diff --git a/includes/admin/class-pr-core-admin-columns.php b/includes/admin/class-pr-core-admin-columns.php index 58adf57..fe33d10 100644 --- a/includes/admin/class-pr-core-admin-columns.php +++ b/includes/admin/class-pr-core-admin-columns.php @@ -19,7 +19,7 @@ class PR_Core_Admin_Columns { * @return array Modified columns. */ public function add_columns( array $columns ): array { - $new = []; + $new = array(); foreach ( $columns as $key => $label ) { $new[ $key ] = $label; diff --git a/includes/admin/class-pr-core-admin.php b/includes/admin/class-pr-core-admin.php index ad54619..a266689 100644 --- a/includes/admin/class-pr-core-admin.php +++ b/includes/admin/class-pr-core-admin.php @@ -25,22 +25,22 @@ 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 +60,7 @@ 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 +79,7 @@ class PR_Core_Admin { wp_enqueue_style( 'pr-core-admin', PR_CORE_PLUGIN_URL . 'assets/css/admin.css', - [], + array(), PR_CORE_VERSION ); } diff --git a/includes/admin/class-pr-core-ajax-handlers.php b/includes/admin/class-pr-core-ajax-handlers.php index 3e516e0..c5bbac2 100644 --- a/includes/admin/class-pr-core-ajax-handlers.php +++ b/includes/admin/class-pr-core-ajax-handlers.php @@ -47,7 +47,7 @@ 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 +74,6 @@ 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' ) ); } } diff --git a/includes/admin/class-pr-core-candidate-queue-page.php b/includes/admin/class-pr-core-candidate-queue-page.php index 0f45493..4433e38 100644 --- a/includes/admin/class-pr-core-candidate-queue-page.php +++ b/includes/admin/class-pr-core-candidate-queue-page.php @@ -71,11 +71,21 @@ 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' ); @@ -109,7 +119,7 @@ class PR_Core_Candidate_Queue_Page { private function handle_actions(): void { $action = sanitize_text_field( $_GET['action'] ?? '' ); - if ( ! in_array( $action, [ 'pr_core_approve', 'pr_core_reject' ], true ) ) { + if ( ! in_array( $action, array( 'pr_core_approve', 'pr_core_reject' ), true ) ) { return; } @@ -128,15 +138,21 @@ 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 '

' . esc_html__( 'Candidate approved and added to dosing data.', 'peptide-repo-core' ) . '

'; - } ); + add_action( + 'admin_notices', + static function () { + echo '

' . esc_html__( 'Candidate approved and added to dosing data.', 'peptide-repo-core' ) . '

'; + } + ); } } else { $repo->reject( $candidate_id, $reviewer_id ); - add_action( 'admin_notices', static function () { - echo '

' . esc_html__( 'Candidate rejected.', 'peptide-repo-core' ) . '

'; - } ); + add_action( + 'admin_notices', + static function () { + echo '

' . esc_html__( 'Candidate rejected.', 'peptide-repo-core' ) . '

'; + } + ); } } } diff --git a/includes/admin/class-pr-core-peptide-metaboxes.php b/includes/admin/class-pr-core-peptide-metaboxes.php index 0da722a..6fe001e 100644 --- a/includes/admin/class-pr-core-peptide-metaboxes.php +++ b/includes/admin/class-pr-core-peptide-metaboxes.php @@ -22,7 +22,7 @@ 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 +31,7 @@ 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 +40,7 @@ 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 +56,7 @@ 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 +64,7 @@ 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 ''; foreach ( $fields as $key => $label ) { diff --git a/includes/admin/class-pr-core-repo-daily-metaboxes.php b/includes/admin/class-pr-core-repo-daily-metaboxes.php index 0393d46..1c2364b 100755 --- a/includes/admin/class-pr-core-repo-daily-metaboxes.php +++ b/includes/admin/class-pr-core-repo-daily-metaboxes.php @@ -29,7 +29,7 @@ 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' @@ -45,7 +45,7 @@ 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( + $author = sanitize_text_field( get_post_meta( $post->ID, '_repo_daily_author', true ) ?: self::DEFAULT_AUTHOR ); $requires_review = get_post_meta( $post->ID, '_repo_daily_clinical_review_required', true ); diff --git a/includes/admin/class-pr-core-settings.php b/includes/admin/class-pr-core-settings.php index 7bc2246..18d8d47 100644 --- a/includes/admin/class-pr-core-settings.php +++ b/includes/admin/class-pr-core-settings.php @@ -48,7 +48,7 @@ class PR_Core_Settings { __( 'Settings', 'peptide-repo-core' ), 'manage_options', 'pr-core-settings', - [ __CLASS__, 'render_page' ] + array( __CLASS__, 'render_page' ) ); } @@ -83,7 +83,7 @@ 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 ───────────────────────────────────────────────── @@ -94,12 +94,28 @@ 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 */ @@ -141,16 +157,48 @@ 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' ] ] ); + register_setting( + self::OPTION_GROUP, + self::SCAN_CADENCE, + array( + 'type' => 'string', + 'default' => 'weekly', + 'sanitize_callback' => array( __CLASS__, 'sanitize_cadence' ), + ) + ); + 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' ), [ __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' ); + 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' ); } /** @return void */ @@ -162,7 +210,11 @@ class PR_Core_Settings { public static function render_cadence_field(): void { $current = get_option( self::SCAN_CADENCE, 'weekly' ); echo ''; @@ -195,7 +247,7 @@ 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'; } /** diff --git a/includes/admin/class-pr-core-verification-metabox.php b/includes/admin/class-pr-core-verification-metabox.php index 386d319..f80f9ce 100644 --- a/includes/admin/class-pr-core-verification-metabox.php +++ b/includes/admin/class-pr-core-verification-metabox.php @@ -21,7 +21,7 @@ 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' @@ -47,7 +47,11 @@ class PR_Core_Verification_Metabox { echo '

' . esc_html__( 'Verification Velocity', 'peptide-repo-core' ) . ':
'; echo '

'; echo '

' . esc_html__( 'Status', 'peptide-repo-core' ) . ':
'; - $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;"', diff --git a/includes/admin/class-pr-core-verification-widget.php b/includes/admin/class-pr-core-verification-widget.php index 885cfe8..723369f 100644 --- a/includes/admin/class-pr-core-verification-widget.php +++ b/includes/admin/class-pr-core-verification-widget.php @@ -23,7 +23,7 @@ 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 +33,38 @@ 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'; - 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', '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 '

