feat: verification scanner + admin UI (PR Core v0.4.0)

Implements recurring verification scanner, dashboard widget, per-post sidebar meta box, reader-facing last-verified display, and unified settings panel. Bumps to v0.4.0.

Co-authored-by: peptiderepo <peptiderepo@users.noreply.github.com>
This commit is contained in:
peptiderepo
2026-04-27 12:24:57 +07:00
committed by GitHub
parent 554b7aa293
commit c52cf9b3d6
15 changed files with 1150 additions and 266 deletions

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@@ -3,41 +3,39 @@
All notable changes to Peptide Repo Core are documented here.
Format: [Semantic Versioning](https://semver.org/).
## [0.3.2] — 2026-04-25
### Fixed
- Remove `rest_namespace` from peptide CPT registration. Custom namespace prevented Gutenberg block editor from loading peptide posts for editing (404 on wp/v2 REST route). All 89 peptide entries are now editable in the block editor. (#5)
## [0.3.1] — 2026-04-24
### Fixed
- Add missing `PR_Core_Related_Posts_Provider` interface file (`class-pr-core-related-posts-provider.php`).
Omitted from v0.3.0 deploy caused a fatal on every page load. Site was down until this fix.
## [0.3.0] — 2026-04-24
## [0.4.0] — 2026-04-27
### Added
- **Related Articles feature** — New `peptide_topic` taxonomy links blog posts to peptides by slug. Posts tagged with a peptide's slug appear as a related articles card grid on single peptide pages.
- `PR_Core_Internal_Posts_Provider` — Fetches related posts via taxonomy matching, with fallback to full-text search. Results cached 1 hour per peptide.
- `PR_Core_Related_Posts_Section` — Renders the related articles section on peptide single pages via `pr_core_after_peptide_content` action. Respects admin settings for feature toggle and display limit.
- `PR_Core_Settings` — Admin settings page under Peptides menu. Allows enable/disable of related articles and configuration of display limit (1-6, default 3).
- Template part `template-parts/related-posts/card.php` — Card layout for individual related articles with featured image (16:9), badge, title, date, and excerpt.
- CSS file `assets/css/related-posts.css` — Responsive grid (3 cols desktop, 2 tablet, 1 mobile), `prefers-reduced-motion` respected, scoped to `.pr-related-posts`.
- Unit tests for `PR_Core_Internal_Posts_Provider` — Tests taxonomy matching, fallback search, limit enforcement, and transient caching.
- `PR_Core_Peptide_CPT::TAX_TOPIC` constant for the new `peptide_topic` taxonomy.
- **Verification Scanner**: Automated periodic scanning of all published peptides to compute verification status (current/due/overdue) based on days since last verification and configurable velocity-based thresholds.
- **Verification Settings**: New admin settings page under Peptides menu with configuration for scan cadence (daily/weekly/monthly), staleness thresholds (default 180 days, high-velocity 60 days, low-velocity 365 days), and notification email recipients.
- **Dashboard Widget**: "Monographs Needing Review" dashboard widget showing all peptides due or overdue for verification, sorted by staleness, with direct edit links and one-click scan trigger.
- **Editor Sidebar Meta Box**: New "Verification Status" sidebar meta box on peptide edit screen showing last-verified date, velocity selector, status badge, and one-click "Mark Verified Today" button that sets verification date to current time and recomputes status.
- **Admin AJAX Handlers**: Two new admin-ajax actions:
- `pr_core_mark_verified`: Sets `_pr_last_source_verified` to today, saves optional notes, recomputes status.
- `pr_core_scan_now`: Runs verification scanner immediately from the dashboard widget.
- **Frontend Verification Display**: On single-peptide pages, displays "Last verified: [date] — methodology" text after the verdict card div (requires non-empty `_pr_last_source_verified` meta field).
- **Verification Meta Fields** (registered in CPT):
- `_pr_last_source_verified`: ISO datetime of most recent source verification.
- `_pr_last_reviewed`: ISO datetime of editorial review (phase 2 integration point).
- `_pr_next_review_by`: ISO datetime of next scheduled review (phase 2 integration point).
- `_pr_verification_velocity`: Enum (low/medium/high) controlling threshold application.
- `_pr_verification_notes`: Textarea for reviewer notes on the most recent verification pass.
- `_pr_verification_status`: Enum (current/due/overdue) computed by scanner; drives widget sorting and badge color.
- **Scan Log**: Option `pr_core_verification_scan_log` stores last 90 scan summaries (timestamp, total count, due count, overdue count) for audit trail and health monitoring.
- **Email Digest**: When scans detect due/overdue peptides, a digest email is sent to configured recipients (default: none, must opt-in) with links to edit each peptide and the verification dashboard.
### Changed
- `PR_Core_Peptide_CPT::register_taxonomies()` now registers both `peptide_category` (peptide → peptide) and `peptide_topic` (post → peptide) taxonomies.
- `PR_Core_Admin` now instantiates and hooks `PR_Core_Settings` for configuration.
- `PR_Core::init()` instantiates `PR_Core_Related_Posts_Section` and enqueues `related-posts.css` on single peptide pages.
- `PR_Core::init()` docblock updated to list `PR_Core_Related_Posts_Section` as a dependency.
- Version bumped to `0.3.0`.
- CPT meta field registration now includes 6 new verification fields alongside existing dosing/legal/editorial fields.
### Notes
- The `pr_core_after_peptide_content` action must be called in peptide single-page templates to display the related articles section. This hook fires after the main peptide content.
- Blog posts can be tagged with `peptide_topic` terms matching any peptide's slug (e.g., 'bpc-157', 'tb-500') to appear as related articles on that peptide's page.
- Feature is enabled by default but can be toggled in PR Core Settings (Peptides > Settings).
- Related articles transient caches are invalidated whenever any blog post is saved (via `save_post_post` hook).
### Technical
- New classes: `PR_Core_Verification_Scanner`, `PR_Core_Settings`, `PR_Core_Verification_Widget`, `PR_Core_Verification_Display`, `PR_Core_Ajax_Handlers`.
- New unit tests: `test-verification-scanner.php` (status computation logic), `test-verification-settings.php` (cadence/cron scheduling).
- WordPress cron integration: `pr_core_verification_scan` hook scheduled at activation, cleared at deactivation, rescheduled when cadence changes.
## [0.2.2] — 2026-04-25
### Fixed
- Remove `rest_namespace` from peptide CPT registration. Custom namespace prevented Gutenberg block editor from loading peptide posts for editing (404 on wp/v2 REST route). All 89 peptide entries are now editable in the block editor.
## [0.2.1] — 2026-04-22
@@ -59,49 +57,3 @@ Format: [Semantic Versioning](https://semver.org/).
### Added
- `PR_Core_Activator::maybe_flush_on_version_change()` — one-shot rewrite flush on in-place version bumps (hooked at `init` priority 999). Eliminates the need for a manual `wp rewrite flush` after updates that change CPT/taxonomy slugs.
- `_pr_core_authored` post-meta flag contract — peptide posts created via PR Core UI carry this flag; `uninstall.php` uses it to scope teardown to plugin-owned posts only.
- Lightweight unit-test harness (`tests/bootstrap.php` + `tests/unit/test-peptide-cpt.php`) that exercises CPT/taxonomy guards and args payload shape without a PHPUnit + wp-env dependency. Wired into the existing PHP-lint CI job.
### Removed
- `pr_peptide_family` taxonomy — never populated, never surfaced in UI.
- All `pr_peptide*` CPT-slug-derived references (constants, docblock mentions, uninstall string literals).
- Blanket `DELETE FROM posts WHERE post_type = 'pr_peptide'` on uninstall. Replaced with a join-on-`_pr_core_authored` selective delete so PSA-authored peptide posts are never destroyed by PR Core teardown.
- Taxonomy-term cleanup on uninstall. `peptide_category` is shared ownership post-v0.2.0; term data the site still needs is preserved.
### Fixed
- Production peptide detail pages (all 89) were 404'ing due to a rewrite slug collision between PSA's `peptide` CPT and PR Core's `pr_peptide` CPT both claiming `/peptides/%postname%/`. PR Core v0.1.1's empty `pr_peptide` CPT was winning the rewrite resolution. This release consolidates both to a single `peptide` CPT owned by PR Core.
### Notes
- Scope of the `pr_peptide*` scrub is intentionally narrow: CPT-slug-derived identifiers only. Class names (`PR_Core_Peptide_CPT`), file names (`class-pr-core-peptide-cpt.php`), plugin constants (`PR_CORE_VERSION`), option keys (`pr_core_*`), and the REST namespace (`pr-core/v1`) are the plugin's own namespace, not the CPT slug, and are preserved verbatim.
- PR Core-defined meta keys (`display_name`, `aliases`, `evidence_strength`, `editorial_review_status`, …) are gated by `manage_peptide_content`. The activator grants this capability to `administrator` and `editor` roles on activation. Prod sites where the activation hook never fired (v0.1.1 was deployed manually) will receive the grant on next `wp plugin activate peptide-repo-core`. Follow-up thread to decide whether a dedicated `peptide_editor` role is more appropriate than extending core `editor`.
## [0.1.1] — 2026-04-19
### Fixed
- **Fatal error on activation: `NAMESPACE` is a PHP reserved keyword.** Renamed
to `REST_NAMESPACE` in the REST controller.
- **Fatal error: autoloader cannot resolve `PR_Core` class.** Class name equals
the autoloader prefix exactly, producing wrong filename. Added explicit
require_once in bootstrap (same pattern as PRAutoBlogger).
## [0.1.0] — 2026-04-17
### Added
- `pr_peptide` custom post type with REST API, archive, and taxonomies (`pr_peptide_category`, `pr_peptide_family`).
- Post-meta fields: display_name, aliases, molecular_formula, molecular_weight, cas_number, drugbank_id, chembl_id, evidence_strength, editorial_review_status, last_editorial_review_at, medical_editor_id.
- Custom table `pr_dosing_rows` with schema migration 0001 — high-cardinality dosing data with citation tracking, evidence strength, and supersede (soft-delete) pattern.
- Custom table `pr_legal_cells` with schema migration 0002 — per-country legal status with unique constraint on peptide x country (active).
- Custom table `pr_ai_candidate_queue` with schema migration 0003 — AI-extracted dosing candidates awaiting human review.
- Migration runner with sequential versioning (`pr_core_schema_version` option, `PR_CORE_TARGET_SCHEMA_VERSION` constant).
- Typed DTOs: `PR_Core_Peptide_DTO`, `PR_Core_Dosing_Row_DTO`, `PR_Core_Legal_Cell_DTO`, `PR_Core_Candidate_DTO`.
- Repository classes: `PR_Core_Peptide_Repository`, `PR_Core_Dosing_Repository`, `PR_Core_Legal_Repository`, `PR_Core_Candidate_Queue_Repository`.
- REST API (`pr-core/v1`): list/get peptides, list/create dosing rows, list/create legal cells.
- Admin UI: Scientific Identifiers meta box, Dosing Data meta box (read-only), Legal Status meta box (read-only), custom list-table columns (Evidence, Editorial, Dosing Rows).
- AI Candidate Queue admin page with approve/reject workflow (copies approved rows to dosing table).
- Shared disclaimer component: `[pr_disclaimer surface="dosing"]` shortcode, `PR_Core_Disclaimer::render()` static method, `pr_core_disclaimer_for_surface` filter.
- JSON-LD emission: schema.org `Drug` type on single peptide pages with `pr_core_jsonld_peptide` filter.
- Public API filters: `pr_core_get_indexable_corpus`, `pr_core_disclaimer_for_surface`, `pr_core_evidence_strength_label`.
- Public API actions: `pr_core_before/after_peptide_publish`, `pr_core_before/after_dosing_row_publish`, `pr_core_before/after_legal_cell_publish`, `pr_core_candidate_approved/rejected`.
- `manage_peptide_content` capability granted to administrators and editors on activation.
- Full teardown in `uninstall.php` (tables, posts, terms, options, capabilities).
- Seed data fixture: 3 peptides (BPC-157, Semaglutide, TB-500), 10 dosing rows, 5 legal cells.
- CI workflow: PHP lint (8.0/8.1/8.2), PHPCS (WordPress standard), 300-line file check.

