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feat: add browsable peptide directory with category filtering, REST API, and extended meta fields (v4.3.0)

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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
2026-04-13 21:30:11 +07:00
parent 0fa2707163
commit ed65b6ab90
28 changed files with 3380 additions and 783 deletions
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12
includes/class-psa-pubchem.php
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@@ -1,8 +1,14 @@
<?php
declare( strict_types=1 );
/**
* PubChem PUG REST API integration for molecular data enrichment.
*
* What: Fetches verified molecular data (formula, weight, SMILES, InChI) from PubChem.
* Who calls it: PSA_AI_Generator::background_generate() during peptide content generation.
* Dependencies: WordPress HTTP API (wp_remote_get), PSA_Config for cache TTL.
*
* @package PeptideSearchAI
* @see includes/class-psa-ai-generator.php
*/
if ( ! defined( 'ABSPATH' ) ) {
@@ -20,7 +26,7 @@ class PSA_PubChem {
* @param string $name Peptide or compound name.
* @return array|WP_Error|null Array of properties, WP_Error on failure, or null if not found.
*/
public static function lookup( $name ) {
public static function lookup( string $name ) {
$options = get_option( 'psa_settings', array() );
$use_pubchem = $options['use_pubchem'] ?? '1';
@@ -79,7 +85,7 @@ class PSA_PubChem {
* @param string $name Compound name.
* @return int|WP_Error|null CID, WP_Error on API failure, or null if not found.
*/
private static function get_cid_by_name( $name ) {
private static function get_cid_by_name( string $name ) {
$url = self::API_BASE . '/compound/name/' . rawurlencode( $name ) . '/cids/JSON';
$response = wp_remote_get(
@@ -112,7 +118,7 @@ class PSA_PubChem {
* @param int $cid PubChem Compound ID.
* @return array|WP_Error|null Properties array, WP_Error on failure, or null if not found.
*/
private static function get_properties( $cid ) {
private static function get_properties( int $cid ) {
$props = 'MolecularFormula,MolecularWeight,IUPACName,CanonicalSMILES,InChI';
$url = self::API_BASE . '/compound/cid/' . (int) $cid . '/property/' . $props . '/JSON';