' . esc_html__( 'All monographs are current. ', 'peptide-repo-core' ); diff --git a/includes/api/class-pr-core-rest-controller.php b/includes/api/class-pr-core-rest-controller.php index f2e8d5e..001ce6c 100644 --- a/includes/api/class-pr-core-rest-controller.php +++ b/includes/api/class-pr-core-rest-controller.php @@ -31,7 +31,7 @@ class PR_Core_Rest_Controller { * @return void */ public function register_hooks(): void { - add_action( 'rest_api_init', [ $this, 'register_routes' ] ); + add_action( 'rest_api_init', array( $this, 'register_routes' ) ); } /** @@ -43,57 +43,105 @@ class PR_Core_Rest_Controller { */ public function register_routes(): void { // GET /peptides - register_rest_route( self::REST_NAMESPACE, '/peptides', [ - 'methods' => 'GET', - 'callback' => [ $this, 'list_peptides' ], - 'permission_callback' => '__return_true', - 'args' => [ - 'category' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ], - 'evidence_strength' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ], - 'search' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ], - 'per_page' => [ 'type' => 'integer', 'default' => 25, 'minimum' => 1, 'maximum' => 100 ], - 'page' => [ 'type' => 'integer', 'default' => 1, 'minimum' => 1 ], - ], - ] ); + register_rest_route( + self::REST_NAMESPACE, + '/peptides', + array( + 'methods' => 'GET', + 'callback' => array( $this, 'list_peptides' ), + 'permission_callback' => '__return_true', + 'args' => array( + 'category' => array( + 'type' => 'string', + 'sanitize_callback' => 'sanitize_text_field', + ), + 'evidence_strength' => array( + 'type' => 'string', + 'sanitize_callback' => 'sanitize_text_field', + ), + 'search' => array( + 'type' => 'string', + 'sanitize_callback' => 'sanitize_text_field', + ), + 'per_page' => array( + 'type' => 'integer', + 'default' => 25, + 'minimum' => 1, + 'maximum' => 100, + ), + 'page' => array( + 'type' => 'integer', + 'default' => 1, + 'minimum' => 1, + ), + ), + ) + ); // GET /peptides/{id} - register_rest_route( self::REST_NAMESPACE, '/peptides/(?P\d+)', [ - 'methods' => 'GET', - 'callback' => [ $this, 'get_peptide' ], - 'permission_callback' => '__return_true', - ] ); + register_rest_route( + self::REST_NAMESPACE, + '/peptides/(?P\d+)', + array( + 'methods' => 'GET', + 'callback' => array( $this, 'get_peptide' ), + 'permission_callback' => '__return_true', + ) + ); // GET /peptides/{id}/dosing - register_rest_route( self::REST_NAMESPACE, '/peptides/(?P\d+)/dosing', [ - 'methods' => 'GET', - 'callback' => [ $this, 'list_dosing' ], - 'permission_callback' => '__return_true', - 'args' => [ - 'route' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ], - 'population' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ], - ], - ] ); + register_rest_route( + self::REST_NAMESPACE, + '/peptides/(?P\d+)/dosing', + array( + 'methods' => 'GET', + 'callback' => array( $this, 'list_dosing' ), + 'permission_callback' => '__return_true', + 'args' => array( + 'route' => array( + 'type' => 'string', + 'sanitize_callback' => 'sanitize_text_field', + ), + 'population' => array( + 'type' => 'string', + 'sanitize_callback' => 'sanitize_text_field', + ), + ), + ) + ); // POST /peptides/{id}/dosing (auth required) - register_rest_route( self::REST_NAMESPACE, '/peptides/(?P\d+)/dosing', [ - 'methods' => 'POST', - 'callback' => [ $this, 'create_dosing' ], - 'permission_callback' => [ $this, 'check_write_permission' ], - ] ); + register_rest_route( + self::REST_NAMESPACE, + '/peptides/(?P\d+)/dosing', + array( + 'methods' => 'POST', + 'callback' => array( $this, 'create_dosing' ), + 'permission_callback' => array( $this, 'check_write_permission' ), + ) + ); // GET /peptides/{id}/legal - register_rest_route( self::REST_NAMESPACE, '/peptides/(?P\d+)/legal', [ - 'methods' => 'GET', - 'callback' => [ $this, 'list_legal' ], - 'permission_callback' => '__return_true', - ] ); + register_rest_route( + self::REST_NAMESPACE, + '/peptides/(?P\d+)/legal', + array( + 'methods' => 'GET', + 'callback' => array( $this, 'list_legal' ), + 'permission_callback' => '__return_true', + ) + ); // POST /peptides/{id}/legal (auth required) - register_rest_route( self::REST_NAMESPACE, '/peptides/(?P\d+)/legal', [ - 'methods' => 'POST', - 'callback' => [ $this, 'create_legal' ], - 'permission_callback' => [ $this, 'check_write_permission' ], - ] ); + register_rest_route( + self::REST_NAMESPACE, + '/peptides/(?P\d+)/legal', + array( + 'methods' => 'POST', + 'callback' => array( $this, 'create_legal' ), + 'permission_callback' => array( $this, 'check_write_permission' ), + ) + ); } /** @@ -109,12 +157,14 @@ class PR_Core_Rest_Controller { if ( $search ) { $peptides = $repo->search( $search, (int) $request->get_param( 'per_page' ) ); } else { - $peptides = $repo->find_all( [ - 'category' => $request->get_param( 'category' ), - 'evidence_strength' => $request->get_param( 'evidence_strength' ), - 'per_page' => $request->get_param( 'per_page' ), - 'page' => $request->get_param( 'page' ), - ] ); + $peptides = $repo->find_all( + array( + 'category' => $request->get_param( 'category' ), + 'evidence_strength' => $request->get_param( 'evidence_strength' ), + 'per_page' => $request->get_param( 'per_page' ), + 'page' => $request->get_param( 'page' ), + ) + ); } $data = array_map( static fn( PR_Core_Peptide_DTO $p ) => $p->to_array(), $peptides ); @@ -133,7 +183,7 @@ class PR_Core_Rest_Controller { $peptide = $repo->find_by_id( (int) $request->get_param( 'id' ) ); if ( ! $peptide ) { - return new \WP_Error( 'not_found', __( 'Peptide not found.', 'peptide-repo-core' ), [ 'status' => 404 ] ); + return new \WP_Error( 'not_found', __( 'Peptide not found.', 'peptide-repo-core' ), array( 'status' => 404 ) ); } return new \WP_REST_Response( $peptide->to_array(), 200 ); @@ -149,10 +199,12 @@ class PR_Core_Rest_Controller { $repo = new PR_Core_Dosing_Repository(); $rows = $repo->find_by_peptide( (int) $request->get_param( 'id' ), - array_filter( [ - 'route' => $request->get_param( 'route' ), - 'population' => $request->get_param( 'population' ), - ] ) + array_filter( + array( + 'route' => $request->get_param( 'route' ), + 'population' => $request->get_param( 'population' ), + ) + ) ); $data = array_map( static fn( PR_Core_Dosing_Row_DTO $r ) => $r->to_array(), $rows ); @@ -176,12 +228,12 @@ class PR_Core_Rest_Controller { $id = $repo->insert( $data ); if ( 0 === $id ) { - return new \WP_Error( 'insert_failed', __( 'Failed to insert dosing row.', 'peptide-repo-core' ), [ 'status' => 500 ] ); + return new \WP_Error( 'insert_failed', __( 'Failed to insert dosing row.', 'peptide-repo-core' ), array( 'status' => 500 ) ); } $row = $repo->find_by_id( $id ); - return new \WP_REST_Response( $row ? $row->to_array() : [ 'id' => $id ], 201 ); + return new \WP_REST_Response( $row ? $row->to_array() : array( 'id' => $id ), 201 ); } /** @@ -208,19 +260,19 @@ class PR_Core_Rest_Controller { public function create_legal( \WP_REST_Request $request ) { $repo = new PR_Core_Legal_Repository(); - $data = $request->get_json_params(); - $data['peptide_id'] = (int) $request->get_param( 'id' ); + $data = $request->get_json_params(); + $data['peptide_id'] = (int) $request->get_param( 'id' ); $data['reviewer_id'] = get_current_user_id(); $id = $repo->insert( $data ); if ( 0 === $id ) { - return new \WP_Error( 'insert_failed', __( 'Failed to insert legal cell.', 'peptide-repo-core' ), [ 'status' => 500 ] ); + return new \WP_Error( 'insert_failed', __( 'Failed to insert legal cell.', 'peptide-repo-core' ), array( 'status' => 500 ) ); } $cell = $repo->find_by_id( $id ); - return new \WP_REST_Response( $cell ? $cell->to_array() : [ 'id' => $id ], 201 ); + return new \WP_REST_Response( $cell ? $cell->to_array() : array( 'id' => $id ), 201 ); } /** diff --git a/includes/class-pr-core-activator.php b/includes/class-pr-core-activator.php index 43efb35..7b11609 100644 --- a/includes/class-pr-core-activator.php +++ b/includes/class-pr-core-activator.php @@ -93,7 +93,7 @@ class PR_Core_Activator { */ private static function add_capabilities(): void { $cap = 'manage_peptide_content'; - $roles = [ 'administrator', 'editor' ]; + $roles = array( 'administrator', 'editor' ); foreach ( $roles as $role_name ) { $role = get_role( $role_name ); @@ -156,4 +156,3 @@ class PR_Core_Activator { } } } - diff --git a/includes/class-pr-core-autoloader.php b/includes/class-pr-core-autoloader.php index 29c5db5..490c534 100644 --- a/includes/class-pr-core-autoloader.php +++ b/includes/class-pr-core-autoloader.php @@ -16,7 +16,7 @@ declare(strict_types=1); class PR_Core_Autoloader { /** @var string[] Directories to scan for class files. */ - private static array $dirs = []; + private static array $dirs = array(); /** * Register the autoloader with SPL. @@ -35,7 +35,7 @@ class PR_Core_Autoloader { self::$dirs[] = trailingslashit( $dir ); } - spl_autoload_register( [ __CLASS__, 'load' ] ); + spl_autoload_register( array( __CLASS__, 'load' ) ); } /** diff --git a/includes/class-pr-core-seed-data.php b/includes/class-pr-core-seed-data.php index 2aefd78..4e7bfc1 100644 --- a/includes/class-pr-core-seed-data.php +++ b/includes/class-pr-core-seed-data.php @@ -24,11 +24,11 @@ class PR_Core_Seed_Data { $dosing = self::seed_dosing_rows( $peptide_ids ); $legal = self::seed_legal_cells( $peptide_ids ); - return [ + return array( 'peptides' => count( $peptide_ids ), 'dosing_rows' => $dosing, 'legal_cells' => $legal, - ]; + ); } /** @@ -37,8 +37,8 @@ class PR_Core_Seed_Data { * @return array Map of slug => post ID. */ private static function seed_peptides(): array { - $peptides = [ - [ + $peptides = array( + array( 'title' => 'BPC-157', 'slug' => 'bpc-157', 'excerpt' => 'Body Protection Compound-157, a pentadecapeptide derived from human gastric juice.', @@ -50,8 +50,8 @@ class PR_Core_Seed_Data { 'drugbank_id' => '', 'chembl_id' => '', 'evidence_strength' => 'observational', - ], - [ + ), + array( 'title' => 'Semaglutide', 'slug' => 'semaglutide', 'excerpt' => 'A GLP-1 receptor agonist approved for type 2 diabetes and chronic weight management.', @@ -63,8 +63,8 @@ class PR_Core_Seed_Data { 'drugbank_id' => 'DB13928', 'chembl_id' => 'CHEMBL3137309', 'evidence_strength' => 'meta-analysis', - ], - [ + ), + array( 'title' => 'TB-500', 'slug' => 'tb-500', 'excerpt' => 'Thymosin Beta-4 fragment, a synthetic peptide used in tissue repair research.', @@ -76,37 +76,41 @@ class PR_Core_Seed_Data { 'drugbank_id' => '', 'chembl_id' => '', 'evidence_strength' => 'preclinical', - ], - ]; + ), + ); - $ids = []; + $ids = array(); foreach ( $peptides as $p ) { - $existing = get_posts( [ - 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, - 'name' => $p['slug'], - 'posts_per_page' => 1, - 'post_status' => 'any', - ] ); + $existing = get_posts( + array( + 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, + 'name' => $p['slug'], + 'posts_per_page' => 1, + 'post_status' => 'any', + ) + ); if ( ! empty( $existing ) ) { $ids[ $p['slug'] ] = $existing[0]->ID; continue; } - $post_id = wp_insert_post( [ - 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, - 'post_title' => $p['title'], - 'post_name' => $p['slug'], - 'post_excerpt' => $p['excerpt'], - 'post_status' => 'publish', - 'post_content' => '', - ] ); + $post_id = wp_insert_post( + array( + 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, + 'post_title' => $p['title'], + 'post_name' => $p['slug'], + 'post_excerpt' => $p['excerpt'], + 'post_status' => 'publish', + 'post_content' => '', + ) + ); if ( is_wp_error( $post_id ) ) { continue; } - foreach ( [ 'display_name', 'aliases', 'molecular_formula', 'molecular_weight', 'cas_number', 'drugbank_id', 'chembl_id', 'evidence_strength' ] as $key ) { + foreach ( array( 'display_name', 'aliases', 'molecular_formula', 'molecular_weight', 'cas_number', 'drugbank_id', 'chembl_id', 'evidence_strength' ) as $key ) { update_post_meta( $post_id, $key, $p[ $key ] ); } update_post_meta( $post_id, 'editorial_review_status', 'published' ); @@ -126,21 +130,145 @@ class PR_Core_Seed_Data { */ private static function seed_dosing_rows( array $peptide_ids ): int { $repo = new PR_Core_Dosing_Repository(); - $rows = [ + $rows = array( // BPC-157 (4 rows). - [ 'peptide' => 'bpc-157', 'dose_min' => 200, 'dose_max' => 300, 'dose_unit' => 'mcg', 'route' => 'subq', 'frequency' => 'twice daily', 'population' => 'healthy', 'evidence_strength' => 'observational', 'study_title' => 'BPC 157 in wound healing review', 'study_year' => 2021, 'citation_pubmed_id' => '34537800' ], - [ 'peptide' => 'bpc-157', 'dose_min' => 500, 'dose_max' => 500, 'dose_unit' => 'mcg', 'route' => 'subq', 'frequency' => 'daily', 'population' => 'healthy', 'evidence_strength' => 'case-series', 'study_title' => 'Subcutaneous BPC-157 in tendon repair', 'study_year' => 2019, 'citation_pubmed_id' => '30915550' ], - [ 'peptide' => 'bpc-157', 