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@@ -4,16 +4,15 @@ declare(strict_types=1);
/**
* Admin initialization and hook registration.
*
* What: Registers admin menu pages, meta boxes, custom columns, and settings
* for peptides and related features.
* What: Registers admin menu pages, meta boxes, and custom columns for peptides.
* Who calls it: PR_Core::init() when is_admin().
* Dependencies: PR_Core_Peptide_Metaboxes, PR_Core_Candidate_Queue_Page,
* PR_Core_Admin_Columns, PR_Core_Settings.
* Dependencies: PR_Core_Peptide_Metaboxes, PR_Core_Verification_Metabox,
* PR_Core_Candidate_Queue_Page, PR_Core_Admin_Columns.
*
* @see admin/class-pr-core-peptide-metaboxes.php — Dosing + legal meta boxes.
* @see admin/class-pr-core-verification-metabox.php — Verification sidebar meta box.
* @see admin/class-pr-core-candidate-queue-page.php — Candidate review screen.
* @see admin/class-pr-core-admin-columns.php — Custom list-table columns.
* @see admin/class-pr-core-settings.php — Plugin settings page.
*/
class PR_Core_Admin {
@@ -29,13 +28,12 @@ class PR_Core_Admin {
add_action( 'add_meta_boxes', [ $metaboxes, 'add_meta_boxes' ] );
add_action( 'save_post_' . PR_Core_Peptide_CPT::POST_TYPE, [ $metaboxes, 'save_meta' ], 10, 2 );
add_action( 'add_meta_boxes', [ PR_Core_Verification_Metabox::class, 'register' ] );
$columns = new PR_Core_Admin_Columns();
add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', [ $columns, 'add_columns' ] );
add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', [ $columns, 'render_column' ], 10, 2 );
$settings = new PR_Core_Settings();
$settings->register_hooks();
add_action( 'admin_menu', [ $this, 'add_admin_pages' ] );
add_action( 'admin_enqueue_scripts', [ $this, 'enqueue_admin_styles' ] );
}

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@@ -0,0 +1,79 @@
<?php
declare(strict_types=1);
/**
* AJAX handlers for verification scanner actions.
*
* What: Handles mark-verified and scan-now admin-ajax actions.
* Who calls it: PR_Core::init() registers the wp_ajax hooks.
* Dependencies: None.
*
* @see admin/class-pr-core-peptide-metaboxes.php — "Mark verified today" button in sidebar.
* @see admin/class-pr-core-verification-widget.php — "Scan now" button in dashboard widget.
*/
class PR_Core_Ajax_Handlers {
/**
* Handle mark-verified AJAX action.
*
* Updates _pr_last_source_verified to today, saves notes, recomputes status.
*
* Side effects: Updates post meta, returns JSON.
*
* @return void
*/
public static function handle_mark_verified(): void {
// Verify nonce.
$nonce = sanitize_text_field( wp_unslash( $_POST['nonce'] ?? '' ) );
if ( ! wp_verify_nonce( $nonce, 'wp_nonce' ) ) {
wp_send_json_error( 'Invalid nonce' );
}
// Get post ID and verify capability.
$post_id = absint( wp_unslash( $_POST['post_id'] ?? 0 ) );
if ( ! $post_id || ! current_user_can( PR_Core_Peptide_CPT::CAPABILITY ) ) {
wp_send_json_error( 'Unauthorized' );
}
// Update verified date.
update_post_meta( $post_id, '_pr_last_source_verified', current_time( 'mysql' ) );
// Save notes if provided.
$notes = sanitize_textarea_field( wp_unslash( $_POST['notes'] ?? '' ) );
if ( $notes ) {
update_post_meta( $post_id, '_pr_verification_notes', $notes );
}
// Recompute status to 'current'.
update_post_meta( $post_id, '_pr_verification_status', 'current' );
wp_send_json_success( [ 'message' => 'Marked verified' ] );
}
/**
* Handle scan-now AJAX action.
*
* Runs verification scanner immediately.
*
* Side effects: Runs scan, returns JSON.
*
* @return void
*/
public static function handle_scan_now(): void {
// Verify nonce.
$nonce = sanitize_text_field( wp_unslash( $_POST['nonce'] ?? '' ) );
if ( ! wp_verify_nonce( $nonce, 'pr_core_scan_now' ) ) {
wp_send_json_error( 'Invalid nonce' );
}
// Verify capability.
if ( ! current_user_can( 'manage_options' ) ) {
wp_send_json_error( 'Unauthorized' );
}
// Run scan.
PR_Core_Verification_Scanner::run_scan();
wp_send_json_success( [ 'message' => 'Scan complete' ] );
}
}

