feat(autobidsify): add public private mode page, local AI support, and Ollama security

backend/package.json

@@ -29,6 +29,7 @@
     "cors": "^2.8.5",
     "dotenv": "^17.2.3",
     "express": "^5.1.0",
+    "express-rate-limit": "^8.5.2",
     "jsonwebtoken": "^9.0.2",
     "nanoid": "^3.3.11",
     "nodemailer": "^7.0.11",

backend/src/controllers/couchdb.controller.js

@@ -513,7 +513,11 @@ const getDatasetFilesManifest = async (req, res) => {
       }
     );
 
-    const files = rows.filter((r) => r.url);
+    const resolveUrl = (url) => {
+      if (!url || url.startsWith("http")) return url;
+      return `https://neurojson.org/io/stat.cgi?action=get&db=${dbName}&doc=${dsName}&${url}`;
+    };
+    const files = rows.filter((r) => r.url).map((r) => ({ ...r, url: resolveUrl(r.url) }));
     const urls = files.map((r) => r.url);
     const baseName = `${dbName}_${dsName}_${exts.join("_")}`;
     const extLabel = exts.join(", ");

backend/src/controllers/ollama.controller.js

@@ -1,12 +1,13 @@
 const OLLAMA_BASE_URL = "http://jin.neu.edu:11434";
+const OLLAMA_MODEL = "qwen3.6:27b";
 
 const proxyChat = async (req, res) => {
-  console.log("🟣 [Ollama] proxyChat hit — model:", req.body.model);
+  console.log("🟣 [Ollama] proxyChat hit — model:", OLLAMA_MODEL);
   try {
     const response = await fetch(`${OLLAMA_BASE_URL}/v1/chat/completions`, {
       method: "POST",
       headers: { "Content-Type": "application/json" },
-      body: JSON.stringify(req.body),
+      body: JSON.stringify({ ...req.body, model: OLLAMA_MODEL }),
     });
 
     const data = await response.json();

backend/src/routes/ollama.public.routes.js

@@ -0,0 +1,17 @@
+const express = require("express");
+const router = express.Router();
+const rateLimit = require("express-rate-limit");
+const { proxyChat, getTags } = require("../controllers/ollama.controller");
+
+const dailyLimit = rateLimit({
+  windowMs: 24 * 60 * 60 * 1000, // 24 hours
+  max: 20,
+  standardHeaders: true,
+  legacyHeaders: false,
+  message: { error: "Daily request limit reached. You can send up to 20 requests per day from this IP." },
+});
+
+router.post("/chat", dailyLimit, proxyChat);
+// router.get("/tags", dailyLimit, getTags);
+
+module.exports = router;

backend/src/routes/ollama.routes.js

@@ -1,8 +1,9 @@
 const express = require("express");
 const router = express.Router();
 const { proxyChat, getTags } = require("../controllers/ollama.controller");
+const { requireAuth } = require("../middleware/auth.middleware");
 
-router.post("/chat", proxyChat);
-router.get("/tags", getTags);
+router.post("/chat", requireAuth, proxyChat);
+// router.get("/tags", requireAuth, getTags);
 
 module.exports = router;

backend/src/server.js

@@ -14,6 +14,7 @@ const datasetsRoutes = require("./routes/datasets.routes");
 const collectionRoutes = require("./routes/collection.route");
 const projectRoutes = require("./routes/projects.routes");
 const ollamaRoutes = require("./routes/ollama.routes");
+const ollamaPublicRoutes = require("./routes/ollama.public.routes");
 
 const app = express();
 const PORT = process.env.PORT || 5000;
@@ -51,6 +52,7 @@ app.use("/api/v1/datasets", datasetsRoutes);
 app.use("/api/v1/collections", collectionRoutes);
 app.use("/api/v1/projects", projectRoutes);
 app.use("/api/v1/ollama", ollamaRoutes);
+app.use("/api/v1/ollama-public", ollamaPublicRoutes);
 
