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Adopt reusable CI standard + PHPUnit conversion (#22)

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Squash-merge of PR #22: adopt shared reusable CI workflow, convert PHPUnit to stubs, update branch-protection contexts.

QA-approved at 05d8094a1d. All required CI checks green.

Agent-Session: 2026-06-17-prcore-ci-deploy
This commit is contained in:
peptiderepo
2026-06-17 01:12:00 +07:00
committed by GitHub
parent d0b5875fd8
commit 665d7fa9e1
72 changed files with 4604 additions and 1212 deletions
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18
includes/admin/class-pr-core-admin-columns.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Admin Columns.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Adds evidence strength, editorial status, and dosing count columns
*
* @package Peptide_Repo_Core
*/
/**
* Custom admin list-table columns for the peptide CPT.
*
@@ -19,7 +31,7 @@ class PR_Core_Admin_Columns {
* @return array<string, string> Modified columns.
*/
public function add_columns( array $columns ): array {
$new = [];
$new = array();
foreach ( $columns as $key => $label ) {
$new[ $key ] = $label;
@@ -44,13 +56,13 @@ class PR_Core_Admin_Columns {
public function render_column( string $column, int $post_id ): void {
switch ( $column ) {
case 'pr_evidence':
$strength = get_post_meta( $post_id, 'evidence_strength', true ) ?: 'preclinical';
$strength = get_post_meta( $post_id, 'evidence_strength', true ) ?: 'preclinical'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$label = apply_filters( 'pr_core_evidence_strength_label', $strength, $strength );
echo esc_html( $label );
break;
case 'pr_editorial':
$status = get_post_meta( $post_id, 'editorial_review_status', true ) ?: 'draft';
$status = get_post_meta( $post_id, 'editorial_review_status', true ) ?: 'draft'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo esc_html( ucfirst( str_replace( '-', ' ', $status ) ) );
break;

34
includes/admin/class-pr-core-admin.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Admin.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Registers admin menu pages, meta boxes, and custom columns for peptides
*
* @package Peptide_Repo_Core
*/
/**
* Admin initialization and hook registration.
*
@@ -25,22 +37,22 @@ class PR_Core_Admin {
*/
public function register_hooks(): void {
$metaboxes = new PR_Core_Peptide_Metaboxes();
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', array( $metaboxes, 'add_meta_boxes' ) );
add_action( 'save_post_' . PR_Core_Peptide_CPT::POST_TYPE, array( $metaboxes, 'save_meta' ), 10, 2 );
add_action( 'add_meta_boxes', [ PR_Core_Verification_Metabox::class, 'register' ] );
add_action( 'add_meta_boxes', array( 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 );
add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', array( $columns, 'add_columns' ) );
add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', array( $columns, 'render_column' ), 10, 2 );
// Repo Daily meta boxes.
$repo_daily_metaboxes = new PR_Core_Repo_Daily_Metaboxes();
add_action( 'add_meta_boxes', [ $repo_daily_metaboxes, 'add_meta_boxes' ] );
add_action( 'save_post_' . PR_Core_Repo_Daily_CPT::POST_TYPE, [ $repo_daily_metaboxes, 'save_meta' ], 10, 2 );
add_action( 'add_meta_boxes', array( $repo_daily_metaboxes, 'add_meta_boxes' ) );
add_action( 'save_post_' . PR_Core_Repo_Daily_CPT::POST_TYPE, array( $repo_daily_metaboxes, 'save_meta' ), 10, 2 );
add_action( 'admin_menu', [ $this, 'add_admin_pages' ] );
add_action( 'admin_enqueue_scripts', [ $this, 'enqueue_admin_styles' ] );
add_action( 'admin_menu', array( $this, 'add_admin_pages' ) );
add_action( 'admin_enqueue_scripts', array( $this, 'enqueue_admin_styles' ) );
}
/**
@@ -60,7 +72,7 @@ class PR_Core_Admin {
__( 'Candidate Queue', 'peptide-repo-core' ) . $badge,
PR_Core_Peptide_CPT::CAPABILITY,
'pr-core-candidates',
[ new PR_Core_Candidate_Queue_Page(), 'render' ]
array( new PR_Core_Candidate_Queue_Page(), 'render' )
);
}
@@ -79,7 +91,7 @@ class PR_Core_Admin {
wp_enqueue_style(
'pr-core-admin',
PR_CORE_PLUGIN_URL . 'assets/css/admin.css',
[],
array(),
PR_CORE_VERSION
);
}