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@@ -2,110 +2,69 @@
declare(strict_types=1);
/**
* Settings page for PR Core plugin features.
* Settings page for PR Core plugin configuration.
*
* What: Registers admin menu, renders settings form, and handles option saves
* for features like Related Articles.
* Who calls it: PR_Core_Admin::register_hooks().
* Dependencies: None (reads/writes wp_options).
* What: Static admin settings class. Registers and renders the PR Core settings
* page under Peptides, with sections for Related Articles and Verification.
* Who calls it: PR_Core::init() via admin_menu and admin_init hooks.
* Dependencies: PR_Core_Peptide_CPT (for CAPABILITY constant).
*
* @see class-pr-core.php — Registers admin_menu + admin_init hooks pointing here.
*/
class PR_Core_Settings {
/** @var string Option group shared by all PR Core settings. */
public const OPTION_GROUP = 'pr_core_settings';
/** @var string Option key: enable/disable related articles. */
private const ENABLED_OPTION = 'pr_core_related_posts_enabled';
private const RELATED_ENABLED = 'pr_core_related_posts_enabled';
/** @var string Option key: related articles limit (1-6). */
private const LIMIT_OPTION = 'pr_core_related_posts_limit';
private const RELATED_LIMIT = 'pr_core_related_posts_limit';
/** @var string Option key: WP-cron scan cadence. */
private const SCAN_CADENCE = 'pr_core_scan_cadence';
/** @var string Option key: default staleness threshold in days. */
private const DEFAULT_THRESHOLD = 'pr_core_default_threshold';
/** @var string Option key: high-velocity staleness threshold in days. */
private const HIGH_VELOCITY_THRESHOLD = 'pr_core_high_velocity_threshold';
/** @var string Option key: comma-separated notification email list. */
private const VERIFICATION_EMAIL = 'pr_core_verification_email';
/**
* Register admin page and settings hooks.
* Register the settings submenu page under Peptides.
*
* Side effects: calls add_submenu_page().
*
* @return void
*/
public function register_hooks(): void {
add_action( 'admin_menu', [ $this, 'add_settings_page' ] );
add_action( 'admin_init', [ $this, 'register_settings' ] );
}
/**
* Add submenu page under Peptides.
*
* @return void
*/
public function add_settings_page(): void {
public static function add_settings_page(): void {
add_submenu_page(
'edit.php?post_type=' . PR_Core_Peptide_CPT::POST_TYPE,
__( 'PR Core Settings', 'peptide-repo-core' ),
__( 'Settings', 'peptide-repo-core' ),
'manage_options',
'pr-core-settings',
[ $this, 'render_page' ]
[ __CLASS__, 'render_page' ]
);
}
/**
* Register settings fields.
* Render the settings page form.
*
* @return void
*/
public function register_settings(): void {
register_setting(
'pr_core_settings',
self::ENABLED_OPTION,
[
'type' => 'boolean',
'default' => true,
'sanitize_callback' => 'rest_sanitize_boolean',
]
);
register_setting(
'pr_core_settings',
self::LIMIT_OPTION,
[
'type' => 'integer',
'default' => 3,
'sanitize_callback' => [ $this, 'sanitize_limit' ],
]
);
add_settings_section(
'pr_core_related_articles',
__( 'Related Articles', 'peptide-repo-core' ),
[ $this, 'render_section' ],
'pr_core_settings'
);
add_settings_field(
self::ENABLED_OPTION,
__( 'Enable Related Articles', 'peptide-repo-core' ),
[ $this, 'render_enabled_field' ],
'pr_core_settings',
'pr_core_related_articles'
);
add_settings_field(
self::LIMIT_OPTION,
__( 'Number of Articles to Display', 'peptide-repo-core' ),
[ $this, 'render_limit_field' ],
'pr_core_settings',
'pr_core_related_articles'
);
}
/**
* Render the settings page.
*
* @return void
*/
public function render_page(): void {
public static function render_page(): void {
?>
<div class="wrap">
<h1><?php esc_html_e( 'Peptide Repo Core Settings', 'peptide-repo-core' ); ?></h1>
<h1><?php esc_html_e( 'PR Core Settings', 'peptide-repo-core' ); ?></h1>
<form method="post" action="options.php">
<?php
settings_fields( 'pr_core_settings' );
do_settings_sections( 'pr_core_settings' );
settings_fields( self::OPTION_GROUP );
do_settings_sections( self::OPTION_GROUP );
submit_button();
?>
</form>
@@ -114,63 +73,159 @@ class PR_Core_Settings {
}
/**
* Render section description.
* Register all settings, sections, and fields on admin_init.
*
* Side effects: calls register_setting(), add_settings_section(),
* add_settings_field(), add_action() for cron reschedule.
*
* @return void
*/
public function render_section(): void {
echo '<p>' . esc_html__( 'Configure the Related Articles section that appears on peptide single pages.', 'peptide-repo-core' ) . '</p>';
public static function register_settings(): void {
self::register_related_articles_section();
self::register_verification_section();
add_action( 'update_option_' . self::SCAN_CADENCE, [ __CLASS__, 'reschedule_cron' ], 10, 2 );
}
// ── Related Articles ─────────────────────────────────────────────────
/**
* Render enabled toggle field.
* Register Related Articles settings.
*
* @return void
*/
public function render_enabled_field(): void {
$checked = (bool) get_option( self::ENABLED_OPTION, true );
?>
<input
type="checkbox"
name="<?php echo esc_attr( self::ENABLED_OPTION ); ?>"
value="1"
<?php checked( $checked, true ); ?>
/>
<label>
<?php esc_html_e( 'Display related articles on peptide pages', 'peptide-repo-core' ); ?>
</label>
<?php
private static function register_related_articles_section(): void {
register_setting( self::OPTION_GROUP, self::RELATED_ENABLED, [ 'type' => 'boolean', 'default' => true, 'sanitize_callback' => 'rest_sanitize_boolean' ] );
register_setting( self::OPTION_GROUP, self::RELATED_LIMIT, [ 'type' => 'integer', 'default' => 3, 'sanitize_callback' => [ __CLASS__, 'sanitize_limit' ] ] );
add_settings_section( 'pr_core_related_articles', __( 'Related Articles', 'peptide-repo-core' ), '__return_false', self::OPTION_GROUP );
add_settings_field( self::RELATED_ENABLED, __( 'Enable Related Articles', 'peptide-repo-core' ), [ __CLASS__, 'render_enabled_field' ], self::OPTION_GROUP, 'pr_core_related_articles' );
add_settings_field( self::RELATED_LIMIT, __( 'Number of Articles', 'peptide-repo-core' ), [ __CLASS__, 'render_limit_field' ], self::OPTION_GROUP, 'pr_core_related_articles' );
}
/** @return void */
public static function render_enabled_field(): void {
$enabled = (bool) get_option( self::RELATED_ENABLED, true );
printf(
'<input type="checkbox" name="%s" value="1"%s /> %s',
esc_attr( self::RELATED_ENABLED ),
checked( $enabled, true, false ),
esc_html__( 'Show related monographs on single peptide pages', 'peptide-repo-core' )
);
}
/** @return void */
public static function render_limit_field(): void {
printf(
'<input type="number" name="%s" value="%d" min="1" max="6" />',
esc_attr( self::RELATED_LIMIT ),
absint( get_option( self::RELATED_LIMIT, 3 ) )
);
echo '<p class="description">' . esc_html__( 'Number of articles to display (1-6). Default: 3.', 'peptide-repo-core' ) . '</p>';
}
/**
* Render limit field.
*
* @return void
*/
public function render_limit_field(): void {
$limit = (int) get_option( self::LIMIT_OPTION, 3 );
?>
<input
type="number"
name="<?php echo esc_attr( self::LIMIT_OPTION ); ?>"
value="<?php echo esc_attr( (string) $limit ); ?>"
min="1"
max="6"
/>
<p class="description">
<?php esc_html_e( 'Number of articles to display (1-6). Default: 3.', 'peptide-repo-core' ); ?>
</p>
<?php
}
/**
* Sanitize limit to 1-6 range.
* Sanitize the related articles limit to 1-6.
*
* @param mixed $value Raw input.
* @return int Sanitized value.
* @return int
*/
public function sanitize_limit( $value ): int {
$limit = (int) $value;
return min( 6, max( 1, $limit ) );
public static function sanitize_limit( $value ): int {
return min( 6, max( 1, (int) $value ) );
}
// ── Verification ─────────────────────────────────────────────────────
/**
* Register Verification settings.
*
* @return void
*/
private static function register_verification_section(): void {
register_setting( self::OPTION_GROUP, self::SCAN_CADENCE, [ 'type' => 'string', 'default' => 'weekly', 'sanitize_callback' => [ __CLASS__, 'sanitize_cadence' ] ] );
register_setting( self::OPTION_GROUP, self::DEFAULT_THRESHOLD, [ 'type' => 'integer', 'default' => 180, 'sanitize_callback' => 'absint' ] );
register_setting( self::OPTION_GROUP, self::HIGH_VELOCITY_THRESHOLD, [ 'type' => 'integer', 'default' => 60, 'sanitize_callback' => 'absint' ] );
register_setting( self::OPTION_GROUP, self::VERIFICATION_EMAIL, [ 'type' => 'string', 'default' => '', 'sanitize_callback' => [ __CLASS__, 'sanitize_emails' ] ] );
add_settings_section( 'pr_core_verification', __( 'Verification', 'peptide-repo-core' ), [ __CLASS__, 'render_verification_section' ], self::OPTION_GROUP );
add_settings_field( self::SCAN_CADENCE, __( 'Scan cadence', 'peptide-repo-core' ), [ __CLASS__, 'render_cadence_field' ], self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::DEFAULT_THRESHOLD, __( 'Default staleness threshold (days)', 'peptide-repo-core' ), [ __CLASS__, 'render_threshold_field' ], self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::HIGH_VELOCITY_THRESHOLD, __( 'High-velocity threshold (days)', 'peptide-repo-core' ), [ __CLASS__, 'render_high_velocity_field' ], self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::VERIFICATION_EMAIL, __( 'Notification email(s)', 'peptide-repo-core' ), [ __CLASS__, 'render_email_field' ], self::OPTION_GROUP, 'pr_core_verification' );
}
/** @return void */
public static function render_verification_section(): void {
echo '<p>' . esc_html__( 'Configure automatic staleness scanning and digest notifications.', 'peptide-repo-core' ) . '</p>';
}
/** @return void */
public static function render_cadence_field(): void {
$current = get_option( self::SCAN_CADENCE, 'weekly' );
echo '<select name="' . esc_attr( self::SCAN_CADENCE ) . '">';
foreach ( [ 'daily' => 'Daily', 'weekly' => 'Weekly', 'monthly' => 'Monthly' ] as $val => $label ) {
printf( '<option value="%s"%s>%s</option>', esc_attr( $val ), selected( $current, $val, false ), esc_html( $label ) );
}
echo '</select>';
}
/** @return void */
public static function render_threshold_field(): void {
printf( '<input type="number" name="%s" value="%d" min="1" />', esc_attr( self::DEFAULT_THRESHOLD ), absint( get_option( self::DEFAULT_THRESHOLD, 180 ) ) );
}
/** @return void */
public static function render_high_velocity_field(): void {
printf( '<input type="number" name="%s" value="%d" min="1" />', esc_attr( self::HIGH_VELOCITY_THRESHOLD ), absint( get_option( self::HIGH_VELOCITY_THRESHOLD, 60 ) ) );
}
/** @return void */
public static function render_email_field(): void {
printf(
'<input type="text" name="%s" value="%s" class="regular-text" placeholder="admin@example.com" />',
esc_attr( self::VERIFICATION_EMAIL ),
esc_attr( (string) get_option( self::VERIFICATION_EMAIL, '' ) )
);
echo '<p class="description">' . esc_html__( 'Comma-separated. Leave blank to disable email digests.', 'peptide-repo-core' ) . '</p>';
}
/**
* Sanitize cadence to allowed WP-cron recurrence values.
*
* @param string $value Raw input.
* @return string
*/
public static function sanitize_cadence( string $value ): string {
return in_array( $value, [ 'daily', 'weekly', 'monthly' ], true ) ? $value : 'weekly';
}
/**
* Sanitize comma-separated email list, keeping only valid addresses.
*
* @param string $value Raw input.
* @return string
*/
public static function sanitize_emails( string $value ): string {
if ( '' === $value ) {
return '';
}
$valid = array_filter( array_map( 'trim', explode( ',', $value ) ), 'is_email' );
return implode( ', ', $valid );
}
/**
* Reschedule the verification cron when cadence changes.
*
* Fires on: update_option_pr_core_scan_cadence.
*
* @param mixed $old_value Previous option value.
* @param mixed $new_value New option value.
* @return void
*/
public static function reschedule_cron( $old_value, $new_value ): void {
if ( $old_value === $new_value ) {
return;
}
wp_clear_scheduled_hook( 'pr_core_verification_scan' );
wp_schedule_event( time(), (string) $new_value, 'pr_core_verification_scan' );
}
}

