feat: initial peptide-repo-core plugin (v0.1.0) — canonical schema sprint
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>
This commit is contained in:
peptiderepo
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<?php
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declare(strict_types=1);
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/**
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* Migration 0001: Create the pr_dosing_rows table.
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*
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* What: Creates the high-cardinality dosing data table (1:many with peptide).
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* Who calls it: PR_Core_Migration_Runner::run_pending().
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* Dependencies: WordPress $wpdb, dbDelta().
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*
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* @see ARCHITECTURE.md — Table schema specification.
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*/
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class PR_Core_Migration_0001_Dosing_Rows {
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/**
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* Create the pr_dosing_rows table.
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*
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* Side effects: database DDL via dbDelta().
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*
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* @return void
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*/
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public function up(): void {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_dosing_rows';
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$charset = $wpdb->get_charset_collate();
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$sql = "CREATE TABLE {$table} (
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id BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
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peptide_id BIGINT UNSIGNED NOT NULL,
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dose_min DECIMAL(12,4) NULL,
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dose_max DECIMAL(12,4) NULL,
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dose_unit VARCHAR(16) NOT NULL,
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route VARCHAR(32) NOT NULL,
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frequency VARCHAR(64) NULL,
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duration_value INT UNSIGNED NULL,
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duration_unit VARCHAR(16) NULL,
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population VARCHAR(32) NOT NULL,
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indication VARCHAR(255) NULL,
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evidence_strength VARCHAR(32) NOT NULL,
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study_title VARCHAR(500) NULL,
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study_year SMALLINT UNSIGNED NULL,
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citation_pubmed_id VARCHAR(16) NULL,
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citation_doi VARCHAR(128) NULL,
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citation_url VARCHAR(500) NULL,
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notes TEXT NULL,
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schema_version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
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source VARCHAR(32) NOT NULL DEFAULT 'manual',
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ai_candidate_id BIGINT UNSIGNED NULL,
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added_by BIGINT UNSIGNED NOT NULL,
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added_at DATETIME NOT NULL,
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reviewed_by BIGINT UNSIGNED NULL,
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reviewed_at DATETIME NULL,
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superseded_by_id BIGINT UNSIGNED NULL,
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PRIMARY KEY (id),
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KEY idx_peptide (peptide_id),
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KEY idx_peptide_route (peptide_id, route),
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KEY idx_peptide_population (peptide_id, population),
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KEY idx_pubmed (citation_pubmed_id)
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) {$charset};";
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dbDelta( $sql );
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}
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}
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<?php
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declare(strict_types=1);
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/**
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* Migration 0002: Create the pr_legal_cells table.
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*
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* What: Creates the per-country legal status table (1:many with peptide).
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* Who calls it: PR_Core_Migration_Runner::run_pending().
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* Dependencies: WordPress $wpdb, dbDelta().
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*
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* Uniqueness: only one active cell per peptide x country (superseded_by_id NULL).
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*
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* @see ARCHITECTURE.md — Table schema specification.
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*/
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class PR_Core_Migration_0002_Legal_Cells {
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/** @var string[] Valid legal status enum values. */
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public const STATUSES = [
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'prescription',
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'ruo',
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'otc',
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'restricted',
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'banned',
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'unclear',
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];
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/**
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* Create the pr_legal_cells table.
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*
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* Side effects: database DDL via dbDelta().
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*
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* @return void
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*/
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public function up(): void {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_legal_cells';
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$charset = $wpdb->get_charset_collate();
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$sql = "CREATE TABLE {$table} (
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id BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
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peptide_id BIGINT UNSIGNED NOT NULL,
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country_code CHAR(2) NOT NULL,
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status VARCHAR(32) NOT NULL,
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regulatory_framework VARCHAR(128) NULL,
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regulatory_text_url VARCHAR(500) NULL,
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regulatory_text_quote TEXT NULL,
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notes TEXT NULL,
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last_verified_at DATETIME NOT NULL,
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schema_version SMALLINT UNSIGNED NOT NULL DEFAULT 1,
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reviewer_id BIGINT UNSIGNED NOT NULL,
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superseded_by_id BIGINT UNSIGNED NULL,
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PRIMARY KEY (id),
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KEY idx_peptide (peptide_id),
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KEY idx_country (country_code)
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) {$charset};";
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dbDelta( $sql );
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// dbDelta doesn't support UNIQUE with nullable columns well.
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// Add the unique constraint manually if not present.
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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$index_exists = $wpdb->get_var(
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$wpdb->prepare(
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"SELECT COUNT(*) FROM information_schema.STATISTICS WHERE TABLE_SCHEMA = %s AND TABLE_NAME = %s AND INDEX_NAME = %s",
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DB_NAME,
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$table,
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'uq_peptide_country_active'
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)
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);
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if ( '0' === $index_exists ) {
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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$wpdb->query(
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"ALTER TABLE {$table} ADD UNIQUE KEY uq_peptide_country_active (peptide_id, country_code, superseded_by_id)"
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);
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}
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}
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}
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<?php
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declare(strict_types=1);
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/**
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* Migration 0003: Create the pr_ai_candidate_queue table.
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*
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* What: Creates the AI-extracted dosing candidate queue table.
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* Who calls it: PR_Core_Migration_Runner::run_pending().
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* Dependencies: WordPress $wpdb, dbDelta().
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*
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* Approved rows are copied into pr_dosing_rows with source='ai-candidate-approved'
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* and ai_candidate_id set; queue row marked 'merged'.
