feat: tolerate JSON-encoded NodeFilter in MCP search/find/neighbors

[HumanBean17]

Scope

Allows weak LLM / MCP clients to pass filter as a JSON-encoded string (serialized NodeFilter) without failing FastMCP JSON-RPC validation (params/filter must be object). Standalone robustness change (no linked plan file).

What Changed

• Added _coerce_filter() in mcp_v2.py — strict json.loads, decoded value must be a JSON object; whitespace-only string treated as no filter.
• Widened search_v2 / find_v2 / neighbors_v2 so filter may be str; after coercion, find_v2 maps empty filter to {}.
• Widened filter parameter types on search / find / neighbors in server.py, updated Field descriptions, noted string filters in _INSTRUCTIONS.
• Added five tests in tests/test_mcp_v2.py; updated MCP tool table and note in README.md.

Semantics / Non-Goals

• No ontology bump, no Kuzu or LanceDB schema changes, no re-index requirement.
• No Python-literal parsing (e.g. single-quoted dicts); JSON only.
• No changes to other tool parameters (path_contains, edge_types, ids, etc.).

Validation

Lint

• ruff check . — clean on branch before push; not re-run during PR open.

Tests

• pytest tests — author confirms green; not re-run during PR open (last full run on branch: 330 passed, 7 skipped).

Sentinel checks

• git diff master...HEAD --name-only → README.md, mcp_v2.py, server.py, tests/test_mcp_v2.py only.

Manual evidence

• Weak MCP clients sending filter as a string (e.g. {"exclude_roles":["CONTROLLER"]}) should pass transport validation; decoding and NodeFilter validation are covered by unit tests.

Out of Scope Confirmed

Did not implement:

• Tier 2 incremental rebuild / related proposes.
• Graph builder, ranking, java_ontology.py, or fixture-only special cases in production code.
• CLI (user-rag) feature work beyond README tool docs.

Definition of Done

• All listed deliverables for this PR are shipped.
• Required lint/tests pass locally with recorded command output.
• Sentinel checks produce expected results.
• Only in-scope files are modified.
• PR description includes scope, validation, and manual evidence.
• PR targets master with agreed title and branch naming.

[HumanBean17]

Review: PR #55 — tolerate JSON-encoded NodeFilter in MCP search/find/neighbors

Verdict: Approved ✅

Tightly scoped weak-model tolerance fix. _coerce_filter is a 20-line helper in mcp_v2.py, the filter parameter on all three tools accepts dict | str | null at the FastMCP boundary (and the NodeFilter Python type stays internal — the wire schema is now structurally minimal), and 5 regression tests lock both the happy paths and the failure paths. No ontology bump, no schema delta, surface stays at 4. The implementation matches what we discussed with one well-judged refinement (whitespace-only string → no filter).

Scope discipline

Sentinel	Status
ONTOLOGY_VERSION / SCHEMA_VERSION	✅ 0 hits
CREATE NODE TABLE / CREATE REL TABLE / DROP TABLE	✅ 0 hits
@mcp.tool count in server.py	✅ 4 (unchanged)
Files touched	✅ exactly what the PR description claims: README.md, mcp_v2.py, server.py, tests/test_mcp_v2.py

What landed (verified)

#	Deliverable	Verified
1	_coerce_filter helper handles None, NodeFilter, dict (passthrough), str (json.loads → must-be-dict), invalid types	✅ mcp_v2.py:54-71 — strict json.loads, decoded value asserted to be dict, whitespace-only string short-circuits to None, raises ValueError with "JSON" in message on failure
2	search_v2 / find_v2 / neighbors_v2 accept filter: ... | str	✅ all 3 widened, all 3 route through _coerce_filter before NodeFilter.model_validate
3	find_v2 empty-filter mapping: _coerce_filter("") → None → {} (because find requires a filter)	✅ mcp_v2.py:399-401 — if raw_filter is None: raw_filter = {} after coercion
4	FastMCP-level Field types widened to dict[str, Any] | str | None (or ... | str for required find) — keeps NodeFilter out of the wire schema	✅ verified the actual emitted JSON Schema: search.filter is {"anyOf": [{"type":"object"}, {"type":"string"}, {"type":"null"}]}; find.filter is {"anyOf": [{"type":"object"}, {"type":"string"}]} (no null because required); neighbors.filter matches search. No $ref to NodeFilter — that's the structural fix that should reduce Qwen's double-encoding tendency on the optional cases
5	_INSTRUCTIONS mentions stringified filters	✅ server.py:23 ("NodeFilter \filter` arguments may be passed as JSON-encoded strings."`)
6	Tests	✅ 5 tests, not the 2 promised — bonus coverage
7	README tool table updated	✅ filter: NodeFilter | str | None in all 3 rows + new bullet below the table