'dose_min' => 10, 'dose_max' => 10, 'dose_unit' => 'mcg', 'route' => 'oral', 'frequency' => 'daily', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'Oral BPC-157 in rat gastric ulcer model', 'study_year' => 2018, 'citation_pubmed_id' => '29869189' ], - [ 'peptide' => 'bpc-157', 'dose_min' => 250, 'dose_max' => 750, 'dose_unit' => 'mcg', 'route' => 'im', 'frequency' => 'daily', 'population' => 'clinical', 'evidence_strength' => 'case-series', 'study_title' => 'Intramuscular BPC-157 for muscle injuries', 'study_year' => 2020, 'citation_pubmed_id' => '33312000' ], + array( + 'peptide' => 'bpc-157', + 'dose_min' => 200, + 'dose_max' => 300, + 'dose_unit' => 'mcg', + 'route' => 'subq', + 'frequency' => 'twice daily', + 'population' => 'healthy', + 'evidence_strength' => 'observational', + 'study_title' => 'BPC 157 in wound healing review', + 'study_year' => 2021, + 'citation_pubmed_id' => '34537800', + ), + array( + 'peptide' => 'bpc-157', + 'dose_min' => 500, + 'dose_max' => 500, + 'dose_unit' => 'mcg', + 'route' => 'subq', + 'frequency' => 'daily', + 'population' => 'healthy', + 'evidence_strength' => 'case-series', + 'study_title' => 'Subcutaneous BPC-157 in tendon repair', + 'study_year' => 2019, + 'citation_pubmed_id' => '30915550', + ), + array( + 'peptide' => 'bpc-157', + 'dose_min' => 10, + 'dose_max' => 10, + 'dose_unit' => 'mcg', + 'route' => 'oral', + 'frequency' => 'daily', + 'population' => 'animal', + 'evidence_strength' => 'preclinical', + 'study_title' => 'Oral BPC-157 in rat gastric ulcer model', + 'study_year' => 2018, + 'citation_pubmed_id' => '29869189', + ), + array( + 'peptide' => 'bpc-157', + 'dose_min' => 250, + 'dose_max' => 750, + 'dose_unit' => 'mcg', + 'route' => 'im', + 'frequency' => 'daily', + 'population' => 'clinical', + 'evidence_strength' => 'case-series', + 'study_title' => 'Intramuscular BPC-157 for muscle injuries', + 'study_year' => 2020, + 'citation_pubmed_id' => '33312000', + ), // Semaglutide (4 rows). - [ 'peptide' => 'semaglutide', 'dose_min' => 0.25, 'dose_max' => 0.25, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'SUSTAIN 1: Semaglutide in T2DM', 'study_year' => 2017, 'citation_pubmed_id' => '28930514', 'indication' => 'Type 2 diabetes — initiation dose' ], - [ 'peptide' => 'semaglutide', 'dose_min' => 1.0, 'dose_max' => 1.0, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'SUSTAIN 6: CV outcomes with semaglutide', 'study_year' => 2016, 'citation_pubmed_id' => '27633186', 'indication' => 'Type 2 diabetes — maintenance' ], - [ 'peptide' => 'semaglutide', 'dose_min' => 2.4, 'dose_max' => 2.4, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'STEP 1: Semaglutide 2.4mg for obesity', 'study_year' => 2021, 'citation_pubmed_id' => '33567185', 'indication' => 'Chronic weight management' ], - [ 'peptide' => 'semaglutide', 'dose_min' => 14, 'dose_max' => 14, 'dose_unit' => 'mg', 'route' => 'oral', 'frequency' => 'daily', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'PIONEER 1: Oral semaglutide in T2DM', 'study_year' => 2019, 'citation_pubmed_id' => '30924169', 'indication' => 'Type 2 diabetes — oral formulation' ], + array( + 'peptide' => 'semaglutide', + 'dose_min' => 0.25, + 'dose_max' => 0.25, + 'dose_unit' => 'mg', + 'route' => 'subq', + 'frequency' => 'weekly', + 'population' => 'clinical', + 'evidence_strength' => 'rct-large', + 'study_title' => 'SUSTAIN 1: Semaglutide in T2DM', + 'study_year' => 2017, + 'citation_pubmed_id' => '28930514', + 'indication' => 'Type 2 diabetes — initiation dose', + ), + array( + 'peptide' => 'semaglutide', + 'dose_min' => 1.0, + 'dose_max' => 1.0, + 'dose_unit' => 'mg', + 'route' => 'subq', + 'frequency' => 'weekly', + 'population' => 'clinical', + 'evidence_strength' => 'rct-large', + 'study_title' => 'SUSTAIN 6: CV outcomes with semaglutide', + 'study_year' => 2016, + 'citation_pubmed_id' => '27633186', + 'indication' => 'Type 2 diabetes — maintenance', + ), + array( + 'peptide' => 'semaglutide', + 'dose_min' => 2.4, + 'dose_max' => 2.4, + 'dose_unit' => 'mg', + 'route' => 'subq', + 'frequency' => 'weekly', + 'population' => 'clinical', + 'evidence_strength' => 'rct-large', + 'study_title' => 'STEP 1: Semaglutide 2.4mg for obesity', + 'study_year' => 2021, + 'citation_pubmed_id' => '33567185', + 'indication' => 'Chronic weight management', + ), + array( + 'peptide' => 'semaglutide', + 'dose_min' => 14, + 'dose_max' => 14, + 'dose_unit' => 'mg', + 'route' => 'oral', + 'frequency' => 'daily', + 'population' => 'clinical', + 'evidence_strength' => 'rct-large', + 'study_title' => 'PIONEER 1: Oral semaglutide in T2DM', + 'study_year' => 2019, + 'citation_pubmed_id' => '30924169', + 'indication' => 'Type 2 diabetes — oral formulation', + ), // TB-500 (2 rows). - [ 'peptide' => 'tb-500', 'dose_min' => 2, 'dose_max' => 2.5, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'twice weekly', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'Thymosin beta-4 promotes dermal healing in rats', 'study_year' => 2007, 'citation_pubmed_id' => '17584560' ], - [ 'peptide' => 'tb-500', 'dose_min' => 5, 'dose_max' => 5, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'TB4 cardiac repair in murine MI model', 'study_year' => 2012, 'citation_pubmed_id' => '22561753' ], - ]; + array( + 'peptide' => 'tb-500', + 'dose_min' => 2, + 'dose_max' => 2.5, + 'dose_unit' => 'mg', + 'route' => 'subq', + 'frequency' => 'twice weekly', + 'population' => 'animal', + 'evidence_strength' => 'preclinical', + 'study_title' => 'Thymosin beta-4 promotes dermal healing in rats', + 'study_year' => 2007, + 'citation_pubmed_id' => '17584560', + ), + array( + 'peptide' => 'tb-500', + 'dose_min' => 5, + 'dose_max' => 5, + 'dose_unit' => 'mg', + 'route' => 'subq', + 'frequency' => 'weekly', + 'population' => 'animal', + 'evidence_strength' => 'preclinical', + 'study_title' => 'TB4 cardiac repair in murine MI model', + 'study_year' => 2012, + 'citation_pubmed_id' => '22561753', + ), + ); $count = 0; foreach ( $rows as $row ) { @@ -156,7 +284,7 @@ class PR_Core_Seed_Data { $row['added_by'] = get_current_user_id() ?: 1; if ( $repo->insert( $row ) > 0 ) { - $count++; + ++$count; } } @@ -171,13 +299,44 @@ class PR_Core_Seed_Data { */ private static function seed_legal_cells( array $peptide_ids ): int { $repo = new PR_Core_Legal_Repository(); - $cells = [ - [ 'peptide' => 'bpc-157', 'country_code' => 'US', 'status' => 'ruo', 'regulatory_framework' => 'Not FDA-approved; available as Research Use Only', 'notes' => 'Compounding pharmacies may dispense under FDA 503A/503B exemptions.' ], - [ 'peptide' => 'bpc-157', 'country_code' => 'GB', 'status' => 'unclear', 'regulatory_framework' => 'Not listed by MHRA', 'notes' => 'No specific scheduling; import for personal use is a grey area.' ], - [ 'peptide' => 'semaglutide', 'country_code' => 'US', 'status' => 'prescription', 'regulatory_framework' => 'FDA-approved (Ozempic, Wegovy, Rybelsus)', 'regulatory_text_url' => 'https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/209637s020lbl.pdf', 'notes' => 'Schedule IV not applicable; requires valid prescription.' ], - [ 'peptide' => 'semaglutide', 'country_code' => 'GB', 'status' => 'prescription', 'regulatory_framework' => 'MHRA-approved (Ozempic, Wegovy)', 'notes' => 'Available via NHS and private prescription.' ], - [ 'peptide' => 'semaglutide', 'country_code' => 'AU', 'status' => 'prescription', 'regulatory_framework' => 'TGA-approved (Ozempic)', 'notes' => 'PBS-listed for type 2 diabetes; Wegovy approval pending as of 2025.' ], - ]; + $cells = array( + array( + 'peptide' => 'bpc-157', + 'country_code' => 'US', + 'status' => 'ruo', + 'regulatory_framework' => 'Not FDA-approved; available as Research Use Only', + 'notes' => 'Compounding pharmacies may dispense under FDA 503A/503B exemptions.', + ), + array( + 'peptide' => 'bpc-157', + 'country_code' => 'GB', + 'status' => 'unclear', + 'regulatory_framework' => 'Not listed by MHRA', + 'notes' => 'No specific scheduling; import for personal use is a grey area.', + ), + array( + 'peptide' => 'semaglutide', + 'country_code' => 'US', + 'status' => 'prescription', + 'regulatory_framework' => 'FDA-approved (Ozempic, Wegovy, Rybelsus)', + 'regulatory_text_url' => 'https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/209637s020lbl.pdf', + 'notes' => 'Schedule IV not applicable; requires valid prescription.', + ), + array( + 'peptide' => 'semaglutide', + 'country_code' => 'GB', + 'status' => 'prescription', + 'regulatory_framework' => 'MHRA-approved (Ozempic, Wegovy)', + 'notes' => 'Available via NHS and private prescription.', + ), + array( + 'peptide' => 'semaglutide', + 'country_code' => 'AU', + 'status' => 'prescription', + 'regulatory_framework' => 'TGA-approved (Ozempic)', + 'notes' => 'PBS-listed for type 2 diabetes; Wegovy approval pending as of 2025.', + ), + ); $count = 0; foreach ( $cells as $cell ) { @@ -192,7 +351,7 @@ class PR_Core_Seed_Data { $cell['reviewer_id'] = get_current_user_id() ?: 1; if ( $repo->insert( $cell ) > 0 ) { - $count++; + ++$count; } } diff --git a/includes/class-pr-core.php b/includes/class-pr-core.php index f7b2315..b4ce83b 100644 --- a/includes/class-pr-core.php +++ b/includes/class-pr-core.php @@ -47,24 +47,24 @@ class PR_Core { // end of init (priority 999) so all CPTs/taxonomies — ours and // anyone else's — are registered first. Handles updates deployed // without a deactivate/reactivate cycle (e.g., SCP/rsync pushes). - add_action( 'init', [ PR_Core_Activator::class, 'maybe_flush_on_version_change' ], 999 ); + add_action( 'init', array( 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' ] ); + add_action( 'pr_core_verification_scan', array( 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' ] ); + add_action( 'wp_ajax_pr_core_mark_verified', array( PR_Core_Ajax_Handlers::class, 'handle_mark_verified' ) ); + add_action( 'wp_ajax_pr_core_scan_now', array( 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' ] ); + add_action( 'admin_menu', array( PR_Core_Settings::class, 'add_settings_page' ) ); + add_action( 'admin_init', array( PR_Core_Settings::class, 'register_settings' ) ); + add_action( 'wp_dashboard_setup', array( PR_Core_Verification_Widget::class, 'register' ) ); $admin = new PR_Core_Admin(); $admin->register_hooks(); @@ -86,7 +86,7 @@ class PR_Core { $related_posts->register_hooks(); // Enqueue related-posts CSS on single peptide pages. - add_action( 'wp_enqueue_scripts', [ $this, 'enqueue_frontend_styles' ] ); + add_action( 'wp_enqueue_scripts', array( $this, 'enqueue_frontend_styles' ) ); // REST API. $rest = new PR_Core_Rest_Controller(); @@ -109,7 +109,7 @@ class PR_Core { wp_enqueue_style( 'pr-core-related-posts', PR_CORE_PLUGIN_URL . 'assets/css/related-posts.css', - [], + array(), PR_CORE_VERSION ); } @@ -125,9 +125,9 @@ class PR_Core { * @return void */ private function register_public_filters(): void { - add_filter( 'pr_core_get_indexable_corpus', [ $this, 'filter_indexable_corpus' ] ); - add_filter( 'pr_core_disclaimer_for_surface', [ $this, 'filter_disclaimer_for_surface' ], 10, 2 ); - add_filter( 'pr_core_evidence_strength_label', [ $this, 'filter_evidence_label' ], 10, 2 ); + add_filter( 'pr_core_get_indexable_corpus', array( $this, 'filter_indexable_corpus' ) ); + add_filter( 'pr_core_disclaimer_for_surface', array( $this, 'filter_disclaimer_for_surface' ), 10, 2 ); + add_filter( 'pr_core_evidence_strength_label', array( $this, 'filter_evidence_label' ), 10, 2 ); } /** @@ -139,17 +139,17 @@ class PR_Core { * @return array> */ public function filter_indexable_corpus( array $entries ): array { - $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' ) ); foreach ( $peptides as $dto ) { - $entries[] = [ + $entries[] = array( 'id' => $dto->id, 'url' => get_permalink( $dto->id ), 'title' => $dto->title, 'body' => $dto->excerpt . "\n" . $dto->content, 'type' => 'peptide_monograph', - ]; + ); } return $entries; @@ -174,14 +174,14 @@ class PR_Core { * @return string Localized label. */ public function filter_evidence_label( string $label, string $strength ): string { - $map = [ - 'preclinical' => __( 'Preclinical', 'peptide-repo-core' ), - 'case-series' => __( 'Case Series', 'peptide-repo-core' ), - 'observational' => __( 'Observational', 'peptide-repo-core' ), - 'rct-small' => __( 'Small RCT', 'peptide-repo-core' ), - 'rct-large' => __( 'Large RCT', 'peptide-repo-core' ), - 'meta-analysis' => __( 'Meta-Analysis', 'peptide-repo-core' ), - ]; + $map = array( + 'preclinical' => __( 'Preclinical', 'peptide-repo-core' ), + 'case-series' => __( 'Case Series', 'peptide-repo-core' ), + 'observational' => __( 'Observational', 'peptide-repo-core' ), + 'rct-small' => __( 'Small RCT', 'peptide-repo-core' ), + 'rct-large' => __( 'Large RCT', 'peptide-repo-core' ), + 'meta-analysis' => __( 'Meta-Analysis', 'peptide-repo-core' ), + ); return $map[ $strength ] ?? $strength; } diff --git a/includes/core/class-pr-core-internal-posts-provider.php b/includes/core/class-pr-core-internal-posts-provider.php index dc7bb49..39b1f8f 100644 --- a/includes/core/class-pr-core-internal-posts-provider.php +++ b/includes/core/class-pr-core-internal-posts-provider.php @@ -33,7 +33,7 @@ class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider public function get_posts( int $peptide_id, int $limit ): array { $peptide = get_post( $peptide_id ); if ( ! $peptide || 'peptide' !