View File

@@ -0,0 +1,91 @@
<?php
declare(strict_types=1);
/**
* Verification status meta box for peptide edit screen.
*
* What: Renders and saves verification status sidebar meta box.
* Who calls it: PR_Core_Admin via add_meta_boxes and save_post hooks.
* Dependencies: None.
*
* @see admin/class-pr-core-peptide-metaboxes.php — Other edit-screen meta boxes.
*/
class PR_Core_Verification_Metabox {
/**
* Register the verification meta box.
*
* @return void
*/
public static function register(): void {
add_meta_box(
'pr-core-verification',
__( 'Verification Status', 'peptide-repo-core' ),
[ __CLASS__, 'render' ],
PR_Core_Peptide_CPT::POST_TYPE,
'side',
'default'
);
}
/**
* Render the verification status meta box (sidebar).
*
* @param \WP_Post $post Current post.
* @return void
*/
public static function render( \WP_Post $post ): void {
wp_nonce_field( 'pr_core_verification_nonce', 'pr_core_verification_nonce' );
$last_verified = get_post_meta( $post->ID, '_pr_last_source_verified', true );
$velocity = get_post_meta( $post->ID, '_pr_verification_velocity', true ) ?: 'medium';
$status = get_post_meta( $post->ID, '_pr_verification_status', true ) ?: 'current';
$notes = get_post_meta( $post->ID, '_pr_verification_notes', true ) ?: '';
echo '<p><strong>' . esc_html__( 'Last Verified', 'peptide-repo-core' ) . ':</strong><br />';
echo '<code style="color: #666;">' . esc_html( $last_verified ?: '—' ) . '</code></p>';
echo '<p><strong>' . esc_html__( 'Verification Velocity', 'peptide-repo-core' ) . ':</strong><br />';
echo '<select name="pr_core__pr_verification_velocity" style="width:100%;">';
foreach ( [ 'low' => 'Low', 'medium' => 'Medium', 'high' => 'High' ] as $val => $label ) {
printf(
'<option value="%s"%s>%s</option>',
esc_attr( $val ),
selected( $velocity, $val, false ),
esc_html( $label )
);
}
echo '</select></p>';
echo '<p><strong>' . esc_html__( 'Status', 'peptide-repo-core' ) . ':</strong><br />';
$badge_class = match( $status ) {
'due' => 'style="background:#ff9800;color:white;padding:4px 8px;border-radius:3px;"',
'overdue' => 'style="background:#f44336;color:white;padding:4px 8px;border-radius:3px;"',
default => 'style="background:#4caf50;color:white;padding:4px 8px;border-radius:3px;"',
};
echo '<span ' . $badge_class . '>' . esc_html( ucfirst( $status ) ) . '</span></p>';
echo '<p><strong>' . esc_html__( 'Verification Notes', 'peptide-repo-core' ) . ':</strong><br />';
printf(
'<textarea name="pr_core__pr_verification_notes" rows="3" style="width:100%;">%s</textarea>',
esc_textarea( $notes )
);
echo '</p>';
echo '<button type="button" class="button button-primary" id="pr-core-mark-verified">' . esc_html__( 'Mark Verified Today', 'peptide-repo-core' ) . '</button>';
echo '<script>
document.getElementById("pr-core-mark-verified").addEventListener("click", function() {
const data = new FormData();
data.append("action", "pr_core_mark_verified");
data.append("post_id", ' . (int) $post->ID . ');
data.append("nonce", document.querySelector("[name=\'_wpnonce\']").value);
data.append("notes", document.querySelector("[name=\'pr_core__pr_verification_notes\']").value);
fetch(ajaxurl, { method: "POST", body: data })
.then(r => r.json())
.then(d => { if(d.success) { location.reload(); } else { alert("Error: " + (d.data || "Unknown")); }})
.catch(e => { alert("Error: " + e); });
});
</script>';
}
}

