feat: add browsable peptide directory with category filtering, REST API, and extended meta fields (v4.3.0)
Adds [peptide_directory] shortcode with card grid, category taxonomy (8 terms), search, pagination, detail modal, and /v1/compounds REST endpoint. Includes 9 new meta fields (half-life, stability, solubility, etc.), admin data tools for migration/re-enrichment, integration hooks for cross-plugin extensibility, dark mode support, and full uninstall cleanup. Refactors AI generator into PSA_OpenRouter + PSA_KB_Builder classes. Adds PHPUnit tests for PostType and Directory classes. Fixes QA findings: dead JS selector, renderError loading state, numeric meta validation, prepared SQL in uninstall. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
peptiderepo
@@ -1,8 +1,15 @@
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<?php
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declare( strict_types=1 );
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/**
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* Custom template rendering for single peptide pages.
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*
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* What: Appends structured peptide data (quick facts, extended data, sections, badges) below post content.
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* Who calls it: WordPress 'the_content' filter on single peptide pages.
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* Dependencies: WordPress post meta API, PSA_Post_Type meta field keys.
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*
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* @package PeptideSearchAI
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* @see includes/class-psa-post-type.php
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* @see includes/class-psa-directory.php — detail modal uses the same data via REST
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*/
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if ( ! defined( 'ABSPATH' ) ) {
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@@ -11,7 +18,7 @@ if ( ! defined( 'ABSPATH' ) ) {
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class PSA_Template {
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public static function init() {
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public static function init(): void {
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add_filter( 'the_content', array( __CLASS__, 'append_peptide_data' ) );
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}
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@@ -21,7 +28,7 @@ class PSA_Template {
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* @param string $content The post content.
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* @return string Modified content.
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*/
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public static function append_peptide_data( $content ) {
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public static function append_peptide_data( string $content ): string {
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if ( ! is_singular( 'peptide' ) || ! in_the_loop() || ! is_main_query() ) {
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return $content;
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}
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@@ -30,17 +37,14 @@ class PSA_Template {
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$source = get_post_meta( $post_id, 'psa_source', true );
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$pubchem_cid = get_post_meta( $post_id, 'psa_pubchem_cid', true );
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// Build template data for filtering.
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$data = array(
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'post_id' => $post_id,
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'source' => $source,
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'pubchem_cid' => $pubchem_cid,
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);
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// Allow filtering of template data before rendering.
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$data = apply_filters( 'psa_template_data', $data, $post_id );
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// Restore values from possibly filtered data.
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$post_id = $data['post_id'] ?? $post_id;
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$source = $data['source'] ?? $source;
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$pubchem_cid = $data['pubchem_cid'] ?? $pubchem_cid;
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@@ -48,38 +52,117 @@ class PSA_Template {
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$html = '<div class="psa-peptide-data">';
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// Quick facts box.
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$html .= self::render_quick_facts( $post_id, $pubchem_cid );
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// Extended research data box (half-life, stability, storage, etc.).
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$html .= self::render_extended_data( $post_id );
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// Detailed sections.
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$html .= self::render_detail_sections( $post_id );
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// Source badge.
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$html .= self::render_source_badge( $source );
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// Integration hook: allow Peptide Community and other plugins to append content.
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ob_start();
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do_action( 'psa_after_peptide_detail', $post_id );
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$html .= ob_get_clean();
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$html .= '</div>';
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return $content . $html;
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}
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/**
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* Render the quick facts table.
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*
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* @param int $post_id Post ID.
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* @param string $pubchem_cid PubChem CID (may be empty).
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* @return string HTML.
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*/
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private static function render_quick_facts( int $post_id, string $pubchem_cid ): string {
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$weight = get_post_meta( $post_id, 'psa_molecular_weight', true );
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$formula = get_post_meta( $post_id, 'psa_molecular_formula', true );
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$seq = get_post_meta( $post_id, 'psa_sequence', true );
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$aliases = get_post_meta( $post_id, 'psa_aliases', true );
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if ( $weight || $formula || $seq ) {
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$html .= '<div class="psa-quick-facts">';
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$html .= '<h3>Quick Facts</h3>';
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$html .= '<table class="psa-facts-table">';
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if ( $aliases ) {
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$html .= '<tr><th>Also Known As</th><td>' . esc_html( $aliases ) . '</td></tr>';
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}
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if ( $seq ) {
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$html .= '<tr><th>Sequence</th><td><code class="psa-sequence">' . esc_html( $seq ) . '</code></td></tr>';
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}
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if ( $formula ) {
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$html .= '<tr><th>Molecular Formula</th><td>' . esc_html( $formula ) . '</td></tr>';
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}
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if ( $weight ) {
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$html .= '<tr><th>Molecular Weight</th><td>' . esc_html( $weight ) . '</td></tr>';
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}
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if ( $pubchem_cid ) {
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$cid_int = intval( $pubchem_cid );
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$html .= '<tr><th>PubChem CID</th><td><a href="https://pubchem.ncbi.nlm.nih.gov/compound/' . $cid_int . '" target="_blank" rel="noopener">' . $cid_int . '</a></td></tr>';
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}
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$html .= '</table>';
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$html .= '</div>';
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if ( ! $weight && ! $formula && ! $seq ) {
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return '';
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}
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// Detailed sections.