== $peptide->post_type ) { - return []; + return array(); } $cache_key = 'pr_core_related_' . $peptide_id; @@ -64,21 +64,23 @@ class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider * @return array */ private function query_by_taxonomy( string $peptide_slug, int $limit ): array { - $query = new WP_Query( [ - 'post_type' => 'post', - 'posts_per_page' => $limit, - 'orderby' => 'date', - 'order' => 'DESC', - 'tax_query' => [ - [ - 'taxonomy' => 'peptide_topic', - 'field' => 'slug', - 'terms' => $peptide_slug, - ], - ], - ] ); + $query = new WP_Query( + array( + 'post_type' => 'post', + 'posts_per_page' => $limit, + 'orderby' => 'date', + 'order' => 'DESC', + 'tax_query' => array( + array( + 'taxonomy' => 'peptide_topic', + 'field' => 'slug', + 'terms' => $peptide_slug, + ), + ), + ) + ); - return $query->posts ?: []; + return $query->posts ?: array(); } /** @@ -89,14 +91,16 @@ class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider * @return array */ private function query_by_search( string $search_term, int $limit ): array { - $query = new WP_Query( [ - 'post_type' => 'post', - 'posts_per_page' => $limit, - 'orderby' => 'date', - 'order' => 'DESC', - 's' => $search_term, - ] ); + $query = new WP_Query( + array( + 'post_type' => 'post', + 'posts_per_page' => $limit, + 'orderby' => 'date', + 'order' => 'DESC', + 's' => $search_term, + ) + ); - return $query->posts ?: []; + return $query->posts ?: array(); } } diff --git a/includes/core/class-pr-core-related-posts-section.php b/includes/core/class-pr-core-related-posts-section.php index 6d65ada..9ba8f1c 100644 --- a/includes/core/class-pr-core-related-posts-section.php +++ b/includes/core/class-pr-core-related-posts-section.php @@ -33,8 +33,8 @@ class PR_Core_Related_Posts_Section { * @return void */ public function register_hooks(): void { - add_action( 'pr_core_after_peptide_content', [ $this, 'render' ] ); - add_action( 'save_post_post', [ $this, 'invalidate_caches' ] ); + add_action( 'pr_core_after_peptide_content', array( $this, 'render' ) ); + add_action( 'save_post_post', array( $this, 'invalidate_caches' ) ); } /** @@ -72,7 +72,7 @@ class PR_Core_Related_Posts_Section { break; } setup_postdata( $post ); - get_template_part( 'template-parts/related-posts/card', null, [ 'post' => $post ] ); + get_template_part( 'template-parts/related-posts/card', null, array( 'post' => $post ) ); ++$count; } wp_reset_postdata(); diff --git a/includes/cpt/class-pr-core-peptide-cpt.php b/includes/cpt/class-pr-core-peptide-cpt.php index d06b97a..5b4d31f 100644 --- a/includes/cpt/class-pr-core-peptide-cpt.php +++ b/includes/cpt/class-pr-core-peptide-cpt.php @@ -31,26 +31,26 @@ class PR_Core_Peptide_CPT { * * @var string[] */ - public const EVIDENCE_STRENGTHS = [ + public const EVIDENCE_STRENGTHS = array( 'preclinical', 'case-series', 'observational', 'rct-small', 'rct-large', 'meta-analysis', - ]; + ); /** * Editorial review status enum values. * * @var string[] */ - public const REVIEW_STATUSES = [ + public const REVIEW_STATUSES = array( 'draft', 'in-review', 'published', 'retired', - ]; + ); /** * Post-meta field definitions (1:1 with peptide). @@ -59,115 +59,115 @@ class PR_Core_Peptide_CPT { * @return array> */ public static function get_meta_fields(): array { - return [ - 'display_name' => [ + return array( + 'display_name' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - 'aliases' => [ + ), + 'aliases' => array( 'type' => 'string', 'default' => '[]', - 'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ], - ], - 'molecular_formula' => [ + 'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ), + ), + 'molecular_formula' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - 'molecular_weight' => [ + ), + 'molecular_weight' => array( 'type' => 'number', 'default' => 0, 'sanitize' => 'floatval', - ], - 'cas_number' => [ + ), + 'cas_number' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - 'drugbank_id' => [ + ), + 'drugbank_id' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - 'chembl_id' => [ + ), + 'chembl_id' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - 'evidence_strength' => [ + ), + 'evidence_strength' => array( 'type' => 'string', 'default' => 'preclinical', - 'sanitize' => [ __CLASS__, 'sanitize_evidence_strength' ], - ], - 'editorial_review_status' => [ + 'sanitize' => array( __CLASS__, 'sanitize_evidence_strength' ), + ), + 'editorial_review_status' => array( 'type' => 'string', 'default' => 'draft', - 'sanitize' => [ __CLASS__, 'sanitize_review_status' ], - ], - 'last_editorial_review_at' => [ + 'sanitize' => array( __CLASS__, 'sanitize_review_status' ), + ), + 'last_editorial_review_at' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - 'medical_editor_id' => [ + ), + 'medical_editor_id' => array( 'type' => 'integer', 'default' => 0, 'sanitize' => 'absint', - ], - '_pr_last_source_verified' => [ + ), + '_pr_last_source_verified' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - '_pr_last_reviewed' => [ + ), + '_pr_last_reviewed' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - '_pr_next_review_by' => [ + ), + '_pr_next_review_by' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_text_field', - ], - '_pr_verification_velocity' => [ + ), + '_pr_verification_velocity' => array( 'type' => 'string', 'default' => 'medium', - 'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_velocity' ], - ], - '_pr_verification_notes' => [ + 'sanitize' => array( PR_Core_Verification_Sanitizers::class, 'sanitize_velocity' ), + ), + '_pr_verification_notes' => array( 'type' => 'string', 'default' => '', 'sanitize' => 'sanitize_textarea_field', - ], - '_pr_verification_status' => [ + ), + '_pr_verification_status' => array( 'type' => 'string', 'default' => 'current', - 'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_status' ], - ], + 'sanitize' => array( PR_Core_Verification_Sanitizers::class, 'sanitize_status' ), + ), // Schema-input meta (v0.6.0): molecular data sourced from PSA psa_* keys via migration 0004. - '_pr_molecular_formula' => [ + '_pr_molecular_formula' => array( 'type' => 'string', 'default' => '', - 'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ], - ], - '_pr_molecular_weight' => [ + 'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ), + ), + '_pr_molecular_weight' => array( 'type' => 'string', 'default' => '', - 'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ], - ], - '_pr_aliases' => [ + 'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ), + ), + '_pr_aliases' => array( 'type' => 'string', 'default' => '[]', - 'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ], - ], + 'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ), + ), // FAQ items (v0.6.0): [{question, answer}] JSON for FAQPage schema. Populated by CMO content sprint. - '_pr_faq_items' => [ + '_pr_faq_items' => array( 'type' => 'string', 'default' => '[]', - 'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ], - ], - ]; + 'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ), + ), + ); } /** @@ -176,9 +176,9 @@ class PR_Core_Peptide_CPT { * @return void */ public function register_hooks(): void { - add_action( 'init', [ __CLASS__, 'register_peptide_post_type' ] ); - add_action( 'init', [ __CLASS__, 'register_taxonomies' ] ); - add_action( 'init', [ __CLASS__, 'register_meta_fields' ] ); + add_action( 'init', array( __CLASS__, 'register_peptide_post_type' ) ); + add_action( 'init', array( __CLASS__, 'register_taxonomies' ) ); + add_action( 'init', array( __CLASS__, 'register_meta_fields' ) ); } /** @@ -193,7 +193,7 @@ class PR_Core_Peptide_CPT { return; } - $labels = [ + $labels = array( 'name' => __( 'Peptides', 'peptide-repo-core' ), 'singular_name' => __( 'Peptide', 'peptide-repo-core' ), 'add_new_item' => __( 'Add New Peptide', 'peptide-repo-core' ), @@ -205,11 +205,11 @@ class PR_Core_Peptide_CPT { 'not_found_in_trash' => __( 'No peptides found in trash', 'peptide-repo-core' ), 'all_items' => __( 'All Peptides', 'peptide-repo-core' ), 'menu_name' => __( 'Peptides', 'peptide-repo-core' ), - ]; + ); // Args harmonized superset of PR Core + PSA for 89 existing posts. // Supports union, capability/role perms preserved, slugs unchanged. - $args = [ + $args = array( 'labels' => $labels, 'public' => true, 'publicly_queryable' => true, @@ -228,9 +228,12 @@ class PR_Core_Peptide_CPT { 'map_meta_cap' => true, 'hierarchical' => false, 'has_archive' => true, - 'rewrite' => [ 'slug' => 'peptides', 'with_front' => false ], - 'supports' => [ 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ], - ]; + 'rewrite' => array( + 'slug' => 'peptides', + 'with_front' => false, + ), + 'supports' => array( 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ), + ); register_post_type( self::POST_TYPE, $args ); } @@ -246,19 +249,26 @@ class PR_Core_Peptide_CPT { 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 ], - ] ); + register_taxonomy( + self::TAX_CATEGORY, + self::POST_TYPE, + array( + 'labels' => array( + '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' => array( + 'slug' => 'peptide-category', + 'with_front' => false, + ), + ) + ); } /** @@ -268,16 +278,20 @@ class PR_Core_Peptide_CPT { */ public static function register_meta_fields(): void { foreach ( self::get_meta_fields() as $key => $config ) { - register_post_meta( self::POST_TYPE, $key, [ - 'type' => $config['type'], - 'single' => true, - 'default' => $config['default'], - 'show_in_rest' => true, - 'sanitize_callback' => $config['sanitize'], - 'auth_callback' => static function () { - return current_user_can( self::CAPABILITY ); - }, - ] ); + register_post_meta( + self::POST_TYPE, + $key, + array( + 'type' => $config['type'], + 'single' => true, + 'default' => $config['default'], + 'show_in_rest' => true, + 'sanitize_callback' => $config['sanitize'], + 'auth_callback' => static function () { + return current_user_can( self::CAPABILITY ); + }, + ) + ); } } diff --git a/includes/cpt/class-pr-core-repo-daily-cpt.php b/includes/cpt/class-pr-core-repo-daily-cpt.php index 2382520..ba4923d 100755 --- a/includes/cpt/class-pr-core-repo-daily-cpt.php +++ b/includes/cpt/class-pr-core-repo-daily-cpt.php @@ -27,7 +27,7 @@ class PR_Core_Repo_Daily_CPT { * @return void */ public function register_hooks(): void { - add_action( 'init', [ __CLASS__, 'register_post_type' ] ); + add_action( 'init', array( __CLASS__, 'register_post_type' ) ); } /** @@ -42,7 +42,7 @@ class PR_Core_Repo_Daily_CPT { return; } - $labels = [ + $labels = array( 'name' => __( 'Repo Daily', 'peptide-repo-core' ), 'singular_name' => __( 'Repo Daily', 'peptide-repo-core' ), 'add_new_item' => __( 'Add New Article', 'peptide-repo-core' ), @@ -54,9 +54,9 @@ class PR_Core_Repo_Daily_CPT { 'not_found_in_trash' => __( 'No articles found in trash', 'peptide-repo-core' ), 'all_items' => __( 'All Articles', 'peptide-repo-core' ), 'menu_name' => __( 'Repo Daily', 'peptide-repo-core' ), - ]; + ); - $args = [ + $args = array( 'labels' => $labels, 'public' => true, 'publicly_queryable' => true, @@ -71,9 +71,12 @@ class PR_Core_Repo_Daily_CPT { 'map_meta_cap' => true, 'hierarchical' => false, 'has_archive' => true, - 'rewrite' => [ 'slug' => 'daily', 'with_front' => false ], - 'supports' => [ 'title', 'editor', 'excerpt', 'thumbnail', 'custom-fields' ], - ]; + 'rewrite' => array( + 'slug' => 'daily', + 'with_front' => false, + ), + 'supports' => array( 'title', 'editor', 'excerpt', 'thumbnail', 'custom-fields' ), + ); register_post_type( self::POST_TYPE, $args ); } diff --git a/includes/cpt/class-pr-core-schema-sanitizers.php b/includes/cpt/class-pr-core-schema-sanitizers.php index 8d9b24f..e08e63d 100644 --- a/includes/cpt/class-pr-core-schema-sanitizers.php +++ b/includes/cpt/class-pr-core-schema-sanitizers.php @@ -67,7 +67,7 @@ class PR_Core_Schema_Sanitizers { return ''; } // 3. Extract the maximal leading run of valid element tokens and separators. - // A valid run must start with an element token ([A-Z][a-z]?\d*), not a separator. + // A valid run must start with an element token ([A-Z][a-z]?\d*), not a separator. $pattern = '/^((?:' . self::FORMULA_TOKEN . '|' . self::FORMULA_SEP . ')+)/u'; if ( preg_match( $pattern, $value, $m ) ) { return $m[1]; @@ -132,7 +132,7 @@ class PR_Core_Schema_Sanitizers { return '[]'; } - $clean = []; + $clean = array(); foreach ( $value as $item ) { if ( ! is_array( $item ) ) { continue; @@ -140,10 +140,10 @@ class PR_Core_Schema_Sanitizers { $question = sanitize_text_field( (string) ( $item['question'] ?? '' ) ); $answer = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) ); if ( '' !