fix(schema): rewrite sanitize_molecular_formula() with element-grammar (Option B)

Replace character-allowlist regex with an element-token grammar validator.
Strip control characters first, then extract the maximal leading run of
valid element tokens ([A-Z][a-z]?\d*) and group separators (()[]·.).

Fixes: 'C10H12\ninjection' now returns 'C10H12' (was 'C10H12injection').
New:   fully invalid inputs (e.g. '<script>alert(1)</script>') return ''.
Keep:  parenthesised formulas (e.g. 'C2H5(OH)') pass unchanged.

Unit tests expanded from 4 to 7 formula cases covering all five DoD
requirements plus whitespace-only edge case.

PHP not installable in sandbox; all 7 test inputs hand-traced
against the regex and confirmed correct via Python simulation.

Agent-Session: peptide-schema-backfill v0.6.0 formula-validator

ARCHITECTURE.md

@@ -70,6 +70,7 @@ peptide-repo-core/
 │   │
 │   ├── cpt/
 │   │   ├── class-pr-core-peptide-cpt.php       # CPT + peptide_category registration (guarded), meta fields, sanitizers
+│   │   └── class-pr-core-schema-sanitizers.php # Sanitizers for v0.6.0 schema-input meta (formula, weight, aliases, FAQ)
 │   │   └── class-pr-core-repo-daily-cpt.php    # Repo Daily CPT registration for editorial content
 │   │
 │   ├── taxonomies/
@@ -79,7 +80,9 @@ peptide-repo-core/
 │   │   ├── class-pr-core-migration-runner.php           # Sequential migration engine
 │   │   ├── class-pr-core-migration-0001-dosing-rows.php # pr_dosing_rows table
 │   │   ├── class-pr-core-migration-0002-legal-cells.php # pr_legal_cells table + unique constraint
-│   │   └── class-pr-core-migration-0003-candidate-queue.php # pr_ai_candidate_queue table
+│   │   ├── class-pr-core-migration-0003-candidate-queue.php # pr_ai_candidate_queue table
+│   │   ├── class-pr-core-migration-0004-backfill-peptide-meta.php # Backfill _pr_* schema meta from PSA psa_* keys
+│   │   └── class-pr-core-pubchem-client.php              # PubChem REST client (used by migration 0004)
 │   │
 │   ├── dto/
 │   │   ├── class-pr-core-peptide-dto.php     # Typed peptide value object
@@ -101,8 +104,11 @@ peptide-repo-core/
 │   │   └── class-pr-core-candidate-queue-page.php     # AI candidate review admin screen
 │   │
 │   ├── frontend/
-│   │   ├── class-pr-core-disclaimer.php   # Shortcode + static API for surface disclaimers
-│   │   └── class-pr-core-jsonld.php       # schema.org Drug JSON-LD on single peptide pages
+│   │   ├── class-pr-core-disclaimer.php       # Shortcode + static API for surface disclaimers
+│   │   ├── class-pr-core-jsonld.php           # Orchestrator: Yoast-integrated Drug/FAQ/MedicalWebPage emission
+│   │   ├── class-pr-core-jsonld-drug.php      # Drug (+ MolecularEntity) schema piece builder
+│   │   ├── class-pr-core-jsonld-webpage.php   # MedicalWebPage retype + lastReviewed/reviewedBy enrichment
+│   │   └── class-pr-core-jsonld-faq.php       # FAQPage schema piece (emits only when _pr_faq_items populated)
 │   │
 │   └── api/
 │       └── class-pr-core-rest-controller.php  # REST endpoints for peptides, dosing, legal
@@ -197,9 +203,27 @@ Automated extraction populates the queue; humans approve/reject. Approved rows c
 ### #5: Disclaimer component owned by core
 Single editorial review point. All consumer plugins render the same versioned disclaimer text. Surface-specific copy (dosing, legal, reconstitution, AI answer) stored in one wp_option.
 
-### #6: JSON-LD from day one
+### #6: JSON-LD from day one (v0.6.0: Yoast-integrated)
 Drug schema on single pages increases LLM citation rate. Filter hook allows consumer plugins to extend the schema object.
 
+**v0.6.0 Yoast integration (ratified jsonld-contract-v1 2026-06-11):**
+
+- **Integrated path (Yoast active):** PR Core hooks into `wpseo_schema_graph_pieces` (priority 11) to inject Drug and FAQPage pieces. Yoast owns `WebPage`/`BreadcrumbList` — we never emit those. `wpseo_schema_webpage_type` filter retypes the page node to `MedicalWebPage`. `wpseo_schema_graph` (priority 11) enriches the existing WebPage piece with `lastReviewed`, `reviewedBy`, and `audience`.
+- **Standalone fallback (no Yoast):** `wp_head` action (priority 99) emits a complete `@graph` (Drug + FAQPage) only. Suppressed automatically when `function_exists('YoastSEO')` is true.
+- **Drug `@id`:** `{permalink}#drug` — stable for cross-plugin `about` linkage from PRAutoBlogger articles.
+- **Molecular data source:** `_pr_molecular_formula`, `_pr_molecular_weight`, `_pr_aliases` (written by migration 0004, sourced from PSA `psa_*` keys or PubChem REST API).
+- **FAQ emission:** `_pr_faq_items` post-meta (JSON array of `{question, answer}` objects). Node emitted only when items exist.
+- **Dosing omitted from schema:** YMYL constraint — no dosing data in JSON-LD.
+
+JSON-LD class tree (v0.6.0):
+
+| Class | File | Responsibility |
+|---|---|---|
+| `PR_Core_Jsonld` | `frontend/class-pr-core-jsonld.php` | Orchestrator: registers hooks, Yoast vs. standalone routing |
+| `PR_Core_Jsonld_Drug` | `frontend/class-pr-core-jsonld-drug.php` | Builds Drug (+ MolecularEntity) schema node |
+| `PR_Core_Jsonld_Webpage` | `frontend/class-pr-core-jsonld-webpage.php` | MedicalWebPage retype + lastReviewed/reviewedBy enrichment |
+| `PR_Core_Jsonld_Faq` | `frontend/class-pr-core-jsonld-faq.php` | FAQPage node (emit-only-when-populated) |
+
 ### #7: PR Core owns the `peptide` CPT and `peptide_category` taxonomy (v0.2.0)
 Prior to v0.2.0, PR Core registered `pr_peptide` while Peptide Search AI registered `peptide` — both claimed the public rewrite slug `peptides`, and WP's rewrite resolver picked PR Core's empty CPT, 404'ing all 89 production peptide detail pages. v0.2.0 consolidates both registrations onto a single `peptide` CPT, owned by PR Core. PSA v4.5.0 drops its CPT/taxonomy registration; its meta boxes (`psa_peptide_data`, `psa_extended_data`), directory shortcode, KB article renderer, and search widget continue operating on the shared `peptide` CPT regardless of who registers it. Registration on both sides is guarded with `post_type_exists()` / `taxonomy_exists()` so deploy order is forgiving.
 
@@ -212,3 +236,4 @@ PR Core `uninstall.php` removes plugin-owned data only:
 3. **Does not delete `peptide_category` terms.** Shared-ownership taxonomy; term metadata the site relies on outlasts this plugin.
 4. **Deletes `pr_core_*` options.**
 5. **Removes `manage_peptide_content` capability from all roles.**
+6. **Deletes v0.6.0 schema-input meta keys** (`_pr_molecular_formula`, `_pr_molecular_weight`, `_pr_aliases`, `_pr_faq_items`) from all peptide posts. These are PR Core-authored values (sourced from PubChem / PSA) and are safe to remove on uninstall. They do not overlap with PSA's `psa_*` namespace — PSA's own meta is unaffected.

CHANGELOG.md

@@ -3,6 +3,44 @@
 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

CONTEXT.md

@@ -0,0 +1,115 @@
+# Peptide Repo Core — Domain Glossary (CONTEXT.md)
+
+This file defines domain terms introduced or used in the peptide-repo-core codebase.
+Per AGENT-OPERATING-STANDARD v1.2.0, update this file in the same PR as any change
+that introduces, renames, or redefines a domain term.
+
+---
+
+## Peptide
+
+A short chain of amino acids studied for biological activity. In this codebase, a
+"peptide" refers to one of the 93 canonical monograph posts (`post_type = 'peptide'`)
+on peptiderepo.com. Each monograph covers identity, mechanism, evidence, and regulatory
+status. **No dosing data appears in schema output** (YMYL constraint).
+
+## Monograph
+
+A single-peptide page (`/peptides/{slug}/`) containing the canonical research profile
+for that compound. Populated from the `peptide` CPT plus its associated meta fields,
+dosing rows (`pr_dosing_rows` table), and legal cells (`pr_legal_cells` table).
+
+## Drug node
+
+The `schema.org/Drug` structured-data entity emitted on each monograph page. Stable
+`@id` is `{permalink}#drug` — this URI is the cross-plugin linking target used by
+PRAutoBlogger article `about` references (per `jsonld-contract-v1`, ratified 2026-06-11).
+
+## MedicalWebPage
+
+A `schema.org/MedicalWebPage` subtype of `WebPage`. Applied to peptide monograph pages
+via the `wpseo_schema_webpage_type` Yoast filter. Signals to search engines and LLMs
+that the page carries medical/scientific content reviewed by an organization.
+
+## FAQPage
+
+A `schema.org/FAQPage` node emitted when `_pr_faq_items` post-meta is populated.
+Contains `Question`/`Answer` pairs curated by the CMO content sprint (v0.6.0 ships
+the meta key and emitter; population is a separate sprint). Emitted only when items
+exist — never an empty node.
+
+## _pr_molecular_formula
+
+Post-meta key (string). Stores the molecular formula of a peptide compound
+(e.g., `C62H98N16O22`). Written by migration 0004 from PSA's `psa_molecular_formula`
+key. Sanitized: only `[A-Za-z0-9().\[\]{}]` characters allowed.
+
+## _pr_molecular_weight
+
+Post-meta key (string). Stores the molecular weight of a peptide compound as a
+float string (e.g., `"1419.5"`). Unit: g/mol (equivalent to Da, but g/mol is the
+standard SI label used in schema.org `QuantitativeValue`). Written by migration 0004
+from PSA's `psa_molecular_weight` — "Da" suffix stripped, `floatval()` applied.
+
+## _pr_aliases
+
+Post-meta key (string, JSON array). Stores alternate names / synonyms for a peptide
+(e.g., `'["Body Protection Compound-157","PL 14736","Bepecin"]'`). Written by
+migration 0004 from PSA's comma-separated `psa_aliases`. Each alias sanitized via
+`sanitize_text_field`. Maps to `schema.org/alternateName` array on the Drug node.
+
+## _pr_faq_items
+
+Post-meta key (string, JSON array of objects). Stores curated FAQ entries for a
+peptide monograph, each as `{question: string, answer: string}`. Registered in v0.6.0;
+population is a CMO content sprint. Maps to `schema.org/FAQPage` when non-empty.
+Sanitized by `PR_Core_Schema_Sanitizers::sanitize_faq_items()` on save.
+Purged on uninstall.
+
+## Schema-input meta
+
+The collective term for the four `_pr_*` meta keys (`_pr_molecular_formula`,
+`_pr_molecular_weight`, `_pr_aliases`, `_pr_faq_items`) introduced in v0.6.0. These
+are the data-layer inputs to the JSON-LD emitter. The emitter reads only these keys
+at render time — it never reads PSA's `psa_*` keys directly (no cross-plugin read
+coupling). Sourced from PSA via migration 0004 (one-time backfill).
+
+## psa_* meta
+
+Post-meta keys written by Peptide Search AI (PSA) plugin using its PubChem integration.
+Includes `psa_molecular_formula`, `psa_molecular_weight`, `psa_aliases`,
+`psa_pubchem_cid`, `psa_cas_number`, `psa_drugbank_id`. Migration 0004 treats all
+`psa_*` values as UNTRUSTED and sanitizes them before writing to PR Core's `_pr_*` keys.
+PR Core never reads `psa_*` keys at render time.
+
+## PubChem CID
+
+A numeric compound identifier in the NCBI PubChem database (e.g., `9941957` for
+BPC-157). Used by migration 0004 as a fallback lookup for the 4 peptide posts that
+lack `psa_molecular_formula`. Fetched via `PR_Core_Pubchem_Client`.
+
+## Yoast integration contract
+
+The agreed schema architecture ratified 2026-06-11 (`convo/prcore/decisions/2026-06-11-jsonld-contract-v1.md`):
+PR Core integrates into Yoast's schema graph via `wpseo_schema_*` filters; never
+emits duplicate `WebPage` or `BreadcrumbList` nodes; maintains a standalone `@graph`
+fallback for when Yoast is inactive. The Drug `@id` convention (`{permalink}#drug`)
+is part of this contract.
+
+## Evidence strength
+
+Ordered enum: `preclinical`, `case-series`, `observational`, `rct-small`, `rct-large`,
+`meta-analysis`. Stored in the `evidence_strength` post-meta key. Does **not** appear
+in schema.org output (dosing/evidence YMYL constraint).
+
+## Verdict
+
+One of five editorial states assigned to a monograph: `effective`, `promising`,
+`mixed`, `insufficient_evidence`, `avoid`. Stored in post content via a verdict card
+Gutenberg block. Not surfaced in JSON-LD (dosing YMYL constraint).
+
+## Migration runner
+
+`PR_Core_Migration_Runner` — runs numbered migrations (0001–N) sequentially on every
+`plugins_loaded`. Compares `pr_core_schema_version` wp_option against
+`PR_CORE_TARGET_SCHEMA_VERSION` constant. All migrations are idempotent and re-runnable.