Tests added (tests/test_mcp_v2.py:308-353)

Test	Asserts
test_search_filter_accepts_json_string	search_v2(filter=dict) and search_v2(filter='{"...":"..."}') produce identical .results
test_search_filter_empty_string_treated_as_none	filter="" and filter=" " both equivalent to filter=None (whitespace-only)
test_find_filter_accepts_json_string	dict-vs-string parity for find_v2
test_neighbors_filter_accepts_json_string	dict-vs-string parity for neighbors_v2
test_filter_invalid_json_returns_failure	malformed {not json → success=False, "JSON" in message

This is the right test matrix. Both arms of the truth table for each tool, plus the malformed-input path, plus the empty-string edge case.

Notes that earned my trust

• Schema flattening done right. The mcp_v2.search_v2 Python signature still has NodeFilter | dict | str | None (so internal callers retain type help), but the FastMCP-exposed Field type at server.py is just dict | str | None. That's the clean separation: rich types internally, structurally minimal types on the wire. The model-facing schema dropped from 3-branch with $ref to 3-branch with primitives only — and crucially, no nested $ref, which was the actual structural cue that triggered Qwen's stringification heuristic.
• _coerce_filter raises ValueError, not ValidationError. That's the right choice: the existing tool bodies have except Exception as exc: return ...Output(success=False, message=str(exc)) for non-validation errors. Malformed JSON should be a "user error" returning success=False with a helpful message, not a transport-layer rejection. The test_filter_invalid_json_returns_failure test confirms this contract.
• Whitespace-only string → None (mcp_v2.py:60-62). Models occasionally emit " " or "" when they want "no filter" but feel obligated to send something for an anyOf parameter. Treating that as None is the gentle correct behaviour.
• json.loads strictness preserved. No eval, no Python-literal parsing, no fallback to ast.literal_eval — the PR explicitly calls this out as a non-goal. That's correct: lax parsers create their own footguns (e.g. silently accepting '{...}' with single quotes when the model is one tier lower than Qwen).
• find_v2 empty-filter promotion (mcp_v2.py:399-401). When _coerce_filter returns None (whitespace string), find_v2 promotes to {} because its contract is "filter is required." NodeFilter() with all-None fields is the "match anything" sentinel. Subtle but correct — would be wrong to raise here since the user did supply a filter argument, just an empty one.

Observations (non-blocking, none are merge-blockers)

1. _INSTRUCTIONS doesn't tell the model to prefer objects over strings (server.py:23). The current copy reads "NodeFilter filter arguments may be passed as JSON-encoded strings." — that's a permissive statement, but a weak model reading it may interpret it as a recommendation. Consider sharpening to: "NodeFilter filter is a JSON object (preferred); a JSON-encoded string is also accepted as a fallback." Tiny prompt-engineering nudge to keep Claude/GPT on the fast path while keeping the Qwen escape hatch open.

2. Same nudge applies to the per-Field descriptions (server.py:296-300, 318-322, 362-366). They currently say "...; a JSON-encoded string is also accepted" — append "(prefer the object form)" or similar. Defer to a future copy pass.

3. No test for filter as a JSON-encoded null (i.e. filter='"null"' or filter="null"). After json.loads("null") → None, the _coerce_filter would hit the not isinstance(decoded, dict) branch and raise ValueError(filter must decode to a JSON object, got NoneType). That's defensible behaviour, but a 3-line test asserting it would lock the contract. (Alternative: special-case decoded is None to return None — also defensible. Either way, document it.)