== $question && '' !== $answer ) { - $clean[] = [ + $clean[] = array( 'question' => $question, 'answer' => $answer, - ]; + ); } } diff --git a/includes/cpt/class-pr-core-topic-taxonomy.php b/includes/cpt/class-pr-core-topic-taxonomy.php index 9dcf5f5..f65fef6 100644 --- a/includes/cpt/class-pr-core-topic-taxonomy.php +++ b/includes/cpt/class-pr-core-topic-taxonomy.php @@ -27,7 +27,7 @@ class PR_Core_Topic_Taxonomy { * @return void */ public function register_hooks(): void { - add_action( 'init', [ __CLASS__, 'register_topic_taxonomy' ] ); + add_action( 'init', array( __CLASS__, 'register_topic_taxonomy' ) ); } /** @@ -45,18 +45,25 @@ class PR_Core_Topic_Taxonomy { return; } - register_taxonomy( self::TAX_TOPIC, 'post', [ - 'labels' => [ - 'name' => __( 'Peptide Topics', 'peptide-repo-core' ), - 'singular_name' => __( 'Peptide Topic', 'peptide-repo-core' ), - ], - 'public' => true, - 'publicly_queryable' => true, - 'show_in_rest' => true, - 'show_ui' => true, - 'show_admin_column' => true, - 'hierarchical' => false, - 'rewrite' => [ 'slug' => 'peptide-topic', 'with_front' => false ], - ] ); + register_taxonomy( + self::TAX_TOPIC, + 'post', + array( + 'labels' => array( + 'name' => __( 'Peptide Topics', 'peptide-repo-core' ), + 'singular_name' => __( 'Peptide Topic', 'peptide-repo-core' ), + ), + 'public' => true, + 'publicly_queryable' => true, + 'show_in_rest' => true, + 'show_ui' => true, + 'show_admin_column' => true, + 'hierarchical' => false, + 'rewrite' => array( + 'slug' => 'peptide-topic', + 'with_front' => false, + ), + ) + ); } } diff --git a/includes/cpt/class-pr-core-verification-sanitizers.php b/includes/cpt/class-pr-core-verification-sanitizers.php index 5b0a932..ee3ee08 100644 --- a/includes/cpt/class-pr-core-verification-sanitizers.php +++ b/includes/cpt/class-pr-core-verification-sanitizers.php @@ -19,7 +19,7 @@ class PR_Core_Verification_Sanitizers { * @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'; + return in_array( $value, array( 'low', 'medium', 'high' ), true ) ? $value : 'medium'; } /** @@ -29,6 +29,6 @@ class PR_Core_Verification_Sanitizers { * @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'; + return in_array( $value, array( 'current', 'due', 'overdue' ), true ) ? $value : 'current'; } } diff --git a/includes/dto/class-pr-core-candidate-dto.php b/includes/dto/class-pr-core-candidate-dto.php index 9183d9e..9f053bf 100644 --- a/includes/dto/class-pr-core-candidate-dto.php +++ b/includes/dto/class-pr-core-candidate-dto.php @@ -74,7 +74,7 @@ class PR_Core_Candidate_DTO { * @return array */ public function to_array(): array { - return [ + return array( 'id' => $this->id, 'peptide_id' => $this->peptide_id, 'dose_min' => $this->dose_min, @@ -90,6 +90,6 @@ class PR_Core_Candidate_DTO { 'extraction_confidence' => $this->extraction_confidence, 'queue_status' => $this->queue_status, 'extracted_at' => $this->extracted_at, - ]; + ); } } diff --git a/includes/dto/class-pr-core-dosing-row-dto.php b/includes/dto/class-pr-core-dosing-row-dto.php index 98724b5..af991a3 100644 --- a/includes/dto/class-pr-core-dosing-row-dto.php +++ b/includes/dto/class-pr-core-dosing-row-dto.php @@ -44,32 +44,32 @@ class PR_Core_Dosing_Row_DTO { * @param array $data Associative array from database row. */ public function __construct( array $data ) { - $this->id = (int) ( $data['id'] ?? 0 ); - $this->peptide_id = (int) ( $data['peptide_id'] ?? 0 ); - $this->dose_min = isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null; - $this->dose_max = isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null; - $this->dose_unit = (string) ( $data['dose_unit'] ?? '' ); - $this->route = (string) ( $data['route'] ?? '' ); - $this->frequency = $data['frequency'] ?? null; - $this->duration_value = isset( $data['duration_value'] ) ? (int) $data['duration_value'] : null; - $this->duration_unit = $data['duration_unit'] ?? null; - $this->population = (string) ( $data['population'] ?? '' ); - $this->indication = $data['indication'] ?? null; - $this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' ); - $this->study_title = $data['study_title'] ?? null; - $this->study_year = isset( $data['study_year'] ) ? (int) $data['study_year'] : null; - $this->citation_pubmed_id = $data['citation_pubmed_id'] ?? null; - $this->citation_doi = $data['citation_doi'] ?? null; - $this->citation_url = $data['citation_url'] ?? null; - $this->notes = $data['notes'] ?? null; - $this->schema_version = (int) ( $data['schema_version'] ?? 1 ); - $this->source = (string) ( $data['source'] ?? 'manual' ); - $this->ai_candidate_id = isset( $data['ai_candidate_id'] ) ? (int) $data['ai_candidate_id'] : null; - $this->added_by = (int) ( $data['added_by'] ?? 0 ); - $this->added_at = (string) ( $data['added_at'] ?? '' ); - $this->reviewed_by = isset( $data['reviewed_by'] ) ? (int) $data['reviewed_by'] : null; - $this->reviewed_at = $data['reviewed_at'] ?? null; - $this->superseded_by_id = isset( $data['superseded_by_id'] ) ? (int) $data['superseded_by_id'] : null; + $this->id = (int) ( $data['id'] ?? 0 ); + $this->peptide_id = (int) ( $data['peptide_id'] ?? 0 ); + $this->dose_min = isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null; + $this->dose_max = isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null; + $this->dose_unit = (string) ( $data['dose_unit'] ?? '' ); + $this->route = (string) ( $data['route'] ?? '' ); + $this->frequency = $data['frequency'] ?? null; + $this->duration_value = isset( $data['duration_value'] ) ? (int) $data['duration_value'] : null; + $this->duration_unit = $data['duration_unit'] ?? null; + $this->population = (string) ( $data['population'] ?? '' ); + $this->indication = $data['indication'] ?? null; + $this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' ); + $this->study_title = $data['study_title'] ?? null; + $this->study_year = isset( $data['study_year'] ) ? (int) $data['study_year'] : null; + $this->citation_pubmed_id = $data['citation_pubmed_id'] ?? null; + $this->citation_doi = $data['citation_doi'] ?? null; + $this->citation_url = $data['citation_url'] ?? null; + $this->notes = $data['notes'] ?? null; + $this->schema_version = (int) ( $data['schema_version'] ?? 1 ); + $this->source = (string) ( $data['source'] ?? 'manual' ); + $this->ai_candidate_id = isset( $data['ai_candidate_id'] ) ? (int) $data['ai_candidate_id'] : null; + $this->added_by = (int) ( $data['added_by'] ?? 0 ); + $this->added_at = (string) ( $data['added_at'] ?? '' ); + $this->reviewed_by = isset( $data['reviewed_by'] ) ? (int) $data['reviewed_by'] : null; + $this->reviewed_at = $data['reviewed_at'] ?? null; + $this->superseded_by_id = isset( $data['superseded_by_id'] ) ? (int) $data['superseded_by_id'] : null; } /** @@ -78,27 +78,27 @@ class PR_Core_Dosing_Row_DTO { * @return array */ public function to_array(): array { - return [ - 'id' => $this->id, - 'peptide_id' => $this->peptide_id, - 'dose_min' => $this->dose_min, - 'dose_max' => $this->dose_max, - 'dose_unit' => $this->dose_unit, - 'route' => $this->route, - 'frequency' => $this->frequency, - 'duration_value' => $this->duration_value, - 'duration_unit' => $this->duration_unit, - 'population' => $this->population, - 'indication' => $this->indication, - 'evidence_strength' => $this->evidence_strength, - 'study_title' => $this->study_title, - 'study_year' => $this->study_year, - 'citation_pubmed_id' => $this->citation_pubmed_id, - 'citation_doi' => $this->citation_doi, - 'citation_url' => $this->citation_url, - 'notes' => $this->notes, - 'source' => $this->source, - 'added_at' => $this->added_at, - ]; + return array( + 'id' => $this->id, + 'peptide_id' => $this->peptide_id, + 'dose_min' => $this->dose_min, + 'dose_max' => $this->dose_max, + 'dose_unit' => $this->dose_unit, + 'route' => $this->route, + 'frequency' => $this->frequency, + 'duration_value' => $this->duration_value, + 'duration_unit' => $this->duration_unit, + 'population' => $this->population, + 'indication' => $this->indication, + 'evidence_strength' => $this->evidence_strength, + 'study_title' => $this->study_title, + 'study_year' => $this->study_year, + 'citation_pubmed_id' => $this->citation_pubmed_id, + 'citation_doi' => $this->citation_doi, + 'citation_url' => $this->citation_url, + 'notes' => $this->notes, + 'source' => $this->source, + 'added_at' => $this->added_at, + ); } } diff --git a/includes/dto/class-pr-core-legal-cell-dto.php b/includes/dto/class-pr-core-legal-cell-dto.php index ea0b8d0..b03a03a 100644 --- a/includes/dto/class-pr-core-legal-cell-dto.php +++ b/includes/dto/class-pr-core-legal-cell-dto.php @@ -59,7 +59,7 @@ class PR_Core_Legal_Cell_DTO { * @return array */ public function to_array(): array { - return [ + return array( 'id' => $this->id, 'peptide_id' => $this->peptide_id, 'country_code' => $this->country_code, @@ -70,6 +70,6 @@ class PR_Core_Legal_Cell_DTO { 'notes' => $this->notes, 'last_verified_at' => $this->last_verified_at, 'is_active' => $this->is_active(), - ]; + ); } } diff --git a/includes/dto/class-pr-core-peptide-dto.php b/includes/dto/class-pr-core-peptide-dto.php index d8b02ed..72ed9a8 100644 --- a/includes/dto/class-pr-core-peptide-dto.php +++ b/includes/dto/class-pr-core-peptide-dto.php @@ -47,7 +47,7 @@ class PR_Core_Peptide_DTO { $this->excerpt = (string) ( $data['excerpt'] ?? '' ); $this->status = (string) ( $data['status'] ?? 'draft' ); $this->display_name = (string) ( $data['display_name'] ?? '' ); - $this->aliases = (array) ( $data['aliases'] ?? [] ); + $this->aliases = (array) ( $data['aliases'] ?? array() ); $this->molecular_formula = (string) ( $data['molecular_formula'] ?? '' ); $this->molecular_weight = (float) ( $data['molecular_weight'] ?? 0 ); $this->cas_number = (string) ( $data['cas_number'] ?? '' ); @@ -57,8 +57,8 @@ class PR_Core_Peptide_DTO { $this->editorial_review_status = (string) ( $data['editorial_review_status'] ?? 'draft' ); $this->last_editorial_review_at = (string) ( $data['last_editorial_review_at'] ?? '' ); $this->medical_editor_id = (int) ( $data['medical_editor_id'] ?? 0 ); - $this->categories = (array) ( $data['categories'] ?? [] ); - $this->families = (array) ( $data['families'] ?? [] ); + $this->categories = (array) ( $data['categories'] ?? array() ); + $this->families = (array) ( $data['families'] ?? array() ); } /** @@ -67,7 +67,7 @@ class PR_Core_Peptide_DTO { * @return array */ public function to_array(): array { - return [ + return array( 'id' => $this->id, 'title' => $this->title, 'slug' => $this->slug, @@ -86,6 +86,6 @@ class PR_Core_Peptide_DTO { 'categories' => $this->categories, 'families' => $this->families, 'url' => get_permalink( $this->id ), - ]; + ); } } diff --git a/includes/frontend/class-pr-core-disclaimer.php b/includes/frontend/class-pr-core-disclaimer.php index e46f7b9..85d641f 100644 --- a/includes/frontend/class-pr-core-disclaimer.php +++ b/includes/frontend/class-pr-core-disclaimer.php @@ -28,13 +28,13 @@ class PR_Core_Disclaimer { * * @var array */ - private const DEFAULTS = [ - 'dosing' => 'The dosing information presented here is compiled from published peer-reviewed literature and is provided for educational and research purposes only. It does not constitute medical advice, diagnosis, or treatment recommendations. Always consult a licensed healthcare professional before making any decisions based on this information.', - 'legal' => 'Legal status information is compiled from publicly available regulatory texts and is current as of the last-verified date shown. Regulatory frameworks change frequently. This information does not constitute legal advice. Verify current regulations with the relevant regulatory authority in your jurisdiction before taking any action.', - 'reconstitution' => 'This calculator is provided for educational purposes only. Always verify your calculations independently and consult a licensed healthcare professional. The results are based on the inputs you provide and standard reconstitution mathematics.', - 'ai-answer' => 'This response was generated by an AI system and may contain errors or omissions. All claims are grounded in the Peptide Repo corpus and cited sources where possible. This is not medical advice. Always verify information with primary sources and consult a licensed healthcare professional.', - 'general' => 'The information on this site is for educational and research purposes only. It is not intended as medical advice, diagnosis, or treatment. Always consult a licensed healthcare professional.', - ]; + private const DEFAULTS = array( + 'dosing' => 'The dosing information presented here is compiled from published