' + data.total + ' peptide' + - (data.total !== 1 ? 's' : '') + ' found
'; - - data.results.forEach(function (item) { - html += ''; - html += '' + esc(item.sequence) + '');
- if (meta.length) html += '';
-
- if (item.excerpt) html += '' + esc(item.excerpt) + '
'; - html += ''; - }); - - $results.html(html).show(); - } - - /** - * Show the pending/in-progress message. - */ - function showPending(name) { - hideAll(); - $pending.find('.psa-pending-inner p').html( - '' + esc(name) + ' is currently being added to our database. Please check back again later.' - ); - $pending.show(); - } - - /** - * Show the invalid peptide message. - */ - function showInvalid(name, reason) { - hideAll(); - $invalid.find('.psa-invalid-text').html( - '' + esc(name) + ' does not appear to be a recognized peptide. Please check the spelling or try a different search term.' - ); - $invalid.show(); - } - - /** - * Perform the search. The backend handles everything: - * - If found: returns results - * - If not found + valid peptide: validates, creates placeholder, queues generation - * - If not found + invalid: returns invalid status - */ - function doSearch(query) { - if (query.length < 2) { - hideAll(); - return; - } - - hideAll(); - $checking.show(); - $results.attr('aria-busy', 'true'); - - $.ajax({ - url: psaAjax.ajaxurl, - method: 'GET', - data: { - action: 'psa_search', - nonce: psaAjax.nonce, - q: query - }, - timeout: 30000, - success: function (response) { - $results.attr('aria-busy', 'false'); - if (!response.success) { - showError(response.data || 'Search failed.'); - return; - } - var d = response.data; - switch (d.status) { - case 'found': - renderResults(d.data); - break; - case 'pending': - showPending(d.peptide_name); - break; - case 'invalid': - showInvalid(query, d.message); - break; - case 'rate_limited': - showError(d.message || 'Too many requests. Please try again later.'); - break; - default: - showError('Unexpected response.'); - } - }, - error: function (jqXHR, textStatus, errorThrown) { - $results.attr('aria-busy', 'false'); - var errorMsg = 'Could not connect to the server. Please try again.'; - if (textStatus === 'timeout') { - errorMsg = 'Request timed out. The server took too long to respond. Please try again.'; - } else if (textStatus === 'error') { - if (jqXHR.status === 0) { - errorMsg = 'Network error. Please check your connection and try again.'; - } else if (jqXHR.status === 500) { - errorMsg = 'Server error. Please try again later.'; - } else if (jqXHR.status === 503) { - errorMsg = 'Server is temporarily unavailable. Please try again later.'; - } - } - showError(errorMsg); - } - }); - } - - // --- Event Handlers (scoped to this instance) --- - - $form.on('submit', function (e) { - e.preventDefault(); - doSearch($input.val().trim()); - }); - - var debouncedSearch = debounce(function () { - var q = $input.val().trim(); - if (q.length >= 2) { - doSearch(q); - } else { - hideAll(); - } - }, 400); - - $input.on('input', debouncedSearch); - } - - // --- Initialize all search instances on page --- - - $(document).ready(function () { - $('.psa-search-wrap').each(function () { - initSearchInstance($(this)); - }); - }); - -})(jQuery); diff --git a/composer.json b/composer.json deleted file mode 100755 index 59495fc..0000000 --- a/composer.json +++ /dev/null @@ -1,36 +0,0 @@ -{ - "name": "peptiderepo/peptide-search-ai", - "description": "Searchable peptide database with AI-powered auto-population for WordPress", - "type": "wordpress-plugin", - "license": "GPL-2.0-or-later", - "authors": [ - { - "name": "Terence", - "role": "Lead Developer" - } - ], - "require": { - "php": ">=7.4" - }, - "require-dev": { - "phpunit/phpunit": "^9.0 || ^10.0", - "squizlabs/php_codesniffer": "^3.7", - "wp-coding-standards/wpcs": "^3.0", - "dealerdirect/phpcodesniffer-composer-installer": "^1.0" - }, - "autoload": { - "psr-4": { - "PSA\\": "includes/" - } - }, - "config": { - "allow-plugins": { - "dealerdirect/phpcodesniffer-composer-installer": true - } - }, - "scripts": { - "test": "phpunit", - "lint": "phpcs", - "lint:fix": "phpcbf" - } -} diff --git a/includes/class-psa-admin.php b/includes/class-psa-admin.php deleted file mode 100755 index c93c56a..0000000 --- a/includes/class-psa-admin.php +++ /dev/null @@ -1,247 +0,0 @@ - array( __CLASS__, 'sanitize_settings' ), - ) - ); - - // OpenRouter Section. - add_settings_section( - 'psa_ai_section', - __( 'OpenRouter API Settings', 'peptide-search-ai' ), - array( __CLASS__, 'render_section_description' ), - 'peptide-search-ai' - ); - add_settings_field( - 'api_key', - __( 'API Key', 'peptide-search-ai' ), - array( __CLASS__, 'render_api_key_field' ), - 'peptide-search-ai', - 'psa_ai_section' - ); - add_settings_field( - 'ai_model', - __( 'Generation Model', 'peptide-search-ai' ), - array( __CLASS__, 'render_model_field' ), - 'peptide-search-ai', - 'psa_ai_section' - ); - add_settings_field( - 'validation_model', - __( 'Validation Model', 'peptide-search-ai' ), - array( __CLASS__, 'render_validation_model_field' ), - 'peptide-search-ai', - 'psa_ai_section' - ); - - // Behavior Section. - add_settings_section( - 'psa_behavior_section', - __( 'Behavior Settings', 'peptide-search-ai' ), - null, - 'peptide-search-ai' - ); - add_settings_field( - 'auto_publish', - __( 'Auto-Publish', 'peptide-search-ai' ), - array( __CLASS__, 'render_publish_field' ), - 'peptide-search-ai', - 'psa_behavior_section' - ); - add_settings_field( - 'use_pubchem', - __( 'PubChem Enrichment', 'peptide-search-ai' ), - array( __CLASS__, 'render_pubchem_field' ), - 'peptide-search-ai', - 'psa_behavior_section' - ); - } - - /** - * Sanitize settings input. - * - * @param array $input Raw input from the form. - * @return array Sanitized settings. - */ - public static function sanitize_settings( $input ) { - return array( - 'api_key' => sanitize_text_field( $input['api_key'] ?? '' ), - 'ai_model' => sanitize_text_field( $input['ai_model'] ?? '' ), - 'validation_model' => sanitize_text_field( $input['validation_model'] ?? '' ), - 'auto_publish' => sanitize_text_field( $input['auto_publish'] ?? 'draft' ), - // Checkbox: if key is absent in POST, it was unchecked → '0'. - 'use_pubchem' => ! empty( $input['use_pubchem'] ) ? '1' : '0', - ); - } - - // ------------------------------------------------------------------------- - // Field renderers - // ------------------------------------------------------------------------- - - public static function render_section_description() { - ?> -- OpenRouter to access AI models. OpenRouter provides a unified API for hundreds of models including open-source options like Gemini Flash, Llama, Mistral, Qwen, and DeepSeek, as well as commercial models.', 'peptide-search-ai' ), - esc_url( 'https://openrouter.ai/' ) - ); - ?> -
- - - - - - -
-
- openrouter.ai/settings/keys.
- define( 'PSA_OPENROUTER_KEY', 'your-key-here' );
-
- google/gemini-2.5-flash.
- openrouter.ai/models.
- meta-llama/llama-4-maverick, deepseek/deepseek-chat-v3-0324, qwen/qwen-2.5-72b-instruct.
-
- google/gemini-2.0-flash-001.
- meta-llama/llama-4-scout, mistralai/mistral-small-3.1-24b-instruct.
-
[peptide_search]
[peptide_search placeholder="Search peptides..."]
GET /wp-json/peptides/v1/search?q=BPC-157
' . $header . '
' . "\n\n" : ''; - - // Overview. - $c .= 'The following potential benefits are based on animal studies and preclinical research. Human clinical trial data is extremely limited.
' . "\n"; - $research = $ai_data['research_benefits'] ?? $ai_data['research_applications'] ?? ''; - $c .= self::research_with_subheadings( $research ); - } - - // Administration & Dosing. - if ( ! empty( $ai_data['administration_dosing'] ) || ! empty( $ai_data['dosage_info'] ) ) { - $c .= 'Important: The following dosing information is derived from animal studies and extrapolated research. This peptide is not approved for human use. This information is provided for educational purposes only.
' . "\n"; - $c .= self::paragraphs( $ai_data['administration_dosing'] ?? $ai_data['dosage_info'] ?? '' ); - } - - // Safety & Side Effects. - if ( ! empty( $ai_data['safety_side_effects'] ) || ! empty( $ai_data['safety_profile'] ) ) { - $c .= 'Medical Disclaimer: The information on this page is provided for educational and research purposes only. This peptide is not approved for human therapeutic use. Nothing on this page constitutes medical advice. Always consult a licensed healthcare professional before using any peptide, supplement, or research chemical.