16
includes/admin/class-pr-core-ajax-handlers.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Ajax Handlers.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Handles mark-verified and scan-now admin-ajax actions
*
* @package Peptide_Repo_Core
*/
/**
* AJAX handlers for verification scanner actions.
*
@@ -47,7 +59,7 @@ class PR_Core_Ajax_Handlers {
// Recompute status to 'current'.
update_post_meta( $post_id, '_pr_verification_status', 'current' );
wp_send_json_success( [ 'message' => 'Marked verified' ] );
wp_send_json_success( array( 'message' => 'Marked verified' ) );
}
/**
@@ -74,6 +86,6 @@ class PR_Core_Ajax_Handlers {
// Run scan.
PR_Core_Verification_Scanner::run_scan();
wp_send_json_success( [ 'message' => 'Scan complete' ] );
wp_send_json_success( array( 'message' => 'Scan complete' ) );
}
}

56
includes/admin/class-pr-core-candidate-queue-page.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Candidate Queue Page.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders a review screen for AI-extracted dosing candidates
*
* @package Peptide_Repo_Core
*/
/**
* Admin page for the AI Candidate Queue.
*
@@ -58,8 +70,8 @@ class PR_Core_Candidate_Queue_Page {
$peptide = $pep_repo->find_by_id( $c->peptide_id );
$name = $peptide ? $peptide->title : '#' . $c->peptide_id;
$dose = $c->dose_min !== null ? number_format( $c->dose_min, 2 ) : '?';
if ( $c->dose_max !== null && $c->dose_max !== $c->dose_min ) {
$dose = null !== $c->dose_min ? number_format( $c->dose_min, 2 ) : '?';
if ( null !== $c->dose_max && $c->dose_max !== $c->dose_min ) {
$dose .= ' – ' . number_format( $c->dose_max, 2 );
}
$dose .= ' ' . esc_html( $c->dose_unit );
@@ -71,11 +83,21 @@ class PR_Core_Candidate_Queue_Page {
$confidence_pct = number_format( $c->extraction_confidence * 100, 0 ) . '%';
$approve_url = wp_nonce_url(
add_query_arg( [ 'action' => 'pr_core_approve', 'candidate_id' => $c->id ] ),
add_query_arg(
array(
'action' => 'pr_core_approve',
'candidate_id' => $c->id,
)
),
'pr_core_queue_action'
);
$reject_url = wp_nonce_url(
add_query_arg( [ 'action' => 'pr_core_reject', 'candidate_id' => $c->id ] ),
add_query_arg(
array(
'action' => 'pr_core_reject',
'candidate_id' => $c->id,
)
),
'pr_core_queue_action'
);
@@ -84,7 +106,7 @@ class PR_Core_Candidate_Queue_Page {
printf( '<td>%s</td>', esc_html( $c->route ) );
printf( '<td>%s</td>', esc_html( $dose ) );
printf( '<td>%s</td>', esc_html( $c->population ) );
printf( '<td>%s</td>', $study ); // Contains escaped HTML + link.
printf( '<td>%s</td>', $study ); // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- $study is pre-escaped HTML.
printf( '<td>%s</td>', esc_html( $confidence_pct ) );
printf(
'<td><a href="%s" class="button button-primary button-small">%s</a> <a href="%s" class="button button-small">%s</a></td>',
@@ -107,9 +129,9 @@ class PR_Core_Candidate_Queue_Page {
* @return void
*/
private function handle_actions(): void {
$action = sanitize_text_field( $_GET['action'] ?? '' );
$action = sanitize_text_field( wp_unslash( $_GET['action'] ?? '' ) ); // phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotValidated
if ( ! in_array( $action, [ 'pr_core_approve', 'pr_core_reject' ], true ) ) {
if ( ! in_array( $action, array( 'pr_core_approve', 'pr_core_reject' ), true ) ) {
return;
}
@@ -117,7 +139,7 @@ class PR_Core_Candidate_Queue_Page {
return;
}
$candidate_id = absint( $_GET['candidate_id'] ?? 0 );
$candidate_id = absint( wp_unslash( $_GET['candidate_id'] ?? 0 ) );
if ( 0 === $candidate_id ) {
return;
}
@@ -128,15 +150,21 @@ class PR_Core_Candidate_Queue_Page {
if ( 'pr_core_approve' === $action ) {
$dosing_id = $repo->approve( $candidate_id, $reviewer_id );
if ( $dosing_id > 0 ) {
add_action( 'admin_notices', static function () {
echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Candidate approved and added to dosing data.', 'peptide-repo-core' ) . '</p></div>';
} );
add_action(
'admin_notices',
static function () {
echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Candidate approved and added to dosing data.', 'peptide-repo-core' ) . '</p></div>';
}
);
}
} else {
$repo->reject( $candidate_id, $reviewer_id );
add_action( 'admin_notices', static function () {
echo '<div class="notice notice-warning is-dismissible"><p>' . esc_html__( 'Candidate rejected.', 'peptide-repo-core' ) . '</p></div>';
} );
add_action(
'admin_notices',
static function () {
echo '<div class="notice notice-warning is-dismissible"><p>' . esc_html__( 'Candidate rejected.', 'peptide-repo-core' ) . '</p></div>';
}
);
}
}
}