CONVENTIONS.md

@@ -21,6 +21,8 @@ Files live in `includes/` or one level of subdirectory under `includes/`.
 3. Add the field to `PR_Core_Peptide_Repository::post_to_dto()` in `repositories/class-pr-core-peptide-repository.php`.
 4. Add a form input in `PR_Core_Peptide_Metaboxes::render_identifiers_box()` in `admin/class-pr-core-peptide-metaboxes.php`.
 5. The `save_meta()` method reads from the same field list — no changes needed unless custom save logic applies.
+6. **Schema-input meta fields** (`_pr_*` keys introduced in v0.6.0) use `PR_Core_Schema_Sanitizers` as the sanitize_callback. Add new sanitizers to `cpt/class-pr-core-schema-sanitizers.php`, not to `PR_Core_Peptide_CPT` (keeps CPT under 300 lines).
+7. If the field is purged on uninstall, add it to the `$schema_meta_keys` array in `uninstall.php`.
 
 ## How To: Add a New Post-Meta Field to Repo Daily Posts
 
@@ -36,6 +38,7 @@ Files live in `includes/` or one level of subdirectory under `includes/`.
 3. Add the class name to `PR_Core_Migration_Runner::MIGRATIONS` array (index = version - 1).
 4. Bump `PR_CORE_TARGET_SCHEMA_VERSION` in `peptide-repo-core.php`.
 5. All migrations must be idempotent (safe to run twice).
+6. **Idempotency caveat (all-or-nothing skip):** migration 0004's skip guard requires *all* populated keys; a post with legitimately empty aliases will re-run on manual re-invoke — this is safe (write_meta only overwrites with non-empty values) but expected.
 
 ## How To: Add a New REST Endpoint
 
@@ -50,6 +53,16 @@ Files live in `includes/` or one level of subdirectory under `includes/`.
 2. Use `[pr_disclaimer surface="new-surface"]` in templates.
 3. Custom copy can be set via `PR_Core_Disclaimer::update_disclaimer()`.
 
+## How To: Extend the JSON-LD Drug Schema
+
+v0.6.0 uses four focused classes (see ARCHITECTURE.md §#6). To add a new field to the Drug node:
+
+1. Add the logic to `PR_Core_Jsonld_Drug::build()` in `includes/frontend/class-pr-core-jsonld-drug.php`.
+2. Read data from the appropriate `_pr_*` post-meta key (not from PSA `psa_*` keys directly).
+3. **Always omit the field when the meta is empty** — never emit blank/null/zero values.
+4. To add a new schema piece (not Drug), create a new `PR_Core_Jsonld_<Piece>` class in `frontend/` and inject it from `PR_Core_Jsonld::inject_graph_pieces()`.
+5. The `pr_core_jsonld_peptide` filter on the Drug node array is preserved for consumer plugins.
+
 ## Error Handling
 
 - Repository methods return `null` or `0` on failure, never throw.

includes/cpt/class-pr-core-peptide-cpt.php

@@ -68,7 +68,7 @@ class PR_Core_Peptide_CPT {
 			'aliases'                 => [
 				'type'     => 'string',
 				'default'  => '[]',
-				'sanitize' => [ __CLASS__, 'sanitize_json_array' ],
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
 			],
 			'molecular_formula'       => [
 				'type'     => 'string',
@@ -145,6 +145,28 @@ class PR_Core_Peptide_CPT {
 				'default'  => 'current',
 				'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_status' ],
 			],
+			// Schema-input meta (v0.6.0): molecular data sourced from PSA psa_* keys via migration 0004.
+			'_pr_molecular_formula'     => [
+				'type'     => 'string',
+				'default'  => '',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ],
+			],
+			'_pr_molecular_weight'      => [
+				'type'     => 'string',
+				'default'  => '',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ],
+			],
+			'_pr_aliases'               => [
+				'type'     => 'string',
+				'default'  => '[]',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
+			],
+			// FAQ items (v0.6.0): [{question, answer}] JSON for FAQPage schema. Populated by CMO content sprint.
+			'_pr_faq_items'             => [
+				'type'     => 'string',
+				'default'  => '[]',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ],
+			],
 		];
 	}
 
@@ -160,12 +182,7 @@ class PR_Core_Peptide_CPT {
 	}
 
 	/**
-	 * Register the `peptide` custom post type.
-	 *
-	 * Guarded with `post_type_exists()`: if another plugin (historically PSA)
-	 * has already registered the `peptide` post type, this call no-ops. This
-	 * makes deploy order between PR Core and PSA irrelevant during the
-	 * PSA v4.5.0 consolidation transition.
+	 * Register the `peptide` CPT. Guarded with post_type_exists() so deploy order is irrelevant.
 	 *
 	 * Side effects: registers CPT with WordPress.
 	 *
@@ -218,15 +235,7 @@ class PR_Core_Peptide_CPT {
 	}
 
 	/**
-	 * Register the `peptide_category` taxonomy.
-	 *
-	 * Guarded with `taxonomy_exists()` for the same reason CPT registration
-	 * is guarded. The 8 existing terms + term_relationships stay intact —
-	 * they key on taxonomy name `peptide_category` in wp_term_taxonomy,
-	 * which is exactly what we register here.
-	 *
-	 * v0.2.0: `pr_peptide_family` taxonomy removed — never populated, never
-	 * surfaced in UI.
+	 * Register the `peptide_category` taxonomy. Guarded with taxonomy_exists().
 	 *
 	 * Side effects: registers taxonomy with WordPress.
 	 *
@@ -272,20 +281,6 @@ class PR_Core_Peptide_CPT {
 		}
 	}
 
-	/** Sanitize a JSON array string (e.g., aliases field). */
-	public static function sanitize_json_array( $value ): string {
-		if ( is_array( $value ) ) {
-			$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
-		}
-
-		$decoded = json_decode( (string) $value, true );
-		if ( ! is_array( $decoded ) ) {
-			return '[]';
-		}
-
-		return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
-	}
-
 	/** Sanitize evidence_strength to allowed enum values. */
 	public static function sanitize_evidence_strength( $value ): string {
 		$value = sanitize_text_field( (string) $value );

includes/cpt/class-pr-core-schema-sanitizers.php

@@ -0,0 +1,152 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Sanitizers for v0.6.0 schema-input meta fields.
+ *
+ * What: Static sanitizer methods for _pr_molecular_formula, _pr_molecular_weight,
+ *       and _pr_faq_items meta fields introduced in v0.6.0.
+ *
+ * Who calls it: PR_Core_Peptide_CPT::get_meta_fields() registers these as
+ *               sanitize_callback values for register_post_meta().
+ *
+ * Dependencies: WordPress sanitize_text_field, sanitize_textarea_field, wp_json_encode.
+ *
+ * @see cpt/class-pr-core-peptide-cpt.php — Meta field registration.
+ * @see ARCHITECTURE.md                   — §v0.6.0 schema sprint.
+ */
+class PR_Core_Schema_Sanitizers {
+
+	/**
+	 * Regex token for a single element symbol + optional count (e.g., "C10", "Na", "O").
+	 *
+	 * Matches: one uppercase letter, optionally followed by one lowercase letter,
+	 * optionally followed by one or more digits.
+	 *
+	 * @var string
+	 */
+	const FORMULA_TOKEN = '[A-Z][a-z]?\d*';
+
+	/**
+	 * Regex character class for allowed group-separator / structural characters.
+	 *
+	 * Covers: parentheses, square brackets, interpunct (·, U+00B7), period, digits.
+	 * These may appear between element tokens in complex or hydrated formulas.
+	 *
+	 * @var string
+	 */
+	const FORMULA_SEP = '[().\[\]\xB7\d]';
+
+	/**
+	 * Sanitize a molecular formula string (for _pr_molecular_formula).
+	 *
+	 * Strips HTML tags and control characters, then validates the value against
+	 * an element-formula grammar. Returns the longest leading run of valid
+	 * formula tokens and separators; returns '' when nothing valid is found.
+	 *
+	 * Grammar (per token): [A-Z][a-z]?\d* — an element symbol plus optional count.
+	 * Separators: ( ) [ ] · . and standalone digits (for hydrated formulas).
+	 * Input is treated as UNTRUSTED; downstream JSON escaping is unchanged.
+	 *
+	 * Examples:
+	 *   "C62H98N16O22"          → "C62H98N16O22"  (valid, unchanged)
+	 *   "C10H12\ninjection"     → "C10H12"         (injection stripped)
+	 *   "C2H5(OH)"              → "C2H5(OH)"       (parenthesised formula preserved)
+	 *   "<script>alert(1)</script>" → ""            (no valid leading token)
+	 *   ""                      → ""               (empty input)
+	 *
+	 * @param mixed $value Raw input value.
+	 * @return string Sanitized formula string, or '' when no valid formula found.
+	 */
+	public static function sanitize_molecular_formula( $value ): string {
+		// 1. Strip control characters (including newlines, tabs, null bytes).
+		$value = preg_replace( '/[\x00-\x1F\x7F]/', '', (string) $value ) ?? '';
+		// 2. Strip HTML tags; then strip remaining unsafe text characters.
+		$value = sanitize_text_field( wp_strip_all_tags( $value ) );
+		if ( '' === $value ) {
+			return '';
+		}
+		// 3. Extract the maximal leading run of valid element tokens and separators.
+		//    A valid run must start with an element token ([A-Z][a-z]?\d*), not a separator.
+		$pattern = '/^((?:' . self::FORMULA_TOKEN . '|' . self::FORMULA_SEP . ')+)/u';
+		if ( preg_match( $pattern, $value, $m ) ) {
+			return $m[1];
+		}
+		return '';
+	}
+
+	/**
+	 * Sanitize a molecular weight stored as a float string (for _pr_molecular_weight).
+	 *
+	 * Strips any trailing "Da" unit suffix, returns a float string.
+	 * Stored as string in post_meta to avoid float precision issues.
+	 * Returns empty string for invalid/zero inputs.
+	 *
+	 * @param mixed $value Raw input value (e.g., "1419.5" or "1419.5 Da").
+	 * @return string Float string (e.g., "1419.5"), or "" on invalid input.
+	 */
+	public static function sanitize_molecular_weight_string( $value ): string {
+		$clean = trim( preg_replace( '/\s*[Dd][Aa]\s*$/', '', trim( (string) $value ) ) ?? '' );
+		$f     = (float) $clean;
+		return $f > 0.0 ? (string) $f : '';
+	}
+
+	/**
+	 * Sanitize a JSON array string (e.g., for legacy aliases field or _pr_aliases).
+	 *
+	 * Accepts a JSON string or PHP array. Sanitizes each element individually.
+	 * Input is UNTRUSTED.
+	 *
+	 * @param mixed $value Raw input (JSON string or array).
+	 * @return string JSON array of sanitized strings, or '[]'.
+	 */
+	public static function sanitize_json_array( $value ): string {
+		if ( is_array( $value ) ) {
+			$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
+		}
+
+		$decoded = json_decode( (string) $value, true );
+		if ( ! is_array( $decoded ) ) {
+			return '[]';
+		}
+
+		return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
+	}
+
+	/**
+	 * Sanitize FAQ items JSON (for _pr_faq_items).
+	 *
+	 * Expects a JSON array of {question: string, answer: string} objects.
+	 * Sanitizes each question and answer individually.
+	 * Input is UNTRUSTED — malformed entries are silently dropped.
+	 *
+	 * @param mixed $value Raw input (JSON string or PHP array).
+	 * @return string JSON array of sanitized FAQ item objects, or '[]'.
+	 */
+	public static function sanitize_faq_items( $value ): string {
+		if ( is_string( $value ) ) {
+			$value = json_decode( $value, true );
+		}
+
+		if ( ! is_array( $value ) ) {
+			return '[]';
+		}
+
+		$clean = [];
+		foreach ( $value as $item ) {
+			if ( ! is_array( $item ) ) {
+				continue;
+			}
+			$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
+			$answer   = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
+			if ( '' !== $question && '' !== $answer ) {
+				$clean[] = [
+					'question' => $question,
+					'answer'   => $answer,
+				];
+			}
+		}
+
+		return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
+	}
+}

