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fix: resolve PHPCS errors and PHPUnit test failures for CI

Browse Source 
Move declare(strict_types=1) after file-level docblock in all 12 class
files to satisfy WordPress Coding Standards docblock placement rule.
Fix multi-line function call formatting in class-psa-admin.php. Align
array double arrows and equals signs. Fix escaped backticks in
AIGeneratorTest heredoc that broke markdown fence stripping tests.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
peptiderepo
2026-04-13 21:38:04 +07:00
parent ed65b6ab90
commit 3bbf927510
14 changed files with 70 additions and 62 deletions
Download Patch File Download Diff File Expand all files Collapse all files

48
includes/class-psa-admin.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Admin settings page for Peptide Search AI. * Admin settings page for Peptide Search AI.
* *
@@ -12,6 +11,7 @@ declare( strict_types=1 );
* @see includes/class-psa-cost-tracker.php * @see includes/class-psa-cost-tracker.php
* @see includes/class-psa-post-type.php * @see includes/class-psa-post-type.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;
@@ -74,21 +74,21 @@ class PSA_Admin {
$api_key_value = ''; $api_key_value = '';
if ( ! empty( $api_key_input ) && '••••••••' !== $api_key_input ) { if ( ! empty( $api_key_input ) && '••••••••' !== $api_key_input ) {
$sanitized = sanitize_text_field( $api_key_input ); $sanitized = sanitize_text_field( $api_key_input );
$encrypted = PSA_Encryption::encrypt( $sanitized ); $encrypted = PSA_Encryption::encrypt( $sanitized );
$api_key_value = ( false !== $encrypted ) ? $encrypted : ''; $api_key_value = ( false !== $encrypted ) ? $encrypted : '';
} else { } else {
$existing = self::get_setting( 'api_key', '' ); $existing = self::get_setting( 'api_key', '' );
$api_key_value = $existing; $api_key_value = $existing;
} }
return array( return array(
'api_key' => $api_key_value, 'api_key' => $api_key_value,
'ai_model' => sanitize_text_field( $input['ai_model'] ?? '' ), 'ai_model' => sanitize_text_field( $input['ai_model'] ?? '' ),
'validation_model' => sanitize_text_field( $input['validation_model'] ?? '' ), 'validation_model' => sanitize_text_field( $input['validation_model'] ?? '' ),
'auto_publish' => sanitize_text_field( $input['auto_publish'] ?? 'draft' ), 'auto_publish' => sanitize_text_field( $input['auto_publish'] ?? 'draft' ),
'use_pubchem' => ! empty( $input['use_pubchem'] ) ? '1' : '0', 'use_pubchem' => ! empty( $input['use_pubchem'] ) ? '1' : '0',
'monthly_budget' => max( 0, floatval( $input['monthly_budget'] ?? PSA_Config::DEFAULT_MONTHLY_BUDGET ) ), 'monthly_budget' => max( 0, floatval( $input['monthly_budget'] ?? PSA_Config::DEFAULT_MONTHLY_BUDGET ) ),
); );
} }
@@ -106,20 +106,28 @@ class PSA_Admin {
if ( 'migrate_categories' === $action && wp_verify_nonce( $nonce, 'psa_migrate_categories' ) ) { if ( 'migrate_categories' === $action && wp_verify_nonce( $nonce, 'psa_migrate_categories' ) ) {
self::run_category_migration(); self::run_category_migration();
add_action( 'admin_notices', function () { add_action(
echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Category migration completed.', 'peptide-search-ai' ) . '</p></div>'; 'admin_notices',
} ); function () {
echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Category migration completed.', 'peptide-search-ai' ) . '</p></div>';
}
);
} }
if ( 'reenrich' === $action && wp_verify_nonce( $nonce, 'psa_reenrich' ) ) { if ( 'reenrich' === $action && wp_verify_nonce( $nonce, 'psa_reenrich' ) ) {
$queued = self::queue_reenrichment(); $queued = self::queue_reenrichment();
add_action( 'admin_notices', function () use ( $queued ) { add_action(
echo '<div class="notice notice-success is-dismissible"><p>' . esc_html( sprintf( 'admin_notices',
/* translators: %d = number of peptides queued */ function () use ( $queued ) {
__( '%d peptides queued for re-enrichment.', 'peptide-search-ai' ), echo '<div class="notice notice-success is-dismissible"><p>' . esc_html(
$queued sprintf(
) ) . '</p></div>'; /* translators: %d = number of peptides queued */
} ); __( '%d peptides queued for re-enrichment.', 'peptide-search-ai' ),
$queued
)
) . '</p></div>';
}
);
} }
} }