40
includes/admin/class-pr-core-peptide-metaboxes.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Peptide Metaboxes.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders and saves three meta boxes on the peptide edit screen
*
* @package Peptide_Repo_Core
*/
/**
* Meta boxes for the peptide edit screen: scientific identifiers, dosing, and legal.
*
@@ -22,7 +34,7 @@ class PR_Core_Peptide_Metaboxes {
add_meta_box(
'pr-core-identifiers',
__( 'Scientific Identifiers', 'peptide-repo-core' ),
[ $this, 'render_identifiers_box' ],
array( $this, 'render_identifiers_box' ),
PR_Core_Peptide_CPT::POST_TYPE,
'normal',
'high'
@@ -31,7 +43,7 @@ class PR_Core_Peptide_Metaboxes {
add_meta_box(
'pr-core-dosing',
__( 'Dosing Data', 'peptide-repo-core' ),
[ $this, 'render_dosing_box' ],
array( $this, 'render_dosing_box' ),
PR_Core_Peptide_CPT::POST_TYPE,
'normal',
'default'
@@ -40,7 +52,7 @@ class PR_Core_Peptide_Metaboxes {
add_meta_box(
'pr-core-legal',
__( 'Legal Status by Country', 'peptide-repo-core' ),
[ $this, 'render_legal_box' ],
array( $this, 'render_legal_box' ),
PR_Core_Peptide_CPT::POST_TYPE,
'normal',
'default'
@@ -56,7 +68,7 @@ class PR_Core_Peptide_Metaboxes {
public function render_identifiers_box( \WP_Post $post ): void {
wp_nonce_field( 'pr_core_save_meta', 'pr_core_meta_nonce' );
$fields = [
$fields = array(
'display_name' => __( 'Display Name', 'peptide-repo-core' ),
'aliases' => __( 'Aliases (JSON array)', 'peptide-repo-core' ),
'molecular_formula' => __( 'Molecular Formula', 'peptide-repo-core' ),
@@ -64,7 +76,7 @@ class PR_Core_Peptide_Metaboxes {
'cas_number' => __( 'CAS Number', 'peptide-repo-core' ),
'drugbank_id' => __( 'DrugBank ID', 'peptide-repo-core' ),
'chembl_id' => __( 'ChEMBL ID', 'peptide-repo-core' ),
];
);
echo '<table class="form-table pr-core-meta-table">';
foreach ( $fields as $key => $label ) {
@@ -73,12 +85,12 @@ class PR_Core_Peptide_Metaboxes {
'<tr><th><label for="pr_core_%1$s">%2$s</label></th><td><input type="text" id="pr_core_%1$s" name="pr_core_%1$s" value="%3$s" class="regular-text" /></td></tr>',
esc_attr( $key ),
esc_html( $label ),
$value
$value // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- esc_attr applied on assignment
);
}
// Evidence strength dropdown.
$current_strength = get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical';
$current_strength = get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<tr><th><label for="pr_core_evidence_strength">' . esc_html__( 'Evidence Strength', 'peptide-repo-core' ) . '</label></th><td><select id="pr_core_evidence_strength" name="pr_core_evidence_strength">';
foreach ( PR_Core_Peptide_CPT::EVIDENCE_STRENGTHS as $strength ) {
$label = apply_filters( 'pr_core_evidence_strength_label', $strength, $strength );
@@ -92,7 +104,7 @@ class PR_Core_Peptide_Metaboxes {
echo '</select></td></tr>';
// Editorial review status.
$current_review = get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft';
$current_review = get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<tr><th><label for="pr_core_editorial_review_status">' . esc_html__( 'Editorial Status', 'peptide-repo-core' ) . '</label></th><td><select id="pr_core_editorial_review_status" name="pr_core_editorial_review_status">';
foreach ( PR_Core_Peptide_CPT::REVIEW_STATUSES as $status ) {
printf(
@@ -134,8 +146,8 @@ class PR_Core_Peptide_Metaboxes {
echo '</tr></thead><tbody>';
foreach ( $rows as $row ) {
$dose = $row->dose_min !== null ? number_format( $row->dose_min, 2 ) : '?';
if ( $row->dose_max !== null && $row->dose_max !== $row->dose_min ) {
$dose = null !== $row->dose_min ? number_format( $row->dose_min, 2 ) : '?';
if ( null !== $row->dose_max && $row->dose_max !== $row->dose_min ) {
$dose .= ' – ' . number_format( $row->dose_max, 2 );
}
$dose .= ' ' . esc_html( $row->dose_unit );
@@ -233,11 +245,11 @@ class PR_Core_Peptide_Metaboxes {
foreach ( $meta_fields as $key => $config ) {
$input_key = 'pr_core_' . $key;
if ( ! isset( $_POST[ $input_key ] ) ) {
if ( ! isset( $_POST[ $input_key ] ) ) { // phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotSanitized -- existence check only; unslash+sanitize below
continue;
}
$raw = wp_unslash( $_POST[ $input_key ] );
$raw = wp_unslash( $_POST[ $input_key ] ); // phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotSanitized -- sanitized via config['sanitize'] callback on next line
$clean = is_callable( $config['sanitize'] )
? call_user_func( $config['sanitize'], $raw )
: sanitize_text_field( (string) $raw );
@@ -246,10 +258,10 @@ class PR_Core_Peptide_Metaboxes {
}
// Set last_editorial_review_at when status changes to published.
$new_review_status = sanitize_text_field( $_POST['pr_core_editorial_review_status'] ?? '' );
$new_review_status = sanitize_text_field( wp_unslash( $_POST['pr_core_editorial_review_status'] ?? '' ) );
if ( 'published' === $new_review_status ) {
$old_status = get_post_meta( $post_id, 'editorial_review_status', true );
if ( $old_status !== 'published' ) {
if ( 'published' !== $old_status ) {
update_post_meta( $post_id, 'last_editorial_review_at', current_time( 'mysql' ) );
update_post_meta( $post_id, 'medical_editor_id', get_current_user_id() );
}

