From e8adce77e98a85f3403b4400c9f167400f31e3f0 Mon Sep 17 00:00:00 2001
From: peptiderepo <peptiderepo@users.noreply.github.com>
Date: Fri, 17 Apr 2026 02:43:13 +0700
Subject: [PATCH] =?UTF-8?q?refactor:=20extract=20PSA=5FPost=5FType=5FMeta?=
 =?UTF-8?q?=20from=20PSA=5FPost=5FType=20(343=E2=86=92193+140)?=
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Meta box registration, rendering (core + extended), and save handler
moved to PSA_Post_Type_Meta. PSA_Post_Type retains CPT/taxonomy
registration, default categories, admin columns, and constants.
Backward-compatible proxy methods on PSA_Post_Type.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
---
 includes/class-psa-post-type-meta.php | 140 ++++++++++++
 includes/class-psa-post-type.php      | 296 +++++++-------------------
 peptide-search-ai.php                 |   1 +
 3 files changed, 214 insertions(+), 223 deletions(-)
 create mode 100644 includes/class-psa-post-type-meta.php

diff --git a/includes/class-psa-post-type-meta.php b/includes/class-psa-post-type-meta.php
new file mode 100644
index 0000000..7f21480
--- /dev/null
+++ b/includes/class-psa-post-type-meta.php
@@ -0,0 +1,140 @@
+<?php
+/**
+ * Meta box rendering and save handlers for the Peptide CPT editor.
+ *
+ * What: Adds and renders meta boxes (core + extended fields), saves meta on post update.
+ * Who calls it: PSA_Post_Type::init_admin() registers hooks that point here.
+ * Dependencies: PSA_Post_Type (META_FIELDS, EXTENDED_META_FIELDS constants).
+ *
+ * @package PeptideSearchAI
+ * @since   4.5.0
+ * @see     includes/class-psa-post-type.php — CPT registration, taxonomy, admin columns.
+ */
+declare( strict_types=1 );
+
+if ( ! defined( 'ABSPATH' ) ) {
+	exit;
+}
+
+class PSA_Post_Type_Meta {
+
+	/** Register meta boxes on the peptide editor screen. */
+	public static function add_meta_boxes(): void {
+		add_meta_box(
+			'psa_peptide_data',
+			'Peptide Scientific Data',
+			array( __CLASS__, 'render_meta_box' ),
+			'peptide',
+			'normal',
+			'high'
+		);
+		add_meta_box(
+			'psa_extended_data',
+			'Extended Research Data',
+			array( __CLASS__, 'render_extended_meta_box' ),
+			'peptide',
+			'normal',
+			'default'
+		);
+	}
+
+	/**
+	 * Render core meta box fields (sequence, molecular data, mechanism, etc.).
+	 *
+	 * @param WP_Post $post The current post object.
+	 */
+	public static function render_meta_box( $post ): void {
+		wp_nonce_field( 'psa_save_meta', 'psa_meta_nonce' );
+
+		$textarea_fields = array(
+			'psa_sequence', 'psa_mechanism', 'psa_research_apps',
+			'psa_safety_profile', 'psa_dosage_info', 'psa_references',
+		);
+
+		echo '<table class="form-table">';
+		foreach ( PSA_Post_Type::META_FIELDS as $key => $label ) {
+			$value = get_post_meta( $post->ID, $key, true );
+			echo '<tr>';
+			echo '<th><label for="' . esc_attr( $key ) . '">' . esc_html( $label ) . '</label></th>';
+			echo '<td>';
+
+			if ( 'psa_source' === $key ) {
+				$options = array(
+					'' => '— Select —', 'ai-generated' => 'AI Generated',
+					'pubchem' => 'PubChem Verified', 'manual' => 'Manual Entry', 'pending' => 'Pending Generation',
+				);
+				echo '<select name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '">';
+				foreach ( $options as $opt_val => $opt_label ) {
+					echo '<option value="' . esc_attr( $opt_val ) . '"' . selected( $value, $opt_val, false ) . '>' . esc_html( $opt_label ) . '</option>';
+				}
+				echo '</select>';
+			} elseif ( in_array( $key, $textarea_fields, true ) ) {
+				echo '<textarea name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" rows="4" class="large-text">' . esc_textarea( $value ) . '</textarea>';