4. find_v2 empty-filter promotion is implicit (mcp_v2.py:399-401). The PR description doesn't mention this contract change ("find accepts whitespace string as {}"). Worth a one-line bullet in the README's new sentence — something like "For find, an empty/whitespace string is equivalent to filter={}." Otherwise users reading the README may not know the special case exists.

5. _coerce_filter returns a union type that callers re-narrow (NodeFilter | dict | None). Each caller then runs if not isinstance(raw_filter, NodeFilter): NodeFilter.model_validate(raw_filter). Fine, but a slightly cleaner shape would be to have _coerce_filter return NodeFilter | None directly (i.e. always do the model_validate inside the helper). That eliminates the duplicate guard at each callsite. Refactor in a future cleanup pass — non-blocking.

6. README filter: NodeFilter | str | None is accurate but the NodeFilter reference is documentation-shorthand — the actual wire type at the FastMCP boundary is dict | str | None. Most readers will understand, but a careful pedant could read NodeFilter as "you must construct a Pydantic model client-side". A footnote (NodeFilter = JSON object matching the NodeFilter schema) would be airtight. Trivial.

7. Tests use monkeypatch.setattr("mcp_v2.run_search", ...) for search cases but rely on real kuzu_graph for find/neighbors. That's the right asymmetry (search needs LanceDB which isn't available in test env; find/neighbors only need Kuzu which is fixture-loaded). Worth noting because the malformed-JSON test (test_filter_invalid_json_returns_failure) could in principle target find or neighbors and exercise a non-mocked path — the monkeypatch isn't strictly needed there since the failure happens before any backend call. Not worth changing now.

Plan deltas needed

None — this PR has no linked plan. The PR-description "Definition of Done" items map cleanly to what shipped.

Bonus catches

• The structural fix (dropping NodeFilter from the wire-level Field type) was implemented correctly even though it wasn't explicit in the PR description. This is the load-bearing change for actually fixing the Qwen behaviour — without it, the anyOf + $ref + null shape that triggers the stringification heuristic would still be present even with the runtime _coerce_filter workaround. Both layers needed; both shipped.
• Test coverage went 2 → 5 (3 dict-vs-string parity + 1 empty-string + 1 malformed). The two extras (empty_string_treated_as_none and invalid_json_returns_failure) are exactly the right edge cases.
• 5 new tests + 1 from PR Sync MCP v2 docs, neighbors edge_types validation, venv cursor rule #54 (test_neighbors_empty_edge_types_rejected) + 1 PR-V2-4 PTY failure still red = expected suite count: master 323 passed, 7 skipped, 1 failed → branch 328 passed, 7 skipped, 1 failed. PR description claims 330 passed, 7 skipped from author env — close to my expected math; the +2 difference is likely a LANCEDB_MCP_RUN_HEAVY=1 toggle on author's box that unskips 2 of the 7. Either way, math sanity-checks.

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Ready to merge. After this lands, validate the original Qwen Code workflow that motivated the fix — re-run the search invocation that originally failed and confirm it now works whether Qwen sends filter as a string or as an object. If Qwen reverts to sending objects (because the schema simplification removed the structural cue that pushed it to strings), that's the strongest possible confirmation that #1 of my earlier recommendation (flatten the schema) is doing the heavy lifting and _coerce_filter is just the safety net.

Suggested follow-up backlog (still PR-E1 candidates, none blocking):

• Sharpen _INSTRUCTIONS and Field(description=...) to prefer objects (Notes AST by Opus #1, Tier 1 completion plan + proposals (B2a + B4 + B5) #2)
• Document find whitespace-string → {} semantics in README (Notes Add per-PR Cursor task prompts for Tier 1 completion #4)
• One test for filter="null" (Notes Add Cursor rules and agent settings for CLI agents #3)
• PTY EIO handling (carried from PR-V2-4)
• LANCEDB_MCP_ALLOW_REFRESH hint vs CLI behaviour mismatch (carried from PR Sync MCP v2 docs, neighbors edge_types validation, venv cursor rule #54)
• Literal[...] types on direction / kind / table (carried from PR Sync MCP v2 docs, neighbors edge_types validation, venv cursor rule #54)