'; - - $kb_post_id = wp_insert_post( - array( - 'post_title' => $title, - 'post_content' => wp_kses_post( $c ), - 'post_type' => 'epkb_post_type_1', - 'post_status' => $post_status, - ), - true - ); - - if ( is_wp_error( $kb_post_id ) ) { - error_log( 'PSA: Failed to create KB article: ' . $kb_post_id->get_error_message() ); - return; - } - - // Assign KB category. - $category_map = array( - 'GH Secretagogues' => 'gh-secretagogues', - 'Healing & Repair' => 'healing-repair', - 'Melanocortin Peptides' => 'melanocortin-peptides', - 'Metabolic & Anti-Aging' => 'metabolic-anti-aging', - 'Nootropic & Neuroprotective' => 'nootropic-neuroprotective', - ); - - $cat_name = trim( $ai_data['category'] ?? '' ); - if ( isset( $category_map[ $cat_name ] ) ) { - $term = get_term_by( 'slug', $category_map[ $cat_name ], 'epkb_post_type_1_category' ); - if ( $term ) { - wp_set_object_terms( $kb_post_id, array( (int) $term->term_id ), 'epkb_post_type_1_category' ); - } - } - - update_post_meta( $peptide_post_id, 'psa_kb_article_id', $kb_post_id ); - update_post_meta( $kb_post_id, 'psa_peptide_post_id', $peptide_post_id ); - - error_log( 'PSA: Created KB article #' . $kb_post_id . ' for "' . $peptide_name . '"' ); - } - - /** - * Convert text to HTML paragraphs. - */ - private static function paragraphs( $text ) { - if ( empty( $text ) ) { - return ''; - } - $text = str_replace( "\r\n", "\n", $text ); - $parts = preg_split( '/\n{2,}/', trim( $text ) ); - $out = ''; - foreach ( $parts as $p ) { - $p = trim( $p ); - if ( '' === $p ) { - continue; - } - $out .= '' . wp_kses_post( $p ) . '
' . "\n"; - } - return $out; - } - - /** - * Parse research text into h3 subheadings + paragraphs. - */ - private static function research_with_subheadings( $text ) { - if ( empty( $text ) ) { - return ''; - } - $text = str_replace( "\r\n", "\n", trim( $text ) ); - $blocks = preg_split( '/\n{2,}/', $text ); - $out = ''; - foreach ( $blocks as $block ) { - $block = trim( $block ); - if ( '' === $block ) { - continue; - } - // If block is short (under 80 chars) and has no period, treat as a subheading. - if ( strlen( $block ) < 80 && strpos( $block, '.' ) === false ) { - $out .= '' . wp_kses_post( $rest ) . '
' . "\n"; - continue; - } - } - $out .= '' . wp_kses_post( $block ) . '
' . "\n"; - } - } - return $out; - } -} diff --git a/includes/class-psa-config.php b/includes/class-psa-config.php deleted file mode 100755 index 7ac6a9e..0000000 --- a/includes/class-psa-config.php +++ /dev/null @@ -1,41 +0,0 @@ - $type, - 'message' => $message, - ), - $http_code - ); - } -} diff --git a/includes/class-psa-post-type.php b/includes/class-psa-post-type.php deleted file mode 100755 index 79043dd..0000000 --- a/includes/class-psa-post-type.php +++ /dev/null @@ -1,162 +0,0 @@ - 'Amino Acid Sequence', - 'psa_molecular_weight' => 'Molecular Weight', - 'psa_molecular_formula' => 'Molecular Formula', - 'psa_aliases' => 'Aliases / Synonyms', - 'psa_mechanism' => 'Mechanism of Action', - 'psa_research_apps' => 'Research Applications', - 'psa_safety_profile' => 'Safety & Side Effects', - 'psa_dosage_info' => 'Dosage Information', - 'psa_references' => 'References & Citations', - 'psa_source' => 'Data Source', - 'psa_pubchem_cid' => 'PubChem CID', - ); - - /** - * Register admin-only hooks (meta boxes, save). - */ - public static function init_admin() { - add_action( 'add_meta_boxes', array( __CLASS__, 'add_meta_boxes' ) ); - add_action( 'save_post_peptide', array( __CLASS__, 'save_meta' ) ); - } - - /** - * Register the peptide CPT. - */ - public static function register_peptide_post_type() { - 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, - ) - ); - } - - /** - * Add meta boxes to the peptide editor. - */ - public static function add_meta_boxes() { - add_meta_box( - 'psa_peptide_data', - 'Peptide Scientific Data', - array( __CLASS__, 'render_meta_box' ), - 'peptide', - 'normal', - 'high' - ); - } - - /** - * Render the meta box fields. - * - * @param WP_Post $post The current post object. - */ - public static function render_meta_box( $post ) { - 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 '| '; - echo ' | '; - - if ( 'psa_source' === $key ) { - $options = array( - '' => '— Select —', - 'ai-generated' => 'AI Generated', - 'pubchem' => 'PubChem Verified', - 'manual' => 'Manual Entry', - 'pending' => 'Pending Generation', - ); - echo ''; - } elseif ( in_array( $key, $textarea_fields, true ) ) { - echo ''; - } else { - echo ''; - } - - echo ' |
|---|
| Also Known As | ' . esc_html( $aliases ) . ' |
|---|---|
| Sequence | ' . esc_html( $seq ) . ' |
| Molecular Formula | ' . esc_html( $formula ) . ' |
| Molecular Weight | ' . esc_html( $weight ) . ' |
| PubChem CID | ' . $cid_int . ' |