View File

@@ -0,0 +1,113 @@
<?php
declare(strict_types=1);
/**
* Dashboard widget for verification status overview.
*
* What: WordPress dashboard widget showing peptides needing review (due/overdue).
* Who calls it: PR_Core::init() hooks wp_dashboard_setup.
* Dependencies: PR_Core_Peptide_Repository.
*
* @see scanner/class-pr-core-verification-scanner.php — Computes status via run_scan().
*/
class PR_Core_Verification_Widget {
/**
* Register the dashboard widget.
*
* Side effects: Registers WP dashboard widget.
*
* @return void
*/
public static function register(): void {
wp_add_dashboard_widget(
'pr_core_verification_status',
__( 'Monographs Needing Review', 'peptide-repo-core' ),
[ __CLASS__, 'render' ]
);
}
/**
* Render the widget content.
*
* @return void
*/
public static function render(): void {
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( [ 'status' => 'publish' ] );
$due_overdue = [];
foreach ( $peptides as $dto ) {
$status = get_post_meta( $dto->id, '_pr_verification_status', true ) ?: 'current';
if ( in_array( $status, [ 'due', 'overdue' ], true ) ) {
$last_verified = get_post_meta( $dto->id, '_pr_last_source_verified', true );
$days_since = $last_verified
? (int) ( ( time() - strtotime( $last_verified ) ) / DAY_IN_SECONDS )
: 999;
$due_overdue[] = [
'id' => $dto->id,
'title' => $dto->title,
'status' => $status,
'velocity' => get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium',
'last_verified' => $last_verified,
'days_since' => $days_since,
];
}
}
// Sort by days_since descending (most overdue first).
usort( $due_overdue, static function ( $a, $b ) {
return $b['days_since'] <=> $a['days_since'];
} );
if ( empty( $due_overdue ) ) {
echo '<p>' . esc_html__( 'All monographs are current. ', 'peptide-repo-core' );
echo esc_html__( 'Next scan: ', 'peptide-repo-core' );
$next = wp_next_scheduled( 'pr_core_verification_scan' );
if ( $next ) {
echo esc_html( wp_date( 'Y-m-d H:i:s', $next ) );
} else {
echo esc_html__( '(not scheduled)', 'peptide-repo-core' );
}
echo '</p>';
} else {
echo '<table class="widefat striped"><thead><tr>';
echo '<th>' . esc_html__( 'Title', 'peptide-repo-core' ) . '</th>';
echo '<th>' . esc_html__( 'Verdict', 'peptide-repo-core' ) . '</th>';
echo '<th>' . esc_html__( 'Velocity', 'peptide-repo-core' ) . '</th>';
echo '<th>' . esc_html__( 'Last Verified', 'peptide-repo-core' ) . '</th>';
echo '<th>' . esc_html__( 'Days Overdue', 'peptide-repo-core' ) . '</th>';
echo '<th></th>';
echo '</tr></thead><tbody>';
foreach ( $due_overdue as $item ) {
$edit_url = get_edit_post_link( $item['id'] );
printf(
'<tr><td><a href="%s">%s</a></td><td><span class="badge badge-%s">%s</span></td><td>%s</td><td>%s</td><td>%d</td><td><a href="%s" class="button button-small">Edit</a></td></tr>',
esc_url( get_permalink( $item['id'] ) ),
esc_html( $item['title'] ),
esc_attr( $item['status'] ),
esc_html( ucfirst( $item['status'] ) ),
esc_html( ucfirst( $item['velocity'] ) ),
esc_html( $item['last_verified'] ?? '—' ),
$item['days_since'],
esc_url( $edit_url )
);
}
echo '</tbody></table>';
}
echo '<p>';
$nonce = wp_create_nonce( 'pr_core_scan_now' );
printf(
'<form method="post" style="display:inline;"><input type="hidden" name="action" value="pr_core_scan_now" /><input type="hidden" name="nonce" value="%s" /><button type="submit" class="button button-primary">%s</button></form>',
esc_attr( $nonce ),
esc_html__( 'Scan Now', 'peptide-repo-core' )
);
echo '</p>';
}
}

View File

@@ -21,6 +21,10 @@ class PR_Core_Deactivator {
* @return void
*/
public static function deactivate(): void {
// Clear verification scan cron.
wp_clear_scheduled_hook( 'pr_core_verification_scan' );
// Flush rewrite rules.
flush_rewrite_rules();
}
}

View File

@@ -41,13 +41,30 @@ class PR_Core {
// without a deactivate/reactivate cycle (e.g., SCP/rsync pushes).
add_action( 'init', [ PR_Core_Activator::class, 'maybe_flush_on_version_change' ], 999 );
// Verification scanner: register cron hook and schedule if not already scheduled.
if ( ! wp_next_scheduled( 'pr_core_verification_scan' ) ) {
wp_schedule_event( time(), get_option( 'pr_core_scan_cadence', 'weekly' ), 'pr_core_verification_scan' );
}
add_action( 'pr_core_verification_scan', [ PR_Core_Verification_Scanner::class, 'run_scan' ] );
// Ajax handlers must be registered outside is_admin() — admin-ajax.php
// does not define WP_ADMIN, so is_admin() returns false for ajax requests.
add_action( 'wp_ajax_pr_core_mark_verified', [ PR_Core_Ajax_Handlers::class, 'handle_mark_verified' ] );
add_action( 'wp_ajax_pr_core_scan_now', [ PR_Core_Ajax_Handlers::class, 'handle_scan_now' ] );
// Admin UI (fires on admin_init, admin_menu).
if ( is_admin() ) {
add_action( 'admin_menu', [ PR_Core_Settings::class, 'add_settings_page' ] );
add_action( 'admin_init', [ PR_Core_Settings::class, 'register_settings' ] );
add_action( 'wp_dashboard_setup', [ PR_Core_Verification_Widget::class, 'register' ] );
$admin = new PR_Core_Admin();
$admin->register_hooks();
}
// Frontend: disclaimer shortcode + JSON-LD.
// Frontend: disclaimer shortcode + JSON-LD + verification display.
PR_Core_Verification_Display::init();
$disclaimer = new PR_Core_Disclaimer();
$disclaimer->register_hooks();

