From 80a0c805231994320d034319b4bc100c5358eae0 Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Thu, 14 May 2026 15:15:52 -0400 Subject: [PATCH 1/4] upgrade packages, fix search bugs, fix examples --- frontend/bun.lock | 337 +++++++++--------- .../{eslint.config.js => eslint.config.ts} | 26 +- frontend/package.json | 65 ++-- frontend/public/mockServiceWorker.js | 2 +- frontend/src/pages/Cart.tsx | 8 +- frontend/src/pages/Home.tsx | 34 +- 6 files changed, 246 insertions(+), 226 deletions(-) rename frontend/{eslint.config.js => eslint.config.ts} (65%) diff --git a/frontend/bun.lock b/frontend/bun.lock index 38d8015..a226820 100644 --- a/frontend/bun.lock +++ b/frontend/bun.lock @@ -4,56 +4,57 @@ "workspaces": { "": { "dependencies": { - "@base-ui/react": "^1.1.0", + "@base-ui/react": "^1.4.1", "@fontsource-variable/outfit": "^5.2.8", "@fontsource-variable/sometype-mono": "^5.2.7", - "@reactuses/core": "^6.1.11", - "@tailwindcss/vite": "^4.1.18", - "@tanstack/react-query": "^5.90.19", + "@reactuses/core": "^6.3.1", + "@tailwindcss/vite": "^4.3.0", + "@tanstack/react-query": "^5.100.10", "@tanstack/react-table": "^8.21.3", "clsx": "^2.1.1", - 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eslintJs.configs.recommended, - typescriptEslint.configs.recommended, - eslintPluginPrettierRecommended, - eslintPluginReactHooks.configs.flat.recommended, - eslintPluginJsxA11y.flatConfigs.recommended, + js.configs.recommended, + tslint.configs.recommended, + prettier, + reactHooks.configs.flat.recommended, + a11y.flatConfigs.recommended, { plugins: { - "better-tailwindcss": eslintPluginBetterTailwindcss, + "better-tailwindcss": tailwind, }, languageOptions: { ecmaVersion: 2020, @@ -45,7 +45,7 @@ export default defineConfig([ /** FORMATTING */ "prettier/prettier": "warn", - ...eslintPluginBetterTailwindcss.configs["recommended-warn"].rules, + ...tailwind.configs["recommended-warn"].rules, /** https://github.com/schoero/eslint-plugin-better-tailwindcss/issues/302 */ "better-tailwindcss/enforce-consistent-line-wrapping": [ "warn", diff --git a/frontend/package.json b/frontend/package.json index db436e2..0b629f3 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -13,56 +13,57 @@ "clean": "rm -rf node_modules dist bun.lock && bun pm cache rm" }, "dependencies": { - "@base-ui/react": "^1.1.0", + "@base-ui/react": "^1.4.1", "@fontsource-variable/outfit": "^5.2.8", "@fontsource-variable/sometype-mono": "^5.2.7", - "@reactuses/core": "^6.1.11", - "@tailwindcss/vite": "^4.1.18", - "@tanstack/react-query": "^5.90.19", + "@reactuses/core": "^6.3.1", + "@tailwindcss/vite": "^4.3.0", + "@tanstack/react-query": "^5.100.10", "@tanstack/react-table": "^8.21.3", "clsx": "^2.1.1", - "gsap": "^3.14.2", + "gsap": "^3.15.0", "highlight.js": "^11.11.1", - "javascript-time-ago": "^2.5.12", - "jotai": "^2.16.2", - "lodash": "^4.17.21", - "lucide-react