Add /upload and /outputs endpoints for file persistence; add / health check

- Wrap FastMCP server in FastAPI app to add extra HTTP routes
- POST /upload: upload local files to server's /data/inputs directory
- GET /outputs/{name}: download files from server's /data/outputs directory
- GET /: health check endpoint for HF Spaces liveness probes
- Mount MCP sub-app at /mcp with correct path handling
- Add python-multipart dependency for file upload support

requirements.txt

@@ -3,6 +3,7 @@ fastmcp==2.14.5
 uvicorn==0.40.0
 fastapi
 starlette==0.52.1
+python-multipart
 
 # Bioinformatics core
 anndata==0.11.4

src/GLUE_Agent_mcp.py

@@ -13,28 +13,89 @@ This MCP Server contains tools extracted from the following tutorial files:
     - glue_train_model: Train GLUE model for multi-omics integration
     - glue_check_integration_consistency: Evaluate integration quality with consistency scores
     - glue_generate_embeddings: Generate cell and feature embeddings from trained GLUE model
+
+Remote endpoint layout
+----------------------
+GET  /            — health check (HF Spaces liveness probe)
+POST /upload      — upload a local file to /data/inputs on the server
+GET  /outputs/... — download a file previously written to /data/outputs
+/mcp              — Streamable HTTP MCP endpoint (used by Claude Code)
 """
 
 import os
+from pathlib import Path
 
+from fastapi import FastAPI, HTTPException, UploadFile
+from fastapi.responses import FileResponse
 from fastmcp import FastMCP
 
-# Import statements (alphabetical order)
 from tools.preprocessing import preprocessing_mcp
 from tools.training import training_mcp
 
-# Server definition and mounting
+# These env vars are set in the Dockerfile; both tool modules honour them too.
+INPUT_DIR = Path(os.getenv("PREPROCESSING_INPUT_DIR", "/data/inputs"))
+OUTPUT_DIR = Path(os.getenv("PREPROCESSING_OUTPUT_DIR", "/data/outputs"))
+
+INPUT_DIR.mkdir(parents=True, exist_ok=True)
+OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+
+# --- MCP server -----------------------------------------------------------
 mcp = FastMCP(name="GLUE_Agent")
 mcp.mount(preprocessing_mcp)
 mcp.mount(training_mcp)
 
-# ASGI app for uvicorn (used when deployed as a remote HTTP server)
-app = mcp.http_app(path="/mcp")
+# --- Outer FastAPI app ----------------------------------------------------
+app = FastAPI(title="GLUE_Agent MCP Server")
+
+
+@app.get("/")
+async def health_check():
+    """Liveness probe for HF Spaces; also confirms the MCP endpoint path."""
+    return {"status": "ok", "mcp_endpoint": "/mcp"}
+
+
+@app.post("/upload")
+async def upload_file(file: UploadFile):
+    """
+    Upload a local file to the server's input directory.
+
+    Usage (from launch_remote_mcp.sh CLAUDE.md template):
+        curl -F "file=@/absolute/local/path" ${REMOTE_MCP_URL}/upload
+    """
+    dest = INPUT_DIR / file.filename
+    dest.parent.mkdir(parents=True, exist_ok=True)
+    content = await file.read()
+    dest.write_bytes(content)
+    return {"filename": file.filename, "path": str(dest), "size": len(content)}
+
+
+@app.get("/outputs/{name:path}")
+async def download_output(name: str):
+    """
+    Download a file previously written by an MCP tool.
+
+    Usage (from launch_remote_mcp.sh CLAUDE.md template):
+        wget ${REMOTE_MCP_URL}/outputs/<output_filename>
+    """
+    # Resolve and guard against path-traversal attacks
+    file_path = (OUTPUT_DIR / name).resolve()
+    if not str(file_path).startswith(str(OUTPUT_DIR.resolve())):
+        raise HTTPException(status_code=400, detail="Invalid file path")
+    if not file_path.is_file():
+        raise HTTPException(status_code=404, detail=f"Output file not found: {name}")
+    return FileResponse(str(file_path), filename=file_path.name)
+
+
+# Mount the MCP ASGI sub-app at /mcp.
+# path="/" because FastAPI strips the "/mcp" prefix before forwarding to the
+# sub-app, so the sub-app must handle requests at its own root.
+app.mount("/mcp", mcp.http_app(path="/"))
 
 if __name__ == "__main__":
-    mcp.run(
-        transport="http",
+    import uvicorn
+
+    uvicorn.run(
+        app,
         host="0.0.0.0",
         port=int(os.getenv("PORT", 7860)),
-        path="/mcp",
-    )
+    )