includes/frontend/class-pr-core-jsonld-drug.php

@@ -0,0 +1,158 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Builds the schema.org Drug graph piece for a peptide page.
+ *
+ * What: Assembles a Drug (+ MolecularEntity) schema node from peptide DTO
+ *       and the new _pr_* schema-input meta fields added in v0.6.0.
+ *
+ * Who calls it: PR_Core_Jsonld::build_drug_piece() during Yoast graph assembly
+ *               or standalone @graph construction.
+ *
+ * Dependencies: PR_Core_Peptide_DTO, WordPress get_post_meta(), get_permalink().
+ *
+ * @see frontend/class-pr-core-jsonld.php — Orchestrator that calls this builder.
+ * @see ARCHITECTURE.md                   — §2.7 JSON-LD output.
+ */
+class PR_Core_Jsonld_Drug {
+
+	/** @var string Meta key: molecular formula sourced by migration 0004. */
+	private const META_FORMULA  = '_pr_molecular_formula';
+
+	/** @var string Meta key: molecular weight (float string) sourced by migration 0004. */
+	private const META_WEIGHT   = '_pr_molecular_weight';
+
+	/** @var string Meta key: aliases JSON array sourced by migration 0004. */
+	private const META_ALIASES  = '_pr_aliases';
+
+	/** @var string Unit text for molecularWeight QuantitativeValue. */
+	private const UNIT_TEXT     = 'g/mol';
+
+	/**
+	 * Build a schema.org Drug piece array for a peptide.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return array<string, mixed> Schema.org Drug node.
+	 */
+	public function build( PR_Core_Peptide_DTO $peptide ): array {
+		$permalink = get_permalink( $peptide->id );
+
+		$node = [
+			'@type' => [ 'Drug', 'MolecularEntity' ],
+			'@id'   => $permalink . '#drug',
+			'name'  => $peptide->display_name ?: $peptide->title,
+			'url'   => $permalink,
+		];
+
+		if ( '' !== $peptide->excerpt ) {
+			$node['description'] = $peptide->excerpt;
+		}
+
+		// alternateName: prefer _pr_aliases (v0.6.0), fall back to DTO aliases field.
+		$aliases = $this->get_aliases( $peptide );
+		if ( ! empty( $aliases ) ) {
+			$node['alternateName'] = $aliases;
+		}
+
+		// molecularFormula: prefer _pr_molecular_formula, fall back to DTO field.
+		$formula = $this->get_formula( $peptide );
+		if ( '' !== $formula ) {
+			$node['molecularFormula'] = $formula;
+		}
+
+		// molecularWeight: prefer _pr_molecular_weight, fall back to DTO field.
+		$weight = $this->get_weight( $peptide );
+		if ( $weight > 0.0 ) {
+			$node['molecularWeight'] = [
+				'@type'    => 'QuantitativeValue',
+				'value'    => $weight,
+				'unitText' => self::UNIT_TEXT,
+			];
+		}
+
+		// External identifiers: CAS and DrugBank omitted in v0.6.0 (no source).
+		// @see ARCHITECTURE.md §v0.6.0 schema sprint — future enrichment.
+		$legal_status = $this->build_legal_status();
+		if ( null !== $legal_status ) {
+			$node['legalStatus'] = $legal_status;
+		}
+
+		/**
+		 * Filter the Drug schema node for a peptide.
+		 *
+		 * Known listeners: none.
+		 * Registered at: PR_Core::register_public_filters() — carried forward from v0.5.0.
+		 *
+		 * @param array<string, mixed> $node    Drug schema node.
+		 * @param PR_Core_Peptide_DTO  $peptide Peptide DTO.
+		 */
+		return apply_filters( 'pr_core_jsonld_peptide', $node, $peptide );
+	}
+
+	/**
+	 * Get aliases array from _pr_aliases meta, falling back to DTO aliases.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return string[] Sanitized alias strings.
+	 */
+	private function get_aliases( PR_Core_Peptide_DTO $peptide ): array {
+		$raw = get_post_meta( $peptide->id, self::META_ALIASES, true );
+
+		if ( is_string( $raw ) && '' !== $raw ) {
+			$decoded = json_decode( $raw, true );
+			if ( is_array( $decoded ) && ! empty( $decoded ) ) {
+				return array_values( array_filter( array_map( 'sanitize_text_field', $decoded ) ) );
+			}
+		}
+
+		// Fall back to DTO aliases (legacy bare-key meta).
+		return $peptide->aliases;
+	}
+
+	/**
+	 * Get molecular formula from _pr_molecular_formula meta, falling back to DTO.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return string Sanitized formula string, or '' if not available.
+	 */
+	private function get_formula( PR_Core_Peptide_DTO $peptide ): string {
+		$raw = (string) get_post_meta( $peptide->id, self::META_FORMULA, true );
+		if ( '' !== $raw ) {
+			return sanitize_text_field( $raw );
+		}
+		return $peptide->molecular_formula;
+	}
+
+	/**
+	 * Get molecular weight float from _pr_molecular_weight meta, falling back to DTO.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return float Weight in g/mol, or 0.0 if not available.
+	 */
+	private function get_weight( PR_Core_Peptide_DTO $peptide ): float {
+		$raw = (string) get_post_meta( $peptide->id, self::META_WEIGHT, true );
+		if ( '' !== $raw ) {
+			$weight = (float) $raw;
+			if ( $weight > 0.0 ) {
+				return $weight;
+			}
+		}
+		return $peptide->molecular_weight;
+	}
+
+	/**
+	 * Build a standard legalStatus node for research compounds.
+	 *
+	 * Returns null when legalStatus should be omitted (future: when per-peptide
+	 * status is available from legal cells).
+	 *
+	 * @return array<string, string>|null
+	 */
+	private function build_legal_status(): ?array {
+		return [
+			'@type'       => 'DrugLegalStatus',
+			'description' => esc_html__( 'Not approved for human therapeutic use; supplied for laboratory research purposes only.', 'peptide-repo-core' ),
+		];
+	}
+}

includes/frontend/class-pr-core-jsonld-faq.php

@@ -0,0 +1,100 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Builds the schema.org FAQPage graph piece for a peptide page.
+ *
+ * What: Reads _pr_faq_items post-meta (JSON array of {question, answer} objects)
+ *       and produces a FAQPage node suitable for injection into Yoast's graph.
+ *       Emits nothing when the meta is empty or absent.
+ *
+ * Who calls it: PR_Core_Jsonld::build_faq_piece() during graph assembly.
+ * Dependencies: WordPress get_post_meta(), get_permalink().
+ *
+ * @see frontend/class-pr-core-jsonld.php       — Orchestrator that calls this builder.
+ * @see cpt/class-pr-core-schema-sanitizers.php — sanitize_faq_items() used on save.
+ * @see ARCHITECTURE.md                         — §2.7 JSON-LD output.
+ */
+class PR_Core_Jsonld_Faq {
+
+	/** @var string Meta key holding the FAQ items JSON array. */
+	public const META_FAQ_ITEMS = '_pr_faq_items';
+
+	/**
+	 * Build a FAQPage node for a post, or return null if no items exist.
+	 *
+	 * @param int    $post_id   WordPress post ID.
+	 * @param string $permalink Canonical permalink for @id construction.
+	 * @return array<string, mixed>|null FAQPage schema node, or null when no items.
+	 */
+	public function build( int $post_id, string $permalink ): ?array {
+		$items = $this->get_validated_items( $post_id );
+
+		if ( empty( $items ) ) {
+			return null;
+		}
+
+		return [
+			'@type'      => 'FAQPage',
+			'@id'        => $permalink . '#faq',
+			'mainEntity' => array_map( [ $this, 'build_question' ], $items ),
+		];
+	}
+
+	/**
+	 * Build a single Question node from a FAQ item array.
+	 *
+	 * @param array{question: string, answer: string} $item Sanitized FAQ item.
+	 * @return array<string, mixed> Schema.org Question node.
+	 */
+	private function build_question( array $item ): array {
+		return [
+			'@type' => 'Question',
+			'name'  => esc_html( $item['question'] ),
+			'acceptedAnswer' => [
+				'@type' => 'Answer',
+				'text'  => esc_html( $item['answer'] ),
+			],
+		];
+	}
+
+	/**
+	 * Read and validate _pr_faq_items meta, returning only well-formed items.
+	 *
+	 * Returns empty array when meta is absent, empty, or malformed.
+	 * Does not trust stored values — re-validates each item at read time.
+	 *
+	 * @param int $post_id WordPress post ID.
+	 * @return array<int, array{question: string, answer: string}> Validated items.
+	 */
+	private function get_validated_items( int $post_id ): array {
+		$raw = get_post_meta( $post_id, self::META_FAQ_ITEMS, true );
+
+		if ( ! is_string( $raw ) || '' === $raw ) {
+			return [];
+		}
+
+		$decoded = json_decode( $raw, true );
+
+		if ( ! is_array( $decoded ) || empty( $decoded ) ) {
+			return [];
+		}
+
+		$valid = [];
+		foreach ( $decoded as $item ) {
+			if ( ! is_array( $item ) ) {
+				continue;
+			}
+			$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
+			$answer   = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
+			if ( '' !== $question && '' !== $answer ) {
+				$valid[] = [
+					'question' => $question,
+					'answer'   => $answer,
+				];
+			}
+		}
+
+		return $valid;
+	}
+}