": "^0.562.0", - "react": "^19.2.3", + "javascript-time-ago": "^2.6.4", + "jotai": "^2.20.0", + "lodash": "^4.18.1", + "lucide-react": "^1.16.0", + "react": "^19.2.6", "react-children-utilities": "^2.10.0", - "react-dom": "^19.2.3", + "react-dom": "^19.2.6", "react-ga4": "^3.0.1", "react-highlight-words": "^0.21.0", - "react-router": "^7.12.0", - "react-time-ago": "^7.3.5", + "react-router": "^7.15.1", + "react-time-ago": "^7.4.4", "seedrandom": "^3.0.5", - "tailwindcss": "^4.1.18", - "zod": "^4.3.6" + "tailwindcss": "^4.3.0", + "zod": "^4.4.3" }, "devDependencies": { - "@eslint/js": "^9.39.2", - "@ianvs/prettier-plugin-sort-imports": "^4.7.0", - "@types/lodash": "^4.17.23", - "@types/react": "^19.2.9", + "@eslint/js": "^10.0.1", + "@ianvs/prettier-plugin-sort-imports": "^4.7.1", + "@types/eslint-plugin-jsx-a11y": "^6.10.1", + "@types/lodash": "^4.17.24", + "@types/react": "^19.2.14", "@types/react-dom": "^19.2.3", "@types/react-highlight-words": "^0.20.1", "@types/seedrandom": "^3.0.8", - "@vitejs/plugin-react": "^5.1.2", - "eslint": "^9.39.2", + "@vitejs/plugin-react": "^6.0.1", + "eslint": "^10.3.0", "eslint-config-prettier": "^10.1.8", - "eslint-plugin-better-tailwindcss": "^4.0.1", + "eslint-plugin-better-tailwindcss": "^4.5.0", "eslint-plugin-jsx-a11y": "^6.10.2", "eslint-plugin-prettier": "^5.5.5", - "eslint-plugin-react-hooks": "^7.0.1", - "globals": "^17.0.0", - "msw": "^2.12.7", - "prettier": "^3.8.0", + "eslint-plugin-react-hooks": "^7.1.1", + "globals": "^17.6.0", + "msw": "^2.14.6", + "prettier": "^3.8.3", "prettier-plugin-jsdoc": "^1.8.0", - "prettier-plugin-tailwindcss": "^0.7.2", - "type-fest": "^5.4.1", - "typescript": "^5.9.3", - "typescript-eslint": "^8.53.1", - "vite": "^7.3.1", - "vite-plugin-svgr": "^4.5.0" + "prettier-plugin-tailwindcss": "^0.8.0", + "type-fest": "^5.6.0", + "typescript": "^6.0.3", + "typescript-eslint": "^8.59.3", + "vite": "^8.0.13", + "vite-plugin-svgr": "^5.2.0" }, "msw": { "workerDirectory": [ diff --git a/frontend/public/mockServiceWorker.js b/frontend/public/mockServiceWorker.js index 80f1930..33dde9e 100644 --- a/frontend/public/mockServiceWorker.js +++ b/frontend/public/mockServiceWorker.js @@ -7,7 +7,7 @@ * - Please do NOT modify this file. */ -const PACKAGE_VERSION = '2.13.6' +const PACKAGE_VERSION = '2.14.6' const INTEGRITY_CHECKSUM = '4db4a41e972cec1b64cc569c66952d82' const IS_MOCKED_RESPONSE = Symbol('isMockedResponse') const activeClientIds = new Set() diff --git a/frontend/src/pages/Cart.tsx b/frontend/src/pages/Cart.tsx index ac846e6..28d9005 100644 --- a/frontend/src/pages/Cart.tsx +++ b/frontend/src/pages/Cart.tsx @@ -22,8 +22,8 @@ import { Mail, Plus, Share2, + SquareArrowRightEnter, Table2, - Terminal, Trash, } from "lucide-react"; import { @@ -283,8 +283,8 @@ export default function Cart() { } > @@ -382,7 +382,7 @@ export default function Cart() { History