 // health check endpoint
 app.get("/api/health", async (req, res) => {

package.json

@@ -50,13 +50,13 @@
     "react-redux": "^8.1.2",
     "react-router-dom": "^6.15.0",
     "react-scripts": "^5.0.1",
-    "react-syntax-highlighter": "^15.6.1",
+    "react-syntax-highlighter": "16.1.1",
     "sharp": "^0.33.5",
     "stats-js": "^1.0.1",
     "stats.js": "0.17.0",
     "three": "0.145.0",
     "typescript": "^5.1.6",
-    "uplot": "1.6.17",
+    "uplot": "1.6.32",
     "web-vitals": "^2.1.0",
     "xlsx": "^0.18.5"
   },

src/components/NavBar/NavItems.tsx

@@ -35,11 +35,13 @@ const NavItems: React.FC = () => {
   const [signupOpen, setSignupOpen] = useState(false);
 
   // Resources dropdown state
-  const [resourcesAnchor, setResourcesAnchor] = useState<null | HTMLElement>(
-    null
-  );
+  const [resourcesAnchor, setResourcesAnchor] = useState<null | HTMLElement>(null);
   const resourcesOpen = Boolean(resourcesAnchor);
 
+  // AutoBIDSify dropdown state
+  const [autobidsifyAnchor, setAutobidsifyAnchor] = useState<null | HTMLElement>(null);
+  const autobidsifyOpen = Boolean(autobidsifyAnchor);
+
   const handleLogout = () => {
     dispatch(logoutUser());
     navigate("/");
@@ -53,6 +55,14 @@ const NavItems: React.FC = () => {
     setResourcesAnchor(null);
   };
 
+  const handleAutobidsifyClick = (event: React.MouseEvent<HTMLElement>) => {
+    setAutobidsifyAnchor(event.currentTarget);
+  };
+
+  const handleAutobidsifyClose = () => {
+    setAutobidsifyAnchor(null);
+  };
+
   const resourcesMenu = [
     {
       category: "Converter",
@@ -378,6 +388,38 @@ const NavItems: React.FC = () => {
             </Grid>
           ))}
 
+          {/* AutoBIDSify Dropdown */}
+          <Grid item>
+            <Box
+              onClick={handleAutobidsifyClick}
+              sx={{ display: "flex", alignItems: "center", gap: 0.5, cursor: "pointer" }}
+            >
+              <Typography
+                align="center"
+                fontWeight={600}
+                lineHeight={"1.5rem"}
+                letterSpacing={"0.05rem"}
+                sx={{
+                  fontSize: { xs: "0.8rem", sm: "1rem" },
+                  color: Colors.white,
+                  transition: "color 0.3s ease, transform 0.3s ease",
+                  textTransform: "uppercase",
+                  "&:hover": { transform: "scale(1.2)" },
+                }}
+              >
+                AutoBIDSify
+              </Typography>
+              <KeyboardArrowDownIcon
+                sx={{
+                  color: Colors.white,
+                  fontSize: "1.2rem",
+                  transition: "transform 0.3s ease",
+                  transform: autobidsifyOpen ? "rotate(180deg)" : "rotate(0deg)",
+                }}
+              />
+            </Box>
+          </Grid>
+
           {/* Resources Dropdown */}
           <Grid item>
             <Box
@@ -511,6 +553,49 @@ const NavItems: React.FC = () => {
           </Box>
         ))}
       </Menu>
+
+      {/* AutoBIDSify Dropdown Menu */}
+      <Menu
+        anchorEl={autobidsifyAnchor}
+        open={autobidsifyOpen}
+        onClose={handleAutobidsifyClose}
+        PaperProps={{
+          sx: {
+            bgcolor: Colors.darkPurple,
+            color: Colors.white,
+            minWidth: "220px",
+            mt: 1,
+          },
+        }}
+      >
+        <MenuItem
+          onClick={() => {
+            window.open("https://github.com/COTILab/autobidsify", "_blank");
+            handleAutobidsifyClose();
+          }}
+          sx={{
+            fontSize: "0.9rem",
+            color: Colors.white,
+            "&:hover": { bgcolor: Colors.purpleGrey, color: Colors.darkPurple },
+          }}
+        >
+          AutoBIDSify (GitHub)
+        </MenuItem>
+        <MenuItem
+          onClick={() => {
+            navigate(RoutesEnum.BIDS_CONVERTER);
+            handleAutobidsifyClose();
+          }}
+          sx={{
+            fontSize: "0.9rem",
+            color: Colors.white,
+            "&:hover": { bgcolor: Colors.purpleGrey, color: Colors.darkPurple },
+          }}
+        >
+          AutoBIDSify Web
+        </MenuItem>
+      </Menu>
+
       <UserLogin
         open={loginOpen}
         onClose={() => setLoginOpen(false)}