peer-reviewed literature and is provided for educational and research purposes only. It does not constitute medical advice, diagnosis, or treatment recommendations. Always consult a licensed healthcare professional before making any decisions based on this information.', + 'legal' => 'Legal status information is compiled from publicly available regulatory texts and is current as of the last-verified date shown. Regulatory frameworks change frequently. This information does not constitute legal advice. Verify current regulations with the relevant regulatory authority in your jurisdiction before taking any action.', + 'reconstitution' => 'This calculator is provided for educational purposes only. Always verify your calculations independently and consult a licensed healthcare professional. The results are based on the inputs you provide and standard reconstitution mathematics.', + 'ai-answer' => 'This response was generated by an AI system and may contain errors or omissions. All claims are grounded in the Peptide Repo corpus and cited sources where possible. This is not medical advice. Always verify information with primary sources and consult a licensed healthcare professional.', + 'general' => 'The information on this site is for educational and research purposes only. It is not intended as medical advice, diagnosis, or treatment. Always consult a licensed healthcare professional.', + ); /** * Register shortcode and any frontend hooks. @@ -42,7 +42,7 @@ class PR_Core_Disclaimer { * @return void */ public function register_hooks(): void { - add_shortcode( 'pr_disclaimer', [ $this, 'shortcode_handler' ] ); + add_shortcode( 'pr_disclaimer', array( $this, 'shortcode_handler' ) ); } /** @@ -52,7 +52,7 @@ class PR_Core_Disclaimer { * @return string Disclaimer HTML. */ public function shortcode_handler( $atts ): string { - $atts = shortcode_atts( [ 'surface' => 'general' ], $atts, 'pr_disclaimer' ); + $atts = shortcode_atts( array( 'surface' => 'general' ), $atts, 'pr_disclaimer' ); return self::render( sanitize_text_field( $atts['surface'] ) ); } @@ -81,7 +81,7 @@ class PR_Core_Disclaimer { */ public static function get_disclaimer_text( string $surface ): string { $custom = get_option( self::COPY_OPTION, '{}' ); - $copy = json_decode( $custom, true ) ?: []; + $copy = json_decode( $custom, true ) ?: array(); if ( ! empty( $copy[ $surface ] ) ) { return (string) $copy[ $surface ]; @@ -110,7 +110,7 @@ class PR_Core_Disclaimer { */ public static function update_disclaimer( string $surface, string $text ): void { $custom = get_option( self::COPY_OPTION, '{}' ); - $copy = json_decode( $custom, true ) ?: []; + $copy = json_decode( $custom, true ) ?: array(); $copy[ sanitize_text_field( $surface ) ] = sanitize_textarea_field( $text ); diff --git a/includes/frontend/class-pr-core-jsonld-drug.php b/includes/frontend/class-pr-core-jsonld-drug.php index aad78d4..9f0a2bc 100644 --- a/includes/frontend/class-pr-core-jsonld-drug.php +++ b/includes/frontend/class-pr-core-jsonld-drug.php @@ -18,16 +18,16 @@ declare(strict_types=1); class PR_Core_Jsonld_Drug { /** @var string Meta key: molecular formula sourced by migration 0004. */ - private const META_FORMULA = '_pr_molecular_formula'; + private const META_FORMULA = '_pr_molecular_formula'; /** @var string Meta key: molecular weight (float string) sourced by migration 0004. */ - private const META_WEIGHT = '_pr_molecular_weight'; + private const META_WEIGHT = '_pr_molecular_weight'; /** @var string Meta key: aliases JSON array sourced by migration 0004. */ - private const META_ALIASES = '_pr_aliases'; + private const META_ALIASES = '_pr_aliases'; /** @var string Unit text for molecularWeight QuantitativeValue. */ - private const UNIT_TEXT = 'g/mol'; + private const UNIT_TEXT = 'g/mol'; /** * Build a schema.org Drug piece array for a peptide. @@ -38,12 +38,12 @@ class PR_Core_Jsonld_Drug { public function build( PR_Core_Peptide_DTO $peptide ): array { $permalink = get_permalink( $peptide->id ); - $node = [ - '@type' => [ 'Drug', 'MolecularEntity' ], + $node = array( + '@type' => array( 'Drug', 'MolecularEntity' ), '@id' => $permalink . '#drug', 'name' => $peptide->display_name ?: $peptide->title, 'url' => $permalink, - ]; + ); if ( '' !== $peptide->excerpt ) { $node['description'] = $peptide->excerpt; @@ -64,11 +64,11 @@ class PR_Core_Jsonld_Drug { // molecularWeight: prefer _pr_molecular_weight, fall back to DTO field. $weight = $this->get_weight( $peptide ); if ( $weight > 0.0 ) { - $node['molecularWeight'] = [ + $node['molecularWeight'] = array( '@type' => 'QuantitativeValue', 'value' => $weight, 'unitText' => self::UNIT_TEXT, - ]; + ); } // External identifiers: CAS and DrugBank omitted in v0.6.0 (no source). @@ -150,9 +150,9 @@ class PR_Core_Jsonld_Drug { * @return array|null */ private function build_legal_status(): ?array { - return [ + return array( '@type' => 'DrugLegalStatus', 'description' => esc_html__( 'Not approved for human therapeutic use; supplied for laboratory research purposes only.', 'peptide-repo-core' ), - ]; + ); } } diff --git a/includes/frontend/class-pr-core-jsonld-faq.php b/includes/frontend/class-pr-core-jsonld-faq.php index baba40d..f3a7883 100644 --- a/includes/frontend/class-pr-core-jsonld-faq.php +++ b/includes/frontend/class-pr-core-jsonld-faq.php @@ -34,11 +34,11 @@ class PR_Core_Jsonld_Faq { return null; } - return [ + return array( '@type' => 'FAQPage', '@id' => $permalink . '#faq', - 'mainEntity' => array_map( [ $this, 'build_question' ], $items ), - ]; + 'mainEntity' => array_map( array( $this, 'build_question' ), $items ), + ); } /** @@ -48,14 +48,14 @@ class PR_Core_Jsonld_Faq { * @return array Schema.org Question node. */ private function build_question( array $item ): array { - return [ - '@type' => 'Question', - 'name' => esc_html( $item['question'] ), - 'acceptedAnswer' => [ + return array( + '@type' => 'Question', + 'name' => esc_html( $item['question'] ), + 'acceptedAnswer' => array( '@type' => 'Answer', 'text' => esc_html( $item['answer'] ), - ], - ]; + ), + ); } /** @@ -71,16 +71,16 @@ class PR_Core_Jsonld_Faq { $raw = get_post_meta( $post_id, self::META_FAQ_ITEMS, true ); if ( ! is_string( $raw ) || '' === $raw ) { - return []; + return array(); } $decoded = json_decode( $raw, true ); if ( ! is_array( $decoded ) || empty( $decoded ) ) { - return []; + return array(); } - $valid = []; + $valid = array(); foreach ( $decoded as $item ) { if ( ! is_array( $item ) ) { continue; @@ -88,10 +88,10 @@ class PR_Core_Jsonld_Faq { $question = sanitize_text_field( (string) ( $item['question'] ?? '' ) ); $answer = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) ); if ( '' !== $question && '' !== $answer ) { - $valid[] = [ + $valid[] = array( 'question' => $question, 'answer' => $answer, - ]; + ); } } diff --git a/includes/frontend/class-pr-core-jsonld-webpage.php b/includes/frontend/class-pr-core-jsonld-webpage.php index 4b51e87..8f48132 100644 --- a/includes/frontend/class-pr-core-jsonld-webpage.php +++ b/includes/frontend/class-pr-core-jsonld-webpage.php @@ -77,7 +77,7 @@ class PR_Core_Jsonld_Webpage { // Yoast may set @type as a plain string OR an array of strings. // Normalise to array so in_array() works regardless of shape. $raw_type = $piece['@type'] ?? ''; - $types = is_array( $raw_type ) ? $raw_type : [ $raw_type ]; + $types = is_array( $raw_type ) ? $raw_type : array( $raw_type ); if ( in_array( 'WebPage', $types, true ) || in_array( 'MedicalWebPage', $types, true ) ) { foreach ( $enrichments as $key => $value ) { @@ -97,7 +97,7 @@ class PR_Core_Jsonld_Webpage { * @return array Enrichment fields to merge into the WebPage node. */ private function build_webpage_enrichments( int $post_id ): array { - $enrichments = []; + $enrichments = array(); // lastReviewed: prefer _pr_last_reviewed, fall back to _pr_last_source_verified, // then post modified date. @@ -118,27 +118,27 @@ class PR_Core_Jsonld_Webpage { if ( $editor_id > 0 ) { $editor = get_userdata( $editor_id ); if ( $editor ) { - $enrichments['reviewedBy'] = [ + $enrichments['reviewedBy'] = array( '@type' => 'Person', 'name' => sanitize_text_field( $editor->display_name ), 'url' => get_author_posts_url( $editor_id ), - ]; + ); } } if ( ! isset( $enrichments['reviewedBy'] ) ) { - $enrichments['reviewedBy'] = [ + $enrichments['reviewedBy'] = array( '@type' => 'Organization', 'name' => 'Peptide Repo', 'url' => home_url(), - ]; + ); } // audience: MedicalAudience for researchers. - $enrichments['audience'] = [ + $enrichments['audience'] = array( '@type' => 'MedicalAudience', 'audienceType' => 'Researcher', - ]; + ); return $enrichments; } diff --git a/includes/frontend/class-pr-core-jsonld.php b/includes/frontend/class-pr-core-jsonld.php index c9ad16e..a0bb103 100644 --- a/includes/frontend/class-pr-core-jsonld.php +++ b/includes/frontend/class-pr-core-jsonld.php @@ -6,6 +6,7 @@ declare(strict_types=1); * * What: Integrates Drug, MedicalWebPage, and FAQPage schema into Yoast's graph * on single peptide pages. When Yoast is inactive, emits a standalone + * * @graph block via wp_head as a fallback. * * Who calls it: PR_Core::init() calls register_hooks(). Yoast hooks fire on @@ -67,19 +68,19 @@ class PR_Core_Jsonld { */ public function register_hooks(): void { // wpseo_schema_webpage_type: retype WebPage -> MedicalWebPage on peptide singles. - add_filter( 'wpseo_schema_webpage_type', [ $this->webpage_enricher, 'retype_to_medical_webpage' ] ); + add_filter( 'wpseo_schema_webpage_type', array( $this->webpage_enricher, 'retype_to_medical_webpage' ) ); // wpseo_schema_graph: two callbacks at different priorities. // Priority 11 -- enrich_webpage_piece: merge lastReviewed/reviewedBy/audience into the - // existing WebPage node that Yoast already emitted. + // existing WebPage node that Yoast already emitted. // Priority 12 -- inject_graph_nodes: append Drug + FAQPage arrays to the graph. - // Must run after enrich_webpage_piece so the WebPage node is already - // enriched before Drug/FAQ are appended. - add_filter( 'wpseo_schema_graph', [ $this->webpage_enricher, 'enrich_webpage_piece' ], 11, 2 ); - add_filter( 'wpseo_schema_graph', [ $this, 'inject_graph_nodes' ], 12, 2 ); + // Must run after enrich_webpage_piece so the WebPage node is already + // enriched before Drug/FAQ are appended. + add_filter( 'wpseo_schema_graph', array( $this->webpage_enricher, 'enrich_webpage_piece' ), 11, 2 ); + add_filter( 'wpseo_schema_graph', array( $this, 'inject_graph_nodes' ), 12, 2 ); // Standalone fallback: emits only when Yoast is not producing output. - add_action( 'wp_head', [ $this, 'emit_standalone_fallback' ], 99 ); + add_action( 'wp_head', array( $this, 'emit_standalone_fallback' ), 99 ); } /** @@ -90,8 +91,8 @@ class PR_Core_Jsonld { * Appending plain Drug/FAQ arrays here is safe -- unlike wpseo_schema_graph_pieces * which calls get_class() and is_needed() on each item expecting objects. * - * @param array> $graph Assembled Yoast graph. - * @param \Yoast\WP\SEO\Context\Meta_Tags_Context|null $context Yoast schema context. + * @param array> $graph Assembled Yoast graph. + * @param \Yoast\WP\SEO\Context\Meta_Tags_Context|null $context Yoast schema context. * @return array> Graph with Drug (and optionally FAQ) appended. */ public function inject_graph_nodes( array $graph, $context ): array { @@ -150,7 +151,7 @@ class PR_Core_Jsonld { } $permalink = get_permalink( (int) $post_id ); - $graph = [ $this->drug_builder->build( $peptide ) ]; + $graph = array( $this->drug_builder->build( $peptide ) ); $faq_node = $this->faq_builder->build( (int) $post_id, $permalink ); if ( null !== $faq_node ) { @@ -160,7 +161,10 @@ class PR_Core_Jsonld { printf( '' . "\n", wp_json_encode( - [ '@context' => 'https://schema.org', '@graph' => $graph ], + array( + '@context' => 'https://schema.org', + '@graph' => $graph, + ), JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE | JSON_PRETTY_PRINT ) ); diff --git a/includes/frontend/class-pr-core-verification-display.php b/includes/frontend/class-pr-core-verification-display.php index 57a1afd..f02b239 100644 --- a/includes/frontend/class-pr-core-verification-display.php +++ b/includes/frontend/class-pr-core-verification-display.php @@ -20,7 +20,7 @@ class PR_Core_Verification_Display { * @return void */ public static function init(): void { - add_filter( 'the_content', [ __CLASS__, 'append_verification_display' ], 20 ); + add_filter( 'the_content', array( __CLASS__, 'append_verification_display' ), 20 ); } /** @@ -63,10 +63,10 @@ class PR_Core_Verification_Display { * @return string HTML block. */ private static function render_verification_block( string $last_verified ): string { - $date_obj = new \DateTime( $last_verified ); + $date_obj = new \DateTime( $last_verified ); $formatted_date = $date_obj->format( get_option( 'date_format' ) ); - $html = '