+			} else {
+				echo '<input type="text" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="regular-text" />';
+			}
+
+			echo '</td></tr>';
+		}
+		echo '</table>';
+	}
+
+	/**
+	 * Render extended meta box fields (half-life, stability, storage, etc.).
+	 *
+	 * @param WP_Post $post The current post object.
+	 */
+	public static function render_extended_meta_box( $post ): void {
+		echo '<table class="form-table">';
+		foreach ( PSA_Post_Type::EXTENDED_META_FIELDS as $key => $label ) {
+			$value = get_post_meta( $post->ID, $key, true );
+			echo '<tr>';
+			echo '<th><label for="' . esc_attr( $key ) . '">' . esc_html( $label ) . '</label></th>';
+			echo '<td>';
+
+			if ( 'psa_vial_size_mg' === $key ) {
+				echo '<input type="number" step="0.01" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="small-text" /> mg';
+			} elseif ( 'psa_amino_acid_count' === $key ) {
+				echo '<input type="number" step="1" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="small-text" />';
+			} else {
+				echo '<input type="text" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="regular-text" />';
+			}
+
+			echo '</td></tr>';
+		}
+		echo '</table>';
+	}
+
+	/**
+	 * Save meta field values (core + extended) on post save.
+	 *
+	 * @param int $post_id The post ID.
+	 */
+	public static function save_meta( int $post_id ): void {
+		// phpcs:ignore WordPress.Security.ValidatedSanitizedInput
+		if ( ! isset( $_POST['psa_meta_nonce'] ) ||
+			 ! wp_verify_nonce( wp_unslash( $_POST['psa_meta_nonce'] ), 'psa_save_meta' ) ) {
+			return;
+		}
+		if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ) {
+			return;
+		}
+		if ( ! current_user_can( 'edit_post', $post_id ) ) {
+			return;
+		}
+
+		$numeric_fields = array( 'psa_vial_size_mg', 'psa_amino_acid_count' );
+		$all_fields     = array_merge( PSA_Post_Type::META_FIELDS, PSA_Post_Type::EXTENDED_META_FIELDS );
+		foreach ( $all_fields as $key => $label ) {
+			if ( isset( $_POST[ $key ] ) ) {
+				$raw = wp_unslash( $_POST[ $key ] );
+				if ( in_array( $key, $numeric_fields, true ) ) {
+					$value = ( '' === trim( $raw ) ) ? '' : (string) max( 0, floatval( $raw ) );
+				} else {
+					$value = sanitize_textarea_field( $raw );
+				}
+				update_post_meta( $post_id, $key, $value );
+			}
+		}
+	}
+}
diff --git a/includes/class-psa-post-type.php b/includes/class-psa-post-type.php
index 3b6c707..37dd354 100755
--- a/includes/class-psa-post-type.php
+++ b/includes/class-psa-post-type.php
@@ -1,14 +1,16 @@
 <?php
 /**
- * Registers the Peptide custom post type, taxonomy, and meta fields.
+ * Registers the Peptide custom post type, taxonomy, and admin columns.
  *
- * What: Registers the 'peptide' CPT, 'peptide_category' taxonomy, meta boxes, and save handlers.
+ * What: CPT registration, taxonomy registration, default category seeding, admin columns.
  * Who calls it: Main plugin file via psa_init() and psa_admin_init() hooks.
- * Dependencies: WordPress CPT API, taxonomy API, meta box API.
+ * Dependencies: WordPress CPT API, taxonomy API.
  *
  * @package PeptideSearchAI
- * @see     includes/class-psa-ai-generator.php  — auto-assigns category term after generation
- * @see     includes/class-psa-directory.php     — reads taxonomy for directory filtering
+ * @since   1.0.0
+ * @see     includes/class-psa-post-type-meta.php — Meta box rendering and save handlers.
+ * @see     includes/class-psa-ai-content.php     — Uses DEFAULT_CATEGORIES for category assignment.
+ * @see     includes/class-psa-directory.php       — Reads taxonomy for directory filtering.
  */
 declare( strict_types=1 );
 
