feat: add browsable peptide directory with category filtering, REST API, and extended meta fields (v4.3.0)
Adds [peptide_directory] shortcode with card grid, category taxonomy (8 terms), search, pagination, detail modal, and /v1/compounds REST endpoint. Includes 9 new meta fields (half-life, stability, solubility, etc.), admin data tools for migration/re-enrichment, integration hooks for cross-plugin extensibility, dark mode support, and full uninstall cleanup. Refactors AI generator into PSA_OpenRouter + PSA_KB_Builder classes. Adds PHPUnit tests for PostType and Directory classes. Fixes QA findings: dead JS selector, renderError loading state, numeric meta validation, prepared SQL in uninstall. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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peptiderepo
@@ -17,19 +17,25 @@ peptide-search-ai/
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│
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├── includes/
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│ ├── class-psa-config.php Configuration constants (rate limits, timeouts, tokens, TTL)
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│ ├── class-psa-error.php [Deprecated] Standardized error response structure
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│ ├── class-psa-post-type.php Custom Post Type (CPT) registration; meta field definitions
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│ ├── class-psa-encryption.php AES-256-CBC encryption for API keys at rest
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│ ├── class-psa-post-type.php CPT registration, peptide_category taxonomy, meta field definitions
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│ ├── class-psa-search.php AJAX search, REST API route, shortcode rendering, cache mgmt
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│ ├── class-psa-ai-generator.php AI calls (validation + generation); OpenRouter integration
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│ ├── class-psa-directory.php Browsable directory: [peptide_directory] shortcode + /v1/compounds REST endpoint
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│ ├── class-psa-ai-generator.php AI pipeline orchestrator (validation, generation, category assignment, meta save)
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│ ├── class-psa-openrouter.php OpenRouter API HTTP layer (retry, rate limit, response parsing)
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│ ├── class-psa-kb-builder.php Echo Knowledge Base article builder from AI data
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│ ├── class-psa-cost-tracker.php API usage logging, monthly budget enforcement, cost estimation
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│ ├── class-psa-pubchem.php PubChem PUG REST API integration for molecular enrichment
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│ ├── class-psa-admin.php Settings page; API key, model, auto-publish configuration
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│ └── class-psa-template.php Single peptide page rendering; quick-facts tables, badges
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│ ├── class-psa-admin.php Settings page, usage dashboard, migration tools, re-enrichment actions
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│ └── class-psa-template.php Single peptide page rendering; quick-facts, extended data, badges
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│
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├── assets/
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│ ├── js/
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│ │ └── peptide-search.js Frontend search, AJAX handler, result rendering (jQuery)
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│ │ ├── peptide-search.js Frontend search, AJAX handler, result rendering (jQuery)
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│ │ └── psa-directory.js Directory grid, category filters, detail modal (vanilla JS)
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│ └── css/
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│ └── peptide-search.css Scoped styles for search UI, results, pending states, badges
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│ ├── peptide-search.css Scoped styles for search UI, results, pending states, badges
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│ └── psa-directory.css Directory card grid, filter pills, modal styles, dark mode support
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│
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└── .github/workflows/
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├── ci.yml PHP lint, PHPCS, JS syntax checks on PR/push
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@@ -94,6 +100,23 @@ graph LR
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style D fill:#ffcdd2
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```
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### Directory REST API Flow (v4.3.0)
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```mermaid
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graph LR
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A["GET /wp-json/peptide-search-ai/v1/compounds"] --> B["Query peptide CPT"]
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B -->|"?category=slug"| C["tax_query on peptide_category"]
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B -->|"?search=term"| D["WP_Query title search"]
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C --> E["Paginated JSON response<br/>(compounds, total, total_pages)"]
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D --> E
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B --> E
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E -->|"?fields=basic"| F["Lightweight: id, name, category, vial_size"]
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E -->|"?fields=full"| G["Full: all meta fields + extras"]
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style A fill:#e3f2fd
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style E fill:#c8e6c9
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```
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### Background Generation Flow
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```mermaid
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@@ -140,10 +163,16 @@ graph TD
