "cytoscape-spread"; +namespace React.JSX { + // eslint-disable-next-line + interface IntrinsicElements { + "nightingale-manager": JSX.HTMLAttributes; + "nightingale-navigation": JSX.HTMLAttributes; + "nightingale-sequence": JSX.HTMLAttributes; + "nightingale-interpro-track": JSX.HTMLAttributes; + } +} + declare module "dom-to-image-more" { import domToImage from "dom-to-image"; export = domToImage;