- Carts you've created from this device + Carts you've created on this device

{ if (!id?.trim()) return; - const result = ontologySearchQuery.data?.find( - (result) => result.id === id, - ); - if (result) addSearch(result); + const result = results.find((result) => result.id === id); + if (!result) return; + addSearch(omit(result, "icon")); const params = new URLSearchParams(); - params.set("raw", search); - navigate(`/search/${result?.id ?? ""}?${params.toString()}`); + params.set("raw", search || result.name); + navigate(`/search/${id}?${params.toString()}`); }} status={ + search.trim() && showStatus({ query: ontologySearchQuery }) && ( ) From 660a6d4b31c786cec09d83f7a2e98d395805914a Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Thu, 14 May 2026 15:19:50 -0400 Subject: [PATCH 2/4] delete bash script --- frontend/bun.lock | 3 -- frontend/package.json | 1 - frontend/src/api/api.ts | 27 +----------- frontend/src/pages/Cart.tsx | 72 ++----------------------------- frontend/src/util/download.ts | 4 -- frontend/src/util/highlighting.ts | 9 ---- 6 files changed, 5 insertions(+), 111 deletions(-) delete mode 100644 frontend/src/util/highlighting.ts diff --git a/frontend/bun.lock b/frontend/bun.lock index a226820..670410f 100644 --- a/frontend/bun.lock +++ b/frontend/bun.lock @@ -13,7 +13,6 @@ "@tanstack/react-table": "^8.21.3", "clsx": "^2.1.1", "gsap": "^3.15.0", - "highlight.js": "^11.11.1", "javascript-time-ago": "^2.6.4", "jotai": "^2.20.0", "lodash": "^4.18.1", @@ -639,8 +638,6 @@ "highlight-words-core": ["highlight-words-core@1.2.3", "", {}, "sha512-m1O9HW3/GNHxzSIXWw1wCNXXsgLlxrP0OI6+ycGUhiUHkikqW3OrwVHz+lxeNBe5yqLESdIcj8PowHQ2zLvUvQ=="], - "highlight.js": ["highlight.js@11.11.1", "", {}, "sha512-Xwwo44whKBVCYoliBQwaPvtd/2tYFkRQtXDWj1nackaV2JPXx3L0+Jvd8/qCJ2p+ML0/XVkJ2q+Mr+UVdpJK5w=="], - "ignore": ["ignore@5.3.2", "", {}, "sha512-hsBTNUqQTDwkWtcdYI2i06Y/nUBEsNEDJKjWdigLvegy8kDuJAS8uRlpkkcQpyEXL0Z/pjDy5HBmMjRCJ2gq+g=="], "import-fresh": ["import-fresh@3.3.1", "", { "dependencies": { "parent-module": "^1.0.0", "resolve-from": "^4.0.0" } }, "sha512-TR3KfrTZTYLPB6jUjfx6MF9WcWrHL9su5TObK4ZkYgBdWKPOFoSoQIdEuTuR82pmtxH2spWG9h6etwfr1pLBqQ=="], diff --git a/frontend/package.json b/frontend/package.json index 0b629f3..46af455 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -22,7 +22,6 @@ "@tanstack/react-table": "^8.21.3", "clsx": "^2.1.1", "gsap": "^3.15.0", - "highlight.js": "^11.11.1", "javascript-time-ago": "^2.6.4", "jotai": "^2.20.0", "lodash": "^4.18.1", diff --git a/frontend/src/api/api.ts b/frontend/src/api/api.ts index 42be892..84b2733 100644 --- a/frontend/src/api/api.ts +++ b/frontend/src/api/api.ts @@ -1,10 +1,9 @@ -import type { Cart, Feedback } from "@/api/types"; -import type { LocalCart, ShareCart } from "@/state/cart"; +import type { Feedback } from "@/api/types"; +import type { ShareCart } from "@/state/cart"; import analytics from "react-ga4"; import z from "zod"; import { api, request } from "@/api"; import { cart, ontologies, samples, studies } from "@/api/types"; -import { dbLink, getDb } from "@/components/Database"; import { downloadBlob } from "@/util/download"; /** type to color map */ @@ -142,25 +141,3 @@ export const downloadCart = async ( if (type === "json") downloadBlob(data, filename, "json"); analytics.event("download_cart", { ids, filename, type }); }; - -/** get download bash script */ -export const getCartScript = (cart: Cart | LocalCart, database: string) => - [ - `#!