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>
181 lines
10 KiB
Markdown
181 lines
10 KiB
Markdown
# Peptide Repo Core — Architecture
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Peptide Repo Core is a WordPress plugin that provides the canonical peptide data layer for the peptiderepo.com ecosystem. It defines the `pr_peptide` custom post type, custom tables for dosing rows and legal status cells, typed repository classes, an AI candidate queue for semi-automated data extraction, a shared disclaimer component, and JSON-LD structured data output. Every consumer plugin (PR Theme, PRAutoBlogger, Peptide News, Peptide Search AI, and all Tier 1 tools) reads peptide data through this plugin's versioned PHP API, never directly.
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---
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## Data Flow
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```
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┌───────────────────────┐
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│ PubMed / Literature │
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└──────────┬────────────┘
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│ (future: extraction pipeline)
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▼
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┌───────────────────────┐
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│ AI Candidate Queue │ pr_ai_candidate_queue table
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│ (pending → review) │ Confidence-sorted
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└──────────┬────────────┘
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│ Approve
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▼
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┌──────────────────┐ ┌───────────────────────┐ ┌──────────────────┐
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│ Admin UI / REST │───▶│ Dosing Repository │───▶│ pr_dosing_rows │
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│ (manual entry) │ │ Legal Repository │ │ pr_legal_cells │
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└──────────────────┘ └───────────────────────┘ └──────────────────┘
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│
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▼
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┌───────────────────────┐
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│ Peptide Repository │ pr_peptide CPT + meta
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└──────────┬────────────┘
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│
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┌───────────────┼───────────────┐
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▼ ▼ ▼
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┌──────────┐ ┌──────────┐ ┌──────────┐
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│ REST API │ │ JSON-LD │ │ Consumer │
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│ pr-core │ │ Drug │ │ Plugins │
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│ /v1/ │ │ schema │ │ via API │
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└──────────┘ └──────────┘ └──────────┘
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```
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---
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## File Tree
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```
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peptide-repo-core/
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├── peptide-repo-core.php # Plugin bootstrap — constants, autoloader, activation hooks
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├── uninstall.php # Full teardown: tables, posts, terms, options, capabilities
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├── ARCHITECTURE.md # This file
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├── CONVENTIONS.md # Naming patterns, extension guides
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├── CHANGELOG.md # Semantic versioning changelog
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│
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├── .github/
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│ └── workflows/
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│ └── ci.yml # PHP lint (8.0-8.2), PHPCS, 300-line check
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│
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├── assets/
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│ └── css/
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│ └── admin.css # Minimal admin meta box styles
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│
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├── includes/
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│ ├── class-pr-core.php # Main orchestrator — boots subsystems, registers public filters
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│ ├── class-pr-core-activator.php # Activation: migrations, capabilities, rewrite flush
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│ ├── class-pr-core-deactivator.php # Deactivation: rewrite flush only (data preserved)
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│ ├── class-pr-core-autoloader.php # SPL autoloader for PR_Core_ prefixed classes
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│ ├── class-pr-core-seed-data.php # Dev fixture: 3 peptides, 10 dosing rows, 5 legal cells
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│ │
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│ ├── cpt/
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│ │ └── class-pr-core-peptide-cpt.php # CPT registration, taxonomies, meta fields, sanitizers
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│ │
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│ ├── migrations/
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│ │ ├── class-pr-core-migration-runner.php # Sequential migration engine
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│ │ ├── class-pr-core-migration-0001-dosing-rows.php # pr_dosing_rows table
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│ │ ├── class-pr-core-migration-0002-legal-cells.php # pr_legal_cells table + unique constraint
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│ │ └── class-pr-core-migration-0003-candidate-queue.php # pr_ai_candidate_queue table
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│ │
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│ ├── dto/
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│ │ ├── class-pr-core-peptide-dto.php # Typed peptide value object
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│ │ ├── class-pr-core-dosing-row-dto.php # Typed dosing row value object
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│ │ ├── class-pr-core-legal-cell-dto.php # Typed legal cell value object
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│ │ └── class-pr-core-candidate-dto.php # Typed candidate queue value object
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│ │
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│ ├── repositories/
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│ │ ├── class-pr-core-peptide-repository.php # CRUD for pr_peptide CPT
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│ │ ├── class-pr-core-dosing-repository.php # CRUD for pr_dosing_rows
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│ │ ├── class-pr-core-legal-repository.php # CRUD for pr_legal_cells
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│ │ └── class-pr-core-candidate-queue-repository.php # CRUD + approve/reject for queue
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│ │
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│ ├── admin/
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│ │ ├── class-pr-core-admin.php # Admin initialization, menu, styles
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│ │ ├── class-pr-core-peptide-metaboxes.php # Identifiers, dosing, legal meta boxes
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│ │ ├── class-pr-core-admin-columns.php # Evidence, editorial, dosing count columns
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│ │ └── class-pr-core-candidate-queue-page.php # AI candidate review admin screen
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│ │
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│ ├── frontend/
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│ │ ├── class-pr-core-disclaimer.php # Shortcode + static API for surface disclaimers
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│ │ └── class-pr-core-jsonld.php # schema.org Drug JSON-LD on single peptide pages
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│ │
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│ └── api/
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│ └── class-pr-core-rest-controller.php # REST endpoints for peptides, dosing, legal
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│
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└── tests/
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├── unit/ # PHPUnit tests (mocked WP)
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└── integration/ # WordPress integration tests
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```
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---
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## Custom Tables
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### `{prefix}pr_dosing_rows`
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High-cardinality dosing data, 1:many with peptide. Indexed on peptide_id, route, population, pubmed_id.