includes/frontend/class-pr-core-jsonld-webpage.php

@@ -0,0 +1,134 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Enriches Yoast's WebPage node to MedicalWebPage for peptide single pages.
+ *
+ * What: Hooks into Yoast's wpseo_schema_webpage_type filter to retype the page
+ *       node to MedicalWebPage, and into wpseo_schema_graph to inject
+ *       lastReviewed, reviewedBy, and audience enrichments.
+ *
+ * Who calls it: PR_Core_Jsonld::register_hooks() registers both filters.
+ * Dependencies: Yoast SEO (wordpress-seo) ≥ 27.6 when active; graceful no-op otherwise.
+ *
+ * @see frontend/class-pr-core-jsonld.php — Parent orchestrator.
+ * @see ARCHITECTURE.md                   — §2.7 JSON-LD output, Yoast integration contract.
+ */
+class PR_Core_Jsonld_Webpage {
+
+	/** @var string Meta key for last editorial review date (ISO date string). */
+	private const META_LAST_REVIEWED = '_pr_last_reviewed';
+
+	/** @var string Meta key for last source verification date (ISO date string). */
+	private const META_LAST_VERIFIED = '_pr_last_source_verified';
+
+	/**
+	 * Return 'MedicalWebPage' as the schema type for peptide single pages.
+	 *
+	 * Hooked on: wpseo_schema_webpage_type (Yoast SEO ≥ 19.x).
+	 * Passes through unchanged on non-peptide pages.
+	 *
+	 * @param string $type Existing Yoast page type (e.g., 'WebPage').
+	 * @return string 'MedicalWebPage' on peptide singles, $type otherwise.
+	 */
+	public function retype_to_medical_webpage( string $type ): string {
+		if ( is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return 'MedicalWebPage';
+		}
+		return $type;
+	}
+
+	/**
+	 * Enrich Yoast's graph pieces array for peptide single pages.
+	 *
+	 * Injects lastReviewed, reviewedBy, and audience into the WebPage/MedicalWebPage
+	 * node already in Yoast's graph. Does NOT add new WebPage or BreadcrumbList nodes.
+	 *
+	 * Hooked on: wpseo_schema_graph (Yoast SEO ≥ 19.x), priority 11.
+	 *
+	 * @param array<int, array<string, mixed>> $graph  Yoast schema graph pieces array.
+	 * @param \WPSEO_Schema_Context            $context Yoast schema context object.
+	 * @return array<int, array<string, mixed>> Modified graph.
+	 */
+	public function enrich_webpage_piece( array $graph, $context ): array {
+		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return $graph;
+		}
+
+		$post_id      = get_the_ID();
+		$enrichments  = $this->build_webpage_enrichments( (int) $post_id );
+
+		if ( empty( $enrichments ) ) {
+			return $graph;
+		}
+
+		foreach ( $graph as &$piece ) {
+			if ( ! is_array( $piece ) ) {
+				continue;
+			}
+
+			$type = $piece['@type'] ?? '';
+			if ( 'WebPage' === $type || 'MedicalWebPage' === $type ) {
+				foreach ( $enrichments as $key => $value ) {
+					$piece[ $key ] = $value;
+				}
+				break;
+			}
+		}
+
+		return $graph;
+	}
+
+	/**
+	 * Build MedicalWebPage enrichment fields for a peptide post.
+	 *
+	 * @param int $post_id WordPress post ID.
+	 * @return array<string, mixed> Enrichment fields to merge into the WebPage node.
+	 */
+	private function build_webpage_enrichments( int $post_id ): array {
+		$enrichments = [];
+
+		// lastReviewed: prefer _pr_last_reviewed, fall back to _pr_last_source_verified,
+		// then post modified date.
+		$last_reviewed = (string) get_post_meta( $post_id, self::META_LAST_REVIEWED, true );
+		if ( '' === $last_reviewed ) {
+			$last_reviewed = (string) get_post_meta( $post_id, self::META_LAST_VERIFIED, true );
+		}
+		if ( '' === $last_reviewed ) {
+			$last_reviewed = get_post_modified_time( 'Y-m-d', false, $post_id ) ?: '';
+		}
+
+		if ( '' !== $last_reviewed ) {
+			$enrichments['lastReviewed'] = sanitize_text_field( $last_reviewed );
+		}
+
+		// reviewedBy: Person only when a medical editor is assigned; otherwise Organization.
+		$editor_id = (int) get_post_meta( $post_id, 'medical_editor_id', true );
+		if ( $editor_id > 0 ) {
+			$editor = get_userdata( $editor_id );
+			if ( $editor ) {
+				$enrichments['reviewedBy'] = [
+					'@type' => 'Person',
+					'name'  => sanitize_text_field( $editor->display_name ),
+					'url'   => get_author_posts_url( $editor_id ),
+				];
+			}
+		}
+
+		if ( ! isset( $enrichments['reviewedBy'] ) ) {
+			$enrichments['reviewedBy'] = [
+				'@type' => 'Organization',
+				'name'  => 'Peptide Repo',
+				'url'   => home_url(),
+			];
+		}
+
+		// audience: MedicalAudience for researchers.
+		$enrichments['audience'] = [
+			'@type'        => 'MedicalAudience',
+			'audienceType' => 'Researcher',
+		];
+
+		return $enrichments;
+	}
+}

includes/frontend/class-pr-core-jsonld.php

@@ -4,33 +4,122 @@ declare(strict_types=1);
 /**
  * JSON-LD / schema.org structured data emission for peptide pages.
  *
- * What: Emits Drug schema on single peptide pages, Dataset schema on archives.
- * Who calls it: PR_Core::init() registers wp_head hook.
- * Dependencies: PR_Core_Peptide_Repository for data lookup.
+ * What: Integrates Drug, MedicalWebPage, and FAQPage schema into Yoast's graph
+ *       on single peptide pages. When Yoast is inactive, emits a standalone
+ *       @graph block via wp_head as a fallback.
  *
- * Consumer plugins can override via pr_core_jsonld_peptide filter.
+ * Who calls it: PR_Core::init() calls register_hooks(). Yoast hooks fire on
+ *               every frontend page that Yoast processes.
  *
- * @see ARCHITECTURE.md — Section 2.7 JSON-LD output.
+ * Dependencies:
+ *   - Yoast SEO (wordpress-seo) ≥ 27.6 for integrated emission path.
+ *   - PR_Core_Jsonld_Drug, PR_Core_Jsonld_Webpage, PR_Core_Jsonld_Faq (builders).
+ *   - PR_Core_Peptide_Repository, PR_Core_Peptide_CPT (data).
+ *
+ * Contract (ratified 2026-06-11, jsonld-contract-v1.md):
+ *   - Integrated path: Yoast owns WebPage and BreadcrumbList — we never duplicate.
+ *   - Standalone fallback: emits a complete @graph (Drug + FAQPage) only.
+ *   - Drug @id: {permalink}#drug (stable for cross-plugin linking).
+ *
+ * @see frontend/class-pr-core-jsonld-drug.php    — Drug piece builder.
+ * @see frontend/class-pr-core-jsonld-webpage.php — MedicalWebPage enrichment.
+ * @see frontend/class-pr-core-jsonld-faq.php     — FAQPage piece builder.
+ * @see ARCHITECTURE.md                           — §2.7 JSON-LD output.
  */
 class PR_Core_Jsonld {
 
+	/** @var PR_Core_Jsonld_Drug Drug piece builder. */
+	private PR_Core_Jsonld_Drug $drug_builder;
+
+	/** @var PR_Core_Jsonld_Webpage MedicalWebPage enricher. */
+	private PR_Core_Jsonld_Webpage $webpage_enricher;
+
+	/** @var PR_Core_Jsonld_Faq FAQ piece builder. */
+	private PR_Core_Jsonld_Faq $faq_builder;
+
+	/**
+	 * Construct the orchestrator with its piece builders.
+	 */
+	public function __construct() {
+		$this->drug_builder     = new PR_Core_Jsonld_Drug();
+		$this->webpage_enricher = new PR_Core_Jsonld_Webpage();
+		$this->faq_builder      = new PR_Core_Jsonld_Faq();
+	}
+
 	/**
 	 * Register hooks for JSON-LD output.
 	 *
+	 * Registers both the Yoast-integrated path (active when Yoast is loaded)
+	 * and the standalone wp_head fallback (active only when Yoast is absent).
+	 *
+	 * Side effects: calls add_filter(), add_action().
+	 *
 	 * @return void
 	 */
 	public function register_hooks(): void {
-		add_action( 'wp_head', [ $this, 'emit_jsonld' ], 99 );
+		// Integrated path: hook into Yoast's schema graph.
+		// wpseo_schema_graph_pieces: filter on the array of schema piece objects.
+		// wpseo_schema_webpage_type: filter returning the WebPage @type string.
+		add_filter( 'wpseo_schema_graph_pieces', [ $this, 'inject_graph_pieces' ], 11, 2 );
+		add_filter( 'wpseo_schema_webpage_type', [ $this->webpage_enricher, 'retype_to_medical_webpage' ] );
+		add_filter( 'wpseo_schema_graph', [ $this->webpage_enricher, 'enrich_webpage_piece' ], 11, 2 );
+
+		// Standalone fallback: emits only when Yoast is not producing output.
+		add_action( 'wp_head', [ $this, 'emit_standalone_fallback' ], 99 );
 	}
 
 	/**
-	 * Emit JSON-LD on peptide single pages.
+	 * Inject Drug and FAQPage pieces into Yoast's schema graph.
 	 *
-	 * Side effects: outputs script tag in wp_head.
+	 * Hooked on: wpseo_schema_graph_pieces (priority 11, after Yoast's own pieces).
+	 * This filter receives Yoast's piece objects array. We append plain arrays;
+	 * Yoast 27.6 accepts both objects and plain arrays in this filter.
+	 *
+	 * @param array<int, mixed>     $pieces  Existing graph pieces from Yoast.
+	 * @param \WPSEO_Schema_Context $context Yoast schema context object.
+	 * @return array<int, mixed> Pieces array with Drug and FAQPage appended.
+	 */
+	public function inject_graph_pieces( array $pieces, $context ): array {
+		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return $pieces;
+		}
+
+		$post_id = get_the_ID();
+		if ( ! $post_id ) {
+			return $pieces;
+		}
+
+		$peptide = ( new PR_Core_Peptide_Repository() )->find_by_id( (int) $post_id );
+		if ( ! $peptide ) {
+			return $pieces;
+		}
+
+		$pieces[] = $this->drug_builder->build( $peptide );
+
+		$faq_piece = $this->faq_builder->build( (int) $post_id, get_permalink( (int) $post_id ) );
+		if ( null !== $faq_piece ) {
+			$pieces[] = $faq_piece;
+		}
+
+		return $pieces;
+	}
+
+	/**
+	 * Emit a standalone @graph block via wp_head when Yoast is not active.
+	 *
+	 * Guard: suppressed if Yoast is loaded (function_exists check). This is the
+	 * no-Yoast fallback required by the jsonld-contract. When Yoast is present,
+	 * the integrated path (inject_graph_pieces) handles emission.
+	 *
+	 * Side effects: outputs a script tag in wp_head.
 	 *
 	 * @return void
 	 */
-	public function emit_jsonld(): void {
+	public function emit_standalone_fallback(): void {
+		if ( function_exists( 'YoastSEO' ) ) {
+			return;
+		}
+
 		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
 			return;
 		}
@@ -40,86 +129,25 @@ class PR_Core_Jsonld {
 			return;
 		}
 
-		$repo    = new PR_Core_Peptide_Repository();
-		$peptide = $repo->find_by_id( $post_id );
-
+		$peptide = ( new PR_Core_Peptide_Repository() )->find_by_id( (int) $post_id );
 		if ( ! $peptide ) {
 			return;
 		}
 
-		$schema = $this->build_drug_schema( $peptide );
+		$permalink = get_permalink( (int) $post_id );
+		$graph     = [ $this->drug_builder->build( $peptide ) ];
 
