1e5999e663
Piece 1 — Backfill migration 0004: copies PSA psa_molecular_formula/weight/aliases
into PR Core _pr_* meta. Idempotent + re-runnable. PubChem REST fallback for 4
posts missing PSA data (MAX_RETRIES=3, exp backoff). All PSA values UNTRUSTED.
PR_CORE_TARGET_SCHEMA_VERSION bumped 3 -> 4.
Piece 2 — Drug node enrichment + stable @id = {permalink}#drug (ratified contract).
Reads _pr_* schema-input meta. molecularWeight in g/mol. Empty-prop guard throughout.
Piece 3 — Yoast-integrated emission via wpseo_schema_graph_pieces (priority 11),
wpseo_schema_webpage_type (MedicalWebPage retype), wpseo_schema_graph (enrichment).
Standalone @graph fallback retained. No duplicate WebPage/BreadcrumbList.
FAQPage emitted only when _pr_faq_items populated.
Supporting: PR_Core_Schema_Sanitizers, PR_Core_Pubchem_Client, CONTEXT.md,
ARCHITECTURE.md, CONVENTIONS.md, CHANGELOG.md, uninstall.php purge.
Tests: test-migration-0004.php (20 assertions), test-jsonld.php (29 assertions).
Agent-Session: peptide-schema-backfill v0.6.0
5.2 KiB
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.