24
includes/admin/class-pr-core-repo-daily-metaboxes.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Repo Daily Metaboxes.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders and saves two meta fields on the repo_daily edit screen
*
* @package Peptide_Repo_Core
*/
/**
* Meta boxes for Repo Daily edit screen: author and clinical review flag.
*
@@ -17,7 +29,11 @@ declare(strict_types=1);
*/
class PR_Core_Repo_Daily_Metaboxes {
/** @var string Default author byline for Repo Daily articles. */
/**
* Default author byline for Repo Daily articles.
*
* @var string Default author byline for Repo Daily articles.
*/
private const DEFAULT_AUTHOR = 'Boo Sheeran';
/**
@@ -29,7 +45,7 @@ class PR_Core_Repo_Daily_Metaboxes {
add_meta_box(
'pr-core-repo-daily-meta',
__( 'Article Settings', 'peptide-repo-core' ),
[ $this, 'render_meta_box' ],
array( $this, 'render_meta_box' ),
PR_Core_Repo_Daily_CPT::POST_TYPE,
'normal',
'default'
@@ -45,8 +61,8 @@ class PR_Core_Repo_Daily_Metaboxes {
public function render_meta_box( \WP_Post $post ): void {
wp_nonce_field( 'pr_core_repo_daily_meta', 'pr_core_repo_daily_nonce' );
$author = sanitize_text_field(
get_post_meta( $post->ID, '_repo_daily_author', true ) ?: self::DEFAULT_AUTHOR
$author = sanitize_text_field(
get_post_meta( $post->ID, '_repo_daily_author', true ) ?: self::DEFAULT_AUTHOR // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
);
$requires_review = get_post_meta( $post->ID, '_repo_daily_clinical_review_required', true );

