LLX Agent MCP Implementation
Provides tools for querying Azure Cosmos DB collections and documents using the MongoDB API, enabling read-only database interactions server-side.
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@LLX Agent MCP Implementationfind today's news about AI"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
LLX Agent — MCP Skills Library
A confidential "skills library": employees use Codex locally, which auto-calls these skills over MCP. The skill code/data run in the cloud and are never downloaded locally, so employees can use the skills but cannot read them.
Full architecture & the 7-phase rollout plan: see
../workflow/mcp structure.md. This README is the operational guide (how to run, change, redeploy); that doc explains the why.
Status: ✅ Live on Azure (since 2026-06-29)
Endpoint |
|
Skills | each skill is its own folder in |
Source (public GitHub) |
|
Azure | RG |
Related MCP server: MCP Practice
How employees connect (Codex)
Each employee needs Codex (≥ 0.144, which can connect to a remote MCP server
directly). Two files go in their .codex folder:
Windows:
C:\Users\<username>\.codex\Mac/Linux:
~/.codex/
File 1 — config.toml (connects to the cloud)
Add this block to their Codex config file — it holds only the URL, no skill content:
[mcp_servers.llx-skills]
url = "https://llx-mcp.delightfuldesert-f5bbaa56.eastus.azurecontainerapps.io/mcp"
startup_timeout_sec = 60
tool_timeout_sec = 120Windows users, also add these two top-level lines (outside any [section]
— e.g. above the block above): some skills (e.g. crf-annotation) need Codex
to run local commands on your own machine, and on Windows, Codex's sandbox can
otherwise silently block this (CreateProcessAsUserW failed: Access is denied) without ever asking you — a known Codex-on-Windows sandbox bug. These
two lines make it ask for permission instead of auto-refusing:
approval_policy = "on-request"
approvals_reviewer = "user"(Copy-paste ready template with both blocks: codex-config.toml.)
Why
urland not acommand/npx mcp-remotebridge: Codex ≥ 0.144 speaks streamable HTTP directly. The npx bridge cold-started slowly and intermittently dropped the handshake; the directurlis more reliable. The timeouts give the cloud container time to wake from idle.
File 2 — AGENTS.md (forces Codex to always use the cloud)
Copy AGENTS.md to ~/.codex/AGENTS.md. This file is required.
Without it, a generic request like "list the database collections" can make Codex
query a local database it happens to find nearby, instead of the cloud skills.
AGENTS.md is a standing company rule that tells Codex: for any company data/skill
request, always use the llx-skills cloud tools — never local files. (Verified:
with the rule in place, even a vague prompt from a folder full of local DB configs
correctly routes to the cloud.)
Then
Save both files, restart Codex, and just ask naturally — Codex auto-calls the matching skill in the cloud.
Skills
Each skill is its own folder in server/skills/ (Claude Agent Skills
layout: SKILL.md + optional *.py code tools). server/skill_loader.py
auto-loads every folder at startup — adding a skill = new folder with a
SKILL.md (copy _example/ as a template) — nothing else to edit.
Current skills:
Folder | What it does |
| Explains what data is in the company Cosmos DB (NL + a |
| Protocol → full itemized clinical-data cost-estimate table (NL only) |
| Protocol → TA/TE/TV/TS/TI trial-design domains per SDTMIG v3.4 (NL only) |
| Blank CRF → SDTM Domain/Variable mapping + annotation placement (NL + 12 code tools wrapping an embedded SDTMIG/pattern knowledge base) |
Project layout
server/
main.py # entry point — auto-loads every skill (rarely touch)
app.py # the shared MCP server instance
skill_loader.py # loads each skills/ folder's SKILL.md + *.py
llm.py # cloud LLM call wrapper — runs a NL skill's instructions
skills/ # ONE FOLDER PER SKILL ← add / edit skills here
requirements.txt # Python dependencies
Dockerfile # how Azure packages the server
codex-config.toml # employee client config (points at the cloud endpoint)
AGENTS.md # employee Codex rule — always use the cloud, never localChange a skill & redeploy
Editing GitHub does NOT auto-update Azure. The full loop:
Add or edit a file in
server/skills/, commit, and push to GitHub.Open Azure Cloud Shell: go to https://portal.azure.com, click the
>_icon in the top bar, choose Bash.Run these two commands (no local Docker / CLI needed):
az acr build --registry cafa6fd6c51facr --image llx-mcp:v8 https://github.com/Cathylixi/LLX-Agent-MCP-Implementation.git
az containerapp update --name llx-mcp --resource-group LLXSolutions --image cafa6fd6c51facr.azurecr.io/llx-mcp:v8(bump v8 to whatever the next tag is — see the tag note below)
Why
update(notup):updateonly swaps the image and keeps the existing ingress and secrets/env vars (like the databaseMONGO_URI). Use it for all redeploys after the first one.Why manual: auto-deploy needs a "service principal", which the org account
ai@llxsolutions.comisn't allowed to create — so we build & deploy by hand.Tag note: each redeploy bumps the tag (
:v2,:v3, … currently:v7) so there's a rollback point if a build turns out broken — check the new revision's status in Container Apps → llx-mcp → Revisions and replicas before assuming a deploy worked;provisioningState: Succeededon thecontainerapp updatecommand does NOT by itself mean the new revision came up healthy (it can still crash-loop and fail to become the active revision).