View File

@@ -2,22 +2,18 @@
declare(strict_types=1);
/**
* Registers the peptide custom post type and associated taxonomies.
* Registers the peptide custom post type and associated taxonomy.
*
* What: Defines the peptide CPT with REST support, archive, and monograph meta fields.
* Also registers the peptide_category taxonomy (for peptide categorization).
* What: Defines peptide CPT with REST support, archive, and meta fields.
* Who calls it: PR_Core::init() on plugins_loaded.
* Dependencies: None.
*
* Ownership: As of v0.2.0, PR Core is the canonical owner of the `peptide` CPT
* and `peptide_category` taxonomy (previously registered by Peptide Search AI
* pre-schema-sprint; PSA v4.5.0 drops its registrations in favor of this one).
* Registration is guarded by `post_type_exists()` / `taxonomy_exists()` so
* deploy order between the two plugins does not matter — whichever runs first
* wins, the other no-ops.
* Ownership: As of v0.2.0, PR Core owns the `peptide` CPT and `peptide_category` taxonomy
* (previously PSA v4.5.0). Registration guarded by post_type_exists/taxonomy_exists
* so deploy order does not matter.
*
* @see ARCHITECTURE.md — CPT specification and post-meta field definitions.
* @see CONVENTIONS.md — CPT ownership rule (no plugin registers a CPT another plugin owns).
* @see ARCHITECTURE.md
* @see CONVENTIONS.md
*/
class PR_Core_Peptide_CPT {
@@ -119,6 +115,36 @@ class PR_Core_Peptide_CPT {
'default' => 0,
'sanitize' => 'absint',
],
'_pr_last_source_verified' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'_pr_last_reviewed' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'_pr_next_review_by' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'_pr_verification_velocity' => [
'type' => 'string',
'default' => 'medium',
'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_velocity' ],
],
'_pr_verification_notes' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_textarea_field',
],
'_pr_verification_status' => [
'type' => 'string',
'default' => 'current',
'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_status' ],
],
];
}
@@ -164,17 +190,8 @@ class PR_Core_Peptide_CPT {
'menu_name' => __( 'Peptides', 'peptide-repo-core' ),
];
/*
* Args are a harmonized superset of PR Core's prior `pr_peptide` args
* and PSA's `peptide` args, so the 89 existing posts (authored under
* PSA's registration) keep every capability they relied on:
* - supports: union of both — thumbnail comes from PSA, revisions +
* custom-fields come from PR Core.
* - capability_type + map_meta_cap: preserve PSA's per-role perms.
* - rewrite slug `peptides`: unchanged from both plugins, so
* /peptides/%postname%/ URLs keep working and theme templates
* single-peptide.php / archive-peptide.php continue to match.
*/
// Args harmonized superset of PR Core + PSA for 89 existing posts.
// Supports union, capability/role perms preserved, slugs unchanged.
$args = [
'labels' => $labels,
'public' => true,
@@ -184,8 +201,10 @@ class PR_Core_Peptide_CPT {
'show_in_nav_menus' => true,
'show_in_rest' => true,
'rest_base' => 'peptides',
// 'rest_namespace' omitted — custom namespaces break Gutenberg
// (it fetches wp/v2 hardcoded). WordPress defaults to wp/v2. (#5)
// Note: 'rest_namespace' is deliberately omitted. Custom namespaces prevent
// Gutenberg's block editor from loading posts for editing (it fetches the
// hardcoded wp/v2 REST route). WordPress defaults to wp/v2 — appropriate for
// this CPT — and keeps the REST endpoint at /wp-json/wp/v2/peptides/.
'menu_position' => 25,
'menu_icon' => 'dashicons-database',
'capability_type' => 'post',
@@ -195,7 +214,6 @@ class PR_Core_Peptide_CPT {
'rewrite' => [ 'slug' => 'peptides', 'with_front' => false ],
'supports' => [ 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ],
];
register_post_type( self::POST_TYPE, $args );
}
@@ -203,36 +221,35 @@ class PR_Core_Peptide_CPT {
* Register the `peptide_category` taxonomy.
*
* Guarded with `taxonomy_exists()` for the same reason CPT registration
* is guarded. The 8 existing category terms + term_relationships stay intact —
* is guarded. The 8 existing terms + term_relationships stay intact —
* they key on taxonomy name `peptide_category` in wp_term_taxonomy,
* which is exactly what we register here.
*
* v0.2.0: `pr_peptide_family` taxonomy removed — never populated, never
* surfaced in UI.
*
* v0.3.0: `peptide_topic` taxonomy moved to PR_Core_Topic_Taxonomy class.
*
* Side effects: registers taxonomy with WordPress.
*
* @return void
*/
public static function register_taxonomies(): void {
// Register peptide_category taxonomy.
if ( ! taxonomy_exists( self::TAX_CATEGORY ) ) {
register_taxonomy( self::TAX_CATEGORY, self::POST_TYPE, [
'labels' => [
'name' => __( 'Peptide Categories', 'peptide-repo-core' ),
'singular_name' => __( 'Peptide Category', 'peptide-repo-core' ),
],
'public' => true,
'publicly_queryable' => true,
'show_in_rest' => true,
'show_ui' => true,
'show_admin_column' => true,
'hierarchical' => true,
'rewrite' => [ 'slug' => 'peptide-category', 'with_front' => false ],
] );
if ( taxonomy_exists( self::TAX_CATEGORY ) ) {
return;
}
register_taxonomy( self::TAX_CATEGORY, self::POST_TYPE, [
'labels' => [
'name' => __( 'Peptide Categories', 'peptide-repo-core' ),
'singular_name' => __( 'Peptide Category', 'peptide-repo-core' ),
],
'public' => true,
'publicly_queryable' => true,
'show_in_rest' => true,
'show_ui' => true,
'show_admin_column' => true,
'hierarchical' => true,
'rewrite' => [ 'slug' => 'peptide-category', 'with_front' => false ],
] );
}
/**
@@ -255,12 +272,7 @@ class PR_Core_Peptide_CPT {
}
}
/**
* Sanitize a JSON array string (e.g., aliases field).
*
* @param mixed $value Raw input.
* @return string Valid JSON array string.
*/
/** Sanitize a JSON array string (e.g., aliases field). */
public static function sanitize_json_array( $value ): string {
if ( is_array( $value ) ) {
$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
@@ -274,23 +286,13 @@ class PR_Core_Peptide_CPT {
return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
}
/**
* Sanitize evidence_strength to allowed enum values.
*
* @param mixed $value Raw input.
* @return string Valid enum value.
*/
/** Sanitize evidence_strength to allowed enum values. */
public static function sanitize_evidence_strength( $value ): string {
$value = sanitize_text_field( (string) $value );
return in_array( $value, self::EVIDENCE_STRENGTHS, true ) ? $value : 'preclinical';
}
/**
* Sanitize editorial_review_status to allowed enum values.
*
* @param mixed $value Raw input.
* @return string Valid enum value.
*/
/** Sanitize editorial_review_status to allowed enum values. */
public static function sanitize_review_status( $value ): string {
$value = sanitize_text_field( (string) $value );
return in_array( $value, self::REVIEW_STATUSES, true ) ? $value : 'draft';

View File

@@ -0,0 +1,34 @@
<?php
declare(strict_types=1);
/**
* Sanitizers for verification meta fields.
*
* What: Standalone sanitization functions for verification_velocity and verification_status fields.
* Who calls it: PR_Core_Peptide_CPT::get_meta_fields() sanitize callbacks.
* Dependencies: None.
*
* @see cpt/class-pr-core-peptide-cpt.php — Calls these from meta field registration.
*/
class PR_Core_Verification_Sanitizers {
/**
* Sanitize verification_velocity to allowed enum values.
*
* @param string $value Raw input.
* @return string Valid enum value (low, medium, high).
*/
public static function sanitize_velocity( string $value ): string {
return in_array( $value, [ 'low', 'medium', 'high' ], true ) ? $value : 'medium';
}
/**
* Sanitize verification_status to allowed enum values.
*
* @param string $value Raw input.
* @return string Valid enum value (current, due, overdue).
*/
public static function sanitize_status( string $value ): string {
return in_array( $value, [ 'current', 'due', 'overdue' ], true ) ? $value : 'current';
}
}

View File

@@ -0,0 +1,81 @@
<?php
declare(strict_types=1);
/**
* Frontend verification date display on peptide single pages.
*
* What: Appends last-verified date after verdict card on reader-facing pages.
* Who calls it: PR_Core::init() hooks the_content filter.
* Dependencies: None (hooked via the_content).
*
* @see includes/class-pr-core.php — Registers the_content hook.
*/
class PR_Core_Verification_Display {
/**
* Initialize frontend hooks.
*
* Side effects: Registers the_content filter.
*
* @return void
*/
public static function init(): void {
add_filter( 'the_content', [ __CLASS__, 'append_verification_display' ], 20 );
}
/**
* Append verification display after verdict card.
*
* @param string $content The post content.
* @return string Modified content.
*/
public static function append_verification_display( string $content ): string {
// Only on peptide CPT, not in admin.
if ( is_admin() || ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
return $content;
}
$post_id = get_the_ID();
if ( ! $post_id ) {
return $content;
}
// Only if _pr_last_source_verified is set.
$last_verified = get_post_meta( $post_id, '_pr_last_source_verified', true );
if ( empty( $last_verified ) ) {
return $content;
}
// Find the verdict card closing div and append after it.
$verdict_close = '</div><!-- .pr-verdict -->';
if ( strpos( $content, $verdict_close ) !== false ) {
$display = self::render_verification_block( $last_verified );
$content = str_replace( $verdict_close, $verdict_close . $display, $content );
}
return $content;
}
/**
* Render the verification block HTML.
*
* @param string $last_verified ISO date string.
* @return string HTML block.
*/
private static function render_verification_block( string $last_verified ): string {
$date_obj = new \DateTime( $last_verified );
$formatted_date = $date_obj->format( get_option( 'date_format' ) );
$html = '<p class="pr-verification-date">';
$html .= esc_html__( 'Last verified: ', 'peptide-repo-core' );
$html .= sprintf(
'<time datetime="%s">%s</time>',
esc_attr( $date_obj->format( 'Y-m-d' ) ),
esc_html( $formatted_date )
);
$html .= ' — <a href="' . esc_url( home_url( '/our-methodology/' ) ) . '">' . esc_html__( 'methodology', 'peptide-repo-core' ) . '</a>';
$html .= '</p>';
return $html;
}
}