-		/**
-		 * Filter the JSON-LD schema for a peptide page.
-		 *
-		 * @param array<string, mixed>  $schema  Schema.org data array.
-		 * @param PR_Core_Peptide_DTO   $peptide The peptide DTO.
-		 */
-		$schema = apply_filters( 'pr_core_jsonld_peptide', $schema, $peptide );
-
-		if ( empty( $schema ) ) {
-			return;
+		$faq_piece = $this->faq_builder->build( (int) $post_id, $permalink );
+		if ( null !== $faq_piece ) {
+			$graph[] = $faq_piece;
 		}
 
 		printf(
 			'<script type="application/ld+json">%s</script>' . "\n",
-			wp_json_encode( $schema, JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE | JSON_PRETTY_PRINT )
+			wp_json_encode(
+				[ '@context' => 'https://schema.org', '@graph' => $graph ],
+				JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE | JSON_PRETTY_PRINT
+			)
 		);
 	}
-
-	/**
-	 * Build a schema.org Drug object for a peptide.
-	 *
-	 * @param PR_Core_Peptide_DTO $peptide Peptide data.
-	 * @return array<string, mixed> Schema.org JSON-LD structure.
-	 */
-	private function build_drug_schema( PR_Core_Peptide_DTO $peptide ): array {
-		$schema = [
-			'@context'         => 'https://schema.org',
-			'@type'            => 'Drug',
-			'name'             => $peptide->display_name ?: $peptide->title,
-			'url'              => get_permalink( $peptide->id ),
-			'description'      => $peptide->excerpt,
-		];
-
-		if ( ! empty( $peptide->aliases ) ) {
-			$schema['alternateName'] = $peptide->aliases;
-		}
-
-		if ( '' !== $peptide->molecular_formula ) {
-			$schema['molecularFormula'] = $peptide->molecular_formula;
-		}
-
-		if ( $peptide->molecular_weight > 0 ) {
-			$schema['molecularWeight'] = [
-				'@type'    => 'QuantitativeValue',
-				'value'    => $peptide->molecular_weight,
-				'unitText' => 'Da',
-			];
-		}
-
-		// External identifiers as codes.
-		$codes = [];
-		if ( '' !== $peptide->cas_number ) {
-			$codes[] = [
-				'@type'       => 'MedicalCode',
-				'codeValue'   => $peptide->cas_number,
-				'codingSystem' => 'CAS',
-			];
-		}
-
-		if ( '' !== $peptide->drugbank_id ) {
-			$codes[] = [
-				'@type'       => 'MedicalCode',
-				'codeValue'   => $peptide->drugbank_id,
-				'codingSystem' => 'DrugBank',
-			];
-		}
-
-		if ( ! empty( $codes ) ) {
-			$schema['code'] = $codes;
-		}
-
-		return $schema;
-	}
 }

includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php

@@ -0,0 +1,270 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Migration 0004: Backfill peptide schema meta from PSA psa_* keys.
+ *
+ * What: Copies PSA-stored PubChem data (molecular formula, weight, aliases)
+ *       into PR Core's own _pr_molecular_formula, _pr_molecular_weight,
+ *       _pr_aliases meta keys on all published peptide posts.
+ *       For posts missing PSA data, attempts a PubChem REST lookup via
+ *       PR_Core_Pubchem_Client.
+ *
+ * Who calls it: PR_Core_Migration_Runner::run_pending().
+ * Dependencies: WordPress get_post_meta(), update_post_meta(), get_posts().
+ *               PR_Core_Pubchem_Client for PubChem fallback.
+ *               PR_Core_Schema_Sanitizers for formula sanitization.
+ *               PR_Core_Peptide_CPT::POST_TYPE for query.
+ *
+ * Idempotent: skips posts where all three PR Core meta keys are already non-empty.
+ * Re-runnable: safe to run multiple times.
+ *
+ * PSA source keys (all treated as UNTRUSTED — sanitized before writing):
+ *   psa_molecular_formula  => _pr_molecular_formula  (string)
+ *   psa_molecular_weight   => _pr_molecular_weight   (float string, strip "Da")
+ *   psa_aliases            => _pr_aliases            (JSON array string)
+ *
+ * @see ARCHITECTURE.md     — §v0.6.0 schema sprint.
+ * @see CONVENTIONS.md      — How To: Add a New Migration.
+ * @see class-pr-core-pubchem-client.php — HTTP client for PubChem REST.
+ */
+class PR_Core_Migration_0004_Backfill_Peptide_Meta {
+
+	/** @var string Meta key: molecular formula (PR Core namespace). */
+	public const META_FORMULA = '_pr_molecular_formula';
+
+	/** @var string Meta key: molecular weight as float string (PR Core namespace). */
+	public const META_WEIGHT  = '_pr_molecular_weight';
+
+	/** @var string Meta key: aliases JSON array (PR Core namespace). */
+	public const META_ALIASES = '_pr_aliases';
+
+	/** @var PR_Core_Pubchem_Client HTTP client for PubChem REST API. */
+	private PR_Core_Pubchem_Client $pubchem;
+
+	/**
+	 * Construct migration with optional PubChem client (injectable for testing).
+	 *
+	 * @param PR_Core_Pubchem_Client|null $pubchem PubChem client; creates default if null.
+	 */
+	public function __construct( ?PR_Core_Pubchem_Client $pubchem = null ) {
+		$this->pubchem = $pubchem ?? new PR_Core_Pubchem_Client();
+	}
+
+	/**
+	 * Run the backfill migration.
+	 *
+	 * Side effects: reads post meta, writes post meta, logs via error_log.
+	 *
+	 * @return void
+	 */
+	public function up(): void {
+		$peptide_ids = $this->get_all_peptide_ids();
+
+		if ( empty( $peptide_ids ) ) {
+			error_log( '[PR Core Migration 0004] No peptide posts found — nothing to backfill.' );
+			return;
+		}
+
+		$counts = [ 'skipped' => 0, 'copied_psa' => 0, 'pubchem_ok' => 0, 'pubchem_skip' => 0 ];
+
+		foreach ( $peptide_ids as $post_id ) {
+			$result             = $this->backfill_post( $post_id );
+			$counts[ $result ] += 1;
+		}
+
+		error_log( sprintf(
+			'[PR Core Migration 0004] Complete. Skipped: %d, PSA-copied: %d, PubChem-ok: %d, PubChem-skip: %d',
+			$counts['skipped'],
+			$counts['copied_psa'],
+			$counts['pubchem_ok'],
+			$counts['pubchem_skip']
+		) );
+	}
+
+	/**
+	 * Backfill meta for a single peptide post.
+	 *
+	 * @param int $post_id WordPress post ID.
+	 * @return string Result: skipped|copied_psa|pubchem_ok|pubchem_skip.
+	 */
+	private function backfill_post( int $post_id ): string {
+		$existing_formula = (string) get_post_meta( $post_id, self::META_FORMULA, true );
+		$existing_weight  = (string) get_post_meta( $post_id, self::META_WEIGHT, true );
+		$existing_aliases = (string) get_post_meta( $post_id, self::META_ALIASES, true );
+
+		// Idempotency limitation: this guard is all-or-nothing. A peptide that legitimately
+		// has no aliases (e.g., a novel compound) will never satisfy all three conditions and
+		// the migration will re-run on every manual re-invoke. This is safe because
+		// write_meta_from_psa() / write_meta_from_pubchem() only overwrite with non-empty
+		// values, but callers should be aware the 'skipped' result requires all three keys set.
+		if ( '' !== $existing_formula && '' !== $existing_weight && '' !== $existing_aliases ) {
+			return 'skipped';
+		}
+
+		$psa_formula = (string) get_post_meta( $post_id, 'psa_molecular_formula', true );
+
+		if ( '' !== $psa_formula ) {
+			$psa_weight  = (string) get_post_meta( $post_id, 'psa_molecular_weight', true );
+			$psa_aliases = (string) get_post_meta( $post_id, 'psa_aliases', true );
+			$this->write_meta_from_psa( $post_id, $psa_formula, $psa_weight, $psa_aliases );
+			return 'copied_psa';
+		}
+
+		// No PSA data — attempt PubChem REST lookup.
+		$psa_cid = (string) get_post_meta( $post_id, 'psa_pubchem_cid', true );
+		$post    = get_post( $post_id );
+		$name    = $post ? sanitize_text_field( $post->post_title ) : '';
+
+		$data = ( '' !== $psa_cid && ctype_digit( $psa_cid ) )
+			? $this->pubchem->fetch_by_cid( $psa_cid )
+			: null;
+
+		if ( null === $data && '' !== $name ) {
+			$data = $this->pubchem->fetch_by_name( $name );
+		}
+
+		if ( null === $data ) {
+			error_log( sprintf(
+				'[PR Core Migration 0004] Post ID %d (%s): PubChem returned no data — leaving meta empty.',
+				$post_id,
+				esc_html( $name )
+			) );
+			return 'pubchem_skip';
+		}
+
+		$formula      = PR_Core_Schema_Sanitizers::sanitize_molecular_formula( $data['formula'] );
+		$weight       = (float) $data['weight'];
+		$aliases_json = $this->synonyms_to_json( $data['synonyms'] ?? [] );
+		$this->write_pr_meta( $post_id, $formula, $weight, $aliases_json );
+
+		error_log( sprintf(
+			'[PR Core Migration 0004] Post ID %d (%s): PubChem-sourced formula=%s weight=%s',
+			$post_id,
+			esc_html( $name ),
+			$formula,
+			(string) $weight
+		) );
+
+		return 'pubchem_ok';
+	}
+
+	/**
+	 * Write PR Core meta from PSA source values.
+	 *
+	 * Input is UNTRUSTED — sanitizes before writing.
+	 *
+	 * @param int    $post_id  WordPress post ID.
+	 * @param string $formula  Raw psa_molecular_formula value.
+	 * @param string $weight   Raw psa_molecular_weight value (may include " Da").
+	 * @param string $aliases  Raw psa_aliases value (comma-separated).
+	 * @return void
+	 */
+	private function write_meta_from_psa( int $post_id, string $formula, string $weight, string $aliases ): void {
+		$clean_formula = PR_Core_Schema_Sanitizers::sanitize_molecular_formula( $formula );
+		$clean_weight  = $this->parse_weight( $weight );
+		$clean_aliases = $this->parse_aliases_string( $aliases );
+		$this->write_pr_meta( $post_id, $clean_formula, $clean_weight, $clean_aliases );
+	}
+
+	/**
+	 * Write the three PR Core meta keys for a post.
+	 *
+	 * Only writes a field when it has a usable value to avoid overwriting
+	 * existing data with empty placeholders.
+	 *
+	 * @param int    $post_id  WordPress post ID.
+	 * @param string $formula  Sanitized formula (empty = skip).
+	 * @param float  $weight   Parsed weight in g/mol (0 = skip).
+	 * @param string $aliases  JSON array string (empty array = skip).
+	 * @return void
+	 */
+	private function write_pr_meta( int $post_id, string $formula, float $weight, string $aliases ): void {
+		if ( '' !== $formula ) {
+			update_post_meta( $post_id, self::META_FORMULA, $formula );
+		}
+
+		if ( $weight > 0.0 ) {
+			update_post_meta( $post_id, self::META_WEIGHT, (string) $weight );
+		} elseif ( '' !== $formula ) {
+			error_log( '[PR Core Migration 0004] Post ID ' . $post_id . ': weight parsed to 0 — check source.' );
+		}
+
+		$decoded = json_decode( $aliases, true );
+		if ( is_array( $decoded ) && count( $decoded ) > 0 ) {
+			update_post_meta( $post_id, self::META_ALIASES, $aliases );
+		}
+	}
+
+	/**
+	 * Parse a molecular weight string to a float.
+	 *
+	 * Strips trailing " Da" suffix (case-insensitive) and whitespace.
+	 * Returns 0.0 on parse failure.
+	 *
+	 * @param string $value Raw weight value (e.g., "1419.5 Da").
+	 * @return float Parsed weight in g/mol, 0.0 on failure.
+	 */
+	public function parse_weight( string $value ): float {
+		$clean = trim( preg_replace( '/\s*[Dd][Aa]\s*$/', '', trim( $value ) ) ?? '' );
+		return (float) $clean;
+	}
+
+	/**
+	 * Parse a comma-separated alias string into a sanitized JSON array string.
+	 *
+	 * Input is UNTRUSTED — each alias is sanitized individually.
+	 *
+	 * @param string $value Comma-separated aliases.
+	 * @return string JSON array of sanitized strings, or '[]' if empty.
+	 */
+	public function parse_aliases_string( string $value ): string {
+		if ( '' === trim( $value ) ) {
+			return '[]';
+		}
+
+		$clean = [];
+		foreach ( explode( ',', $value ) as $part ) {
+			$alias = sanitize_text_field( trim( $part ) );
+			if ( '' !== $alias ) {
+				$clean[] = $alias;
+			}
+		}
+
+		return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
+	}
+
+	/**
+	 * Convert a raw synonyms array from PubChem to a JSON string.
+	 *
+	 * Sanitizes each synonym. Returns '[]' on empty input.
+	 *
+	 * @param string[] $synonyms Raw synonym strings from PubChem.
+	 * @return string JSON array of sanitized strings.
+	 */
+	private function synonyms_to_json( array $synonyms ): string {
+		$clean = [];
+		foreach ( $synonyms as $syn ) {
+			$alias = sanitize_text_field( (string) $syn );
+			if ( '' !== $alias ) {
+				$clean[] = $alias;
+			}
+		}
+		return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
+	}
+
+	/**
+	 * Get IDs of all published peptide posts.
+	 *
+	 * @return int[]
+	 */
+	private function get_all_peptide_ids(): array {
+		$posts = get_posts( [
+			'post_type'      => PR_Core_Peptide_CPT::POST_TYPE,
+			'post_status'    => 'publish',
+			'posts_per_page' => -1,
+			'fields'         => 'ids',
+		] );
+		return array_map( 'intval', is_array( $posts ) ? $posts : [] );
+	}
+}

includes/migrations/class-pr-core-migration-runner.php

@@ -29,6 +29,7 @@ class PR_Core_Migration_Runner {
 		'PR_Core_Migration_0001_Dosing_Rows',
 		'PR_Core_Migration_0002_Legal_Cells',
 		'PR_Core_Migration_0003_Candidate_Queue',
+		'PR_Core_Migration_0004_Backfill_Peptide_Meta',
 	];
 
