feat(autobidsify): folder browsing, executor workflow, and UI refinements

.github/workflows/node.js.yml

@@ -0,0 +1,31 @@
+# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs
+
+name: Node.js CI
+
+on:
+  push:
+    branches: [ "dev", "main" ]
+  pull_request:
+    branches: [ "dev", "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [18.x, 20.x, 22.x]
+        # See supported Node.js release schedule at https://nodejs.org/en/about/releases/
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Use Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v4
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: 'yarn' # Cache yarn dependencies
+    - run: yarn install
+    - run: yarn build --if-present
+    - run: yarn test

.github/workflows/validation.yml

@@ -0,0 +1,43 @@
+name: Validate NeuroJson_io Project
+
+on:
+  push:
+    branches:
+      - dev
+      - main
+  pull_request:
+    branches:
+      - dev
+      - main
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v3
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: '18'
+
+      - name: Install dependencies
+        run: yarn install
+
+      - name: Compile TypeScript
+        run: yarn build
+
+      - name: Run Linter
+        run: yarn lint
+
+     # - name: Check for exposed environment variables
+     #   run: |
+     #     if [ -f ".env" ]; then
+     #       echo "Error: .env file found. Environment variables should not be exposed." >&2
+     #       exit 1
+     #     fi
+
+      - name: Run Security Audit
+        run: yarn audit --level moderate

backend/services/email.service.js

@@ -21,18 +21,23 @@ class EmailService {
   }
 
   async createTestTransporter() {
-    const testAccount = await nodemailer.createTestAccount();
-    this.transporter = nodemailer.createTransport({
-      host: "smtp.ethereal.email",
-      port: 587,
-      secure: false,
-      auth: {
-        user: testAccount.user,
-        pass: testAccount.pass,
-      },
-    });
-    console.log("📧 Using Ethereal email for development");
-    console.log("Preview emails at: https://ethereal.email");
+    try {
+      const testAccount = await nodemailer.createTestAccount();
+      this.transporter = nodemailer.createTransport({
+        host: "smtp.ethereal.email",
+        port: 587,
+        secure: false,
+        auth: {
+          user: testAccount.user,
+          pass: testAccount.pass,
+        },
+      });
+      console.log("📧 Using Ethereal email for development");
+      console.log("Preview emails at: https://ethereal.email");
+    } catch (err) {
+      console.warn("⚠️  Ethereal unavailable, email disabled in dev:", err.message);
+      this.transporter = null;
+    }
   }
 
   async sendVerificationEmail(user, token) {

backend/src/routes/ollama.routes.js

@@ -3,7 +3,7 @@ const router = express.Router();
 const { proxyChat, getTags } = require("../controllers/ollama.controller");
 const { requireAuth } = require("../middleware/auth.middleware");
 
-router.post("/chat", requireAuth, proxyChat);
+router.post("/bidsify", requireAuth, proxyChat);
 // router.get("/tags", requireAuth, getTags);
 
 module.exports = router;

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

@@ -1,12 +1,11 @@
 // src/components/DatasetOrganizer/DropZone.tsx
-import { processFile, processFolder, processZip } from "./utils/fileProcessors";
+import { processFile, processFolder, processFolderFromFiles, processZip } from "./utils/fileProcessors";
 import { CloudUpload, Add, CheckCircle } from "@mui/icons-material";
 import {
   Box,
   Typography,
   Paper,
   Button,
-  TextField,
   CircularProgress,
 } from "@mui/material";
 import { Colors } from "design/theme";
@@ -38,6 +37,7 @@ const DropZone: React.FC<DropZoneProps> = ({
   const [isDragging, setIsDragging] = useState(false);
   const [isProcessing, setIsProcessing] = useState(false); // ← add
   const fileInputRef = useRef<HTMLInputElement>(null);
+  const folderInputRef = useRef<HTMLInputElement>(null);
   // const [basePath, setBasePath] = useState<string>(""); // change
 
   const handleDragOver = (e: React.DragEvent) => {
@@ -117,6 +117,24 @@ const DropZone: React.FC<DropZoneProps> = ({
     }
   };
 