2
includes/class-psa-ai-generator.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Handles AI content generation for new peptide entries. * Handles AI content generation for new peptide entries.
* *
@@ -13,6 +12,7 @@ declare( strict_types=1 );
* @see includes/class-psa-pubchem.php * @see includes/class-psa-pubchem.php
* @see includes/class-psa-post-type.php * @see includes/class-psa-post-type.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-config.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Configuration constants for Peptide Search AI. * Configuration constants for Peptide Search AI.
* *
@@ -9,6 +8,7 @@ declare( strict_types=1 );
* *
* @package PeptideSearchAI * @package PeptideSearchAI
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-cost-tracker.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Tracks API usage costs and enforces monthly budget limits. * Tracks API usage costs and enforces monthly budget limits.
* *
@@ -10,6 +9,7 @@ declare( strict_types=1 );
* *
* @package PeptideSearchAI * @package PeptideSearchAI
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-directory.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Browsable peptide directory — REST endpoint, shortcode, and data formatting. * Browsable peptide directory — REST endpoint, shortcode, and data formatting.
* *
@@ -12,6 +11,7 @@ declare( strict_types=1 );
* @see includes/class-psa-search.php — existing search shortcode (separate from directory) * @see includes/class-psa-search.php — existing search shortcode (separate from directory)
* @see assets/js/psa-directory.js — frontend grid, filter, modal logic * @see assets/js/psa-directory.js — frontend grid, filter, modal logic
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-encryption.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Handles encryption/decryption of sensitive data at rest. * Handles encryption/decryption of sensitive data at rest.
* *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
* @see includes/class-psa-admin.php * @see includes/class-psa-admin.php
* @see includes/class-psa-ai-generator.php * @see includes/class-psa-ai-generator.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-kb-builder.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Echo Knowledge Base article builder for generated peptide content. * Echo Knowledge Base article builder for generated peptide content.
* *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
* @package PeptideSearchAI * @package PeptideSearchAI
* @see includes/class-psa-ai-generator.php * @see includes/class-psa-ai-generator.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

32
includes/class-psa-openrouter.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* OpenRouter API communication layer. * OpenRouter API communication layer.
* *
@@ -12,6 +11,7 @@ declare( strict_types=1 );
* @see includes/class-psa-ai-generator.php * @see includes/class-psa-ai-generator.php
* @see includes/class-psa-cost-tracker.php * @see includes/class-psa-cost-tracker.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;
@@ -90,15 +90,15 @@ class PSA_OpenRouter {
array( array(
'timeout' => 120, 'timeout' => 120,
'headers' => array( 'headers' => array(
'Content-Type' => 'application/json', 'Content-Type' => 'application/json',
'Authorization' => 'Bearer ' . $api_key, 'Authorization' => 'Bearer ' . $api_key,
'HTTP-Referer' => $site_url, 'HTTP-Referer' => $site_url,
'X-Title' => $site_name, 'X-Title' => $site_name,
), ),
'body' => wp_json_encode( 'body' => wp_json_encode(
array( array(
'model' => $model, 'model' => $model,
'messages' => array( 'messages' => array(
array( array(
'role' => 'system', 'role' => 'system',
'content' => 'You are a scientific database assistant. Return only valid JSON.', 'content' => 'You are a scientific database assistant. Return only valid JSON.',
@@ -108,8 +108,8 @@ class PSA_OpenRouter {
'content' => $prompt, 'content' => $prompt,
), ),
), ),
'max_tokens' => $max_tokens, 'max_tokens' => $max_tokens,
'temperature' => 0.3, 'temperature' => 0.3,
) )
), ),
) )
@@ -152,13 +152,13 @@ class PSA_OpenRouter {
PSA_Cost_Tracker::log_api_call( PSA_Cost_Tracker::log_api_call(
array( array(
'provider' => 'openrouter', 'provider' => 'openrouter',
'model' => $model, 'model' => $model,
'prompt_tokens' => $prompt_tokens, 'prompt_tokens' => $prompt_tokens,
'completion_tokens' => $completion_tokens, 'completion_tokens' => $completion_tokens,
'request_type' => $request_type, 'request_type' => $request_type,
'peptide_name' => $peptide_name, 'peptide_name' => $peptide_name,
'success' => true, 'success' => true,
) )
); );

2
includes/class-psa-post-type.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Registers the Peptide custom post type, taxonomy, and meta fields. * Registers the Peptide custom post type, taxonomy, and meta fields.
* *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
* @see includes/class-psa-ai-generator.php — auto-assigns category term after generation * @see includes/class-psa-ai-generator.php — auto-assigns category term after generation
* @see includes/class-psa-directory.php — reads taxonomy for directory filtering * @see includes/class-psa-directory.php — reads taxonomy for directory filtering
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-pubchem.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* PubChem PUG REST API integration for molecular data enrichment. * PubChem PUG REST API integration for molecular data enrichment.
* *
@@ -10,6 +9,7 @@ declare( strict_types=1 );
* @package PeptideSearchAI * @package PeptideSearchAI
* @see includes/class-psa-ai-generator.php * @see includes/class-psa-ai-generator.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-search.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Handles AJAX search, the [peptide_search] shortcode, and the REST API endpoint. * Handles AJAX search, the [peptide_search] shortcode, and the REST API endpoint.
* *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
* @see includes/class-psa-ai-generator.php * @see includes/class-psa-ai-generator.php
* @see includes/class-psa-config.php * @see includes/class-psa-config.php
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

