feat(mcp): ensure_kb + ground_paper grounding tools (+ fastmcp 3.x test fix)#28
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…reen baseline) fastmcp 3.2.4 removed mcp._tool_manager; the @mcp.tool() functions remain directly callable at module level. Replace _tool_manager._tools[name].fn access with a module-attr lookup (_tool_fn) and mcp._list_tools() for enumeration; accommodate generate_report's new message_id kwarg in the fake engine; refresh stale tool-count constants (15->49; ==->>= for the non-exhaustive EXPECTED_TOOLS). 8 failing -> 21 passing. Pre-existing issue, surfaced while adding grounding tools. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Two thin MCP tools for ASB grounding, composing existing tools: - ensure_kb(doi, mode='paper'): idempotently create + ingest a per-paper KB named asb-paper-<doi> (matches the ASB binder slug). Skips re-ingest when the KB already has chunks. Reuses create_knowledge_base + add_dois_to_kb. - ground_paper(doi, question, tier='paper'|'si'): ensure_kb, then a RAG query (generate_report) scoped to that KB; tier='si' steers toward the SI. Both degrade gracefully to _json_error; registered in _TOOL_NAMES. 14 new tests. Perspicacite side of the asb-skill-collections grounding consolidation: /ground and the binder can now install + query a skill's source-paper KB via the MCP. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
lfnothias
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Jun 23, 2026
PR #28 added the ensure_kb and ground_paper MCP tools but did not add their required-argument fixtures to _TOOL_ARGS, so test_tool_inventory invoked them with no args and raised TypeError, failing CI. Add the missing entries using the existing fake-DOI convention. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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What
Adds the Perspicacité side of the ASB grounding consolidation — two thin MCP tools so an agent (via the asb-skill-collections
/groundcommand or the bundled binder) can install + query a skill's source-paper KB on demand:ensure_kb(doi, mode="paper")— idempotently create + ingest a per-paper KB namedasb-paper-<doi>(slug matches the ASB binder convention exactly). Returnsstatus: "exists"(skips re-ingest when the KB already has chunks) or"created"with chunk counts. Reusescreate_knowledge_base+add_dois_to_kb.ground_paper(doi, question, tier="paper"|"si")—ensure_kb, then a RAG query (generate_report) scoped to that paper's KB.tier="si"steers retrieval toward the supplementary information. Returns{kb_slug, answer, sources}.Both are thin compositions of existing tools, degrade gracefully to
_json_error(never raise), and are registered in_TOOL_NAMES.Why
This is the MCP-owned, on-first-query grounding path designed in the asb-skill-collections consolidation (asb side already merged: HolobiomicsLab/asb-skill-collections#5, #6). The asb packs ship the
/groundcommand + binder; these tools are what make the KB "auto-install + query via the MCP" in-session.Commits
test(mcp)— fastmcp 3.x test migration (separate commit). The MCP test suite was red at baseline (8/21 failing):fastmcp3.2.4 removedmcp._tool_manager, which the tests still used. Migrated to module-attr tool access (_tool_fn) +mcp._list_tools()enumeration; accommodatedgenerate_report's newmessage_idkwarg; refreshed stale tool-count constants. 8 failing → 21 passing. (Pre-existing issue, surfaced while adding these tools.)feat(mcp)— the two tools + 14 new tests (idempotency, create path, zero-chunk re-ingest, graceful failure, SI hint, error propagation).Suite: 35 passed (
tests/test_mcp_server.py, via.venv).Notes / review points
generate_reporthas nocontextparam, so thetier="si"hint is prepended to the query string rather than passed separately. If you'd prefer a first-classcontext/SI-steering arg ongenerate_report, say so and I'll wire it.ensure_kb'smodeparam is reserved (currently unused) to match the agreed signature./ground, but if you want async/background ingest, that's a follow-up.🤖 Generated with Claude Code