808b2509d8
Implements ADR-0002: canonical peptide schema as shared data layer for the peptiderepo.com ecosystem. All Tier 1 tools (Reconstitution Calculator, Dosage Reference, Legal Status Tracker, PSA enhancements) build on this. Includes: - pr_peptide CPT with REST, taxonomies, 11 meta fields - 3 custom tables: pr_dosing_rows, pr_legal_cells, pr_ai_candidate_queue - Sequential migration runner with schema versioning - 4 typed DTOs and 4 repository classes (full CRUD) - REST API (pr-core/v1): 6 endpoints (read public, write auth-gated) - Admin UI: 3 meta boxes, custom columns, AI candidate queue page - Shared disclaimer component (shortcode + static API) - JSON-LD Drug schema emission on single peptide pages - Seed data fixture (3 peptides, 10 dosing rows, 5 legal cells) - Full teardown in uninstall.php - CI: PHP lint 8.0-8.2, PHPCS WordPress, 300-line check All 22 PHP files under 300 lines. Highest: peptide-cpt at 265. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
202 lines
9.6 KiB
PHP
202 lines
9.6 KiB
PHP
<?php
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declare(strict_types=1);
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/**
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* Seed data fixture for development and testing.
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*
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* What: Creates 3 peptide posts, 10 dosing rows, and 5 legal cells.
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* Who calls it: WP-CLI command or admin action (manual trigger only).
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* Dependencies: PR_Core_Peptide_CPT, PR_Core_Dosing_Repository, PR_Core_Legal_Repository.
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*
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* @see ARCHITECTURE.md — Seed data specification.
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*/
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class PR_Core_Seed_Data {
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/**
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* Run the seed to populate the database with sample data.
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*
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* Side effects: creates posts, inserts dosing rows and legal cells.
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*
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* @return array{peptides: int, dosing_rows: int, legal_cells: int} Counts of created records.
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*/
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public static function run(): array {
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$peptide_ids = self::seed_peptides();
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$dosing = self::seed_dosing_rows( $peptide_ids );
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$legal = self::seed_legal_cells( $peptide_ids );
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return [
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'peptides' => count( $peptide_ids ),
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'dosing_rows' => $dosing,
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'legal_cells' => $legal,
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];
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}
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/**
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* Create 3 canonical peptide posts.
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*
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* @return array<string, int> Map of slug => post ID.
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*/
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private static function seed_peptides(): array {
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$peptides = [
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[
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'title' => 'BPC-157',
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'slug' => 'bpc-157',
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'excerpt' => 'Body Protection Compound-157, a pentadecapeptide derived from human gastric juice.',
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'display_name' => 'BPC-157',
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'aliases' => '["Body Protection Compound-157","Bepecin","PL 14736","PL-10"]',
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'molecular_formula' => 'C62H98N16O22',
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'molecular_weight' => 1419.53,
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'cas_number' => '137525-51-0',
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'drugbank_id' => '',
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'chembl_id' => '',
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'evidence_strength' => 'observational',
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],
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[
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'title' => 'Semaglutide',
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'slug' => 'semaglutide',
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'excerpt' => 'A GLP-1 receptor agonist approved for type 2 diabetes and chronic weight management.',
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'display_name' => 'Semaglutide',
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'aliases' => '["Ozempic","Wegovy","Rybelsus"]',
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'molecular_formula' => 'C187H291N45O59',
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'molecular_weight' => 4113.58,
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'cas_number' => '910463-68-2',
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'drugbank_id' => 'DB13928',
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'chembl_id' => 'CHEMBL3137309',
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'evidence_strength' => 'meta-analysis',
