upload_protocol

THE RISK

Medium Risk

Why upload_protocol needs a policy

Uploading a protocol file creates or modifies executable instructions on lab automation hardware. While not destructive (the upload is reversible via deletion or overwrite), it is a Write action that configures robot behavior.

From the tool's definition Tool uploads a protocol file to an Opentrons robot, which modifies robot state and configuration but does not irreversibly delete data. The description explicitly states 'Upload a protocol file', indicating file creation/modification on the robot.

Documented attack patterns abuse exactly the kind of access upload_protocol gives an agent:

POLICY

How to control upload_protocol

PolicyLayer is an MCP gateway — it sits between your AI agents and Opentrons MCP Server, and nothing reaches the server without passing your rules. This is the rule we recommend for upload_protocol:

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "upload_protocol": {
      "limits": [
        {
          "counter": "upload_protocol_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

upload_protocol stays usable, but capped — an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

Create a free account and register Opentrons MCP Server — nothing to install.
Add this policy — paste it, or build it visually.
Point your MCP client (Claude, Cursor, anything) at your gateway URL.

LIMIT THIS TOOL →

Free to start. No card required.

EXPLORE

Related tools and policies

More Opentrons MCP Server tools

Execute control_run Control run execution (play, pause, stop, resume) Execute home_robot Home robot axes or specific pipette Execute poll_error_endpoint_and_fix Fetch specific JSON error report and automatically fix protocols Execute create_run Create a new protocol run on the robot Write control_lights Turn robot lights on or off Read get_api_overview Get high-level overview of the Opentrons HTTP API structure and capabilities Read get_endpoint_details Get comprehensive details about a specific API endpoint Read get_protocols List all protocols stored on the robot

All 14 Opentrons MCP Server tools →

Write tools on other servers

M-Team MCP Server download_torrent YouTube MCP Server generate_video_title Android Forensics ADB MCP Server combine_reports 0xarchive web3_signup

Go deeper

The MCP Attack Database → Documented attack patterns against MCP deployments — and the policies that stop them.
Argument validation → Checking tool call arguments against schema and policy before they run.
Scoped token → Per-person credentials that grant a defined subset of servers and tools.
Rate Limiting MCP Tool Calls: A Practical Guide →
MCP Security: Why Prompt Guardrails Aren't Enough →

FAQ

Questions about upload_protocol

What does the upload_protocol tool do? +

Upload a protocol file to an Opentrons robot. It is categorised as a Write tool in the Opentrons MCP Server MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

How do I enforce a policy on upload_protocol? +

Register the Opentrons MCP Server MCP server in PolicyLayer and add a rule for upload_protocol: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Opentrons MCP Server. Nothing to install.

What risk level is upload_protocol? +

upload_protocol is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit upload_protocol? +

Yes. Add a rate_limit block to the upload_protocol rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.

How do I block upload_protocol completely? +

Set action: deny in the PolicyLayer policy for upload_protocol. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.

What MCP server provides upload_protocol? +

upload_protocol is provided by the Opentrons MCP Server MCP server (yerbymatey/opentrons-mcp). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.

Enforce policy on every Opentrons MCP Server tool call.

Start from Opentrons MCP Server, add the rest of your stack, and see everything your agents can call. Then put policy on all of it.

CHECK YOUR STACK →