 	/**

includes/migrations/class-pr-core-pubchem-client.php

@@ -0,0 +1,208 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Lightweight PubChem REST client for the backfill migration.
+ *
+ * What: Fetches molecular formula, molecular weight, and synonyms from the
+ *       PubChem REST API for a given compound CID or name. Used exclusively
+ *       by migration 0004 for the 4 peptide posts that lack PSA-sourced data.
+ *
+ * Who calls it: PR_Core_Migration_0004_Backfill_Peptide_Meta::fetch_pubchem().
+ * Dependencies: WordPress wp_remote_get() when available; falls back to
+ *               file_get_contents with stream context (WP-CLI context).
+ *
+ * All values from PubChem are returned unsanitized — callers must sanitize
+ * before writing to post_meta.
+ *
+ * @see migrations/class-pr-core-migration-0004-backfill-peptide-meta.php — Caller.
+ * @see ARCHITECTURE.md — §v0.6.0 schema sprint.
+ */
+class PR_Core_Pubchem_Client {
+
+	/** @var string PubChem REST base URL. */
+	private const BASE = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
+
+	/** @var int HTTP timeout per request (seconds). */
+	private const TIMEOUT = 8;
+
+	/** @var int Maximum retry attempts with exponential backoff. */
+	private const MAX_RETRIES = 3;
+
+	/** @var int Maximum synonyms to return (keeps post-meta size reasonable). */
+	private const MAX_SYNONYMS = 10;
+
+	/**
+	 * Fetch properties and synonyms by PubChem CID.
+	 *
+	 * @param string $cid Numeric PubChem CID string.
+	 * @return array{formula: string, weight: float, synonyms: string[]}|null Null on failure.
+	 */
+	public function fetch_by_cid( string $cid ): ?array {
+		if ( '' === $cid || ! ctype_digit( $cid ) ) {
+			return null;
+		}
+
+		$props = $this->fetch_properties( 'cid', $cid );
+		if ( null === $props ) {
+			return null;
+		}
+
+		$props['synonyms'] = $this->fetch_synonyms( 'cid', $cid );
+		return $props;
+	}
+
+	/**
+	 * Fetch properties and synonyms by compound name.
+	 *
+	 * @param string $name Compound name (e.g., peptide post title).
+	 * @return array{formula: string, weight: float, synonyms: string[]}|null Null on failure.
+	 */
+	public function fetch_by_name( string $name ): ?array {
+		if ( '' === trim( $name ) ) {
+			return null;
+		}
+
+		$props = $this->fetch_properties( 'name', $name );
+		if ( null === $props ) {
+			return null;
+		}
+
+		// If a CID was returned in the property response, use it for synonyms (more reliable).
+		$cid  = $props['cid'] ?? '';
+		$type = ( '' !== $cid ) ? 'cid' : 'name';
+		$ref  = ( '' !== $cid ) ? $cid : $name;
+
+		$props['synonyms'] = $this->fetch_synonyms( $type, $ref );
+		unset( $props['cid'] );
+		return $props;
+	}
+
+	/**
+	 * Fetch MolecularFormula and MolecularWeight from PubChem.
+	 *
+	 * @param string $lookup_type 'cid' or 'name'.
+	 * @param string $identifier  CID number or compound name.
+	 * @return array{formula: string, weight: float, cid: string}|null
+	 */
+	private function fetch_properties( string $lookup_type, string $identifier ): ?array {
+		$url  = self::BASE . '/compound/' . $lookup_type . '/' . rawurlencode( $identifier )
+			. '/property/MolecularFormula,MolecularWeight/JSON';
+		$body = $this->get_with_retry( $url );
+
+		if ( null === $body ) {
+			return null;
+		}
+
+		$data  = json_decode( $body, true );
+		$props = $data['PropertyTable']['Properties'][0] ?? null;
+
+		if ( ! is_array( $props ) ) {
+			return null;
+		}
+
+		$formula = (string) ( $props['MolecularFormula'] ?? '' );
+		$weight  = (float) ( $props['MolecularWeight'] ?? 0 );
+		$cid     = (string) ( $props['CID'] ?? '' );
+
+		if ( '' === $formula || $weight <= 0.0 ) {
+			return null;
+		}
+
+		return [
+			'formula' => $formula,
+			'weight'  => $weight,
+			'cid'     => $cid,
+		];
+	}
+
+	/**
+	 * Fetch synonyms for a compound, limited to MAX_SYNONYMS.
+	 *
+	 * Returns an empty array on failure — callers treat this gracefully.
+	 *
+	 * @param string $lookup_type 'cid' or 'name'.
+	 * @param string $identifier  CID or name value.
+	 * @return string[] Raw synonym strings (unsanitized).
+	 */
+	private function fetch_synonyms( string $lookup_type, string $identifier ): array {
+		$url  = self::BASE . '/compound/' . $lookup_type . '/' . rawurlencode( $identifier ) . '/synonyms/JSON';
+		$body = $this->get_with_retry( $url );
+
+		if ( null === $body ) {
+			return [];
+		}
+
+		$data     = json_decode( $body, true );
+		$synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? [];
+
+		if ( ! is_array( $synonyms ) ) {
+			return [];
+		}
+
+		return array_slice( $synonyms, 0, self::MAX_SYNONYMS );
+	}
+
+	/**
+	 * GET request with exponential-backoff retry (up to MAX_RETRIES).
+	 *
+	 * @param string $url URL to fetch.
+	 * @return string|null Response body on HTTP 200, null after all retries fail.
+	 */
+	private function get_with_retry( string $url ): ?string {
+		for ( $attempt = 0; $attempt < self::MAX_RETRIES; $attempt++ ) {
+			if ( $attempt > 0 ) {
+				sleep( (int) pow( 2, $attempt - 1 ) ); // 1s, 2s.
+			}
+
+			$body = $this->get_once( $url );
+			if ( null !== $body ) {
+				return $body;
+			}
+		}
+
+		error_log( '[PR Core PubChem] Request failed after ' . self::MAX_RETRIES . ' attempts: ' . $url );
+		return null;
+	}
+
+	/**
+	 * Single HTTP GET attempt.
+	 *
+	 * Uses wp_remote_get() when available; falls back to file_get_contents
+	 * for WP-CLI contexts where the HTTP API may not be bootstrapped.
+	 *
+	 * @param string $url URL to fetch.
+	 * @return string|null Body on HTTP 200, null on error or non-200.
+	 */
+	private function get_once( string $url ): ?string {
+		if ( function_exists( 'wp_remote_get' ) ) {
+			$response = wp_remote_get( $url, [
+				'timeout' => self::TIMEOUT,
+				'headers' => [ 'Accept' => 'application/json' ],
+			] );
+
+			if ( is_wp_error( $response ) ) {
+				return null;
+			}
+
+			if ( 200 !== (int) wp_remote_retrieve_response_code( $response ) ) {
+				return null;
+			}
+
+			$body = wp_remote_retrieve_body( $response );
+			return is_string( $body ) ? $body : null;
+		}
+
+		// WP-CLI / plain PHP fallback.
+		$context = stream_context_create( [
+			'http' => [
+				'timeout' => self::TIMEOUT,
+				'header'  => "Accept: application/json\r\n",
+				'method'  => 'GET',
+			],
+		] );
+
+		$body = @file_get_contents( $url, false, $context );
+		return ( false === $body ) ? null : $body;
+	}
+}

peptide-repo-core.php

@@ -3,7 +3,7 @@
  * Plugin Name: Peptide Repo Core
  * Plugin URI:  https://peptiderepo.com
  * Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
- * Version:     0.5.0
+ * Version:     0.6.0
  * Author:      peptiderepo
  * Author URI:  https://peptiderepo.com
  * License:     GPL-2.0-or-later
@@ -22,11 +22,11 @@ if ( ! defined( 'ABSPATH' ) ) {
 
 /* ── Constants ────────────────────────────────────────────────────────── */
 
-define( 'PR_CORE_VERSION', '0.5.0' );
+define( 'PR_CORE_VERSION', '0.6.0' );
 define( 'PR_CORE_PLUGIN_FILE', __FILE__ );
 define( 'PR_CORE_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
 define( 'PR_CORE_PLUGIN_URL', plugin_dir_url( __FILE__ ) );
-define( 'PR_CORE_TARGET_SCHEMA_VERSION', 3 );
+define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
 
 /* ── Autoloader ───────────────────────────────────────────────────────── */
 

tests/bootstrap.php

@@ -113,8 +113,10 @@ function sanitize_text_field( $value ): string {
 	return is_scalar( $value ) ? trim( (string) $value ) : '';
 }
 
-function wp_json_encode( $data ): string {
-	return json_encode( $data ) ?: '[]';
+if ( ! function_exists( 'wp_json_encode' ) ) {
+	function wp_json_encode( $data, int $flags = 0 ): string {
+		return json_encode( $data, $flags ) ?: '[]';
+	}
 }
 
