test: cover deeply nested evidence traversal in the reference plugin

[cmungall]

What

Adds a test suite verifying that ReferenceValidationPlugin recursively discovers and validates evidence nested 2+ levels below the tree root, e.g.:

Community (root) -> MemberRecord  -> EvidenceItem (reference + snippet)
Community (root) -> Interaction   -> EvidenceItem

The existing test_schema.yaml only exercised 1-level nesting (Statement -> Evidence). This mirrors real-world schemas like CommunityMech (MicrobialCommunity -> TaxonomicComposition -> EvidenceItem).

Coverage

• process() path: traversal through members and interactions, multiple members × multiple evidence, valid snippets pass / invalid snippets caught.
• Field detection: implements annotations (reference + excerpt) discovered on EvidenceItem at depth; root class correctly has none.
• Full linkml.validator.Validator pipeline (the same path the CLI validate data uses).

Why a separate PR

These tests are independent of the full-text/PDF framework in #48 (they don't touch that subsystem) and pass against the current plugin on main — the recursive traversal already works; this locks in that behavior. Keeping them out of #48 keeps that PR focused.

10 tests, all green (pytest + mypy + ruff). New fixtures: a deep-nesting schema and valid/invalid data files.

Ref: CultureBotAI/CommunityMech#3

🤖 Generated with Claude Code

[claude]

Claude finished @cmungall's task in 1m 30s —— View job

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Review: deep nested evidence traversal tests

• Read the new test files and fixtures
• Read the plugin under test (reference_validation_plugin.py)
• Assess code quality, correctness, coverage
• Post review feedback

This is a clean, well-documented, test-only PR that locks in recursive traversal behavior already present on main. I traced the new tests against ReferenceValidationPlugin._validate_instance and the fixtures — the wiring is correct:

• Community → members[MemberRecord] → evidence[EvidenceItem] recursion is handled by the isinstance(value, list) branch (plugin lines 265–273), and EvidenceItem exposes reference (implements: linkml:authoritative_reference) + snippet (implements: linkml:excerpt), which the legacy-URI detection in _find_reference_fields/_find_excerpt_fields picks up. ✅
• Fixtures back the assertions: PMID_TEST001.txt contains "Protein X functions in cell cycle regulation" and "plays a critical role in DNA repair"; PMID_TEST002.txt contains "Protein Y inhibits apoptosis" — so the valid-data test legitimately expects 0 errors, and the fabricated snippets in the invalid data legitimately fail. ✅
• Tests are hermetic: references are pre-seeded into a tmp_path cache and rate_limit_delay=0.0, so no network. ✅

Suggestions (all non-blocking)

1. Duplicated cache-seeding boilerplate. The fixture-copy loop appears 3× — in the plugin_with_fixtures fixture (lines 59–62) and inlined in both full-pipeline tests (lines 318–321, 375–378). Worth extracting a small helper to keep them in sync:

def _seed_cache(cache_dir: Path) -> None:
    for pattern in ("*.md", "*.txt"):
        for f in FIXTURES_DIR.glob(pattern):
            (cache_dir / f.name).write_text(f.read_text())

Fix this →

2. "Bug reproduction" wording is slightly misleading. Comments call these "the core bug reproduction" / "the actual bug" (lines 105, 113–115), but the PR body states the behavior already works on main. These are regression guards, not repros — consider rewording so a future reader doesn't go hunting for a live bug.

3. Coverage gap vs. the PR's "2+ levels" claim. Every test nests exactly 2 levels (Community → Container → EvidenceItem). To truly cover "2+", consider one case at 3 levels (e.g. Community → MemberRecord → sub-container → EvidenceItem), which is closer to arbitrarily-deep real schemas. Optional, but it would make the title literally true.

4. No mixed valid+invalid-in-one-tree case. test_deep_nesting_multiple_members_multiple_evidence uses all-invalid snippets and asserts >= 3. A tree that mixes valid and invalid evidence and asserts exactly the invalid count would guard against false positives on the valid siblings (the >= assertions can't catch over-reporting). Minor.

5. FIXTURES_DIR is implicitly required. The plugin_with_fixtures fixture silently no-ops if tests/fixtures/ were ever empty/missing, which would turn the == 0 valid-data assertion into a vacuous pass (no cache → ... actually it'd fail to find refs). Not a real problem today since the dir is populated, just noting the implicit dependency.

Verdict

Solid, hermetic, well-isolated regression coverage that mirrors the real CommunityMech pattern. None of the above blocks merge — they're polish. Nice work keeping it decoupled from #48.

Note: I was unable to execute pytest/mypy/ruff in this environment (command approval), so the green-build claim rests on CI. I verified correctness by reading the plugin, schema, data, and fixtures.