Sidebar chat

.gitignore

@@ -69,3 +69,5 @@ api-e2e/validation.js
 .vs/
 .nx
 .turbo
+.claude/
+.vercel

package.json

@@ -177,6 +177,7 @@
     "gl-matrix": "2.3.2",
     "history": "4.10.1",
     "html-webpack-plugin": "^5.3.2",
+    "html2canvas": "^1.4.1",
     "igv": "^2.11.2",
     "imports-loader": "^0.8.0",
     "jStat": "^1.7.0",

packages/chat-sidebar-server/.gitignore

@@ -0,0 +1,8 @@
+node_modules
+dist
+public
+.vercel
+.env
+.env.local
+.env.*.local
+*.log

packages/chat-sidebar-server/.vercelignore

@@ -0,0 +1,6 @@
+node_modules
+.env
+.env.local
+.env.*.local
+dist
+*.log

packages/chat-sidebar-server/api/chat/health.ts

@@ -0,0 +1,8 @@
+import type { VercelRequest, VercelResponse } from '@vercel/node';
+import { MODEL } from '../../src/core.js';
+import { applyCors } from '../../src/cors.js';
+
+export default function handler(req: VercelRequest, res: VercelResponse) {
+    if (applyCors(req, res)) return;
+    res.json({ ok: true, model: MODEL });
+}

packages/chat-sidebar-server/api/chat/highlights.ts

@@ -0,0 +1,32 @@
+import type { VercelRequest, VercelResponse } from '@vercel/node';
+import { runHighlights } from '../../src/core.js';
+import { applyCors } from '../../src/cors.js';
+
+export const config = {
+    maxDuration: 60,
+};
+
+export default async function handler(
+    req: VercelRequest,
+    res: VercelResponse
+) {
+    if (applyCors(req, res)) return;
+    if (req.method !== 'POST') {
+        res.status(405).json({ error: 'Method not allowed' });
+        return;
+    }
+    const { studyId, inventory, model } = (req.body ?? {}) as any;
+    if (!studyId || typeof studyId !== 'string') {
+        res.status(400).json({ error: 'studyId (string) required' });
+        return;
+    }
+    try {
+        const result = await runHighlights({ studyId, inventory, model });
+        res.json(result);
+    } catch (err: any) {
+        console.error('highlights failed:', err);
+        res.status(500).json({
+            error: err?.message ?? 'Claude call failed',
+        });
+    }
+}

packages/chat-sidebar-server/api/chat/models.ts

@@ -0,0 +1,27 @@
+import type { VercelRequest, VercelResponse } from '@vercel/node';
+import { getShortlistedModels } from '../../src/pricing.js';
+import { applyCors } from '../../src/cors.js';
+
+export const config = {
+    maxDuration: 30,
+};
+
+export default async function handler(
+    req: VercelRequest,
+    res: VercelResponse
+) {
+    if (applyCors(req, res)) return;
+    if (req.method !== 'GET') {
+        res.status(405).json({ error: 'Method not allowed' });
+        return;
+    }
+    try {
+        const models = await getShortlistedModels();
+        res.json({ models });
+    } catch (err: any) {
+        console.error('models failed:', err);
+        res.status(500).json({
+            error: err?.message ?? 'Could not fetch model catalog',
+        });
+    }
+}

packages/chat-sidebar-server/api/chat/paper-status.ts

@@ -0,0 +1,39 @@
+import type { VercelRequest, VercelResponse } from '@vercel/node';
+import { getPaperContext } from '../../src/core.js';
+import { applyCors } from '../../src/cors.js';
+
+export const config = {
+    // First call per study still has to fetch PMC; subsequent ones hit the
+    // in-memory cache and return immediately.
+    maxDuration: 30,
+};
+
+export default async function handler(
+    req: VercelRequest,
+    res: VercelResponse
+) {
+    if (applyCors(req, res)) return;
+    if (req.method !== 'GET') {
+        res.status(405).json({ error: 'Method not allowed' });
+        return;
+    }
+    const studyId = req.query.studyId;
+    if (!studyId || typeof studyId !== 'string') {
+        res.status(400).json({ error: 'studyId (string) required' });
+        return;
+    }
+    try {
+        const paper = await getPaperContext(studyId);
+        res.json({
+            studyId,
+            source: paper.source,
+            paperUrl: paper.paperUrl,
+            studyName: paper.study.name,
+        });
+    } catch (err: any) {
+        console.error('paper-status failed:', err);
+        res.status(500).json({
+            error: err?.message ?? 'paper status failed',
+        });
+    }
+}

packages/chat-sidebar-server/api/chat/suggest.ts

@@ -0,0 +1,41 @@
+import type { VercelRequest, VercelResponse } from '@vercel/node';
+import { runSuggest } from '../../src/core.js';
+import { applyCors } from '../../src/cors.js';
+
+export const config = {
+    maxDuration: 60, // Pro tier cap; first call on a fresh paper can take 15-30s.
+};
+
+export default async function handler(
+    req: VercelRequest,
+    res: VercelResponse
+) {
+    if (applyCors(req, res)) return;
+    if (req.method !== 'POST') {
+        res.status(405).json({ error: 'Method not allowed' });
+        return;
+    }
+    const { studyId, genes, tab, preset, userPrompt, screenshot, model } =
+        (req.body ?? {}) as any;
+    if (!studyId || typeof studyId !== 'string') {
+        res.status(400).json({ error: 'studyId (string) required' });
+        return;
+    }
+    try {
+        const result = await runSuggest({
+            studyId,
+            genes,
+            tab,
+            preset,
+            userPrompt,
+            screenshot,
+            model,
+        });
+        res.json(result);
+    } catch (err: any) {
+        console.error('suggest failed:', err);
+        res.status(500).json({
+            error: err?.message ?? 'Claude call failed',
+        });
+    }
+}

packages/chat-sidebar-server/package.json

@@ -0,0 +1,29 @@
+{
+    "name": "chat-sidebar-server",
+    "private": true,
+    "version": "0.1.0",
+    "description": "Backend for the cBioPortal chat sidebar. Fetches paper text from PMC/PubMed and proxies Claude API calls.",
+    "type": "module",
+    "scripts": {
+        "dev": "tsx watch src/server.ts",
+        "start": "tsx src/server.ts",
+        "vercel-dev": "vercel dev --listen 4000",
+        "vercel-build": "cd ../.. && pnpm --filter chat-sidebar build && rm -rf packages/chat-sidebar-server/public && mkdir -p packages/chat-sidebar-server/public && cp -R packages/chat-sidebar/dist/. packages/chat-sidebar-server/public/"
+    },
+    "dependencies": {
+        "ai": "^6.0.188",
+        "cors": "^2.8.5",
+        "dotenv": "^16.4.5",
+        "express": "^4.21.2",
+        "zod": "4.4.3"
+    },
+    "devDependencies": {
+        "@types/cors": "^2.8.17",
+        "@types/express": "^4.17.21",
+        "@types/node": "^22.10.0",
+        "@vercel/node": "^3.2.0",
+        "tsx": "^4.19.2",
+        "typescript": "^5.7.2",
+        "vercel": "^39.0.0"
+    }
+}