134
includes/admin/class-pr-core-settings-renderer.php Normal file
View File

@@ -0,0 +1,134 @@
<?php
/**
* Settings Renderer.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Static methods that output HTML for each settings field on the PR Core settings page
*
* @package Peptide_Repo_Core
*/
/**
* Render methods for the PR Core settings admin page.
*
* What: Static methods that output HTML for each settings field on the PR Core settings page.
* Who calls it: PR_Core_Settings — register_*_section() methods reference these via add_settings_field().
* Dependencies: PR_Core_Settings (for option key constants).
*
* @see admin/class-pr-core-settings.php — Settings registration and sanitization.
*/
class PR_Core_Settings_Renderer {
/**
* Render the settings page form.
*
* @return void
*/
public static function render_page(): void {
?>
<div class="wrap">
<h1><?php esc_html_e( 'PR Core Settings', 'peptide-repo-core' ); ?></h1>
<form method="post" action="options.php">
<?php
settings_fields( self::OPTION_GROUP );
do_settings_sections( self::OPTION_GROUP );
submit_button();
?>
</form>
</div>
<?php
}
/**
* Render output.
*
* @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' )
);
}
/**
* Render output.
*
* @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 output.
*
* @return void
*/
public static function render_verification_section(): void {
echo '<p>' . esc_html__( 'Configure automatic staleness scanning and digest notifications.', 'peptide-repo-core' ) . '</p>';
}
/**
* Render output.
*
* @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 ( array(
'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>';
}
/**
* Render output.
*
* @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 ) ) );
}
/**
* Render output.
*
* @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 ) ) );
}
/**
* Render output.
*
* @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>';
}
}

