Fix fix_boolean_patterns recursion under nested combinators in if (#187)

[adamjtaylor]

Summary

• scripts/linkml_to_flat_synapse_jsonschema.py::fix_boolean_patterns() only rewrote pattern: "^true$" → const: true when the if clause had properties directly. It did not descend into if.anyOf[], if.oneOf[], if.allOf[], or if.not — so LinkML rules emitted as if: { anyOf: [...] } shipped with pattern: "^true$" against boolean fields. pattern is a string-only keyword, so those branches silently never matched and the conditional required never fired (e.g. PANEL_NAME was not enforced when PROTEIN_MEASURED: true).
• Extends the walk so every subschema reachable inside an if clause is visited (anyOf, oneOf, allOf, not, and nested if/then/else), applying the same boolean-pattern → const rewrite wherever a properties map is found.
• Adds six unit tests covering direct if.properties, if.anyOf, if.oneOf, if.not, true/false variants, and a regression test confirming string-typed patterns are left alone.

Fixes #187.

Test plan

• PYTHONPATH=. python -m pytest tests/test_linkml_schema_conversion.py -v → 22 passed (16 existing + 6 new)
• Black-formatted with the project's existing style
• Downstream regen: after merge, regenerating JSON_Schemas/v1.5.0/HTAN.SpatialLevel3-v1.5.0-schema.json should now show "const": true inside the if.anyOf[] branches for PROTEIN_MEASURED instead of "pattern": "^true$". Per CLAUDE.md, that regen lands in a separate downstream PR.

🤖 Generated with Claude Code

[github-actions]

HTAN Schema Review — ✅ Approved

Automated review by htan-claude · commit 977312c6a6a890f249975230f3a6d6eaeec071aa

This is a clean, well-scoped PR — the fix is targeted, the tests cover all the new recursive paths, and all three reviewers agree there's nothing to flag.

Tip

All checklist items pass — no issues found.

Files Changed

• scripts/linkml_to_flat_synapse_jsonschema.py
• tests/test_linkml_schema_conversion.py

Checklist Results

Check	Result	Notes
Inheritance correctness	N/A	No LinkML YAML schema files changed
Inlining of nested objects	N/A	No LinkML YAML schema files changed
Slot completeness (range, title, description)	N/A	No LinkML YAML schema files changed
Enum integrity (alphabetical, descriptions)	N/A	No LinkML YAML schema files changed
Generated artifacts	PASS	Downstream JSON schema regen is correctly deferred to a follow-on PR per CLAUDE.md; 22 unit tests pass including 6 new cases covering all recursive combinator paths

Verdict

APPROVE

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_{Rules defined in CLAUDE.md · To update review rules, edit CLAUDE.md and open a PR to main}

[aditigopalan]

LGTM!