'; + $html = '

'; $html .= esc_html__( 'Last verified: ', 'peptide-repo-core' ); $html .= sprintf( '', diff --git a/includes/migrations/class-pr-core-migration-0002-legal-cells.php b/includes/migrations/class-pr-core-migration-0002-legal-cells.php index c3f5564..3d0640b 100644 --- a/includes/migrations/class-pr-core-migration-0002-legal-cells.php +++ b/includes/migrations/class-pr-core-migration-0002-legal-cells.php @@ -15,14 +15,14 @@ declare(strict_types=1); class PR_Core_Migration_0002_Legal_Cells { /** @var string[] Valid legal status enum values. */ - public const STATUSES = [ + public const STATUSES = array( 'prescription', 'ruo', 'otc', 'restricted', 'banned', 'unclear', - ]; + ); /** * Create the pr_legal_cells table. @@ -61,7 +61,7 @@ class PR_Core_Migration_0002_Legal_Cells { // phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery $index_exists = $wpdb->get_var( $wpdb->prepare( - "SELECT COUNT(*) FROM information_schema.STATISTICS WHERE TABLE_SCHEMA = %s AND TABLE_NAME = %s AND INDEX_NAME = %s", + 'SELECT COUNT(*) FROM information_schema.STATISTICS WHERE TABLE_SCHEMA = %s AND TABLE_NAME = %s AND INDEX_NAME = %s', DB_NAME, $table, 'uq_peptide_country_active' diff --git a/includes/migrations/class-pr-core-migration-0003-candidate-queue.php b/includes/migrations/class-pr-core-migration-0003-candidate-queue.php index e8665ae..d3944f2 100644 --- a/includes/migrations/class-pr-core-migration-0003-candidate-queue.php +++ b/includes/migrations/class-pr-core-migration-0003-candidate-queue.php @@ -16,12 +16,12 @@ declare(strict_types=1); class PR_Core_Migration_0003_Candidate_Queue { /** @var string[] Valid queue status enum values. */ - public const STATUSES = [ + public const STATUSES = array( 'pending', 'approved', 'rejected', 'merged', - ]; + ); /** * Create the pr_ai_candidate_queue table. diff --git a/includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php b/includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php index fc8c7d9..2fd32c2 100644 --- a/includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php +++ b/includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php @@ -34,7 +34,7 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta { public const META_FORMULA = '_pr_molecular_formula'; /** @var string Meta key: molecular weight as float string (PR Core namespace). */ - public const META_WEIGHT = '_pr_molecular_weight'; + public const META_WEIGHT = '_pr_molecular_weight'; /** @var string Meta key: aliases JSON array (PR Core namespace). */ public const META_ALIASES = '_pr_aliases'; @@ -66,20 +66,27 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta { return; } - $counts = [ 'skipped' => 0, 'copied_psa' => 0, 'pubchem_ok' => 0, 'pubchem_skip' => 0 ]; + $counts = array( + 'skipped' => 0, + 'copied_psa' => 0, + 'pubchem_ok' => 0, + 'pubchem_skip' => 0, + ); foreach ( $peptide_ids as $post_id ) { $result = $this->backfill_post( $post_id ); $counts[ $result ] += 1; } - error_log( sprintf( - '[PR Core Migration 0004] Complete. Skipped: %d, PSA-copied: %d, PubChem-ok: %d, PubChem-skip: %d', - $counts['skipped'], - $counts['copied_psa'], - $counts['pubchem_ok'], - $counts['pubchem_skip'] - ) ); + error_log( + sprintf( + '[PR Core Migration 0004] Complete. Skipped: %d, PSA-copied: %d, PubChem-ok: %d, PubChem-skip: %d', + $counts['skipped'], + $counts['copied_psa'], + $counts['pubchem_ok'], + $counts['pubchem_skip'] + ) + ); } /** @@ -125,26 +132,30 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta { } if ( null === $data ) { - error_log( sprintf( - '[PR Core Migration 0004] Post ID %d (%s): PubChem returned no data — leaving meta empty.', - $post_id, - esc_html( $name ) - ) ); + error_log( + sprintf( + '[PR Core Migration 0004] Post ID %d (%s): PubChem returned no data — leaving meta empty.', + $post_id, + esc_html( $name ) + ) + ); return 'pubchem_skip'; } $formula = PR_Core_Schema_Sanitizers::sanitize_molecular_formula( $data['formula'] ); $weight = (float) $data['weight']; - $aliases_json = $this->synonyms_to_json( $data['synonyms'] ?? [] ); + $aliases_json = $this->synonyms_to_json( $data['synonyms'] ?? array() ); $this->write_pr_meta( $post_id, $formula, $weight, $aliases_json ); - error_log( sprintf( - '[PR Core Migration 0004] Post ID %d (%s): PubChem-sourced formula=%s weight=%s', - $post_id, - esc_html( $name ), - $formula, - (string) $weight - ) ); + error_log( + sprintf( + '[PR Core Migration 0004] Post ID %d (%s): PubChem-sourced formula=%s weight=%s', + $post_id, + esc_html( $name ), + $formula, + (string) $weight + ) + ); return 'pubchem_ok'; } @@ -223,7 +234,7 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta { return '[]'; } - $clean = []; + $clean = array(); foreach ( explode( ',', $value ) as $part ) { $alias = sanitize_text_field( trim( $part ) ); if ( '' !== $alias ) { @@ -243,7 +254,7 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta { * @return string JSON array of sanitized strings. */ private function synonyms_to_json( array $synonyms ): string { - $clean = []; + $clean = array(); foreach ( $synonyms as $syn ) { $alias = sanitize_text_field( (string) $syn ); if ( '' !== $alias ) { @@ -259,12 +270,14 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta { * @return int[] */ private function get_all_peptide_ids(): array { - $posts = get_posts( [ - 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, - 'post_status' => 'publish', - 'posts_per_page' => -1, - 'fields' => 'ids', - ] ); - return array_map( 'intval', is_array( $posts ) ? $posts : [] ); + $posts = get_posts( + array( + 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, + 'post_status' => 'publish', + 'posts_per_page' => -1, + 'fields' => 'ids', + ) + ); + return array_map( 'intval', is_array( $posts ) ? $posts : array() ); } } diff --git a/includes/migrations/class-pr-core-migration-runner.php b/includes/migrations/class-pr-core-migration-runner.php index b53e2e1..820cd01 100644 --- a/includes/migrations/class-pr-core-migration-runner.php +++ b/includes/migrations/class-pr-core-migration-runner.php @@ -25,12 +25,12 @@ class PR_Core_Migration_Runner { * * @var string[] */ - private const MIGRATIONS = [ + private const MIGRATIONS = array( 'PR_Core_Migration_0001_Dosing_Rows', 'PR_Core_Migration_0002_Legal_Cells', 'PR_Core_Migration_0003_Candidate_Queue', 'PR_Core_Migration_0004_Backfill_Peptide_Meta', - ]; + ); /** * Run all pending migrations up to PR_CORE_TARGET_SCHEMA_VERSION. @@ -90,7 +90,7 @@ class PR_Core_Migration_Runner { * @return string Absolute file path. */ private function class_to_file( string $class ): string { - $suffix = substr( $class, 8 ); // Strip 'PR_Core_'. + $suffix = substr( $class, 8 ); // Strip 'PR_Core_'. $filename = 'class-pr-core-' . str_replace( '_', '-', strtolower( $suffix ) ) . '.php'; return PR_CORE_PLUGIN_DIR . 'includes/migrations/' . $filename; diff --git a/includes/migrations/class-pr-core-pubchem-client.php b/includes/migrations/class-pr-core-pubchem-client.php index 994bac0..4c111ff 100644 --- a/includes/migrations/class-pr-core-pubchem-client.php +++ b/includes/migrations/class-pr-core-pubchem-client.php @@ -109,11 +109,11 @@ class PR_Core_Pubchem_Client { return null; } - return [ + return array( 'formula' => $formula, 'weight' => $weight, 'cid' => $cid, - ]; + ); } /** @@ -130,14 +130,14 @@ class PR_Core_Pubchem_Client { $body = $this->get_with_retry( $url ); if ( null === $body ) { - return []; + return array(); } $data = json_decode( $body, true ); - $synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? []; + $synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? array(); if ( ! is_array( $synonyms ) ) { - return []; + return array(); } return array_slice( $synonyms, 0, self::MAX_SYNONYMS ); @@ -176,10 +176,13 @@ class PR_Core_Pubchem_Client { */ private function get_once( string $url ): ?string { if ( function_exists( 'wp_remote_get' ) ) { - $response = wp_remote_get( $url, [ - 'timeout' => self::TIMEOUT, - 'headers' => [ 'Accept' => 'application/json' ], - ] ); + $response = wp_remote_get( + $url, + array( + 'timeout' => self::TIMEOUT, + 'headers' => array( 'Accept' => 'application/json' ), + ) + ); if ( is_wp_error( $response ) ) { return null; @@ -194,13 +197,15 @@ class PR_Core_Pubchem_Client { } // WP-CLI / plain PHP fallback. - $context = stream_context_create( [ - 'http' => [ - 'timeout' => self::TIMEOUT, - 'header' => "Accept: application/json\r\n", - 'method' => 'GET', - ], - ] ); + $context = stream_context_create( + array( + 'http' => array( + 'timeout' => self::TIMEOUT, + 'header' => "Accept: application/json\r\n", + 'method' => 'GET', + ), + ) + ); $body = @file_get_contents( $url, false, $context ); return ( false === $body ) ? null : $body; diff --git a/includes/repositories/class-pr-core-candidate-queue-repository.php b/includes/repositories/class-pr-core-candidate-queue-repository.php index b66beac..210d163 100644 --- a/includes/repositories/class-pr-core-candidate-queue-repository.php +++ b/includes/repositories/class-pr-core-candidate-queue-repository.php @@ -47,15 +47,15 @@ class PR_Core_Candidate_Queue_Repository { global $wpdb; $table = $wpdb->prefix . 'pr_ai_candidate_queue'; - $where = [ 'queue_status = %s' ]; - $params = [ sanitize_text_field( $status ) ]; + $where = array( 'queue_status = %s' ); + $params = array( sanitize_text_field( $status ) ); if ( $peptide_id > 0 ) { $where[] = 'peptide_id = %d'; $params[] = $peptide_id; } - $params[] = $limit; + $params[] = $limit; $where_sql = implode( ' AND ', $where ); // phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery @@ -65,7 +65,7 @@ class PR_Core_Candidate_Queue_Repository { ...$params ), ARRAY_A - ) ?: []; + ) ?: array(); return array_map( static fn( array $row ) => new PR_Core_Candidate_DTO( $row ), @@ -85,7 +85,7 @@ class PR_Core_Candidate_Queue_Repository { global $wpdb; $table = $wpdb->prefix . 'pr_ai_candidate_queue'; - $row = [ + $row = array( 'peptide_id' => absint( $data['peptide_id'] ?? 0 ), 'dose_min' => isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null, 'dose_max' => isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null, @@ -106,7 +106,7 @@ class PR_Core_Candidate_Queue_Repository { 'extraction_confidence' => (float) ( $data['extraction_confidence'] ?? 0 ), 'queue_status' => 'pending', 'extracted_at' => current_time( 'mysql' ), - ]; + ); // phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery $result = $wpdb->insert( $table, $row ); @@ -134,30 +134,32 @@ class PR_Core_Candidate_Queue_Repository { // Copy candidate data into a dosing row. $dosing_repo = new PR_Core_Dosing_Repository(); - $dosing_id = $dosing_repo->insert( [ - 'peptide_id' => $candidate->peptide_id, - 'dose_min' => $candidate->dose_min, - 'dose_max' => $candidate->dose_max, - 'dose_unit' => $candidate->dose_unit, - 'route' => $candidate->route, - 'frequency' => $candidate->frequency, - 'duration_value' => $candidate->duration_value, - 'duration_unit' => $candidate->duration_unit, - 'population' => $candidate->population, - 'indication' => $candidate->indication, - 'evidence_strength' => $candidate->evidence_strength, - 'study_title' => $candidate->study_title, - 'study_year' => $candidate->study_year, - 'citation_pubmed_id' => $candidate->citation_pubmed_id, - 'citation_doi' => $candidate->citation_doi, - 'citation_url' => $candidate->citation_url, - 'notes' => $candidate->notes, - 'source' => 'ai-candidate-approved', - 'ai_candidate_id' => $candidate_id, - 'added_by' => $reviewer_id, - 'reviewed_by' => $reviewer_id, - 'reviewed_at' => current_time( 'mysql' ), - ] ); + $dosing_id = $dosing_repo->insert( + array( + 'peptide_id' => $candidate->peptide_id, + 'dose_min' => $candidate->dose_min, + 'dose_max' => $candidate->dose_max, + 'dose_unit' => $candidate->dose_unit, + 'route' => $candidate->route, + 'frequency' => $candidate->frequency, + 'duration_value' => $candidate->duration_value, + 'duration_unit' => $candidate->duration_unit, + 'population' => $candidate->population, + 'indication' => $candidate->indication, + 'evidence_strength' => $candidate->evidence_strength, + 'study_title' => $candidate->study_title, + 'study_year' => $candidate->study_year, + 'citation_pubmed_id' => $candidate->citation_pubmed_id, + 'citation_doi' => $candidate->citation_doi, + 'citation_url' => $candidate->citation_url, + 'notes' => $candidate->notes, + 'source' => 'ai-candidate-approved', + 'ai_candidate_id' => $candidate_id, + 'added_by' => $reviewer_id, + 'reviewed_by' => $reviewer_id, + 'reviewed_at' => current_time( 'mysql' ), + ) + ); if ( 0 === $dosing_id ) { return 0; @@ -224,15 +226,15 @@ class PR_Core_Candidate_Queue_Repository { // phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery $result = $wpdb->update( $table, - [ + array( 'queue_status' => sanitize_text_field( $status ), 'reviewed_by' => $reviewer_id, 'reviewed_at' => current_time( 'mysql' ), 'reviewer_notes' => sanitize_textarea_field( $notes ), - ], - [ 'id' => $id ], - [ '%s', '%d', '%s', '%s' ], - [ '%d' ] + ), + array( 'id' => $id ), + array( '%s', '%d', '%s', '%s' ), + array( '%d' ) ); return false !