View File

@@ -0,0 +1,199 @@
<?php
declare(strict_types=1);
/**
* Verification scanner for peptide monographs.
*
* What: Runs periodic scans of all published peptides, computes verification status
* (current/due/overdue), logs results, and sends digest notifications.
* Who calls it: PR_Core::init() hooks wp_schedule_event; runs via wp_cron.
* Dependencies: PR_Core_Peptide_Repository, wp_mail().
*
* @see admin/class-pr-core-settings.php — Cadence and threshold settings.
* @see cpt/class-pr-core-peptide-cpt.php — Verification meta field specs.
*/
class PR_Core_Verification_Scanner {
const DEFAULT_THRESHOLD_DAYS = 180;
const HIGH_VELOCITY_THRESHOLD = 60;
const LOW_VELOCITY_THRESHOLD = 365;
const SCAN_LOG_OPTION_KEY = 'pr_core_verification_scan_log';
const MAX_LOG_ENTRIES = 90;
/**
* Run verification scan on all published peptides.
*
* Side effects: Updates _pr_verification_status, appends to scan log, sends email.
*
* @return void
*/
public static function run_scan(): void {
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( [ 'status' => 'publish' ] );
$due_peptides = [];
$overdue_peptides = [];
foreach ( $peptides as $dto ) {
$last_verified = get_post_meta( $dto->id, '_pr_last_source_verified', true );
$velocity = get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium';
// Empty verified date = treat as overdue.
if ( empty( $last_verified ) ) {
update_post_meta( $dto->id, '_pr_verification_status', 'overdue' );
$overdue_peptides[] = $dto;
continue;
}
// Delegate to compute_status() — keeps logic testable without DB calls.
$status = self::compute_status( $last_verified, $velocity );
update_post_meta( $dto->id, '_pr_verification_status', $status );
if ( 'due' === $status ) {
$due_peptides[] = $dto;
} elseif ( 'overdue' === $status ) {
$overdue_peptides[] = $dto;
}
}
// Log the scan result.
self::log_scan( count( $peptides ), count( $due_peptides ), count( $overdue_peptides ) );
// Send digest email if configured and there are items needing review.
if ( ! empty( $due_peptides ) || ! empty( $overdue_peptides ) ) {
self::send_digest_email( $due_peptides, $overdue_peptides );
}
}
/**
* Compute verification status for a single peptide.
*
* Extracted for direct unit-testability without database or WP-cron dependencies.
*
* @param string $last_verified YYYY-MM-DD date of last source verification. Empty = overdue.
* @param string $velocity Velocity tier: high | medium | low.
* @return string Status: current | due | overdue.
*/
public static function compute_status( string $last_verified, string $velocity ): string {
if ( empty( $last_verified ) ) {
return 'overdue';
}
$days_since = ( time() - strtotime( $last_verified ) ) / DAY_IN_SECONDS;
$threshold = match ( $velocity ) {
'high' => (int) get_option( 'pr_core_high_velocity_threshold', self::HIGH_VELOCITY_THRESHOLD ),
'low' => self::LOW_VELOCITY_THRESHOLD,
default => (int) get_option( 'pr_core_default_threshold', self::DEFAULT_THRESHOLD_DAYS ),
};
return $days_since < ( $threshold * 0.9 )
? 'current'
: ( $days_since < $threshold ? 'due' : 'overdue' );
}
/**
* Log scan summary to WP option, keeping last N entries.
*
* @param int $total Total peptides scanned.
* @param int $due Count of due peptides.
* @param int $overdue Count of overdue peptides.
* @return void
*/
private static function log_scan( int $total, int $due, int $overdue ): void {
$log = get_option( self::SCAN_LOG_OPTION_KEY, [] );
if ( ! is_array( $log ) ) {
$log = [];
}
$log[] = [
'timestamp' => current_time( 'mysql' ),
'total' => $total,
'due' => $due,
'overdue' => $overdue,
];
// Keep only the last MAX_LOG_ENTRIES.
if ( count( $log ) > self::MAX_LOG_ENTRIES ) {
$log = array_slice( $log, -self::MAX_LOG_ENTRIES );
}
update_option( self::SCAN_LOG_OPTION_KEY, $log );
}
/**
* Send digest email to configured recipient(s).
*
* @param array<PR_Core_Peptide_DTO> $due_peptides Peptides due for review.
* @param array<PR_Core_Peptide_DTO> $overdue_peptides Peptides overdue for review.
* @return void
*/
private static function send_digest_email( array $due_peptides, array $overdue_peptides ): void {
$recipients = get_option( 'pr_core_verification_email', '' );
if ( empty( $recipients ) ) {
return;
}
// Parse comma-separated emails.
$emails = array_map( 'trim', explode( ',', $recipients ) );
$emails = array_filter( $emails, static function ( $email ) {
return is_email( $email );
} );
if ( empty( $emails ) ) {
return;
}
$subject = sprintf(
'[Peptide Repo] Verification digest: %d due, %d overdue',
count( $due_peptides ),
count( $overdue_peptides )
);
$body = self::build_email_body( $due_peptides, $overdue_peptides );
wp_mail( $emails, $subject, $body, [ 'Content-Type: text/html; charset=UTF-8' ] );
}
/**
* Build HTML email body for digest.
*
* @param array<PR_Core_Peptide_DTO> $due_peptides Peptides due for review.
* @param array<PR_Core_Peptide_DTO> $overdue_peptides Peptides overdue for review.
* @return string HTML email body.
*/
private static function build_email_body( array $due_peptides, array $overdue_peptides ): string {
$body = '<h2>Verification Digest</h2>';
if ( ! empty( $overdue_peptides ) ) {
$body .= '<h3>Overdue for review (' . count( $overdue_peptides ) . ')</h3><ul>';
foreach ( $overdue_peptides as $dto ) {
$edit_url = get_edit_post_link( $dto->id );
$body .= sprintf(
'<li><a href="%s">%s</a></li>',
esc_url( $edit_url ),
esc_html( $dto->title )
);
}
$body .= '</ul>';
}
if ( ! empty( $due_peptides ) ) {
$body .= '<h3>Due for review (' . count( $due_peptides ) . ')</h3><ul>';
foreach ( $due_peptides as $dto ) {
$edit_url = get_edit_post_link( $dto->id );
$body .= sprintf(
'<li><a href="%s">%s</a></li>',
esc_url( $edit_url ),
esc_html( $dto->title )
);
}
$body .= '</ul>';
}
$body .= '<p><a href="' . esc_url( admin_url( 'index.php?page=pr-core-verification' ) ) . '">View verification dashboard</a></p>';
return $body;
}
}

View File

@@ -3,7 +3,7 @@
* Plugin Name: Peptide Repo Core
* Plugin URI: https://peptiderepo.com
* Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
* Version: 0.3.2
* Version: 0.4.0
* Author: peptiderepo
* Author URI: https://peptiderepo.com
* License: GPL-2.0-or-later
@@ -22,7 +22,7 @@ if ( ! defined( 'ABSPATH' ) ) {
/* ── Constants ────────────────────────────────────────────────────────── */
define( 'PR_CORE_VERSION', '0.3.2' );
define( 'PR_CORE_VERSION', '0.4.0' );
define( 'PR_CORE_PLUGIN_FILE', __FILE__ );
define( 'PR_CORE_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
define( 'PR_CORE_PLUGIN_URL', plugin_dir_url( __FILE__ ) );