src/components/Routes.tsx

@@ -1,3 +1,4 @@
+import BidsConverterPage from "pages/BidsConverterPage";
 import ScrollToTop from "./ScrollToTop";
 import CompleteProfile from "./User/CompleteProfile";
 import CollectionDetailPage from "./User/Dashboard/CollectionDetailPage";
@@ -68,6 +69,7 @@ const Routes = () => (
           element={<CollectionDetailPage />}
         />
         <Route path="/projects/:projectId" element={<DatasetOrganizer />} />
+        <Route path={RoutesEnum.BIDS_CONVERTER} element={<BidsConverterPage />} />
       </Route>
     </RouterRoutes>
   </>

src/components/SearchPage/DatasetCard.tsx

@@ -59,6 +59,18 @@ interface DatasetCardProps {
 }
 
 /** ---------- utility helpers ---------- **/
+// Some iolinks records (older openneuro links view) store a relative path like
+// "file=sub-01/anat/sub-01_T1w.nii&size=1" instead of a full stat.cgi URL.
+// Reconstruct the full URL so the browser can follow it.
+const resolveFileUrl = (
+  dbname: string,
+  dsname: string,
+  url?: string
+): string => {
+  if (!url) return "";
+  if (url.startsWith("http")) return url;
+  return `https://neurojson.org/io/stat.cgi?action=get&db=${dbname}&doc=${dsname}&${url}`;
+};
 const normalize = (s: string) =>
   s
     ?.replace(/[\u2018\u2019\u2032]/g, "'") // curly → straight
@@ -504,7 +516,7 @@ const DatasetCard: React.FC<DatasetCardProps> = ({
                   return (
                     <li key={i}>
                       <MuiLink
-                        href={v.url}
+                        href={resolveFileUrl(dbname, dsname, v.url)}
                         target="_blank"
                         rel="noopener noreferrer"
                         underline="hover"

src/components/User/Dashboard/DatasetOrganizer/FileTree.tsx

@@ -522,7 +522,7 @@ const FileTree: React.FC<FileTreeProps> = ({
           }}
         >
           <Box>
-            <Typography variant="subtitle2" fontWeight="600">
+            <Typography variant="subtitle2" fontWeight={800}>
               Virtual File System
             </Typography>
             <Typography variant="caption" color="text.secondary">
@@ -631,12 +631,11 @@ const FileTree: React.FC<FileTreeProps> = ({
                   borderColor: "divider",
                 }}
               >
-                <FolderSpecial sx={{ color: Colors.darkGreen, fontSize: 16 }} />
                 <Typography
-                  variant="caption"
-                  sx={{ color: Colors.darkGreen, fontWeight: 600 }}
+                  variant="body2"
+                  sx={{ color: Colors.darkPurple, fontWeight: 400 }}
                 >
-                  Saved Outputs
+                  BIDS Conversion Package Preview
                 </Typography>
               </Box>
               {outputFiles