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- Max tokens: 4096
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- Called via WP-Cron (non-blocking)
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- **API Call:** `includes/class-psa-ai-generator.php` → `PSA_AI_Generator::call_openrouter()` (private static method)
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- **API Call:** `includes/class-psa-openrouter.php` → `PSA_OpenRouter::send_request()`
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- Endpoint: `https://openrouter.ai/api/v1/chat/completions`
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- Requires API key: database `psa_settings['api_key']` or constant `PSA_OPENROUTER_KEY`
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- Retry logic: 3 retries with exponential backoff (5s base delay)
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- Response parsing via `PSA_OpenRouter::parse_response()` (strips think tags, code fences)
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- **KB Article Creation:** `includes/class-psa-kb-builder.php` → `PSA_KB_Builder::create_article()`
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- Creates Echo Knowledge Base articles from AI-generated data
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- Builds structured HTML with h2/h3 headings, category assignment
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- Cross-references peptide post ↔ KB article via post meta
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**Configuration:** `Settings > Peptide Search AI` in WordPress admin
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- API Key field (or via `PSA_OPENROUTER_KEY` in wp-config.php for security)
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@@ -264,6 +293,31 @@ All stored on peptide posts as post meta:
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| `psa_generation_attempts` | Retry counter | Integer | System (temporary) |
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| `psa_generation_error` | Error message (if generation failed) | Text | System (temporary) |
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| `psa_generation_completed` | Generation completion timestamp | Unix timestamp | System |
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| `psa_half_life` | Half-life display (e.g., "~4-6 hours") | Text | AI (v4.3.0) |
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| `psa_stability` | Stability info (e.g., "28 Days at 2°C") | Text | AI (v4.3.0) |
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| `psa_solubility` | Reconstitution solvent | Text | AI (v4.3.0) |
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| `psa_vial_size_mg` | Common vial size in mg | Float | AI (v4.3.0) |
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| `psa_storage_lyophilized` | Storage conditions (powder) | Text | AI (v4.3.0) |
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| `psa_storage_reconstituted` | Storage conditions (solution) | Text | AI (v4.3.0) |
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| `psa_typical_dose_mcg` | Typical research dose range | Text | AI (v4.3.0) |
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| `psa_cycle_parameters` | Cycle/protocol phase info | Text | AI (v4.3.0) |
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| `psa_amino_acid_count` | Number of amino acids | Integer | Derived from sequence (v4.3.0) |
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### Taxonomy: peptide_category (v4.3.0)
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Hierarchical taxonomy registered on the `peptide` CPT. Pre-populated terms:
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Tissue Repair, Lipid Metabolism, Aging Research, Dermatological, Metabolic, Growth Hormone, Immunology, Endocrine.
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Auto-assigned during AI generation via `PSA_AI_Generator::assign_category_term()`.
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Migration for existing peptides via admin "Migrate Existing Peptides to Categories" button.
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### Integration Hooks (v4.3.0)
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| Hook | Type | Description |
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|------|------|-------------|
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| `psa_after_peptide_detail` | Action | Fired when a single peptide is rendered (single page or modal). Receives `$post_id`. |
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| `psa_directory_card_extras` | Filter | Allows adding HTML to directory cards (e.g., observation count badge). |
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| `psa_rest_compound_data` | Filter | Allows enriching REST compound data before response. Receives `$data`, `$post_id`. |
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### Options (Plugin Settings)
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@@ -349,10 +403,15 @@ $psa_settings = array(
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## Testing
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**CI Pipeline:** `.github/workflows/ci.yml`
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- PHP 7.4, 8.1, 8.3 syntax checks
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- PHPUnit tests across PHP 7.4, 8.1, 8.3
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- PHP syntax checks across PHP 7.4, 8.1, 8.3
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- WordPress Coding Standards (PHPCS) validation
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- JavaScript syntax checks (Node.js)
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**Post-Deploy:** `.github/workflows/deploy.yml`
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- HTTP health check verifies site returns 200
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- REST API smoke test verifies `/wp-json/peptides/v1/search?q=BPC-157` responds
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**Manual Testing Checklist:**
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- Search for existing peptide → results appear
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- Search for new peptide (valid) → "pending" message → check back → content generated
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