2
includes/class-psa-template.php
View File

@@ -1,5 +1,4 @@
<?php <?php
declare( strict_types=1 );
/** /**
* Custom template rendering for single peptide pages. * Custom template rendering for single peptide pages.
* *
@@ -11,6 +10,7 @@ declare( strict_types=1 );
* @see includes/class-psa-post-type.php * @see includes/class-psa-post-type.php
* @see includes/class-psa-directory.php — detail modal uses the same data via REST * @see includes/class-psa-directory.php — detail modal uses the same data via REST
*/ */
declare( strict_types=1 );
if ( ! defined( 'ABSPATH' ) ) { if ( ! defined( 'ABSPATH' ) ) {
exit; exit;

28
peptide-search-ai.php
View File

@@ -129,20 +129,20 @@ function psa_enqueue_frontend_assets() {
'ajaxurl' => admin_url( 'admin-ajax.php' ), 'ajaxurl' => admin_url( 'admin-ajax.php' ),
'nonce' => wp_create_nonce( 'psa_search_nonce' ), 'nonce' => wp_create_nonce( 'psa_search_nonce' ),
'i18n' => array( 'i18n' => array(
'error' => __( 'Error:', 'peptide-search-ai' ), 'error' => __( 'Error:', 'peptide-search-ai' ),
'searchFailed' => __( 'Search failed.', 'peptide-search-ai' ), 'searchFailed' => __( 'Search failed.', 'peptide-search-ai' ),
'unexpected' => __( 'Unexpected response.', 'peptide-search-ai' ), 'unexpected' => __( 'Unexpected response.', 'peptide-search-ai' ),
'rateLimited' => __( 'Too many requests. Please try again later.', 'peptide-search-ai' ), 'rateLimited' => __( 'Too many requests. Please try again later.', 'peptide-search-ai' ),
'networkError' => __( 'Could not connect to the server. Please try again.', 'peptide-search-ai' ), 'networkError' => __( 'Could not connect to the server. Please try again.', 'peptide-search-ai' ),
'timeout' => __( 'Request timed out. The server took too long to respond. Please try again.', 'peptide-search-ai' ), 'timeout' => __( 'Request timed out. The server took too long to respond. Please try again.', 'peptide-search-ai' ),
'connectionError' => __( 'Network error. Please check your connection and try again.', 'peptide-search-ai' ), 'connectionError' => __( 'Network error. Please check your connection and try again.', 'peptide-search-ai' ),
'serverError' => __( 'Server error. Please try again later.', 'peptide-search-ai' ), 'serverError' => __( 'Server error. Please try again later.', 'peptide-search-ai' ),
'unavailable' => __( 'Server is temporarily unavailable. Please try again later.', 'peptide-search-ai' ), 'unavailable' => __( 'Server is temporarily unavailable. Please try again later.', 'peptide-search-ai' ),
'peptidesFound' => __( 'peptide(s) found', 'peptide-search-ai' ), 'peptidesFound' => __( 'peptide(s) found', 'peptide-search-ai' ),
'pendingMsg' => __( 'is currently being added to our database. Please check back again later.', 'peptide-search-ai' ), 'pendingMsg' => __( 'is currently being added to our database. Please check back again later.', 'peptide-search-ai' ),
'invalidMsg' => __( 'does not appear to be a recognized peptide. Please check the spelling or try a different search term.', 'peptide-search-ai' ), 'invalidMsg' => __( 'does not appear to be a recognized peptide. Please check the spelling or try a different search term.', 'peptide-search-ai' ),
'verified' => __( 'Verified', 'peptide-search-ai' ), 'verified' => __( 'Verified', 'peptide-search-ai' ),
'curated' => __( 'Curated', 'peptide-search-ai' ), 'curated' => __( 'Curated', 'peptide-search-ai' ),
), ),
) )
); );

4
tests/unit/AIGeneratorTest.php
View File

@@ -116,9 +116,9 @@ class AIGeneratorTest extends TestCase {
*/ */
public function test_parse_response_with_markdown_fences() { public function test_parse_response_with_markdown_fences() {
$response_text = <<<JSON $response_text = <<<JSON
\`\`\`json ```json
{"is_valid": true, "canonical_name": "Semaglutide", "reason": "GLP-1 agonist"} {"is_valid": true, "canonical_name": "Semaglutide", "reason": "GLP-1 agonist"}
\`\`\` ```
JSON; JSON;
$result = PSA_OpenRouter::parse_response( $response_text ); $result = PSA_OpenRouter::parse_response( $response_text );