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