/bin/bash`, - `# Meta2Onto data cart download script`, - `# Generated: ${new Date().toISOString()}`, - "id" in cart ? `# ID: ${cart.id}` : "", - "name" in cart ? `# Name: ${cart.name}` : "", - `# Studies: ${cart.studies.length}`, - ...cart.studies.map(({ id }) => [ - `# Download ${id} from ${database}`, - `wget "${dbLink(getDb(database).link, id)}" -O ${id}_${database}.zip`, - ]), - `# Extract`, - `for file in *.zip; do unzip "$file"; done`, - `echo "Download complete"`, - ] - .flat() - .map((line) => line.trimEnd()) - .filter(Boolean) - .join("\n"); diff --git a/frontend/src/pages/Cart.tsx b/frontend/src/pages/Cart.tsx index 28d9005..713efbc 100644 --- a/frontend/src/pages/Cart.tsx +++ b/frontend/src/pages/Cart.tsx @@ -29,15 +29,13 @@ import { import { cartLookup, downloadCart, - getCartScript, shareCart, studyBatchLookup, } from "@/api/api"; import ActionButton, { copy } from "@/components/ActionButton"; import Ago from "@/components/Ago"; -import BigRadios from "@/components/BigRadios"; import Button from "@/components/Button"; -import DatabaseBadge, { databases } from "@/components/Database"; +import DatabaseBadge from "@/components/Database"; import Dialog from "@/components/Dialog"; import Heading from "@/components/Heading"; import Link from "@/components/Link"; @@ -55,8 +53,6 @@ import { createdCartsAtom, removeFromCart, } from "@/state/cart"; -import { downloadSh } from "@/util/download"; -import { highlightBash } from "@/util/highlighting"; import { formatNumber } from "@/util/string"; export default function Cart() { @@ -274,13 +270,8 @@ export default function Cart() { - } + title="Export supported studies to Refine.bio" + content={<>hello world} > ); - -/** bash download script popup */ -const DownloadScript = ({ - name, - cart, -}: { - name: string; - cart: LocalCart | Cart; -}) => { - const [database, setDatabase] = useState(databases[0].id as Database["id"]); - - /** script text */ - const script = getCartScript(cart, database); - - return ( - <> -
- - Database to download from - - } - options={databases.map(({ id }) => ({ - value: id, - render: , - }))} - value={database} - onChange={setDatabase} - /> - -
- -
-
- Bash script to download cart directly from database -
- - 
-          
-
-
- -
- - copy(script)}> - - Copy - -
- - ); -}; diff --git a/frontend/src/util/download.ts b/frontend/src/util/download.ts index 92e607b..20d91ee 100755 --- a/frontend/src/util/download.ts +++ b/frontend/src/util/download.ts @@ -48,7 +48,3 @@ export const downloadBlob = (data: Blob, filename: string, ext: string) => /** download string as text file */ export const downloadTxt = (data: string, filename: string) => download(getUrl(data, "text/plain;charset=utf-8"), filename, "txt"); - -/** download string as bash file */ -export const downloadSh = (data: string, filename: string) => - download(getUrl(data, "text/x-shellscript;charset=utf-8"), filename, "sh"); diff --git a/frontend/src/util/highlighting.ts b/frontend/src/util/highlighting.ts deleted file mode 100644 index 3aad228..0000000 --- a/frontend/src/util/highlighting.ts +++ /dev/null @@ -1,9 +0,0 @@ -import hljs from "highlight.js/lib/core"; -import bash from "highlight.js/lib/languages/bash"; - -/** register languages */ -hljs.registerLanguage("bash", bash); - -/** syntax highlight bash to html */ -export const highlightBash = (code: string) => - hljs.highlight(code, { language: "bash" }).value; From f8f84c1a14552e871fceb463b71a5f64c8d82c11 Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Thu, 14 May 2026 15:57:20 -0400 Subject: [PATCH 3/4] implement refine bio export --- frontend/src/api/refine.bio.ts | 37 +++++++++ frontend/src/pages/Cart.tsx | 138 ++++++++++++++++++++++++--------- frontend/src/pages/Search.tsx | 12 +-- frontend/src/pages/user.ts | 15 ++++ 4 files changed, 159 insertions(+), 43 deletions(-) create mode 100644 frontend/src/api/refine.bio.ts create mode 100644 frontend/src/pages/user.ts diff --git a/frontend/src/api/refine.bio.ts b/frontend/src/api/refine.bio.ts new file mode 100644 index 0000000..69798e1 --- /dev/null +++ b/frontend/src/api/refine.bio.ts @@ -0,0 +1,37 @@ +import analytics from "react-ga4"; +import * as z from "zod"; +import { request } from "@/api"; + +const api = `https://api.refine.bio/v1`; + +export const dataset = z.object({ + id: z.string().optional(), + data: z.unknown().optional(), + success: z.boolean().optional(), + failure_reason: z.string().optional(), +}); + +/** export cart of studies to refine.bio dataset */ +export const makeDataset = async (ids: string[], email = "") => { + const url = new URL(`${api}/dataset/`); + const options = { + method: "POST", + headers: { "Content-Type": "application/json" }, + body: { + data: Object.fromEntries(ids.map((id) => [id, ["ALL"]])), + aggregate_by: "ALL", + scale_by: "NONE", + email_address: email, + email_ccdl_ok: !!email, + notify_me: !!email, + start: true, + quantile_normalize: true, + quant_sf_only: true, + svd_algorithm: "NONE", + }, + } as const; + const data = await request(url, dataset, options); + analytics.event("refine.bio_make_dataset", { ids, data }); + if (!data.success) throw Error(data.failure_reason ?? "Unknown error"); + return data; +}; diff --git a/frontend/src/pages/Cart.tsx b/frontend/src/pages/Cart.tsx index 713efbc..28b66a0 100644 --- a/frontend/src/pages/Cart.tsx +++ b/frontend/src/pages/Cart.tsx @@ -1,8 +1,6 @@ import type { ColumnSort } from "@tanstack/react-table"; import type { Cart } from "@/api/types"; -import type { Database } from "@/components/Database"; import type { Limit } from "@/components/Pagination"; -import type { LocalCart } from "@/state/cart"; import { useEffect, useState } from "react"; import { useParams } from "react-router"; import { @@ -32,6 +30,7 @@ import { shareCart, studyBatchLookup, } from "@/api/api"; +import { makeDataset } from "@/api/refine.bio"; import ActionButton, { copy } from "@/components/ActionButton"; import Ago from "@/components/Ago"; import Button from "@/components/Button"; @@ -45,6 +44,7 @@ import Popover from "@/components/Popover"; import Status, { showStatus } from "@/components/Status"; import Table from "@/components/Table"; import Textbox from "@/components/Textbox"; +import { useUser } from "@/pages/user"; import { addCreatedCart, cartAtom, @@ -75,10 +75,11 @@ export default function Cart() { /** remote, shared cart */ const sharedCart = cartLookupQuery.data; + /** current cart */ + const cart = localCart || sharedCart; + /** cart study ids */ - const studyIds = ((localCart || sharedCart).studies || []).map( - (study) => study.id, - ); + const studyIds = (cart.studies || []).map((study) => study.id); /** cart size */ const size = studyIds.length || 0; @@ -125,8 +126,8 @@ export default function Cart() { onSuccess: addCreatedCart, }); - /** share url */ - const shareUrl = + /** share cart result link */ + const shareLink = !shared && shareMutation.data ? new URL(`${window.location.origin}/cart/${shareMutation.data.id}`) : ""; @@ -141,6 +142,25 @@ export default function Cart() { /** created carts */ const createdCarts = useAtomValue(createdCartsAtom); + /** filter study ids by ones that are in refine.bio */ + const refineBioStudyIds = studyDetails + .filter((study) => study.database.includes("Refine.bio")) + .map((study) => study.id); + + /** export to refine.bio */ + const refineBioMutation = useMutation({ + mutationKey: ["refine-bio", refineBioStudyIds], + mutationFn: () => makeDataset(refineBioStudyIds), + }); + + /** export refio.bio result link */ + const refineBioLink = refineBioMutation.data + ? new URL(`https://www.refine.bio/dataset/${refineBioMutation.data.id}`) + : ""; + + /** user self-identification */ + const { userEmail, setUserEmail } = useUser(); + return ( <> @@ -173,57 +193,54 @@ export default function Cart() { title="Share Cart" content={ <> - {!shareUrl && !showStatus({ query: shareMutation }) && ( - <> -
Save this cart to a public link
- - - - )} - - - - {shareUrl && ( + {showStatus({ query: shareMutation }) ? ( + + ) : shareLink ? ( <>
-

Cart saved to:

+

Cart saved to

event.target.select()} />
copy(String(shareUrl))} + onClick={() => copy(String(shareLink))} > Copy - -
-

Start fresh cart:

+

Start fresh cart

+ ) : ( + <> +
Save this cart to a public link
+ + + )} } @@ -238,7 +255,7 @@ export default function Cart() { )} - {(localCart || sharedCart) && ( + {cart && ( <> hello world} + title="Export to Refine.bio" + content={ + <> + {showStatus({ query: refineBioMutation }) ? ( + + ) : refineBioLink ? ( + <> +

Cart exported to

+ event.target.select()} + /> +
+ copy(String(refineBioLink))} + > + + Copy + + + +
+ + ) : ( + <> +
+ Export supported studies in this cart to a + Refine.bio dataset +
+ + + + )} + + } >