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],
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[
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'title' => 'TB-500',
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'slug' => 'tb-500',
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'excerpt' => 'Thymosin Beta-4 fragment, a synthetic peptide used in tissue repair research.',
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'display_name' => 'TB-500',
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'aliases' => '["Thymosin Beta-4","Tβ4"]',
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'molecular_formula' => 'C212H350N56O78S',
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'molecular_weight' => 4963.44,
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'cas_number' => '77591-33-4',
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'drugbank_id' => '',
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'chembl_id' => '',
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'evidence_strength' => 'preclinical',
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],
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];
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$ids = [];
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foreach ( $peptides as $p ) {
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$existing = get_posts( [
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'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
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'name' => $p['slug'],
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'posts_per_page' => 1,
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'post_status' => 'any',
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] );
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if ( ! empty( $existing ) ) {
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$ids[ $p['slug'] ] = $existing[0]->ID;
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continue;
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}
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$post_id = wp_insert_post( [
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'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
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'post_title' => $p['title'],
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'post_name' => $p['slug'],
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'post_excerpt' => $p['excerpt'],
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'post_status' => 'publish',
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'post_content' => '',
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] );
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if ( is_wp_error( $post_id ) ) {
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continue;
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}
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foreach ( [ 'display_name', 'aliases', 'molecular_formula', 'molecular_weight', 'cas_number', 'drugbank_id', 'chembl_id', 'evidence_strength' ] as $key ) {
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update_post_meta( $post_id, $key, $p[ $key ] );
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}
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update_post_meta( $post_id, 'editorial_review_status', 'published' );
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update_post_meta( $post_id, 'last_editorial_review_at', current_time( 'mysql' ) );
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$ids[ $p['slug'] ] = $post_id;
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}
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return $ids;
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}
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/**
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* Seed 10 dosing rows across the 3 peptides.
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*
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* @param array<string, int> $peptide_ids Map of slug => post ID.
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* @return int Number of rows inserted.
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*/
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private static function seed_dosing_rows( array $peptide_ids ): int {
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$repo = new PR_Core_Dosing_Repository();
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$rows = [
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// BPC-157 (4 rows).
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[ 'peptide' => 'bpc-157', 'dose_min' => 200, 'dose_max' => 300, 'dose_unit' => 'mcg', 'route' => 'subq', 'frequency' => 'twice daily', 'population' => 'healthy', 'evidence_strength' => 'observational', 'study_title' => 'BPC 157 in wound healing review', 'study_year' => 2021, 'citation_pubmed_id' => '34537800' ],
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[ 'peptide' => 'bpc-157', 'dose_min' => 500, 'dose_max' => 500, 'dose_unit' => 'mcg', 'route' => 'subq', 'frequency' => 'daily', 'population' => 'healthy', 'evidence_strength' => 'case-series', 'study_title' => 'Subcutaneous BPC-157 in tendon repair', 'study_year' => 2019, 'citation_pubmed_id' => '30915550' ],
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[ 'peptide' => 'bpc-157', 'dose_min' => 10, 'dose_max' => 10, 'dose_unit' => 'mcg', 'route' => 'oral', 'frequency' => 'daily', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'Oral BPC-157 in rat gastric ulcer model', 'study_year' => 2018, 'citation_pubmed_id' => '29869189' ],
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[ 'peptide' => 'bpc-157', 'dose_min' => 250, 'dose_max' => 750, 'dose_unit' => 'mcg', 'route' => 'im', 'frequency' => 'daily', 'population' => 'clinical', 'evidence_strength' => 'case-series', 'study_title' => 'Intramuscular BPC-157 for muscle injuries', 'study_year' => 2020, 'citation_pubmed_id' => '33312000' ],
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// Semaglutide (4 rows).