226
includes/admin/class-pr-core-settings.php
View File

@@ -1,4 +1,10 @@
<?php
/**
* Settings.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
@@ -13,25 +19,25 @@ declare(strict_types=1);
*/
class PR_Core_Settings {
/** @var string Option group shared by all PR Core settings. */
/** @var string Option group shared by all PR Core settings. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
public const OPTION_GROUP = 'pr_core_settings';
/** @var string Option key: enable/disable related articles. */
/** @var string Option key: enable/disable related articles. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const RELATED_ENABLED = 'pr_core_related_posts_enabled';
/** @var string Option key: related articles limit (1-6). */
/** @var string Option key: related articles limit (1-6). */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const RELATED_LIMIT = 'pr_core_related_posts_limit';
/** @var string Option key: WP-cron scan cadence. */
/** @var string Option key: WP-cron scan cadence. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const SCAN_CADENCE = 'pr_core_scan_cadence';
/** @var string Option key: default staleness threshold in days. */
/** @var string Option key: default staleness threshold in days. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const DEFAULT_THRESHOLD = 'pr_core_default_threshold';
/** @var string Option key: high-velocity staleness threshold in days. */
/** @var string Option key: high-velocity staleness threshold in days. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const HIGH_VELOCITY_THRESHOLD = 'pr_core_high_velocity_threshold';
/** @var string Option key: comma-separated notification email list. */
/** @var string Option key: comma-separated notification email list. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const VERIFICATION_EMAIL = 'pr_core_verification_email';
/**
@@ -48,28 +54,17 @@ class PR_Core_Settings {
__( 'Settings', 'peptide-repo-core' ),
'manage_options',
'pr-core-settings',
[ __CLASS__, 'render_page' ]
array( __CLASS__, 'render_page' )
);
}
/**
* Render the settings page form.
* Render the settings page HTML. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_page(): void {
?>
<div class="wrap">
<h1><?php esc_html_e( 'PR Core Settings', 'peptide-repo-core' ); ?></h1>
<form method="post" action="options.php">
<?php
settings_fields( self::OPTION_GROUP );
do_settings_sections( self::OPTION_GROUP );
submit_button();
?>
</form>
</div>
<?php
PR_Core_Settings_Renderer::render_page();
}
/**
@@ -83,10 +78,10 @@ class PR_Core_Settings {
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 );
add_action( 'update_option_' . self::SCAN_CADENCE, array( __CLASS__, 'reschedule_cron' ), 10, 2 );
}
// ── Related Articles ─────────────────────────────────────────────────
// ── Related Articles ─────────────────────────────────────────────────.
/**
* Register Related Articles settings.
@@ -94,33 +89,46 @@ class PR_Core_Settings {
* @return void
*/
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' ] ] );
register_setting(
self::OPTION_GROUP,
self::RELATED_ENABLED,
array(
'type' => 'boolean',
'default' => true,
'sanitize_callback' => 'rest_sanitize_boolean',
)
);
register_setting(
self::OPTION_GROUP,
self::RELATED_LIMIT,
array(
'type' => 'integer',
'default' => 3,
'sanitize_callback' => array( __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' );
add_settings_field( self::RELATED_ENABLED, __( 'Enable Related Articles', 'peptide-repo-core' ), array( __CLASS__, 'render_enabled_field' ), self::OPTION_GROUP, 'pr_core_related_articles' );
add_settings_field( self::RELATED_LIMIT, __( 'Number of Articles', 'peptide-repo-core' ), array( __CLASS__, 'render_limit_field' ), self::OPTION_GROUP, 'pr_core_related_articles' );
}
/** @return void */
/**
* Render the enable/disable checkbox field. Delegates to PR_Core_Settings_Renderer.
*
* @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' )
);
PR_Core_Settings_Renderer::render_enabled_field();
}
/** @return void */
/**
* Render the article count limit field. Delegates to PR_Core_Settings_Renderer.
*
* @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>';
PR_Core_Settings_Renderer::render_limit_field();
}
/**
@@ -133,7 +141,7 @@ class PR_Core_Settings {
return min( 6, max( 1, (int) $value ) );
}
// ── Verification ─────────────────────────────────────────────────────
// ── Verification ─────────────────────────────────────────────────────.
/**
* Register Verification settings.
@@ -141,51 +149,93 @@ class PR_Core_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, '' ) )
register_setting(
self::OPTION_GROUP,
self::SCAN_CADENCE,
array(
'type' => 'string',
'default' => 'weekly',
'sanitize_callback' => array( __CLASS__, 'sanitize_cadence' ),
)
);
echo '<p class="description">' . esc_html__( 'Comma-separated. Leave blank to disable email digests.', 'peptide-repo-core' ) . '</p>';
register_setting(
self::OPTION_GROUP,
self::DEFAULT_THRESHOLD,
array(
'type' => 'integer',
'default' => 180,
'sanitize_callback' => 'absint',
)
);
register_setting(
self::OPTION_GROUP,
self::HIGH_VELOCITY_THRESHOLD,
array(
'type' => 'integer',
'default' => 60,
'sanitize_callback' => 'absint',
)
);
register_setting(
self::OPTION_GROUP,
self::VERIFICATION_EMAIL,
array(
'type' => 'string',
'default' => '',
'sanitize_callback' => array( __CLASS__, 'sanitize_emails' ),
)
);
add_settings_section( 'pr_core_verification', __( 'Verification', 'peptide-repo-core' ), array( __CLASS__, 'render_verification_section' ), self::OPTION_GROUP );
add_settings_field( self::SCAN_CADENCE, __( 'Scan cadence', 'peptide-repo-core' ), array( __CLASS__, 'render_cadence_field' ), self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::DEFAULT_THRESHOLD, __( 'Default staleness threshold (days)', 'peptide-repo-core' ), array( __CLASS__, 'render_threshold_field' ), self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::HIGH_VELOCITY_THRESHOLD, __( 'High-velocity threshold (days)', 'peptide-repo-core' ), array( __CLASS__, 'render_high_velocity_field' ), self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::VERIFICATION_EMAIL, __( 'Notification email(s)', 'peptide-repo-core' ), array( __CLASS__, 'render_email_field' ), self::OPTION_GROUP, 'pr_core_verification' );
}
/**
* Render the verification section header. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_verification_section(): void {
PR_Core_Settings_Renderer::render_verification_section();
}
/**
* Render the scan cadence select field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_cadence_field(): void {
PR_Core_Settings_Renderer::render_cadence_field();
}
/**
* Render the score threshold input field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_threshold_field(): void {
PR_Core_Settings_Renderer::render_threshold_field();
}
/**
* Render the high-velocity scan toggle field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_high_velocity_field(): void {
PR_Core_Settings_Renderer::render_high_velocity_field();
}
/**
* Render the alert email input field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_email_field(): void {
PR_Core_Settings_Renderer::render_email_field();
}
/**
@@ -195,7 +245,7 @@ class PR_Core_Settings {
* @return string
*/
public static function sanitize_cadence( string $value ): string {
return in_array( $value, [ 'daily', 'weekly', 'monthly' ], true ) ? $value : 'weekly';
return in_array( $value, array( 'daily', 'weekly', 'monthly' ), true ) ? $value : 'weekly';
}
/**

