Adopt galaxy-mcp code-mode (draft, needs live testing)#118
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Introduces a getDiscoveryMode() helper that reads galaxy.discoveryMode from ~/.loom/config.json -- "code" by default, "full" to opt back into the legacy named-tool catalog. Malformed values fall through to "code" so a hand-edited typo can't silently re-bloat the per-turn token budget. No call sites yet; the actual mcp.json wiring lands in the next commit.
bin/loom.js seeds mcp.json with the galaxy-mcp[code-mode] extra and GALAXY_MCP_DISCOVERY_MODE=code when credentials are present. The profiles syncMcpConfig path mirrors the same shape on every profile save/switch, defensively rewriting args so older installs that pre-date discovery mode get the [code-mode] extra on next reconnect instead of hitting the server's RuntimeError at import time. The discovery mode is read from config so a "full" override flows through both paths.
The agent now sees three meta-tools (search / get_schema / run_galaxy_tool) instead of the ~40 named ones, so the system-prompt block and the topic docs need to teach that surface explicitly: search to discover, get_schema before the first call so parameter names aren't guessed, run_galaxy_tool to invoke. Routing logic (heavy -> Galaxy, light -> local, UDT for glue) is unchanged -- only the tool-call surface flips. UDT lifecycle, IWC search, and invocation-recording guidance now read via the meta-tool shape.
Adds a gotchas section explaining the discovery-mode trade-off (token budget vs search quality) and the one-liner config edit (galaxy.discoveryMode = "full") that flips Loom back to the legacy named-tool surface. Standalone commit so it can be cherry-picked or reverted without touching the wiring.
Auto-merge across release/install pipeline, error humanizer, version check, and the pi.dev rebrand. No code-mode logic affected.
bin/loom.js (initial mcp.json template) and profiles.ts (syncMcpConfig rewrite) both build the uvx package spec from the discovery mode using identical `galaxy-mcp[code-mode]>=1.4.0` literals. Lifting the spec into a tiny helper next to getDiscoveryMode means the version constraint lives in one place; if we bump it later, no risk of one site drifting from the other.
Code-mode routes every Galaxy call through one meta-tool,
galaxy_run_galaxy_tool({ name, args }), so the tool_* events all carry the
meta-tool name instead of the real tool. That silently broke the bits that key
off the tool name: the galaxy_create_history hook never set currentHistoryId
(so /status loses its history line and the init-gate nags), the galaxy_connect
hooks went dead, and -- worse -- the credential redaction stopped firing on
connect/set_profile, so an api_key could land in activity.jsonl in plaintext.
Added a small resolver that recovers the underlying tool from the meta-tool args
(present on tool_execution_start, remembered per toolCallId for the end/result
hooks). Named mode is unchanged. Redaction now resolves the same way before the
whole-object guard, and the status label shows the real tool name in code-mode.
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Draft -- not ready to merge. Needs live-Galaxy verification (see below).
Summary
Switches Loom's Galaxy MCP integration to galaxy-mcp's code-mode surface
to cut ~10-15k tokens per turn off the request. Instead of shipping the
~40 named tools (history/dataset/job/tool/workflow/IWC/user-tool ops) as
the full catalog, the server collapses to three meta-tools (
search,get_schema,run_galaxy_tool) toggled byGALAXY_MCP_DISCOVERY_MODE=code.Server side already shipped in galaxy-mcp 1.4.0; this PR is the Loom-side
wiring + prompt rewrite + opt-out knob.
What changed
bin/loom.jsseedsmcp.jsonwithgalaxy-mcp[code-mode]>=1.4.0andGALAXY_MCP_DISCOVERY_MODE=codewhen credentials are present.extensions/loom/profiles.ts:syncMcpConfigmirrors the same shape onevery profile save/switch and defensively rewrites
argsso oldinstalls that pre-date discovery mode get the
[code-mode]extra onnext reconnect (otherwise the server throws RuntimeError at import).
shared/loom-config.{js,d.ts}gain agalaxy.discoveryModefield(default
"code", opt back into"full"to restore the named-toolcatalog). Malformed values fall through to
"code".extensions/loom/context.tsGalaxy guidance block rewritten to teachthe meta-tool surface (
search->get_schema->run_galaxy_tool),including UDT lifecycle and IWC search. Routing logic (heavy ->
Galaxy, light -> local, UDT for glue) unchanged.
docs/agent/galaxy-routing.md+docs/agent/commands.mdupdated tomatch.
docs/agent/gotchas.mddocuments the"full"opt-out.tests/discovery-mode.test.tscovers the defaulter.Why draft
Everything below still needs to happen on a live Galaxy server:
tools appear in the MCP handshake (
search,get_schema,run_galaxy_tool).search->get_schema->run_galaxy_tool({ name: "get_histories" })and gets back a sensible answer.
short question. Expectation: 10-15k drop. Numbers go in this PR
description when collected.
realistic queries (alignment, variant calling, IWC RNA-seq).
"full"opt-out path still works for users who hita search-quality miss.
Test plan (local, already passing)
npm run typecheckcleannpx tsc --noEmitinapp/cleantests/discovery-mode.test.ts5/5tests/profiles.test.ts13/13 (touched bysyncMcpConfig)npm test-- 181 pass, 2 failures inagent-manager.test.tsare pre-existing onmain(Electron mockissue, unrelated)
Out of scope
gtn_*,skills_fetch,galaxy_invocation_*) -- registered viapi.registerTool, not MCP,so they don't ride this transform. ~1k tokens combined; not worth a
separate code-mode pass.