feat: Galaxy-SynBioCAD digital-kernel adapter + MCP discovery tools - #273
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LamaSu wants to merge 4 commits into
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feat: Galaxy-SynBioCAD digital-kernel adapter + MCP discovery tools#273LamaSu wants to merge 4 commits into
LamaSu wants to merge 4 commits into
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Exposes the brsynth/galaxytools synthetic-biology & metabolic-engineering suite (~50 tools: RetroPath2.0, rpTools, Selenzyme, PartsGenie, DNA-Bot, DNA Weaver, StrainDesign, OptDOE, iCFree, AMN) as a PCC digital kernel via kernel-sdk's DigitalKernelManifest + createKernelHandler. - catalog.json: deterministically generated from the Galaxy tool XMLs (63 tools, 491 typed input params, 87 outputs, 13 pipeline stages), each with a JSON-Schema input/output contract that agents pick from. - one catalog-driven executor over the Galaxy REST API + a mock-first transport; toWorkflowStep() composes tools into a mixed digital+physical DAG. - GalaxyRestClient verified live against galaxy-synbiocad.org (health, listTools, short-id -> toolshed tool_id resolution). 27/27 tests pass. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01S57C9JofbpCJA8y2i2oYgd
Adds three discovery tools — pcc_galaxy_synbiocad_stages / _list_tools / _tool_schema — that expose the @pcc/adapter-galaxy-synbiocad catalog (~50 synthetic-biology / metabolic-engineering tools with full JSON-Schema I/O) to any MCP client. Reads the local catalog, no network. 6 end-to-end smoke tests over the in-memory transport; full mcp-server suite green (77 tests). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01S57C9JofbpCJA8y2i2oYgd
- scripts/serve.mjs: node:http server for the kernel job handler. Answers the gateway touchstone dry-run with 2xx and runs real jobs (signed evidence bundle). - scripts/register-kernel.mjs: build manifest -> POST /api/kernels/register -> self-verify (builder self-auth via X-Agent-Id) against a PCC gateway. - README: corrected live-verification status + a deploy/register runbook. Serve wrapper locally verified end-to-end: GET / + dryRun + real retropath2 job all return 200; the dryRun path satisfies routes/kernel-marketplace runSmokeTest. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01S57C9JofbpCJA8y2i2oYgd
Proven end-to-end against pcc-gateway-staging: provision -> serve.mjs ->
cloudflared tunnel -> register -> verify -> status "verified" (kernel appears in
the marketplace listing). The /verify POST 400'd on an empty body when
content-type is application/json; send `{}`. Also documents that
BUILDER_AGENT_ID must equal the gateway operator_id (from /api/auth/provision)
for builder self-verify.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01S57C9JofbpCJA8y2i2oYgd
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Summary
Adds
@pcc/adapter-galaxy-synbiocad— a PCC digital-kernel adapter for theGalaxy-SynBioCAD tool suite (brsynth/galaxytools;
Faulon lab, Nature Communications 2022) —
plus MCP-server discovery tools that surface its catalog to any agent.
Galaxy-SynBioCAD is computational (retrosynthesis, FBA, enzyme selection, DNA design), so it
registers via kernel-sdk's
DigitalKernelManifest+createKernelHandler, not the physicalMachineAdapterpath. It composes with physical kernels: design a pathway → synthesize the DNA→ run it on an OT-2 (via
@pcc/adapter-pylabrobot) in one CWM DAG.What's in it
50a72b98— the adaptersrc/catalog.json— deterministically generated from the Galaxy tool XMLs byscripts/build_catalog.py: 63 tools, 491 typed input params, 87 outputs, 13 pipeline stages.Every tool ships a JSON-Schema (Draft-07)
input_schema/output_schema— themachine-readable menu agents pick from.
<expand macro>params resolved (StrainDesign),deprecated standalone wrappers flagged, dotted param paths (
adv.topx,sink.emptysink) thatmap 1:1 to Galaxy's
|nested-input convention.execute({tool_id, params})runs any tool over the GalaxyREST API (
GalaxyRestClient) or a deterministicMockGalaxyClient(mock-first, per PCC convention).toWorkflowStep(id)— the composition bridge: any tool → aDigitalWorkflowStep(carriesinputSchema/outputSchema/dependsOn) that composes with physical steps.72671234— MCP wiringpackages/mcp-server:pcc_galaxy_synbiocad_{stages, list_tools, tool_schema}— surface the catalog to any MCP client (local read, no network).Live verification (against galaxy-synbiocad.org — v21.09, 350 tools installed)
health()✅,listTools()✅ (350), 40/50 advertised tools present on the public server.(
toolshed.g2.bx.psu.edu/repos/tduigou/retropath2/retropath2/3.9.1+galaxy0), not the shortcatalog id
retropath2. AddedresolveServerToolId()(short → server's latest toolshed id,case-insensitive for
PartsGenie) and verified it live.Tests
tscclean.tscclean.tweetnacl, already in-repo via kernel-sdk → clean Gate-A).Honest gaps / not in scope
GalaxyRestClient's authenticated job-execution path is implemented-to-spec andmock-tested, but not yet run against a live server — that needs a Galaxy API key (anonymous
POST /api/histories→ 403).registerKernelis not called here — it requires a deployed HTTPS endpoint (thegateway runs a touchstone smoke test). The MCP wiring already makes the tools discoverable today.
🤖 Generated with Claude Code
https://claude.ai/code/session_01S57C9JofbpCJA8y2i2oYgd