View File

@@ -0,0 +1,128 @@
<?php
/**
* Unit tests for PR_Core_Verification_Scanner::compute_status().
*
* Run: php tests/unit/test-verification-scanner.php
* Exit code 0 = all pass, 1 = any failure.
*
* What's covered:
* - Empty last_verified → overdue.
* - Days < 90% of threshold → current.
* - Days >= 90% and < 100% of threshold → due.
* - Days >= threshold → overdue.
* - Boundary: exactly at 90% → due (not current).
* - high velocity applies 60-day threshold from option.
* - low velocity applies 365-day constant (not option).
* - medium/default applies 180-day threshold from option.
*
* @package PeptideRepoCore
*/
declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs needed by the scanner ──────────────────────────────
if ( ! defined( 'DAY_IN_SECONDS' ) ) {
define( 'DAY_IN_SECONDS', 86400 );
}
/** @var array<string, mixed> $GLOBALS['pr_core_options'] Mocked option store. */
$GLOBALS['pr_core_options'] = [];
if ( ! function_exists( 'get_option' ) ) {
function get_option( string $key, $default = false ) {
return $GLOBALS['pr_core_options'][ $key ] ?? $default;
}
}
// ── Load the scanner class ──────────────────────────────────────────────
require_once __DIR__ . '/../../includes/scanner/class-pr-core-verification-scanner.php';
// ── Helper: build a date N days ago ────────────────────────────────────
function days_ago( int $days ): string {
return gmdate( 'Y-m-d', time() - ( $days * DAY_IN_SECONDS ) );
}
echo "== PR_Core_Verification_Scanner::compute_status() unit tests ==\n\n";
// ── Empty last_verified ─────────────────────────────────────────────────
echo "Empty last_verified:\n";
pr_assert_equals(
'overdue',
PR_Core_Verification_Scanner::compute_status( '', 'medium' ),
'empty string → overdue'
);
// ── Medium velocity (default 180-day threshold) ─────────────────────────
echo "\nMedium velocity (threshold=180, option default):\n";
$GLOBALS['pr_core_options'] = [];
// 160 days ago → 160 < 162 (90% of 180) → current.
pr_assert_equals( 'current', PR_Core_Verification_Scanner::compute_status( days_ago( 160 ), 'medium' ), '160 days → current' );
// 163 days ago → 163 >= 162 and < 180 → due.
pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago( 163 ), 'medium' ), '163 days → due' );
// 180 days ago → 180 >= 180 → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 180 ), 'medium' ), '180 days → overdue' );
// 200 days ago → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 200 ), 'medium' ), '200 days → overdue' );
// ── 90% boundary exactness ──────────────────────────────────────────────
echo "\n90% boundary (threshold=100):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 100 ];
// 89 days → 89 < 90 (90% of 100) → current.
pr_assert_equals( 'current', PR_Core_Verification_Scanner::compute_status( days_ago( 89 ), 'medium' ), '89 days (threshold 100) → current' );
// 90 days → 90 >= 90 and < 100 → due.
pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago( 90 ), 'medium' ), '90 days (threshold 100) → due (at boundary)' );
// 100 days → 100 >= 100 → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 100 ), 'medium' ), '100 days (threshold 100) → overdue' );
// ── High velocity (60-day threshold from option) ────────────────────────
echo "\nHigh velocity (threshold=60 from option):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_high_velocity_threshold' => 60 ];
// 50 days → 50 < 54 (90% of 60) → current.
pr_assert_equals( 'current', PR_Core_Verification_Scanner::compute_status( days_ago( 50 ), 'high' ), 'high: 50 days → current' );
// 55 days → 55 >= 54, < 60 → due.
pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago( 55 ), 'high' ), 'high: 55 days → due' );
// 61 days → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 61 ), 'high' ), 'high: 61 days → overdue' );
// ── Low velocity (365-day constant — ignores option) ────────────────────
echo "\nLow velocity (threshold=365, constant, ignores option):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 999 ]; // Should be ignored for low.
// 300 days → 300 < 328.5 (90% of 365) → current.
pr_assert_equals( 'current', PR_Core_Verification_Scanner::compute_status( days_ago( 300 ), 'low' ), 'low: 300 days → current' );
// 340 days → 340 >= 328.5, < 365 → due.
pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago( 340 ), 'low' ), 'low: 340 days → due' );
// 366 days → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 366 ), 'low' ), 'low: 366 days → overdue' );
// ── Unknown velocity falls through to medium/default ────────────────────
echo "\nUnknown velocity (falls to default/medium):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 180 ];
pr_assert_equals( 'current', PR_Core_Verification_Scanner::compute_status( days_ago( 100 ), 'unknown' ), 'unknown velocity: 100 days → current (uses default 180)' );
// ── Summary ─────────────────────────────────────────────────────────────
exit( pr_test_summary() );

View File

@@ -0,0 +1,131 @@
<?php
/**
* Unit tests for PR_Core_Settings verification methods.
*
* Run: php tests/unit/test-verification-settings.php
* Exit code 0 = all pass, 1 = any failure.
*
* What's covered:
* - sanitize_cadence() accepts valid values, rejects invalid → 'weekly'.
* - sanitize_emails() filters invalid addresses, preserves valid ones.
* - reschedule_cron() no-ops when old === new value.
* - reschedule_cron() clears + reschedules when value changes.
*
* @package PeptideRepoCore
*/
declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs needed by the settings class ───────────────────────
$GLOBALS['pr_core_options'] = [];
$GLOBALS['pr_core_cron_calls'] = [];
if ( ! function_exists( 'get_option' ) ) {
function get_option( string $key, $default = false ) {
return $GLOBALS['pr_core_options'][ $key ] ?? $default;
}
}
if ( ! function_exists( 'update_option' ) ) {
function update_option( string $key, $value ): bool {
$GLOBALS['pr_core_options'][ $key ] = $value;
return true;
}
}
if ( ! function_exists( 'register_setting' ) ) {
function register_setting( string $group, string $option, array $args = [] ): void {}
}
if ( ! function_exists( 'add_settings_section' ) ) {
function add_settings_section( string $id, string $title, $cb, string $page ): void {}
}
if ( ! function_exists( 'add_settings_field' ) ) {
function add_settings_field( string $id, string $title, $cb, string $page, string $section = '' ): void {}
}
if ( ! function_exists( 'is_email' ) ) {
function is_email( string $email ): bool {
return (bool) filter_var( $email, FILTER_VALIDATE_EMAIL );
}
}
if ( ! function_exists( 'wp_clear_scheduled_hook' ) ) {
function wp_clear_scheduled_hook( string $hook ): void {
$GLOBALS['pr_core_cron_calls'][] = [ 'action' => 'clear', 'hook' => $hook ];
}
}
if ( ! function_exists( 'wp_schedule_event' ) ) {
function wp_schedule_event( int $timestamp, string $recurrence, string $hook ): void {
$GLOBALS['pr_core_cron_calls'][] = [ 'action' => 'schedule', 'hook' => $hook, 'recurrence' => $recurrence ];
}
}
// ── Load the settings class ─────────────────────────────────────────────
require_once __DIR__ . '/../../includes/cpt/class-pr-core-peptide-cpt.php';
require_once __DIR__ . '/../../includes/admin/class-pr-core-settings.php';
echo "== PR_Core_Settings verification methods unit tests ==\n\n";
// ── sanitize_cadence() ──────────────────────────────────────────────────
echo "sanitize_cadence():\n";
pr_assert_equals( 'daily', PR_Core_Settings::sanitize_cadence( 'daily' ), 'daily → daily' );
pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( 'weekly' ), 'weekly → weekly' );
pr_assert_equals( 'monthly', PR_Core_Settings::sanitize_cadence( 'monthly' ), 'monthly → monthly' );
pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( 'hourly' ), 'hourly (invalid) → weekly default' );
pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( '' ), 'empty → weekly default' );
pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( 'DAILY' ), 'uppercase → weekly (case-sensitive)' );
// ── sanitize_emails() ───────────────────────────────────────────────────
echo "\nsanitize_emails():\n";
pr_assert_equals( '', PR_Core_Settings::sanitize_emails( '' ), 'empty → empty' );
pr_assert_equals( 'admin@example.com', PR_Core_Settings::sanitize_emails( 'admin@example.com' ), 'valid single → kept' );
pr_assert_equals( '', PR_Core_Settings::sanitize_emails( 'not-an-email' ), 'invalid single → empty' );
pr_assert_equals( 'a@test.com, b@test.com', PR_Core_Settings::sanitize_emails( 'a@test.com, b@test.com' ), 'valid pair → both kept' );
pr_assert_equals( 'good@test.com', PR_Core_Settings::sanitize_emails( 'good@test.com, bad-email' ), 'mixed → only valid kept' );
pr_assert_equals( 'trimmed@test.com', PR_Core_Settings::sanitize_emails( ' trimmed@test.com ' ), 'whitespace trimmed around valid email' );
// ── reschedule_cron(): no-op when same value ────────────────────────────
echo "\nreschedule_cron() — no-op when value unchanged:\n";
$GLOBALS['pr_core_cron_calls'] = [];
PR_Core_Settings::reschedule_cron( 'weekly', 'weekly' );
pr_assert( empty( $GLOBALS['pr_core_cron_calls'] ), 'no cron calls when old === new' );
// ── reschedule_cron(): clears + reschedules on change ───────────────────
echo "\nreschedule_cron() — reschedules when value changes:\n";
$GLOBALS['pr_core_cron_calls'] = [];
PR_Core_Settings::reschedule_cron( 'weekly', 'daily' );
$actions = array_column( $GLOBALS['pr_core_cron_calls'], 'action' );
pr_assert( in_array( 'clear', $actions, true ), 'wp_clear_scheduled_hook was called' );
pr_assert( in_array( 'schedule', $actions, true ), 'wp_schedule_event was called' );
$schedule_call = null;
foreach ( $GLOBALS['pr_core_cron_calls'] as $call ) {
if ( 'schedule' === $call['action'] ) {
$schedule_call = $call;
break;
}
}
pr_assert( null !== $schedule_call, 'schedule call found' );
pr_assert_equals( 'pr_core_verification_scan', $schedule_call['hook'] ?? '', 'rescheduled hook = pr_core_verification_scan' );
pr_assert_equals( 'daily', $schedule_call['recurrence'] ?? '', 'rescheduled with new cadence "daily"' );
// Clear fires before schedule (correct ordering).
$clear_idx = array_search( 'clear', $actions, true );
$schedule_idx = array_search( 'schedule', $actions, true );
pr_assert( $clear_idx < $schedule_idx, 'clear fires before schedule' );
// ── Summary ─────────────────────────────────────────────────────────────
exit( pr_test_summary() );