Refine bio export

frontend/eslint.config.js → frontend/eslint.config.ts

@@ -1,22 +1,22 @@
-import eslintJs from "@eslint/js";
-import eslintPluginBetterTailwindcss from "eslint-plugin-better-tailwindcss";
-import eslintPluginJsxA11y from "eslint-plugin-jsx-a11y";
-import eslintPluginPrettierRecommended from "eslint-plugin-prettier/recommended";
-import eslintPluginReactHooks from "eslint-plugin-react-hooks";
+import js from "@eslint/js";
+import tailwind from "eslint-plugin-better-tailwindcss";
+import a11y from "eslint-plugin-jsx-a11y";
+import prettier from "eslint-plugin-prettier/recommended";
+import reactHooks from "eslint-plugin-react-hooks";
 import { defineConfig, globalIgnores } from "eslint/config";
 import globals from "globals";
-import typescriptEslint from "typescript-eslint";
+import tslint from "typescript-eslint";
 
 export default defineConfig([
   globalIgnores(["dist", "public"]),
-  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",

frontend/package.json

@@ -13,56 +13,56 @@
     "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",
-    "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",
+    "gsap": "^3.15.0",
+    "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": [

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()

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");

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;
+};

frontend/src/components/Textbox.tsx

@@ -27,7 +27,7 @@ export default function Textbox({
   );
   return multi ? (
     <textarea
-      className={clsx("min-h-[calc(3lh+--spacing(4))]", _class)}
+      className={clsx("min-h-[calc(3lh+(--spacing(4)))]", _class)}
       onChange={(event) => onChange?.(event.currentTarget.value)}
       {...(props as ComponentPropsWithRef<"textarea">)}
     />