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peptiderepo 808b2509d8 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>

2026-04-17 07:36:12 +07:00

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Peptide Repo Core — Conventions

Naming

Class prefix: PR_Core_ — all classes use this prefix.
Hook prefix: pr_core_ — all actions and filters start with this.
Option prefix: pr_core_ — all wp_options keys start with this.
Table prefix: pr_ — custom tables use {wpdb->prefix}pr_*.
CSS prefix: .pr-core- — admin and frontend styles.
Text domain: peptide-repo-core.

File Naming

Autoloader convention: PR_Core_Foo_Bar maps to class-pr-core-foo-bar.php. Files live in includes/ or one level of subdirectory under includes/.

How To: Add a New Post-Meta Field

Add the field to PR_Core_Peptide_CPT::get_meta_fields() in cpt/class-pr-core-peptide-cpt.php.
Add the field to PR_Core_Peptide_DTO constructor and to_array() in dto/class-pr-core-peptide-dto.php.
Add the field to PR_Core_Peptide_Repository::post_to_dto() in repositories/class-pr-core-peptide-repository.php.
Add a form input in PR_Core_Peptide_Metaboxes::render_identifiers_box() in admin/class-pr-core-peptide-metaboxes.php.
The save_meta() method reads from the same field list — no changes needed unless custom save logic applies.

How To: Add a New Migration

Create includes/migrations/class-pr-core-migration-NNNN-description.php.
The class must be named PR_Core_Migration_NNNN_Description with a public up() method.
Add the class name to PR_Core_Migration_Runner::MIGRATIONS array (index = version - 1).
Bump PR_CORE_TARGET_SCHEMA_VERSION in peptide-repo-core.php.
All migrations must be idempotent (safe to run twice).

How To: Add a New REST Endpoint

Add a register_rest_route() call in PR_Core_Rest_Controller::register_routes().
Implement the callback method in the same class.
Use check_write_permission() for any write endpoints.
Return typed DTOs via ->to_array() for consistent response shape.

How To: Add a New Disclaimer Surface

Add a default text entry in PR_Core_Disclaimer::DEFAULTS.
Use [pr_disclaimer surface="new-surface"] in templates.
Custom copy can be set via PR_Core_Disclaimer::update_disclaimer().

Error Handling

Repository methods return null or 0 on failure, never throw.
REST endpoints return WP_Error with appropriate HTTP status codes.
All database queries use $wpdb->prepare() for parameterization.
Admin actions verify nonces and capabilities before processing.

Evidence Strength Enum

Ordered weakest to strongest: preclinical, case-series, observational, rct-small, rct-large, meta-analysis. Validated by PR_Core_Peptide_CPT::sanitize_evidence_strength().

Legal Status Enum

Values: prescription, ruo, otc, restricted, banned, unclear. Validated by PR_Core_Legal_Repository::sanitize_row().

Supersede Pattern (Soft Delete)

Dosing rows and legal cells use a superseded_by_id column instead of hard deletes. When a correction is needed, the old row gets superseded_by_id set to the new row's ID. Queries for "active" data filter on superseded_by_id IS NULL. This preserves full audit history.

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