@@ -18,10 +20,7 @@ if ( ! defined( 'ABSPATH' ) ) {
 
 class PSA_Post_Type {
 
-	/**
-	 * Default peptide category terms pre-populated on activation.
-	 * Key = slug, value = display name.
-	 */
+	/** Default peptide category terms pre-populated on activation. slug => display name. */
 	const DEFAULT_CATEGORIES = array(
 		'tissue-repair'    => 'Tissue Repair',
 		'lipid-metabolism' => 'Lipid Metabolism',
@@ -48,10 +47,7 @@ class PSA_Post_Type {
 		'psa_pubchem_cid'       => 'PubChem CID',
 	);
 
-	/**
-	 * Extended meta fields added in v4.3.0 for the directory feature.
-	 * Separated from META_FIELDS so existing code continues to work unchanged.
-	 */
+	/** Extended meta fields added in v4.3.0 for the directory feature. */
 	const EXTENDED_META_FIELDS = array(
 		'psa_half_life'              => 'Half-Life',
 		'psa_stability'              => 'Stability',
@@ -64,93 +60,72 @@ class PSA_Post_Type {
 		'psa_amino_acid_count'       => 'Amino Acid Count',
 	);
 
-	/**
-	 * Register admin-only hooks (meta boxes, save, admin columns).
-	 */
+	/** Register admin-only hooks (meta boxes, save, admin columns). */
 	public static function init_admin(): void {
-		add_action( 'add_meta_boxes', array( __CLASS__, 'add_meta_boxes' ) );
-		add_action( 'save_post_peptide', array( __CLASS__, 'save_meta' ) );
+		add_action( 'add_meta_boxes', array( 'PSA_Post_Type_Meta', 'add_meta_boxes' ) );
+		add_action( 'save_post_peptide', array( 'PSA_Post_Type_Meta', 'save_meta' ) );
 		add_filter( 'manage_peptide_posts_columns', array( __CLASS__, 'add_admin_columns' ) );
 		add_action( 'manage_peptide_posts_custom_column', array( __CLASS__, 'render_admin_column' ), 10, 2 );
 	}
 
-	/**
-	 * Register the peptide CPT.
-	 */
+	/** Register the peptide CPT. */
 	public static function register_peptide_post_type(): void {
 		if ( post_type_exists( 'peptide' ) ) {
 			return;
 		}
 
-		$labels = array(
-			'name'               => 'Peptides',
-			'singular_name'      => 'Peptide',
-			'menu_name'          => 'Peptides',
-			'add_new'            => 'Add Peptide',
-			'add_new_item'       => 'Add New Peptide',
-			'edit_item'          => 'Edit Peptide',
-			'new_item'           => 'New Peptide',
-			'view_item'          => 'View Peptide',
-			'search_items'       => 'Search Peptides',
-			'not_found'          => 'No peptides found',
-			'not_found_in_trash' => 'No peptides found in Trash',
-		);
-
-		register_post_type(
-			'peptide',
-			array(
-				'labels'             => $labels,
-				'public'             => true,
-				'has_archive'        => true,
-				'rewrite'            => array( 'slug' => 'peptides' ),
-				'supports'           => array( 'title', 'editor', 'thumbnail', 'excerpt' ),
-				'menu_icon'          => 'dashicons-database',
-				'show_in_rest'       => true,
-				'capability_type'    => 'post',
-				'hierarchical'       => false,
-			)
-		);
+		register_post_type( 'peptide', array(
+			'labels'          => array(
+				'name'               => 'Peptides',
+				'singular_name'      => 'Peptide',
+				'menu_name'          => 'Peptides',
+				'add_new'            => 'Add Peptide',
+				'add_new_item'       => 'Add New Peptide',
+				'edit_item'          => 'Edit Peptide',
+				'new_item'           => 'New Peptide',
+				'view_item'          => 'View Peptide',
+				'search_items'       => 'Search Peptides',
+				'not_found'          => 'No peptides found',
+				'not_found_in_trash' => 'No peptides found in Trash',
+			),
+			'public'          => true,
+			'has_archive'     => true,
+			'rewrite'         => array( 'slug' => 'peptides' ),
+			'supports'        => array( 'title', 'editor', 'thumbnail', 'excerpt' ),
+			'menu_icon'       => 'dashicons-database',
+			'show_in_rest'    => true,
+			'capability_type' => 'post',
+			'hierarchical'    => false,
+		) );
 	}
 