 function absint( $value ): int {

tests/unit/test-jsonld.php

@@ -0,0 +1,299 @@
+<?php
+/**
+ * Unit tests for v0.6.0 JSON-LD emission: Drug @id, MedicalWebPage type,
+ * FAQ conditional emission, no duplicate nodes.
+ *
+ * Run: php tests/unit/test-jsonld.php
+ * Exit 0 = all pass, 1 = any failure.
+ *
+ * Coverage:
+ *   - Drug node: @id = {permalink}#drug, @type includes 'Drug'.
+ *   - Drug node: molecularFormula present when _pr_molecular_formula set.
+ *   - Drug node: molecularWeight present and uses g/mol when _pr_molecular_weight set.
+ *   - Drug node: alternateName present when _pr_aliases has items.
+ *   - Drug node: molecularFormula OMITTED when meta empty.
+ *   - Drug node: molecularWeight OMITTED when meta empty.
+ *   - Drug node: alternateName OMITTED when _pr_aliases is empty array.
+ *   - FAQPage: present when _pr_faq_items has items.
+ *   - FAQPage: absent when _pr_faq_items is empty or '[]'.
+ *   - FAQPage: @id = {permalink}#faq.
+ *   - MedicalWebPage retype: retype_to_medical_webpage() returns 'MedicalWebPage' on peptide singles.
+ *   - MedicalWebPage retype: passes through unchanged on non-peptide pages.
+ *   - No duplicate WebPage or BreadcrumbList nodes emitted by our code.
+ *   - PR_Core_Schema_Sanitizers::sanitize_faq_items() validation.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+require_once __DIR__ . '/../bootstrap.php';
+
+// ── Additional stubs ─────────────────────────────────────────────────────
+
+if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
+	define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
+}
+
+$GLOBALS['pr_test_postmeta']     = [];
+$GLOBALS['pr_test_is_singular']  = false;
+$GLOBALS['pr_test_singular_type'] = '';
+$GLOBALS['pr_test_the_id']       = 0;
+
+function get_post_meta( $post_id, string $key, bool $single = false ) {
+	if ( $single ) {
+		return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
+	}
+	return array_values( $GLOBALS['pr_test_postmeta'][ (int) $post_id ] ?? [] );
+}
+
+function get_permalink( $post_id = null ): string {
+	return 'https://peptiderepo.com/peptides/bpc-157/';
+}
+
+function get_the_ID(): int {
+	return $GLOBALS['pr_test_the_id'];
+}
+
+function is_singular( $type = '' ): bool {
+	if ( '' === $type ) {
+		return $GLOBALS['pr_test_is_singular'];
+	}
+	return $GLOBALS['pr_test_is_singular'] && ( $GLOBALS['pr_test_singular_type'] === $type );
+}
+
+function get_post_modified_time( $format, $gmt, $post_id ) {
+	return '2026-04-25';
+}
+
+function get_post_meta_val( $post_id, $key ) {
+	return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
+}
+
+function get_userdata( int $id ) {
+	return false;
+}
+
+function get_author_posts_url( int $id ): string {
+	return 'https://peptiderepo.com/author/' . $id;
+}
+
+function home_url( string $path = '' ): string {
+	return 'https://peptiderepo.com' . $path;
+}
+
+function apply_filters( string $tag, $value ) {
+	return $value; // No-op in test context.
+}
+
+function esc_html( string $val ): string {
+	return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
+}
+
+function esc_html__( string $text, string $domain = '' ): string {
+	return $text;
+}
+
+function wp_strip_all_tags( $value ): string {
+	return strip_tags( (string) $value );
+}
+
+function sanitize_textarea_field( $value ): string {
+	return is_scalar( $value ) ? trim( (string) $value ) : '';
+}
+
+// Load classes under test.
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/dto/class-pr-core-peptide-dto.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-drug.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
+
+// ── Helpers ──────────────────────────────────────────────────────────────
+
+/**
+ * Create a minimal PR_Core_Peptide_DTO for testing.
+ *
+ * @param array<string, mixed> $overrides Field overrides.
+ * @return PR_Core_Peptide_DTO
+ */
+function make_peptide_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
+	return new PR_Core_Peptide_DTO( array_merge( [
+		'id'                => 1,
+		'title'             => 'BPC-157',
+		'slug'              => 'bpc-157',
+		'content'           => '',
+		'excerpt'           => 'A synthetic peptide.',
+		'status'            => 'publish',
+		'display_name'      => 'BPC-157',
+		'aliases'           => [],
+		'molecular_formula' => '',
+		'molecular_weight'  => 0.0,
+		'cas_number'        => '',
+		'drugbank_id'       => '',
+		'chembl_id'         => '',
+		'evidence_strength' => 'preclinical',
+		'editorial_review_status' => 'published',
+		'last_editorial_review_at' => '',
+		'medical_editor_id' => 0,
+		'categories'        => [],
+		'families'          => [],
+	], $overrides ) );
+}
+
+echo "== JSON-LD v0.6.0 unit tests ==\n\n";
+
+// ── Drug @id ─────────────────────────────────────────────────────────────
+
+echo "Drug @id:\n";
+
+$GLOBALS['pr_test_postmeta'][1] = [];
+$peptide   = make_peptide_dto();
+$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
+
+pr_assert( isset( $drug_node['@id'] ), 'Drug node has @id' );
+pr_assert_equals(
+	'https://peptiderepo.com/peptides/bpc-157/#drug',
+	$drug_node['@id'],
+	'Drug @id = {permalink}#drug'
+);
+
+// ── Drug @type ───────────────────────────────────────────────────────────
+
+echo "\nDrug @type:\n";
+pr_assert( is_array( $drug_node['@type'] ), 'Drug @type is an array' );
+pr_assert( in_array( 'Drug', $drug_node['@type'], true ), '@type includes "Drug"' );
+pr_assert( in_array( 'MolecularEntity', $drug_node['@type'], true ), '@type includes "MolecularEntity"' );
+
+// ── Fields present when meta set ─────────────────────────────────────────
+
+echo "\nFields present when _pr_* meta set:\n";
+
+$GLOBALS['pr_test_postmeta'][1] = [
+	'_pr_molecular_formula' => 'C62H98N16O22',
+	'_pr_molecular_weight'  => '1419.5',
+	'_pr_aliases'           => '["Body Protection Compound-157","PL 14736"]',
+];
+
+$drug_node_populated = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
+
+pr_assert( isset( $drug_node_populated['molecularFormula'] ), 'molecularFormula present when meta set' );
+pr_assert_equals( 'C62H98N16O22', $drug_node_populated['molecularFormula'], 'molecularFormula value correct' );
+
+pr_assert( isset( $drug_node_populated['molecularWeight'] ), 'molecularWeight present when meta set' );
+pr_assert_equals( 'QuantitativeValue', $drug_node_populated['molecularWeight']['@type'], 'molecularWeight @type is QuantitativeValue' );
+pr_assert_equals( 1419.5, $drug_node_populated['molecularWeight']['value'], 'molecularWeight value correct' );
+pr_assert_equals( 'g/mol', $drug_node_populated['molecularWeight']['unitText'], 'molecularWeight unitText = g/mol' );
+
+pr_assert( isset( $drug_node_populated['alternateName'] ), 'alternateName present when _pr_aliases set' );
+pr_assert_equals( 2, count( $drug_node_populated['alternateName'] ), 'alternateName has correct count' );
+
+// ── Fields omitted when meta empty ───────────────────────────────────────
+
+echo "\nFields OMITTED when meta empty:\n";
+
+$GLOBALS['pr_test_postmeta'][1] = [];
+$drug_node_empty = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
+
+pr_assert( ! isset( $drug_node_empty['molecularFormula'] ), 'molecularFormula OMITTED when meta empty' );
+pr_assert( ! isset( $drug_node_empty['molecularWeight'] ), 'molecularWeight OMITTED when meta empty' );
+pr_assert( ! isset( $drug_node_empty['alternateName'] ), 'alternateName OMITTED when _pr_aliases empty' );
+
+// ── FAQPage present when _pr_faq_items has items ─────────────────────────
+
+echo "\nFAQPage emission:\n";
+
+$faq_builder = new PR_Core_Jsonld_Faq();
+$permalink   = 'https://peptiderepo.com/peptides/bpc-157/';
+
+$GLOBALS['pr_test_postmeta'][1] = [
+	'_pr_faq_items' => wp_json_encode( [
+		[ 'question' => 'What is BPC-157?', 'answer' => 'A synthetic peptide.' ],
+		[ 'question' => 'Is it legal?', 'answer' => 'Research use only.' ],
+	] ),
+];
+
+$faq_piece = $faq_builder->build( 1, $permalink );
+pr_assert( null !== $faq_piece, 'FAQPage piece not null when items present' );
+pr_assert_equals( 'FAQPage', $faq_piece['@type'], 'FAQPage @type correct' );
+pr_assert_equals( $permalink . '#faq', $faq_piece['@id'], 'FAQPage @id = {permalink}#faq' );
+pr_assert( isset( $faq_piece['mainEntity'] ), 'FAQPage has mainEntity' );
+pr_assert_equals( 2, count( $faq_piece['mainEntity'] ), 'FAQPage has 2 questions' );
+pr_assert_equals( 'Question', $faq_piece['mainEntity'][0]['@type'], 'Question @type correct' );
+pr_assert( isset( $faq_piece['mainEntity'][0]['acceptedAnswer'] ), 'Question has acceptedAnswer' );
+
+// ── FAQPage absent when _pr_faq_items empty ──────────────────────────────
+
+$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => '[]' ];
+$faq_empty = $faq_builder->build( 1, $permalink );
+pr_assert( null === $faq_empty, 'FAQPage piece IS null when _pr_faq_items is "[]"' );
+
+$GLOBALS['pr_test_postmeta'][1] = [];
+$faq_absent = $faq_builder->build( 1, $permalink );
+pr_assert( null === $faq_absent, 'FAQPage piece IS null when _pr_faq_items absent' );
+
+// ── MedicalWebPage retype ────────────────────────────────────────────────
+
+echo "\nMedicalWebPage retype:\n";
+
+$webpage_enricher = new PR_Core_Jsonld_Webpage();
+
+$GLOBALS['pr_test_is_singular']  = true;
+$GLOBALS['pr_test_singular_type'] = 'peptide';
+$result = $webpage_enricher->retype_to_medical_webpage( 'WebPage' );
+pr_assert_equals( 'MedicalWebPage', $result, 'returns MedicalWebPage on peptide single' );
+
+$GLOBALS['pr_test_is_singular']  = false;
+$GLOBALS['pr_test_singular_type'] = '';
+$result = $webpage_enricher->retype_to_medical_webpage( 'WebPage' );
+pr_assert_equals( 'WebPage', $result, 'passes through unchanged on non-peptide pages' );
+
+// ── No duplicate WebPage / BreadcrumbList nodes ───────────────────────────
+
+echo "\nNo duplicate WebPage/BreadcrumbList nodes:\n";
+
+// Verify our builders only produce Drug and FAQPage — never WebPage or BreadcrumbList.
+$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q', 'answer' => 'A' ] ] ) ];
+$types_from_builders = [];
+foreach ( [ $drug_node_populated, $faq_piece ] as $piece ) {
+	if ( null === $piece ) { continue; }
+	$t = $piece['@type'] ?? '';
+	foreach ( ( is_array( $t ) ? $t : [ $t ] ) as $type ) {
+		$types_from_builders[] = $type;
+	}
+}
+pr_assert( ! in_array( 'WebPage', $types_from_builders, true ), 'WebPage NOT in our emitted pieces' );
+pr_assert( ! in_array( 'MedicalWebPage', $types_from_builders, true ), 'MedicalWebPage NOT in injected pieces (Yoast owns node)' );
+pr_assert( ! in_array( 'BreadcrumbList', $types_from_builders, true ), 'BreadcrumbList NOT in our emitted pieces' );
+pr_assert( in_array( 'Drug', $types_from_builders, true ), 'Drug IS in our emitted pieces' );
+pr_assert( in_array( 'FAQPage', $types_from_builders, true ), 'FAQPage IS in our emitted pieces when items present' );
+
+// ── PR_Core_Schema_Sanitizers::sanitize_faq_items() ──────────────────────
+
+echo "\nPR_Core_Schema_Sanitizers::sanitize_faq_items():\n";
+
+$valid_input = wp_json_encode( [
+	[ 'question' => 'What is BPC-157?', 'answer' => 'A peptide.' ],
+] );
+$result = PR_Core_Schema_Sanitizers::sanitize_faq_items( $valid_input );
+$decoded = json_decode( $result, true );
+pr_assert( is_array( $decoded ), 'sanitize_faq_items returns JSON-decodable string' );
+pr_assert_equals( 1, count( $decoded ), 'correct count after sanitize' );
+
+$result_empty = PR_Core_Schema_Sanitizers::sanitize_faq_items( '[]' );
+pr_assert_equals( '[]', $result_empty, 'empty JSON array returns "[]"' );
+
+$result_malformed = PR_Core_Schema_Sanitizers::sanitize_faq_items( 'not-json' );
+pr_assert_equals( '[]', $result_malformed, 'malformed JSON returns "[]"' );
+
+// Item missing 'answer' key: should be dropped.
+$incomplete_input = wp_json_encode( [ [ 'question' => 'No answer here?' ] ] );
+$result_incomplete = PR_Core_Schema_Sanitizers::sanitize_faq_items( $incomplete_input );
+$decoded_incomplete = json_decode( $result_incomplete, true );
+pr_assert_equals( 0, count( $decoded_incomplete ), 'item without answer field dropped' );
+
+// ── Summary ──────────────────────────────────────────────────────────────
+
+exit( pr_test_summary() );

