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peptide-repo-core v0.6.0: peptide schema backfill + Yoast-integrated Drug/MedicalWebPage/FAQ (#19)

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Backfill psa_*->_pr_* meta (migration 0004 + PubChem fallback); enrich Drug node with {permalink}#drug @id + molecularFormula/Weight/alternateName; rewrite emitter into Yoast schema graph (MedicalWebPage retype + FAQPage, no duplicate nodes).

QA: APPROVE (independent) — qa-reviews/peptide-repo-core/2026-06-13-817690c1b6ec2118ddcf3b8cfe8bc5ea7f3933b3.md

Agent-Session: peptide-schema-backfill v0.6.0 merge
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peptiderepo
2026-06-13 13:09:56 +07:00
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CHANGELOG.md
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All notable changes to Peptide Repo Core are documented here.
Format: [Semantic Versioning](https://semver.org/).
## [0.6.0] — 2026-06-13
### Added
- **Backfill migration 0004** (`class-pr-core-migration-0004-backfill-peptide-meta.php`): Copies PSA-stored PubChem data into new `_pr_*` schema-input meta keys across all published peptide posts. Source: `psa_molecular_formula` → `_pr_molecular_formula`, `psa_molecular_weight` → `_pr_molecular_weight` (strip "Da", floatval), `psa_aliases` → `_pr_aliases` (comma-split, sanitize, JSON array). For 4 posts without PSA data (igf-1-lr3, cagrilintide, ghk-cu, epitalon), falls back to PubChem REST API via new `PR_Core_Pubchem_Client`. Migration is idempotent + re-runnable; skips posts where all three keys are already populated.
- **Schema-input meta keys** (registered in CPT, v0.6.0):
- `_pr_molecular_formula` — sanitized molecular formula string.
- `_pr_molecular_weight` — float as string (g/mol); "Da" suffix normalized out.
- `_pr_aliases` — JSON array of sanitized alternate names.
- `_pr_faq_items` — JSON array of `{question, answer}` objects for FAQPage emission.
- **`PR_Core_Schema_Sanitizers`** (`cpt/class-pr-core-schema-sanitizers.php`): Static sanitizers for the four schema-input meta keys, split from `PR_Core_Peptide_CPT` to keep the CPT file under 300 lines.
- **`PR_Core_Pubchem_Client`** (`migrations/class-pr-core-pubchem-client.php`): Lightweight PubChem REST client with CID/name lookup, synonym fetch, and MAX_RETRIES=3 exponential backoff. Used exclusively by migration 0004.
- **Yoast-integrated JSON-LD emission** (replaces standalone `wp_head` script):
- `PR_Core_Jsonld_Drug` — builds Drug (+ MolecularEntity) schema node with stable `@id = {permalink}#drug`, reads `_pr_*` schema-input meta, `alternateName`/`molecularFormula`/`molecularWeight` (g/mol) emitted only when non-empty.
- `PR_Core_Jsonld_Webpage` — retypes Yoast's WebPage to `MedicalWebPage` via `wpseo_schema_webpage_type`; enriches it with `lastReviewed`, `reviewedBy` (Person or Organization), and `audience` via `wpseo_schema_graph`.
- `PR_Core_Jsonld_Faq` — builds FAQPage node from `_pr_faq_items`; emitted only when items exist.
- `PR_Core_Jsonld` — orchestrator hooking all three builders into Yoast's graph; maintains standalone `@graph` fallback when Yoast is inactive.
- **`CONTEXT.md`** — new domain glossary covering all new terms (`_pr_*` keys, Drug node, MedicalWebPage, FAQPage, Yoast integration contract, PubChem CID).
### Changed
- `PR_Core_Jsonld` rewritten: replaces standalone `wp_head` script-tag emission with Yoast graph-filter integration. Standalone `@graph` retained as fallback only. **No duplicate WebPage/BreadcrumbList** — Yoast owns those.
- `PR_Core_Peptide_CPT::get_meta_fields()` — adds 4 new `_pr_*` fields; existing `aliases`/`molecular_formula`/`molecular_weight` fields unchanged.
- `PR_Core_Migration_Runner::MIGRATIONS` — adds `PR_Core_Migration_0004_Backfill_Peptide_Meta` at index 3.
- `PR_CORE_TARGET_SCHEMA_VERSION` bumped from 3 to 4.
- `uninstall.php` — purges `_pr_molecular_formula`, `_pr_molecular_weight`, `_pr_aliases`, `_pr_faq_items` from all peptide posts on uninstall.
- `ARCHITECTURE.md` — §#6 JSON-LD rewritten; §2.9 uninstall spec updated; file tree updated for new classes.
- `CONVENTIONS.md` — schema-input meta convention added; Yoast JSON-LD extension pattern added.
### Fixed
- `tests/unit/test-migration-0004.php`: `error_log()` stub now guarded with `function_exists()` to prevent PHP fatal redeclaration error in CI PHP Lint (8.1/8.2/8.3).
- `tests/bootstrap.php`: `wp_json_encode` stub updated to accept `int $flags = 0` second argument, matching production call signature; guarded with `function_exists()`.
- `cpt/class-pr-core-schema-sanitizers.php`: `sanitize_molecular_formula()` rewritten from character-allowlist to element-formula grammar validation (Option B). Now strips control characters first, then extracts the maximal leading run of valid `[A-Z][a-z]?\d*` element tokens and group separators. Inputs containing trailing English words (e.g., `"C10H12\ninjection"`) correctly return the formula prefix only (`"C10H12"`); fully invalid inputs (e.g., `"<script>alert(1)</script>"`) return `""`. Parenthesised formulas (e.g., `"C2H5(OH)"`) preserved unchanged. Seven-case unit test coverage added.
### Technical
- Schema version: `PR_CORE_TARGET_SCHEMA_VERSION` = 4.
- New test files: `tests/unit/test-migration-0004.php`, `tests/unit/test-jsonld.php`.
- Yoast filter names verified against Yoast 27.6: `wpseo_schema_graph_pieces`, `wpseo_schema_webpage_type`, `wpseo_schema_graph`.
- No CAS/DrugBank emission in v0.6.0 (no reliable source — documented in ARCHITECTURE.md for future enrichment sprint).
## [0.5.0] — 2026-04-27
### Added