-	/**
-	 * Register the peptide_category taxonomy on the peptide CPT.
-	 * Called from psa_init() after CPT registration.
-	 */
+	/** Register the peptide_category taxonomy on the peptide CPT. */
 	public static function register_taxonomy(): void {
 		if ( taxonomy_exists( 'peptide_category' ) ) {
 			return;
 		}
 
-		$labels = array(
-			'name'              => __( 'Peptide Categories', 'peptide-search-ai' ),
-			'singular_name'     => __( 'Peptide Category', 'peptide-search-ai' ),
-			'search_items'      => __( 'Search Categories', 'peptide-search-ai' ),
-			'all_items'         => __( 'All Categories', 'peptide-search-ai' ),
-			'edit_item'         => __( 'Edit Category', 'peptide-search-ai' ),
-			'update_item'       => __( 'Update Category', 'peptide-search-ai' ),
-			'add_new_item'      => __( 'Add New Category', 'peptide-search-ai' ),
-			'new_item_name'     => __( 'New Category Name', 'peptide-search-ai' ),
-			'menu_name'         => __( 'Categories', 'peptide-search-ai' ),
-		);
-
-		register_taxonomy(
-			'peptide_category',
-			'peptide',
-			array(
-				'labels'            => $labels,
-				'hierarchical'      => true,
-				'public'            => true,
-				'show_in_rest'      => true,
-				'show_admin_column' => true,
-				'rewrite'           => array( 'slug' => 'peptide-category' ),
-			)
-		);
+		register_taxonomy( 'peptide_category', 'peptide', array(
+			'labels'            => array(
+				'name'          => __( 'Peptide Categories', 'peptide-search-ai' ),
+				'singular_name' => __( 'Peptide Category', 'peptide-search-ai' ),
+				'search_items'  => __( 'Search Categories', 'peptide-search-ai' ),
+				'all_items'     => __( 'All Categories', 'peptide-search-ai' ),
+				'edit_item'     => __( 'Edit Category', 'peptide-search-ai' ),
+				'update_item'   => __( 'Update Category', 'peptide-search-ai' ),
+				'add_new_item'  => __( 'Add New Category', 'peptide-search-ai' ),
+				'new_item_name' => __( 'New Category Name', 'peptide-search-ai' ),
+				'menu_name'     => __( 'Categories', 'peptide-search-ai' ),
+			),
+			'hierarchical'      => true,
+			'public'            => true,
+			'show_in_rest'      => true,
+			'show_admin_column' => true,
+			'rewrite'           => array( 'slug' => 'peptide-category' ),
+		) );
 	}
 
-	/**
-	 * Pre-populate default category terms on activation.
-	 * Safe to call multiple times — skips existing terms.
-	 */
+	/** Pre-populate default category terms on activation. Idempotent. */
 	public static function populate_default_categories(): void {
 		foreach ( self::DEFAULT_CATEGORIES as $slug => $name ) {
 			if ( ! term_exists( $slug, 'peptide_category' ) ) {
@@ -159,138 +134,6 @@ class PSA_Post_Type {
 		}
 	}
 