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[ 'peptide' => 'semaglutide', 'dose_min' => 0.25, 'dose_max' => 0.25, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'SUSTAIN 1: Semaglutide in T2DM', 'study_year' => 2017, 'citation_pubmed_id' => '28930514', 'indication' => 'Type 2 diabetes — initiation dose' ],
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[ 'peptide' => 'semaglutide', 'dose_min' => 1.0, 'dose_max' => 1.0, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'SUSTAIN 6: CV outcomes with semaglutide', 'study_year' => 2016, 'citation_pubmed_id' => '27633186', 'indication' => 'Type 2 diabetes — maintenance' ],
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[ 'peptide' => 'semaglutide', 'dose_min' => 2.4, 'dose_max' => 2.4, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'STEP 1: Semaglutide 2.4mg for obesity', 'study_year' => 2021, 'citation_pubmed_id' => '33567185', 'indication' => 'Chronic weight management' ],
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[ 'peptide' => 'semaglutide', 'dose_min' => 14, 'dose_max' => 14, 'dose_unit' => 'mg', 'route' => 'oral', 'frequency' => 'daily', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'PIONEER 1: Oral semaglutide in T2DM', 'study_year' => 2019, 'citation_pubmed_id' => '30924169', 'indication' => 'Type 2 diabetes — oral formulation' ],
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// TB-500 (2 rows).
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[ 'peptide' => 'tb-500', 'dose_min' => 2, 'dose_max' => 2.5, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'twice weekly', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'Thymosin beta-4 promotes dermal healing in rats', 'study_year' => 2007, 'citation_pubmed_id' => '17584560' ],
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[ 'peptide' => 'tb-500', 'dose_min' => 5, 'dose_max' => 5, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'TB4 cardiac repair in murine MI model', 'study_year' => 2012, 'citation_pubmed_id' => '22561753' ],
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];
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$count = 0;
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foreach ( $rows as $row ) {
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$slug = $row['peptide'];
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unset( $row['peptide'] );
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if ( ! isset( $peptide_ids[ $slug ] ) ) {
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continue;
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}
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$row['peptide_id'] = $peptide_ids[ $slug ];
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$row['source'] = 'manual';
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$row['added_by'] = get_current_user_id() ?: 1;
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if ( $repo->insert( $row ) > 0 ) {
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$count++;
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}
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}
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return $count;
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}
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/**
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* Seed 5 legal cells across BPC-157 and Semaglutide.
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*
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* @param array<string, int> $peptide_ids Map of slug => post ID.
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* @return int Number of cells inserted.
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*/
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private static function seed_legal_cells( array $peptide_ids ): int {
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$repo = new PR_Core_Legal_Repository();
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$cells = [
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[ 'peptide' => 'bpc-157', 'country_code' => 'US', 'status' => 'ruo', 'regulatory_framework' => 'Not FDA-approved; available as Research Use Only', 'notes' => 'Compounding pharmacies may dispense under FDA 503A/503B exemptions.' ],
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[ 'peptide' => 'bpc-157', 'country_code' => 'GB', 'status' => 'unclear', 'regulatory_framework' => 'Not listed by MHRA', 'notes' => 'No specific scheduling; import for personal use is a grey area.' ],
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[ 'peptide' => 'semaglutide', 'country_code' => 'US', 'status' => 'prescription', 'regulatory_framework' => 'FDA-approved (Ozempic, Wegovy, Rybelsus)', 'regulatory_text_url' => 'https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/209637s020lbl.pdf', 'notes' => 'Schedule IV not applicable; requires valid prescription.' ],
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[ 'peptide' => 'semaglutide', 'country_code' => 'GB', 'status' => 'prescription', 'regulatory_framework' => 'MHRA-approved (Ozempic, Wegovy)', 'notes' => 'Available via NHS and private prescription.' ],
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[ 'peptide' => 'semaglutide', 'country_code' => 'AU', 'status' => 'prescription', 'regulatory_framework' => 'TGA-approved (Ozempic)', 'notes' => 'PBS-listed for type 2 diabetes; Wegovy approval pending as of 2025.' ],
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];
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$count = 0;
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foreach ( $cells as $cell ) {
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$slug = $cell['peptide'];
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unset( $cell['peptide'] );
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if ( ! isset( $peptide_ids[ $slug ] ) ) {
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continue;
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}
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$cell['peptide_id'] = $peptide_ids[ $slug ];
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$cell['reviewer_id'] = get_current_user_id() ?: 1;
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if ( $repo->insert( $cell ) > 0 ) {
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$count++;
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}
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}
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return $count;
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}
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}
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