Talk to the MCP over HTTP, because stdio cannot work where this runs

[adamjohnwright]

The live destination spawns node and speaks over a pipe. That works on a developer's machine and cannot work in the deployed container:

$ docker exec biochat_beta_guest sh -c 'command -v node || echo NO NODE'
NO NODE

$ docker inspect biochat_beta_guest --format '{{range .HostConfig.Binds}}...'
  /home/awright/git/reactome_chatbot/config.yml:/app/config.yml
  /home/awright/git/reactome_chatbot/embeddings:/app/embeddings

The image is Python, has no node, and doesn't mount reactome-mcp. REACTOME_MCP_SERVER can never be satisfied there.

The feature worked on every machine it was tested on and none that it ships to — the same shape as the streaming bug fixed in #218, and found the same way: by asking where it actually runs rather than where it was written.

Two transports

variable	transport	where
REACTOME_MCP_URL	Streamable HTTP	anywhere, including the container
REACTOME_MCP_SERVER	stdio, spawning node	a developer's machine only

REACTOME_MCP_URL wins when both are set. stdio stays for local development, where the repo and node both exist.

create_mcp_tools already took a ToolCaller Protocol, so the HTTP client drops in beside the stdio one with no change to the tools or the graph.

Two protocol details, both pinned by tests

Easy to get wrong, and neither fails in a way that points at the cause:

• The session id arrives in the mcp-session-id response header of initialize and must be resent on every later request. Omit it and the server answers 400.
• Replies come back SSE-framed (event: message / data: {...}) rather than as bare JSON, even for a single reply to a POST. Parsing the body as JSON gets a decode error on text that is perfectly valid. The last data: line wins, since a stream may carry progress notifications first.

Verified against a real server

End to end, and through the compiled graph with a callback handler:

tools over HTTP : 5
species         : **Total:** 96
answer          : Reactome covers a total of 96 species...
streamed        : 46 tokens

8 tests against httpx.MockTransport; full suite passes; ruff, ruff format, mypy clean across 103 files.

What this unblocks

Beta can now have the live destination. Run reactome-mcp as a sibling container and set REACTOME_MCP_URL — no node in the chatbot image, nothing mounted, no change to how the chatbot is built.

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