-	/**
-	 * Add meta boxes to the peptide editor.
-	 */
-	public static function add_meta_boxes(): void {
-		add_meta_box(
-			'psa_peptide_data',
-			'Peptide Scientific Data',
-			array( __CLASS__, 'render_meta_box' ),
-			'peptide',
-			'normal',
-			'high'
-		);
-		add_meta_box(
-			'psa_extended_data',
-			'Extended Research Data',
-			array( __CLASS__, 'render_extended_meta_box' ),
-			'peptide',
-			'normal',
-			'default'
-		);
-	}
-
-	/**
-	 * Render the core meta box fields.
-	 *
-	 * @param WP_Post $post The current post object.
-	 * @return void
-	 */
-	public static function render_meta_box( $post ): void {
-		wp_nonce_field( 'psa_save_meta', 'psa_meta_nonce' );
-
-		$textarea_fields = array(
-			'psa_sequence',
-			'psa_mechanism',
-			'psa_research_apps',
-			'psa_safety_profile',
-			'psa_dosage_info',
-			'psa_references',
-		);
-
-		echo '<table class="form-table">';
-		foreach ( self::META_FIELDS as $key => $label ) {
-			$value = get_post_meta( $post->ID, $key, true );
-			echo '<tr>';
-			echo '<th><label for="' . esc_attr( $key ) . '">' . esc_html( $label ) . '</label></th>';
-			echo '<td>';
-
-			if ( 'psa_source' === $key ) {
-				$options = array(
-					''             => '— Select —',
-					'ai-generated' => 'AI Generated',
-					'pubchem'      => 'PubChem Verified',
-					'manual'       => 'Manual Entry',
-					'pending'      => 'Pending Generation',
-				);
-				echo '<select name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '">';
-				foreach ( $options as $opt_val => $opt_label ) {
-					echo '<option value="' . esc_attr( $opt_val ) . '"' . selected( $value, $opt_val, false ) . '>' . esc_html( $opt_label ) . '</option>';
-				}
-				echo '</select>';
-			} elseif ( in_array( $key, $textarea_fields, true ) ) {
-				echo '<textarea name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" rows="4" class="large-text">' . esc_textarea( $value ) . '</textarea>';
-			} else {
-				echo '<input type="text" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="regular-text" />';
-			}
-
-			echo '</td></tr>';
-		}
-		echo '</table>';
-	}
-
-	/**
-	 * Render the extended meta box fields (half-life, stability, storage, etc.).
-	 *
-	 * @param WP_Post $post The current post object.
-	 * @return void
-	 */
-	public static function render_extended_meta_box( $post ): void {
-		echo '<table class="form-table">';
-		foreach ( self::EXTENDED_META_FIELDS as $key => $label ) {
-			$value = get_post_meta( $post->ID, $key, true );
-			echo '<tr>';
-			echo '<th><label for="' . esc_attr( $key ) . '">' . esc_html( $label ) . '</label></th>';
-			echo '<td>';
-
-			if ( 'psa_vial_size_mg' === $key ) {
-				echo '<input type="number" step="0.01" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="small-text" /> mg';
-			} elseif ( 'psa_amino_acid_count' === $key ) {
-				echo '<input type="number" step="1" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="small-text" />';
-			} else {
-				echo '<input type="text" name="' . esc_attr( $key ) . '" id="' . esc_attr( $key ) . '" value="' . esc_attr( $value ) . '" class="regular-text" />';
-			}
-
-			echo '</td></tr>';
-		}
-		echo '</table>';
-	}
-
-	/**
-	 * Save meta field values (core + extended).
-	 *
-	 * @param int $post_id The post ID.
-	 */
-	public static function save_meta( int $post_id ): void {
-		// phpcs:ignore WordPress.Security.ValidatedSanitizedInput
-		if ( ! isset( $_POST['psa_meta_nonce'] ) ||