32
includes/admin/class-pr-core-verification-metabox.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Metabox.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders and saves verification status sidebar meta box
*
* @package Peptide_Repo_Core
*/
/**
* Verification status meta box for peptide edit screen.
*
@@ -21,7 +33,7 @@ class PR_Core_Verification_Metabox {
add_meta_box(
'pr-core-verification',
__( 'Verification Status', 'peptide-repo-core' ),
[ __CLASS__, 'render' ],
array( __CLASS__, 'render' ),
PR_Core_Peptide_CPT::POST_TYPE,
'side',
'default'
@@ -38,16 +50,20 @@ class PR_Core_Verification_Metabox {
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 ) ?: '';
$velocity = get_post_meta( $post->ID, '_pr_verification_velocity', true ) ?: 'medium'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$status = get_post_meta( $post->ID, '_pr_verification_status', true ) ?: 'current'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$notes = get_post_meta( $post->ID, '_pr_verification_notes', true ) ?: ''; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<p><strong>' . esc_html__( 'Last Verified', 'peptide-repo-core' ) . ':</strong><br />';
echo '<code style="color: #666;">' . esc_html( $last_verified ?: '—' ) . '</code></p>';
echo '<code style="color: #666;">' . esc_html( $last_verified ?: '—' ) . '</code></p>'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
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 ) {
foreach ( array(
'low' => 'Low',
'medium' => 'Medium',
'high' => 'High',
) as $val => $label ) {
printf(
'<option value="%s"%s>%s</option>',
esc_attr( $val ),
@@ -58,12 +74,12 @@ class PR_Core_Verification_Metabox {
echo '</select></p>';
echo '<p><strong>' . esc_html__( 'Status', 'peptide-repo-core' ) . ':</strong><br />';
$badge_class = match( $status ) {
$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 '<span ' . $badge_class . '>' . esc_html( ucfirst( $status ) ) . '</span></p>'; // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- badge_class is a hardcoded match expression
echo '<p><strong>' . esc_html__( 'Verification Notes', 'peptide-repo-core' ) . ':</strong><br />';
printf(

49
includes/admin/class-pr-core-verification-widget.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Widget.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* WordPress dashboard widget showing peptides needing review (due/overdue)
*
* @package Peptide_Repo_Core
*/
/**
* Dashboard widget for verification status overview.
*
@@ -23,7 +35,7 @@ class PR_Core_Verification_Widget {
wp_add_dashboard_widget(
'pr_core_verification_status',
__( 'Monographs Needing Review', 'peptide-repo-core' ),
[ __CLASS__, 'render' ]
array( __CLASS__, 'render' )
);
}
@@ -33,35 +45,38 @@ class PR_Core_Verification_Widget {
* @return void
*/
public static function render(): void {
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( [ 'status' => 'publish' ] );
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( array( 'status' => 'publish' ) );
$due_overdue = [];
$due_overdue = array();
foreach ( $peptides as $dto ) {
$status = get_post_meta( $dto->id, '_pr_verification_status', true ) ?: 'current';
$status = get_post_meta( $dto->id, '_pr_verification_status', true ) ?: 'current'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
if ( in_array( $status, [ 'due', 'overdue' ], true ) ) {
if ( in_array( $status, array( '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',
$due_overdue[] = array(
'id' => $dto->id,
'title' => $dto->title,
'status' => $status,
'velocity' => get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'last_verified' => $last_verified,
'days_since' => $days_since,
];
'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'];
} );
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' );
@@ -93,7 +108,7 @@ class PR_Core_Verification_Widget {
esc_html( ucfirst( $item['status'] ) ),
esc_html( ucfirst( $item['velocity'] ) ),
esc_html( $item['last_verified'] ?? '—' ),
$item['days_since'],
(int) $item['days_since'], // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- cast to int, safe
esc_url( $edit_url )
);
}