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*
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* @see ARCHITECTURE.md — AI-assist candidate-extraction pipeline.
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*/
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class PR_Core_Migration_0003_Candidate_Queue {
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/** @var string[] Valid queue status enum values. */
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public const STATUSES = [
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'pending',
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'approved',
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'rejected',
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'merged',
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];
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/**
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* Create the pr_ai_candidate_queue table.
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*
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* Side effects: database DDL via dbDelta().
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*
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* @return void
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*/
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public function up(): void {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_ai_candidate_queue';
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$charset = $wpdb->get_charset_collate();
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$sql = "CREATE TABLE {$table} (
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id BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
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peptide_id BIGINT UNSIGNED NOT NULL,
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dose_min DECIMAL(12,4) NULL,
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dose_max DECIMAL(12,4) NULL,
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dose_unit VARCHAR(16) NOT NULL,
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route VARCHAR(32) NOT NULL,
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frequency VARCHAR(64) NULL,
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duration_value INT UNSIGNED NULL,
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duration_unit VARCHAR(16) NULL,
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population VARCHAR(32) NOT NULL,
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indication VARCHAR(255) NULL,
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evidence_strength VARCHAR(32) NOT NULL,
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study_title VARCHAR(500) NULL,
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study_year SMALLINT UNSIGNED NULL,
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citation_pubmed_id VARCHAR(16) NULL,
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citation_doi VARCHAR(128) NULL,
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citation_url VARCHAR(500) NULL,
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notes TEXT NULL,
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extraction_confidence FLOAT NOT NULL DEFAULT 0,
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queue_status VARCHAR(16) NOT NULL DEFAULT 'pending',
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extracted_at DATETIME NOT NULL,
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reviewed_by BIGINT UNSIGNED NULL,
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reviewed_at DATETIME NULL,
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reviewer_notes TEXT NULL,
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PRIMARY KEY (id),
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KEY idx_peptide (peptide_id),
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KEY idx_status (queue_status),
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KEY idx_confidence (extraction_confidence),
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KEY idx_peptide_status (peptide_id, queue_status)
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) {$charset};";
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dbDelta( $sql );
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}
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}
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97
includes/migrations/class-pr-core-migration-runner.php
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97
includes/migrations/class-pr-core-migration-runner.php
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<?php
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declare(strict_types=1);
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/**
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* Schema migration runner.
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*
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* What: Compares current schema version against target, runs pending migrations.
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* Who calls it: PR_Core::init() on every plugins_loaded, PR_Core_Activator on activation.
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* Dependencies: WordPress $wpdb, dbDelta().
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*
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* Migrations are numbered sequentially (0001, 0002, ...). Each migration class
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* must implement up() and optionally down(). All migrations are idempotent.
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*
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* @see peptide-repo-core.php — Defines PR_CORE_TARGET_SCHEMA_VERSION.
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* @see CONVENTIONS.md — "How To: Add a New Migration".
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*/
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class PR_Core_Migration_Runner {
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/** @var string Option key storing current schema version. */
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private const VERSION_OPTION = 'pr_core_schema_version';
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/**
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* Ordered list of migration classes.
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* Index 0 = migration 1 (bumps schema to version 1).
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*
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* @var string[]
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*/
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private const MIGRATIONS = [
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'PR_Core_Migration_0001_Dosing_Rows',
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'PR_Core_Migration_0002_Legal_Cells',
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'PR_Core_Migration_0003_Candidate_Queue',
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];
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/**
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* Run all pending migrations up to PR_CORE_TARGET_SCHEMA_VERSION.
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*
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* Side effects: creates/alters database tables, updates schema version option.
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*
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* @return void
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*/
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public function run_pending(): void {
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$current = (int) get_option( self::VERSION_OPTION, 0 );
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$target = PR_CORE_TARGET_SCHEMA_VERSION;
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if ( $current >= $target ) {
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return;
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}
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require_once ABSPATH . 'wp-admin/includes/upgrade.php';
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for ( $i = $current; $i < $target; $i++ ) {
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if ( ! isset( self::MIGRATIONS[ $i ] ) ) {
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break;
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}
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$class = self::MIGRATIONS[ $i ];
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if ( ! class_exists( $class ) ) {
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// Migration file not autoloaded — load explicitly.
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$file = $this->class_to_file( $class );
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if ( file_exists( $file ) ) {
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require_once $file;
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}
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}
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if ( class_exists( $class ) ) {
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$migration = new $class();
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$migration->up();
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}
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update_option( self::VERSION_OPTION, $i + 1 );
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}
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}
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/**
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* Get current schema version.
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*
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* @return int
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*/
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public function get_current_version(): int {
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return (int) get_option( self::VERSION_OPTION, 0 );
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}
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/**
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* Convert migration class name to file path.
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*
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* PR_Core_Migration_0001_Dosing_Rows => migrations/class-pr-core-migration-0001-dosing-rows.php
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*
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* @param string $class Fully-qualified class name.
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* @return string Absolute file path.
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*/
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private function class_to_file( string $class ): string {
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$suffix = substr( $class, 8 ); // Strip 'PR_Core_'.
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$filename = 'class-pr-core-' . str_replace( '_', '-', strtolower( $suffix ) ) . '.php';
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return PR_CORE_PLUGIN_DIR . 'includes/migrations/' . $filename;
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}
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}
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