== $result; diff --git a/includes/repositories/class-pr-core-dosing-repository.php b/includes/repositories/class-pr-core-dosing-repository.php index 1a9934e..a47d975 100644 --- a/includes/repositories/class-pr-core-dosing-repository.php +++ b/includes/repositories/class-pr-core-dosing-repository.php @@ -39,12 +39,12 @@ class PR_Core_Dosing_Repository { * @param array $filters Optional: route, population, evidence_strength. * @return PR_Core_Dosing_Row_DTO[] */ - public function find_by_peptide( int $peptide_id, array $filters = [] ): array { + public function find_by_peptide( int $peptide_id, array $filters = array() ): array { global $wpdb; $table = $wpdb->prefix . 'pr_dosing_rows'; - $where = [ 'peptide_id = %d', 'superseded_by_id IS NULL' ]; - $params = [ $peptide_id ]; + $where = array( 'peptide_id = %d', 'superseded_by_id IS NULL' ); + $params = array( $peptide_id ); if ( ! empty( $filters['route'] ) ) { $where[] = 'route = %s'; @@ -70,7 +70,7 @@ class PR_Core_Dosing_Repository { ...$params ), ARRAY_A - ) ?: []; + ) ?: array(); return array_map( static fn( array $row ) => new PR_Core_Dosing_Row_DTO( $row ), @@ -92,7 +92,7 @@ class PR_Core_Dosing_Repository { global $wpdb; $table = $wpdb->prefix . 'pr_dosing_rows'; - $row = $this->sanitize_row( $data ); + $row = $this->sanitize_row( $data ); $row['added_at'] = current_time( 'mysql' ); $row['schema_version'] = 1; @@ -137,10 +137,10 @@ class PR_Core_Dosing_Repository { // phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery $wpdb->update( $table, - [ 'superseded_by_id' => $new_id ], - [ 'id' => $old_id ], - [ '%d' ], - [ '%d' ] + array( 'superseded_by_id' => $new_id ), + array( 'id' => $old_id ), + array( '%d' ), + array( '%d' ) ); return $new_id; @@ -172,7 +172,7 @@ class PR_Core_Dosing_Repository { * @return array Sanitized row. */ private function sanitize_row( array $data ): array { - return [ + return array( 'peptide_id' => absint( $data['peptide_id'] ?? 0 ), 'dose_min' => isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null, 'dose_max' => isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null, @@ -195,6 +195,6 @@ class PR_Core_Dosing_Repository { 'added_by' => absint( $data['added_by'] ?? get_current_user_id() ), 'reviewed_by' => isset( $data['reviewed_by'] ) ? absint( $data['reviewed_by'] ) : null, 'reviewed_at' => $data['reviewed_at'] ?? null, - ]; + ); } } diff --git a/includes/repositories/class-pr-core-legal-repository.php b/includes/repositories/class-pr-core-legal-repository.php index f6abbbf..110dc7a 100644 --- a/includes/repositories/class-pr-core-legal-repository.php +++ b/includes/repositories/class-pr-core-legal-repository.php @@ -52,7 +52,7 @@ class PR_Core_Legal_Repository { $peptide_id ), ARRAY_A - ) ?: []; + ) ?: array(); return array_map( static fn( array $row ) => new PR_Core_Legal_Cell_DTO( $row ), @@ -101,7 +101,7 @@ class PR_Core_Legal_Repository { strtoupper( sanitize_text_field( $country_code ) ) ), ARRAY_A - ) ?: []; + ) ?: array(); return array_map( static fn( array $row ) => new PR_Core_Legal_Cell_DTO( $row ), @@ -161,10 +161,10 @@ class PR_Core_Legal_Repository { // phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery $wpdb->update( $table, - [ 'superseded_by_id' => $new_id ], - [ 'id' => $old_id ], - [ '%d' ], - [ '%d' ] + array( 'superseded_by_id' => $new_id ), + array( 'id' => $old_id ), + array( '%d' ), + array( '%d' ) ); return $new_id; @@ -184,7 +184,7 @@ class PR_Core_Legal_Repository { $status = 'unclear'; } - return [ + return array( 'peptide_id' => absint( $data['peptide_id'] ?? 0 ), 'country_code' => strtoupper( sanitize_text_field( $data['country_code'] ?? '' ) ), 'status' => $status, @@ -195,6 +195,6 @@ class PR_Core_Legal_Repository { 'last_verified_at' => sanitize_text_field( $data['last_verified_at'] ?? current_time( 'mysql' ) ), 'schema_version' => 1, 'reviewer_id' => absint( $data['reviewer_id'] ?? get_current_user_id() ), - ]; + ); } } diff --git a/includes/repositories/class-pr-core-peptide-repository.php b/includes/repositories/class-pr-core-peptide-repository.php index c7903ba..932e4d1 100644 --- a/includes/repositories/class-pr-core-peptide-repository.php +++ b/includes/repositories/class-pr-core-peptide-repository.php @@ -36,12 +36,14 @@ class PR_Core_Peptide_Repository { * @return PR_Core_Peptide_DTO|null */ public function find_by_slug( string $slug ): ?PR_Core_Peptide_DTO { - $posts = get_posts( [ - 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, - 'name' => sanitize_title( $slug ), - 'posts_per_page' => 1, - 'post_status' => 'any', - ] ); + $posts = get_posts( + array( + 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, + 'name' => sanitize_title( $slug ), + 'posts_per_page' => 1, + 'post_status' => 'any', + ) + ); return ! empty( $posts ) ? $this->post_to_dto( $posts[0] ) : null; } @@ -56,14 +58,16 @@ class PR_Core_Peptide_Repository { public function search( string $query, int $limit = 20 ): array { $query = sanitize_text_field( $query ); - $posts = get_posts( [ - 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, - 's' => $query, - 'posts_per_page' => $limit, - 'post_status' => 'publish', - ] ); + $posts = get_posts( + array( + 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, + 's' => $query, + 'posts_per_page' => $limit, + 'post_status' => 'publish', + ) + ); - return array_map( [ $this, 'post_to_dto' ], $posts ); + return array_map( array( $this, 'post_to_dto' ), $posts ); } /** @@ -73,23 +77,25 @@ class PR_Core_Peptide_Repository { * evidence_strength, per_page, page. * @return PR_Core_Peptide_DTO[] */ - public function find_all( array $filters = [] ): array { - $args = [ + public function find_all( array $filters = array() ): array { + $args = array( 'post_type' => PR_Core_Peptide_CPT::POST_TYPE, 'posts_per_page' => (int) ( $filters['per_page'] ?? 100 ), 'paged' => (int) ( $filters['page'] ?? 1 ), 'orderby' => 'title', 'order' => 'ASC', - ]; + ); $args['post_status'] = $filters['status'] ?? 'publish'; if ( ! empty( $filters['category'] ) ) { - $args['tax_query'] = [ [ - 'taxonomy' => PR_Core_Peptide_CPT::TAX_CATEGORY, - 'field' => 'slug', - 'terms' => sanitize_text_field( $filters['category'] ), - ] ]; + $args['tax_query'] = array( + array( + 'taxonomy' => PR_Core_Peptide_CPT::TAX_CATEGORY, + 'field' => 'slug', + 'terms' => sanitize_text_field( $filters['category'] ), + ), + ); } // v0.2.0: `family` filter silently ignored — `pr_peptide_family` taxonomy @@ -98,15 +104,17 @@ class PR_Core_Peptide_Repository { // REST schema in a future minor bump. if ( ! empty( $filters['evidence_strength'] ) ) { - $args['meta_query'] = [ [ - 'key' => 'evidence_strength', - 'value' => sanitize_text_field( $filters['evidence_strength'] ), - ] ]; + $args['meta_query'] = array( + array( + 'key' => 'evidence_strength', + 'value' => sanitize_text_field( $filters['evidence_strength'] ), + ), + ); } $posts = get_posts( $args ); - return array_map( [ $this, 'post_to_dto' ], $posts ); + return array_map( array( $this, 'post_to_dto' ), $posts ); } /** @@ -128,34 +136,36 @@ class PR_Core_Peptide_Repository { */ private function post_to_dto( \WP_Post $post ): PR_Core_Peptide_DTO { $aliases_raw = get_post_meta( $post->ID, 'aliases', true ); - $aliases = json_decode( $aliases_raw ?: '[]', true ) ?: []; + $aliases = json_decode( $aliases_raw ?: '[]', true ) ?: array(); - $categories = wp_get_post_terms( $post->ID, PR_Core_Peptide_CPT::TAX_CATEGORY, [ 'fields' => 'names' ] ); + $categories = wp_get_post_terms( $post->ID, PR_Core_Peptide_CPT::TAX_CATEGORY, array( 'fields' => 'names' ) ); // v0.2.0: `pr_peptide_family` taxonomy removed. DTO `families` field // preserved as empty array to keep the REST response shape stable for // clients; will be dropped in a future minor bump with a release note. - $families = []; + $families = array(); - return new PR_Core_Peptide_DTO( [ - 'id' => $post->ID, - 'title' => $post->post_title, - 'slug' => $post->post_name, - 'content' => $post->post_content, - 'excerpt' => $post->post_excerpt, - 'status' => $post->post_status, - 'display_name' => get_post_meta( $post->ID, 'display_name', true ) ?: '', - 'aliases' => $aliases, - 'molecular_formula' => get_post_meta( $post->ID, 'molecular_formula', true ) ?: '', - 'molecular_weight' => (float) get_post_meta( $post->ID, 'molecular_weight', true ), - 'cas_number' => get_post_meta( $post->ID, 'cas_number', true ) ?: '', - 'drugbank_id' => get_post_meta( $post->ID, 'drugbank_id', true ) ?: '', - 'chembl_id' => get_post_meta( $post->ID, 'chembl_id', true ) ?: '', - 'evidence_strength' => get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical', - 'editorial_review_status' => get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft', - 'last_editorial_review_at' => get_post_meta( $post->ID, 'last_editorial_review_at', true ) ?: '', - 'medical_editor_id' => (int) get_post_meta( $post->ID, 'medical_editor_id', true ), - 'categories' => is_array( $categories ) ? $categories : [], - 'families' => $families, - ] ); + return new PR_Core_Peptide_DTO( + array( + 'id' => $post->ID, + 'title' => $post->post_title, + 'slug' => $post->post_name, + 'content' => $post->post_content, + 'excerpt' => $post->post_excerpt, + 'status' => $post->post_status, + 'display_name' => get_post_meta( $post->ID, 'display_name', true ) ?: '', + 'aliases' => $aliases, + 'molecular_formula' => get_post_meta( $post->ID, 'molecular_formula', true ) ?: '', + 'molecular_weight' => (float) get_post_meta( $post->ID, 'molecular_weight', true ), + 'cas_number' => get_post_meta( $post->ID, 'cas_number', true ) ?: '', + 'drugbank_id' => get_post_meta( $post->ID, 'drugbank_id', true ) ?: '', + 'chembl_id' => get_post_meta( $post->ID, 'chembl_id', true ) ?: '', + 'evidence_strength' => get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical', + 'editorial_review_status' => get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft', + 'last_editorial_review_at' => get_post_meta( $post->ID, 'last_editorial_review_at', true ) ?: '', + 'medical_editor_id' => (int) get_post_meta( $post->ID, 'medical_editor_id', true ), + 'categories' => is_array( $categories ) ? $categories : array(), + 'families' => $families, + ) + ); } } diff --git a/includes/scanner/class-pr-core-verification-scanner.php b/includes/scanner/class-pr-core-verification-scanner.php index 6c9201b..eee4431 100644 --- a/includes/scanner/class-pr-core-verification-scanner.php +++ b/includes/scanner/class-pr-core-verification-scanner.php @@ -28,11 +28,11 @@ class PR_Core_Verification_Scanner { * @return void */ public static function run_scan(): 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_peptides = []; - $overdue_peptides = []; + $due_peptides = array(); + $overdue_peptides = array(); foreach ( $peptides as $dto ) { $last_verified = get_post_meta( $dto->id, '_pr_last_source_verified', true ); @@ -102,17 +102,17 @@ class PR_Core_Verification_Scanner { * @return void */ private static function log_scan( int $total, int $due, int $overdue ): void { - $log = get_option( self::SCAN_LOG_OPTION_KEY, [] ); + $log = get_option( self::SCAN_LOG_OPTION_KEY, array() ); if ( ! is_array( $log ) ) { - $log = []; + $log = array(); } - $log[] = [ + $log[] = array( 'timestamp' => current_time( 'mysql' ), 'total' => $total, 'due' => $due, 'overdue' => $overdue, - ]; + ); // Keep only the last MAX_LOG_ENTRIES. if ( count( $log ) > self::MAX_LOG_ENTRIES ) { @@ -137,9 +137,12 @@ class PR_Core_Verification_Scanner { // Parse comma-separated emails. $emails = array_map( 'trim', explode( ',', $recipients ) ); - $emails = array_filter( $emails, static function ( $email ) { - return is_email( $email ); - } ); + $emails = array_filter( + $emails, + static function ( $email ) { + return is_email( $email ); + } + ); if ( empty( $emails ) ) { return; @@ -153,7 +156,7 @@ class PR_Core_Verification_Scanner { $body = self::build_email_body( $due_peptides, $overdue_peptides ); - wp_mail( $emails, $subject, $body, [ 'Content-Type: text/html; charset=UTF-8' ] ); + wp_mail( $emails, $subject, $body, array( 'Content-Type: text/html; charset=UTF-8' ) ); } /** @@ -170,7 +173,7 @@ class PR_Core_Verification_Scanner { $body .= '

Overdue for review (' . count( $overdue_peptides ) . ')