-			 ! wp_verify_nonce( wp_unslash( $_POST['psa_meta_nonce'] ), 'psa_save_meta' ) ) {
-			return;
-		}
-		if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ) {
-			return;
-		}
-		if ( ! current_user_can( 'edit_post', $post_id ) ) {
-			return;
-		}
-
-		$numeric_fields = array( 'psa_vial_size_mg', 'psa_amino_acid_count' );
-		$all_fields     = array_merge( self::META_FIELDS, self::EXTENDED_META_FIELDS );
-		foreach ( $all_fields as $key => $label ) {
-			if ( isset( $_POST[ $key ] ) ) {
-				$raw = wp_unslash( $_POST[ $key ] );
-				if ( in_array( $key, $numeric_fields, true ) ) {
-					// Numeric fields: store as non-negative number or empty string.
-					$value = ( '' === trim( $raw ) ) ? '' : (string) max( 0, floatval( $raw ) );
-				} else {
-					$value = sanitize_textarea_field( $raw );
-				}
-				update_post_meta( $post_id, $key, $value );
-			}
-		}
-	}
-
 	/**
 	 * Add custom columns to the peptide admin list.
 	 *
@@ -301,7 +144,6 @@ class PSA_Post_Type {
 		$new = array();
 		foreach ( $columns as $key => $label ) {
 			$new[ $key ] = $label;
-			// Insert source column after title.
 			if ( 'title' === $key ) {
 				$new['psa_source'] = __( 'Source', 'peptide-search-ai' );
 			}
@@ -319,11 +161,8 @@ class PSA_Post_Type {
 		if ( 'psa_source' === $column ) {
 			$source = get_post_meta( $post_id, 'psa_source', true );
 			$labels = array(
-				'ai-generated' => 'AI',
-				'pubchem'      => 'PubChem',
-				'manual'       => 'Manual',
-				'pending'      => 'Pending',
-				'failed'       => 'Failed',
+				'ai-generated' => 'AI', 'pubchem' => 'PubChem',
+				'manual' => 'Manual', 'pending' => 'Pending', 'failed' => 'Failed',
 			);
 			echo esc_html( $labels[ $source ] ?? '—' );
 		}
@@ -335,9 +174,20 @@ class PSA_Post_Type {
 	 * @return array<string> Meta keys.
 	 */
 	public static function get_all_meta_keys(): array {
-		return array_merge(
-			array_keys( self::META_FIELDS ),
-			array_keys( self::EXTENDED_META_FIELDS )
-		);
+		return array_merge( array_keys( self::META_FIELDS ), array_keys( self::EXTENDED_META_FIELDS ) );
 	}
+
+	// ── Backward-compatible proxies (meta boxes moved to PSA_Post_Type_Meta) ──
+
+	/** @see PSA_Post_Type_Meta::add_meta_boxes() */
+	public static function add_meta_boxes(): void { PSA_Post_Type_Meta::add_meta_boxes(); }
+
+	/** @see PSA_Post_Type_Meta::render_meta_box() */
+	public static function render_meta_box( $post ): void { PSA_Post_Type_Meta::render_meta_box( $post ); }
+
+	/** @see PSA_Post_Type_Meta::render_extended_meta_box() */
+	public static function render_extended_meta_box( $post ): void { PSA_Post_Type_Meta::render_extended_meta_box( $post ); }
+
+	/** @see PSA_Post_Type_Meta::save_meta() */
+	public static function save_meta( int $post_id ): void { PSA_Post_Type_Meta::save_meta( $post_id ); }
 }
diff --git a/peptide-search-ai.php b/peptide-search-ai.php
index 79bb92e..caee81a 100755
--- a/peptide-search-ai.php
+++ b/peptide-search-ai.php
@@ -23,6 +23,7 @@ define( 'PSA_PLUGIN_FILE', __FILE__ );
 require_once PSA_PLUGIN_DIR . 'includes/class-psa-config.php';
 require_once PSA_PLUGIN_DIR . 'includes/class-psa-encryption.php';
 require_once PSA_PLUGIN_DIR . 'includes/class-psa-post-type.php';
+require_once PSA_PLUGIN_DIR . 'includes/class-psa-post-type-meta.php';
 require_once PSA_PLUGIN_DIR . 'includes/class-psa-search-handler.php';
 require_once PSA_PLUGIN_DIR . 'includes/class-psa-search.php';
 require_once PSA_PLUGIN_DIR . 'includes/class-psa-cost-tracker.php';