requirements.txtgotcha:mcpis pinned to1.28.1. Don't remove the version pin — an unpinnedmcpinstall once pulled inmcp 2.0.0, which restructured the package and brokefrom mcp.server.fastmcp import FastMCPinapp.py, crash-looping every replica withModuleNotFoundError: No module named 'mcp.server.fastmcp'until it was re-pinned.
Connecting a database (Azure Cosmos DB)
The server can query the company database server-side and return only the results, so employees never see the database address or password. Connected since 2026-06-29.
Database: Azure Cosmos DB (MongoDB API), database
llxdocument, clusterllx-solutions-msft5.Driver:
pymongo[srv]inrequirements.txt(the+srvURI needs dnspython).Skill: the database skill is the
describe-databasefolder inserver/skills/(itstools.pyreads the connection string from theMONGO_URIenv var and queries the DB server-side).Full write-up:
../workflow/connecting database.md.
Golden rules: (1) the connection string is a secret — it lives in an encrypted Azure secret, never in the code/GitHub; (2) expose specific, read-only query skills, never a generic "run any SQL" skill.
How it was deployed (run in Azure Cloud Shell)
# 1. build the image (includes pymongo[srv])
az acr build --registry cafa6fd6c51facr --image llx-mcp:v2 https://github.com/Cathylixi/LLX-Agent-MCP-Implementation.git
# 2. store the connection string as an encrypted secret
# (copy the value from AI-for-Word/backend/.env line 8; keep the single quotes)
az containerapp secret set --name llx-mcp --resource-group LLXSolutions --secrets mongo-uri='<CONNECTION_STRING>'
# 3. deploy the image AND wire the secret to the MONGO_URI env var
az containerapp update --name llx-mcp --resource-group LLXSolutions --image cafa6fd6c51facr.azurecr.io/llx-mcp:v2 --set-env-vars MONGO_URI=secretref:mongo-uriTo change the connection string later, re-run step 2 only (then restart a revision). To add new DB query skills, edit
main.pyand redeploy (steps 1 + 3).If the connection times out: open the Cosmos DB in the portal → Networking → allow access from Azure services / public Azure datacenters.
Verify it's working
After deploying (or any time), check the live server with a quick MCP client:
pip install mcp # once
python - <<'PY'
import asyncio
from mcp import ClientSession
from mcp.client.streamable_http import streamablehttp_client
URL = "https://llx-mcp.delightfuldesert-f5bbaa56.eastus.azurecontainerapps.io/mcp"
async def main():
async with streamablehttp_client(URL) as (r, w, _):
async with ClientSession(r, w) as s:
await s.initialize()
print([t.name for t in (await s.list_tools()).tools])
print((await s.call_tool("db_list_collections", {})).content[0].text)
asyncio.run(main())
PYExpect it to print the available tool names and the database collections. (Or in
Codex with the config.toml above, just ask it to list the collections.)
⚠️ Security gap (fix before real data)
The endpoint has no authentication — anyone with the URL can call it.
✅ Outsiders cannot read the skill code/prompts (those stay server-side).
⚠️ But they can call the skills, get the results, see tool names, and burn cost.
Fine for the fake-data demo. Once skills return real confidential data, add token auth so only employees can call them.
Local development (optional)
To test changes on your own machine before deploying:
pip install -r requirements.txt
python server/main.py # serves at http://127.0.0.1:8000/mcpTemporarily point your Codex config.toml at http://127.0.0.1:8000/mcp (same
block, just swap the URL), open Codex, and try a skill. Restart the server after
each code change (a stale server keeps the old port 8000 and your new skill won't
show up).
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