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Supersede pattern: corrections create a new row and set `superseded_by_id` on the old one.
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### `{prefix}pr_legal_cells`
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Per-country legal status, 1:many with peptide. Unique constraint on (peptide_id, country_code, superseded_by_id) — only one active cell per peptide x country.
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### `{prefix}pr_ai_candidate_queue`
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AI-extracted dosing candidates. Status flow: pending → approved/rejected → merged (if approved). Approved rows copy into `pr_dosing_rows` with `source = 'ai-candidate-approved'`.
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---
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## Public API
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### Repositories (typed DTOs, never raw objects)
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- `PR_Core_Peptide_Repository` — find_by_id, find_by_slug, search, find_all, count
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- `PR_Core_Dosing_Repository` — find_by_id, find_by_peptide, insert, supersede, count_by_peptide
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- `PR_Core_Legal_Repository` — find_by_id, find_by_peptide, find_by_peptide_and_country, find_by_country, insert, supersede
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- `PR_Core_Candidate_Queue_Repository` — find_by_id, find_by_status, insert, approve, reject, count_by_status
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### Filters
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- `pr_core_get_indexable_corpus` — returns `{ id, url, title, body, type }` entries for search indexing
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- `pr_core_disclaimer_for_surface` — returns disclaimer text for a given surface identifier
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- `pr_core_evidence_strength_label` — maps enum value to localized label
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- `pr_core_jsonld_peptide` — filter JSON-LD schema before output
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- `pr_core_register_peptide_fields` — add computed fields to peptide DTO (planned)
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### Actions
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- `pr_core_before_peptide_publish`, `pr_core_after_peptide_publish`
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- `pr_core_before_dosing_row_publish`, `pr_core_after_dosing_row_publish`
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- `pr_core_before_legal_cell_publish`, `pr_core_after_legal_cell_publish`
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- `pr_core_candidate_approved`, `pr_core_candidate_rejected`
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### REST API (namespace: `pr-core/v1`)
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| Method | Endpoint | Auth | Description |
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|--------|----------|------|-------------|
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| GET | /peptides | Public | List peptides with filters |
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| GET | /peptides/{id} | Public | Single peptide |
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| GET | /peptides/{id}/dosing | Public | Dosing rows for peptide |
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| POST | /peptides/{id}/dosing | manage_peptide_content | Add dosing row |
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| GET | /peptides/{id}/legal | Public | Legal cells for peptide |
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| POST | /peptides/{id}/legal | manage_peptide_content | Add legal cell |
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---
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## Key Decisions
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### #1: Separate plugin for canonical schema
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Consumer plugins read through versioned PHP API + hooks, never direct table access. Decouples domain schema from feature lifecycle. See ADR-0002.
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### #2: Custom tables for dosing and legal data
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Post-meta doesn't scale for high-cardinality data queried by multiple dimensions (peptide + route + population). Custom tables with proper indexes.
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### #3: Supersede pattern instead of hard deletes
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Corrections create new rows; old rows get `superseded_by_id`. Preserves full audit trail for regulatory accountability.
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### #4: AI candidate queue with human-in-the-loop
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Automated extraction populates the queue; humans approve/reject. Approved rows copy into dosing table with provenance tracking (`source`, `ai_candidate_id`).
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### #5: Disclaimer component owned by core
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Single editorial review point. All consumer plugins render the same versioned disclaimer text. Surface-specific copy (dosing, legal, reconstitution, AI answer) stored in one wp_option.
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### #6: JSON-LD from day one
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Drug schema on single pages increases LLM citation rate. Filter hook allows consumer plugins to extend the schema object.
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