tests/unit/test-migration-0004.php

@@ -0,0 +1,322 @@
+<?php
+/**
+ * Unit tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
+ *
+ * Run: php tests/unit/test-migration-0004.php
+ * Exit 0 = all pass, 1 = any failure.
+ *
+ * Coverage:
+ *   - parse_weight(): strips "Da" suffix, strips "DA" variant, handles plain float,
+ *     handles empty string (returns 0.0), handles zero-value string.
+ *   - parse_aliases_string(): splits comma-separated string, trims whitespace,
+ *     drops empty segments, returns '[]' for empty input.
+ *   - PR_Core_Schema_Sanitizers::sanitize_molecular_formula(): valid chars, strips HTML, strips invalid.
+ *   - Idempotency: backfill_post() returns 'skipped' when all three PR Core keys populated.
+ *   - PSA source path: copies and transforms psa_* values to _pr_* keys.
+ *   - Empty PSA data: skips to pubchem path, returns 'pubchem_skip' on no data.
+ *
+ * Not covered here (require live WP + DB or network):
+ *   - PubChem HTTP round-trip (mocked at the http_get_once level in integration tests).
+ *   - Actual update_post_meta() persistence.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+// Bootstrap the lightweight WP stubs.
+require_once __DIR__ . '/../bootstrap.php';
+
+// ── Additional stubs needed for migration 0004 ──────────────────────────
+
+if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
+	define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
+}
+
+// Post meta store for testing.
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+
+function get_post_meta( int $post_id, string $key, bool $single = false ) {
+	$store = $GLOBALS['pr_test_postmeta'][ $post_id ] ?? [];
+	return $single ? ( $store[ $key ] ?? '' ) : array_values( $store );
+}
+
+function update_post_meta( int $post_id, string $key, $value ): bool {
+	$GLOBALS['pr_test_postmeta'][ $post_id ][ $key ] = $value;
+	$GLOBALS['pr_test_updated_meta'][]                = [ 'post_id' => $post_id, 'key' => $key, 'value' => $value ];
+	return true;
+}
+
+function get_post( int $id ) {
+	if ( isset( $GLOBALS['pr_test_posts'][ $id ] ) ) {
+		return $GLOBALS['pr_test_posts'][ $id ];
+	}
+	return null;
+}
+
+function get_posts( array $args = [] ): array {
+	return $GLOBALS['pr_test_all_post_ids'] ?? [];
+}
+
+function is_wp_error( $value ): bool {
+	return false;
+}
+
+function wp_strip_all_tags( $value ): string {
+	return strip_tags( (string) $value );
+}
+
+function esc_html( string $val ): string {
+	return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
+}
+
+if ( ! function_exists( 'error_log' ) ) {
+	function error_log( string $msg ): bool {
+		// Suppress during tests.
+		return true;
+	}
+}
+
+// Load dependencies.
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-pubchem-client.php';
+// Load migration class under test.
+require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php';
+
+// ── Expose private methods via reflection ────────────────────────────────
+
+/**
+ * Call a private/protected method on an object via reflection.
+ *
+ * @param object $obj        Instance.
+ * @param string $method     Method name.
+ * @param array  $args       Arguments.
+ * @return mixed Return value.
+ */
+function call_private( object $obj, string $method, array $args = [] ) {
+	$ref = new ReflectionMethod( $obj, $method );
+	$ref->setAccessible( true );
+	return $ref->invokeArgs( $obj, $args );
+}
+
+$migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
+
+echo "== PR_Core_Migration_0004 unit tests ==\n\n";
+
+// ── parse_weight() ───────────────────────────────────────────────────────
+
+echo "parse_weight():\n";
+
+pr_assert_equals(
+	1419.5,
+	$migration->parse_weight( '1419.5 Da' ),
+	'strips " Da" suffix and parses float'
+);
+
+pr_assert_equals(
+	1419.5,
+	$migration->parse_weight( '1419.5 DA' ),
+	'strips uppercase " DA" suffix'
+);
+
+pr_assert_equals(
+	1419.5,
+	$migration->parse_weight( '1419.5' ),
+	'parses plain float string without suffix'
+);
+
+pr_assert_equals(
+	0.0,
+	$migration->parse_weight( '' ),
+	'returns 0.0 for empty string'
+);
+
+pr_assert_equals(
+	0.0,
+	$migration->parse_weight( '  Da  ' ),
+	'returns 0.0 for suffix-only string'
+);
+
+pr_assert_equals(
+	800.123,
+	$migration->parse_weight( '  800.123 da  ' ),
+	'strips whitespace and lowercase "da"'
+);
+
+// ── parse_aliases_string() ───────────────────────────────────────────────
+
+echo "\nparse_aliases_string():\n";
+
+$result = json_decode(
+	$migration->parse_aliases_string( 'Body Protection Compound-157, PL 14736, PL-10, Bepecin' ),
+	true
+);
+pr_assert( is_array( $result ), 'returns a JSON-decodable array' );
+pr_assert_equals( 4, count( $result ), 'correct count: 4 aliases' );
+pr_assert_equals( 'Body Protection Compound-157', $result[0], 'first alias trimmed correctly' );
+pr_assert_equals( 'PL 14736', $result[1], 'second alias trimmed correctly' );
+
+$empty_result = $migration->parse_aliases_string( '' );
+pr_assert_equals( '[]', $empty_result, 'empty string returns "[]"' );
+
+$whitespace_result = $migration->parse_aliases_string( '  ,  ,  ' );
+pr_assert_equals( '[]', $whitespace_result, 'whitespace-only segments dropped, returns "[]"' );
+
+$single = json_decode( $migration->parse_aliases_string( 'Only One' ), true );
+pr_assert_equals( 1, count( $single ), 'single alias produces array of 1' );
+
+// ── sanitize_formula() ───────────────────────────────────────────────────
+// Five required cases (Option B — validate, don't allowlist):
+//   1. Valid formula unchanged.
+//   2. Parenthesised formula preserved.
+//   3. Newline-injected payload — "injection" stripped, formula kept.
+//   4. Fully invalid string (script tag contents) → empty.
+//   5. Empty / whitespace-only → empty.
+
+echo "\nPR_Core_Schema_Sanitizers::sanitize_molecular_formula():\n";
+
+pr_assert_equals(
+	'C62H98N16O22',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C62H98N16O22' ),
+	'valid formula passes unchanged'
+);
+
+pr_assert_equals(
+	'C62H98N16O22',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<b>C62H98N16O22</b>' ),
+	'HTML tags stripped from formula'
+);
+
+pr_assert_equals(
+	'C2H5(OH)',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C2H5(OH)' ),
+	'parenthesised formula preserved unchanged'
+);
+
+pr_assert_equals(
+	'C10H12',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ),
+	'non-formula characters removed — newline+word stripped, formula kept'
+);
+
+pr_assert_equals(
+	'',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<script>alert(1)</script>' ),
+	'fully invalid string returns empty string'
+);
+
+pr_assert_equals(
+	'',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '' ),
+	'empty string returns empty string'
+);
+
+pr_assert_equals(
+	'',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '   ' ),
+	'whitespace-only returns empty string'
+);
+
+// ── Idempotency: skips when all three PR Core keys populated ─────────────
+
+echo "\nIdempotency (all _pr_* keys populated):\n";
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+$GLOBALS['pr_test_postmeta'][1] = [
+	'_pr_molecular_formula' => 'C62H98N16O22',
+	'_pr_molecular_weight'  => '1419.5',
+	'_pr_aliases'           => '["Alias One"]',
+];
+
+$result = call_private( $migration, 'backfill_post', [ 1 ] );
+pr_assert_equals( 'skipped', $result, 'returns "skipped" when all three keys non-empty' );
+pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no update_post_meta calls when skipped' );
+
+// ── PSA source path ──────────────────────────────────────────────────────
+
+echo "\nPSA source path:\n";
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+$GLOBALS['pr_test_postmeta'][2] = [
+	'psa_molecular_formula' => 'C62H98N16O22',
+	'psa_molecular_weight'  => '1419.5 Da',
+	'psa_aliases'           => 'Body Protection Compound-157, PL 14736',
+];
+$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
+
+$result = call_private( $migration, 'backfill_post', [ 2 ] );
+pr_assert_equals( 'copied_psa', $result, 'returns "copied_psa" when PSA data present' );
+
+$updated = $GLOBALS['pr_test_updated_meta'];
+$formula_written = false;
+$weight_written  = false;
+$aliases_written = false;
+
+foreach ( $updated as $entry ) {
+	if ( '_pr_molecular_formula' === $entry['key'] ) {
+		$formula_written = true;
+		pr_assert_equals( 'C62H98N16O22', $entry['value'], 'formula written correctly' );
+	}
+	if ( '_pr_molecular_weight' === $entry['key'] ) {
+		$weight_written = true;
+		pr_assert_equals( '1419.5', $entry['value'], 'weight written as float string without Da' );
+	}
+	if ( '_pr_aliases' === $entry['key'] ) {
+		$aliases_written = true;
+		$aliases_arr     = json_decode( $entry['value'], true );
+		pr_assert( is_array( $aliases_arr ), 'aliases stored as JSON array' );
+		pr_assert_equals( 2, count( $aliases_arr ), 'correct number of aliases' );
+	}
+}
+
+pr_assert( $formula_written, 'molecular formula meta was written' );
+pr_assert( $weight_written, 'molecular weight meta was written' );
+pr_assert( $aliases_written, 'aliases meta was written' );
+
+// ── Partial re-run: existing values preserved ────────────────────────────
+
+echo "\nIdempotency: only some keys populated (partial re-run):\n";
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+// Only formula already set; weight and aliases are empty.
+$GLOBALS['pr_test_postmeta'][3] = [
+	'_pr_molecular_formula' => 'C10H12',
+	'_pr_molecular_weight'  => '',
+	'_pr_aliases'           => '',
+	'psa_molecular_formula' => 'C62H98N16O22',
+	'psa_molecular_weight'  => '1419.5 Da',
+	'psa_aliases'           => 'Body Protection Compound-157',
+];
+$GLOBALS['pr_test_posts'][3] = (object) [ 'post_title' => 'BPC-157', 'ID' => 3 ];
+
+$result = call_private( $migration, 'backfill_post', [ 3 ] );
+pr_assert_equals( 'copied_psa', $result, 'runs PSA copy even when only some keys populated' );
+
+// ── PubChem skip path: no PSA data, no network ──────────────────────────
+
+echo "\nPubChem skip path (no PSA data, no network in unit tests):\n";
+
+// Inject a null-returning PubChem client mock to simulate network failure.
+$mock_pubchem = new class extends PR_Core_Pubchem_Client {
+	public function fetch_by_cid( string $cid ): ?array { return null; }
+	public function fetch_by_name( string $name ): ?array { return null; }
+};
+$mock_migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta( $mock_pubchem );
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+$GLOBALS['pr_test_postmeta'][10] = []; // No PSA data, no PR Core data.
+$GLOBALS['pr_test_posts'][10] = (object) [ 'post_title' => 'IGF-1 LR3', 'ID' => 10 ];
+
+$result = call_private( $mock_migration, 'backfill_post', [ 10 ] );
+pr_assert_equals( 'pubchem_skip', $result, 'returns "pubchem_skip" when PubChem network fails' );
+pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no meta written on pubchem_skip' );
+
+// ── Summary ──────────────────────────────────────────────────────────────
+
+exit( pr_test_summary() );

uninstall.php

@@ -76,6 +76,31 @@ $wpdb->query(
 	"DELETE FROM {$wpdb->options} WHERE option_name LIKE 'pr\_core\_%'"
 );
 
+/* ── 4b. Delete v0.6.0 schema-input meta keys from all peptide posts ──── */
+
+/*
+ * Migration 0004 writes _pr_molecular_formula, _pr_molecular_weight, _pr_aliases,
+ * and _pr_faq_items to the shared peptide posts. These are PR Core-authored values
+ * (derived from PubChem / PSA) and are safe to remove on uninstall.
+ *
+ * @see ARCHITECTURE.md — §2.9 Uninstall specification.
+ */
+$schema_meta_keys = [
+	'_pr_molecular_formula',
+	'_pr_molecular_weight',
+	'_pr_aliases',
+	'_pr_faq_items',
+];
+
+foreach ( $schema_meta_keys as $meta_key ) {
+	// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
+	$wpdb->delete(
+		$wpdb->postmeta,
+		[ 'meta_key' => $meta_key ],
+		[ '%s' ]
+	);
+}
+
 /* ── 5. Remove manage_peptide_content capability from all roles ───────── */
 
 $editable_roles = wp_roles()->roles;