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$html = '<div class="psa-quick-facts">';
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$html .= '<h3>Quick Facts</h3>';
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$html .= '<table class="psa-facts-table">';
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if ( $aliases ) {
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$html .= '<tr><th>Also Known As</th><td>' . esc_html( $aliases ) . '</td></tr>';
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}
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if ( $seq ) {
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$html .= '<tr><th>Sequence</th><td><code class="psa-sequence">' . esc_html( $seq ) . '</code></td></tr>';
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}
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if ( $formula ) {
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$html .= '<tr><th>Molecular Formula</th><td>' . esc_html( $formula ) . '</td></tr>';
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}
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if ( $weight ) {
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$html .= '<tr><th>Molecular Weight</th><td>' . esc_html( $weight ) . '</td></tr>';
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}
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if ( $pubchem_cid ) {
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$cid_int = intval( $pubchem_cid );
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$html .= '<tr><th>PubChem CID</th><td><a href="https://pubchem.ncbi.nlm.nih.gov/compound/' . $cid_int . '" target="_blank" rel="noopener">' . $cid_int . '</a></td></tr>';
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}
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$html .= '</table></div>';
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return $html;
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}
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/**
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* Render the extended research data table (v4.3.0 fields).
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*
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* @param int $post_id Post ID.
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* @return string HTML (empty string if no extended data).
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*/
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private static function render_extended_data( int $post_id ): string {
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$fields = array(
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'psa_half_life' => 'Half-Life',
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'psa_stability' => 'Stability',
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'psa_solubility' => 'Solubility',
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'psa_vial_size_mg' => 'Vial Size',
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'psa_storage_lyophilized' => 'Storage (Lyophilized)',
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'psa_storage_reconstituted' => 'Storage (Reconstituted)',
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'psa_typical_dose_mcg' => 'Typical Research Dose',
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'psa_cycle_parameters' => 'Cycle Parameters',
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'psa_amino_acid_count' => 'Amino Acid Count',
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);
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$rows = '';
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foreach ( $fields as $key => $label ) {
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$value = get_post_meta( $post_id, $key, true );
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if ( ! empty( $value ) ) {
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$display = $value;
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if ( 'psa_vial_size_mg' === $key ) {
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$display = floatval( $value ) . ' mg';
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}
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$rows .= '<tr><th>' . esc_html( $label ) . '</th><td>' . esc_html( $display ) . '</td></tr>';
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}
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}
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if ( empty( $rows ) ) {
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return '';
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}
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return '<div class="psa-quick-facts">' .
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'<h3>Research Parameters</h3>' .
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'<table class="psa-facts-table">' . $rows . '</table>' .
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'</div>';
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}
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/**
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* Render detailed text sections (mechanism, research apps, safety, etc.).
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*
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* @param int $post_id Post ID.
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* @return string HTML.
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*/
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private static function render_detail_sections( int $post_id ): string {
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$detail_fields = array(
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'psa_mechanism' => 'Mechanism of Action',
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'psa_research_apps' => 'Research Applications',
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@@ -88,6 +171,7 @@ class PSA_Template {
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'psa_references' => 'References',
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);
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$html = '';
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foreach ( $detail_fields as $key => $label ) {
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$value = get_post_meta( $post_id, $key, true );
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if ( ! empty( $value ) ) {
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@@ -98,34 +182,43 @@ class PSA_Template {
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}
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}
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// Source badge.
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if ( $source && 'pending' !== $source ) {
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$badges = array(
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'ai-generated' => array(
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'label' => 'AI-Generated Content',
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'class' => 'psa-badge-ai',
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),
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'pubchem' => array(
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'label' => 'PubChem Verified',
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'class' => 'psa-badge-verified',
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),
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'manual' => array(
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'label' => 'Manually Curated',
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'class' => 'psa-badge-manual',
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),
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);
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$badge = $badges[ $source ] ?? $badges['ai-generated'];
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return $html;
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}
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$html .= '<div class="psa-source-badge ' . esc_attr( $badge['class'] ) . '">';
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$html .= esc_html( $badge['label'] );
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if ( 'ai-generated' === $source ) {
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$html .= ' — This entry was automatically generated and may contain inaccuracies. Please verify critical information with primary sources.';
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}
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$html .= '</div>';
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/**
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* Render the source badge.
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*
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* @param string $source The data source value.
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* @return string HTML (empty if source is empty or 'pending').
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*/
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private static function render_source_badge( string $source ): string {
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if ( ! $source || 'pending' === $source ) {
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return '';
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}
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$badges = array(
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'ai-generated' => array(
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'label' => 'AI-Generated Content',
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'class' => 'psa-badge-ai',
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),
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'pubchem' => array(
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'label' => 'PubChem Verified',
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'class' => 'psa-badge-verified',
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),
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'manual' => array(
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'label' => 'Manually Curated',
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'class' => 'psa-badge-manual',
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),
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);
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$badge = $badges[ $source ] ?? $badges['ai-generated'];
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$html = '<div class="psa-source-badge ' . esc_attr( $badge['class'] ) . '">';
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$html .= esc_html( $badge['label'] );
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if ( 'ai-generated' === $source ) {
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$html .= ' — This entry was automatically generated and may contain inaccuracies. Please verify critical information with primary sources.';
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}
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$html .= '</div>';
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return $content . $html;
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return $html;
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}
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}
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