+  const handleFolderSelect = async (e: React.ChangeEvent<HTMLInputElement>) => {
+    const selectedFiles = Array.from(e.target.files || []);
+    if (selectedFiles.length === 0) return;
+    setIsProcessing(true);
+
+    // Auto-detect root folder name from webkitRelativePath (e.g. "myDataset/sub-01/file.nii")
+    const rootFolder = selectedFiles[0].webkitRelativePath.split("/")[0];
+    if (rootFolder && !baseDirectoryPath) setBaseDirectoryPath(rootFolder);
+
+    try {
+      const items = await processFolderFromFiles(selectedFiles, baseDirectoryPath);
+      setFiles((prev) => [...prev, ...items]);
+    } finally {
+      setIsProcessing(false);
+      e.target.value = "";
+    }
+  };
+
   return (
     <Box sx={{ display: "flex", flexDirection: "column", gap: 2 }}>
       {/* Show file count if files exist */}
@@ -136,7 +154,7 @@ const DropZone: React.FC<DropZoneProps> = ({
         onDragOver={handleDragOver}
         onDragLeave={handleDragLeave}
         onDrop={handleDrop}
-        onClick={() => fileInputRef.current?.click()}
+        onClick={(e) => { if (e.target === e.currentTarget) fileInputRef.current?.click(); }}
         sx={{
           border: `2px dashed ${isDragging ? Colors.purple : Colors.lightGray}`,
           borderRadius: 2,
@@ -198,13 +216,24 @@ const DropZone: React.FC<DropZoneProps> = ({
               📁 Folders • 🗜️ ZIP files • 📄 Documents (.json, .txt, .md) • 📊
               Office (.docx, .pdf, .xlsx)
             </Typography>
-            <Button
-              variant="outlined"
-              startIcon={<Add />}
-              sx={{ borderColor: Colors.purple, color: Colors.purple }}
-            >
-              Or Click to Browse
-            </Button>
+            <Box sx={{ display: "flex", gap: 1, justifyContent: "center" }}>
+              <Button
+                variant="outlined"
+                startIcon={<Add />}
+                onClick={(e) => { e.stopPropagation(); fileInputRef.current?.click(); }}
+                sx={{ borderColor: Colors.purple, color: Colors.purple }}
+              >
+                Browse Files
+              </Button>
+              <Button
+                variant="outlined"
+                startIcon={<Add />}
+                onClick={(e) => { e.stopPropagation(); folderInputRef.current?.click(); }}
+                sx={{ borderColor: Colors.purple, color: Colors.purple }}
+              >
+                Browse Folder
+              </Button>
+            </Box>
           </>
         )}
         <input
@@ -215,19 +244,14 @@ const DropZone: React.FC<DropZoneProps> = ({
           onChange={handleFileSelect}
           accept=".nii,.nii.gz,.snirf,.h5,.hdf5,.jnii,.jmsh,.json,.txt,.md,.zip,.docx,.pdf,.xlsx,.xls,.mat,.dcm,.nirs"
         />
+        <input
+          ref={folderInputRef}
+          type="file"
+          hidden
+          onChange={handleFolderSelect}
+          {...{ webkitdirectory: "", mozdirectory: "" } as any}
+        />
       </Paper>
-      <TextField
-        label="Directory Path (actual data path)"
-        placeholder="example: /Users/username/Desktop/Downloads"
-        // value={basePath} // change
-        // onChange={(e) => setBasePath(e.target.value)} //change
-        value={baseDirectoryPath} // ✅ CHANGE: Use prop
-        onChange={(e) => setBaseDirectoryPath(e.target.value)} // ✅ CHANGE: Use prop setter
-        fullWidth
-        size="small"
-        sx={{ mb: 2 }}
-        helperText="Enter the folder path where these files are located"
-      />
     </Box>
   );
 };

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

@@ -20,6 +20,7 @@ import {
   Paper,
   Button,
   TextField,
+  Alert,
   Dialog,
   DialogTitle,
   DialogContent,
@@ -37,6 +38,8 @@ interface FileTreeProps {
   setSelectedIds: React.Dispatch<React.SetStateAction<Set<string>>>;
   expandedIds: Set<string>;
   setExpandedIds: React.Dispatch<React.SetStateAction<Set<string>>>;
+  baseDirectoryPath: string;
+  setBaseDirectoryPath: (path: string) => void;
 }
 
 const FileTree: React.FC<FileTreeProps> = ({
@@ -46,6 +49,8 @@ const FileTree: React.FC<FileTreeProps> = ({
   setSelectedIds,
   expandedIds,
   setExpandedIds,
+  baseDirectoryPath,
+  setBaseDirectoryPath,
 }) => {
   const [noteDialogOpen, setNoteDialogOpen] = useState(false);
   const [editingNoteId, setEditingNoteId] = useState<string | null>(null);
@@ -521,6 +526,20 @@ const FileTree: React.FC<FileTreeProps> = ({
             // alignItems: "center",
           }}
         >
+          <TextField
+            label="Root Directory Path"
+            placeholder="/Users/username/Desktop/my-dataset"
+            value={baseDirectoryPath}
+            onChange={(e) => setBaseDirectoryPath(e.target.value)}
+            size="small"
+            sx={{ mb: 0.75 }}
+            fullWidth
+          />
+          <Alert severity="info" sx={{ py: 0.5, mb: 1.5, fontSize: "0.75rem" }}>
+            {baseDirectoryPath
+              ? <>All dropped files must be inside <Box component="span" sx={{ fontFamily: "monospace", fontWeight: 600 }}>{baseDirectoryPath}</Box> on your machine.</>
+              : "All dropped files must be inside this root folder on your machine."}
+          </Alert>
           <Box>
             <Typography variant="subtitle2" fontWeight={800}>
               Virtual File System
@@ -635,7 +654,7 @@ const FileTree: React.FC<FileTreeProps> = ({
                   variant="body2"
                   sx={{ color: Colors.darkPurple, fontWeight: 400 }}
                 >
-                  BIDS Conversion Package Preview
+                  BIDS Conversion Bundle Preview
                 </Typography>
               </Box>
               {outputFiles