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Adopt reusable CI standard + PHPUnit conversion (#22)

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Squash-merge of PR #22: adopt shared reusable CI workflow, convert PHPUnit to stubs, update branch-protection contexts.

QA-approved at 05d8094a1d. All required CI checks green.

Agent-Session: 2026-06-17-prcore-ci-deploy
This commit is contained in:
peptiderepo
2026-06-17 01:12:00 +07:00
committed by GitHub
parent d0b5875fd8
commit 665d7fa9e1
72 changed files with 4604 additions and 1212 deletions
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73
includes/migrations/class-pr-core-pubchem-client.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Pubchem Client.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Fetches molecular formula, molecular weight, and synonyms from the
*
* @package Peptide_Repo_Core
*/
/**
* Lightweight PubChem REST client for the backfill migration.
*
@@ -20,16 +32,32 @@ declare(strict_types=1);
*/
class PR_Core_Pubchem_Client {
/** @var string PubChem REST base URL. */
/**
* PubChem REST base URL.
*
* @var string PubChem REST base URL.
*/
private const BASE = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
/** @var int HTTP timeout per request (seconds). */
/**
* HTTP timeout per request (seconds).
*
* @var int HTTP timeout per request (seconds).
*/
private const TIMEOUT = 8;
/** @var int Maximum retry attempts with exponential backoff. */
/**
* Maximum retry attempts with exponential backoff.
*
* @var int Maximum retry attempts with exponential backoff.
*/
private const MAX_RETRIES = 3;
/** @var int Maximum synonyms to return (keeps post-meta size reasonable). */
/**
* Maximum synonyms to return (keeps post-meta size reasonable).
*
* @var int Maximum synonyms to return (keeps post-meta size reasonable).
*/
private const MAX_SYNONYMS = 10;
/**
@@ -109,11 +137,11 @@ class PR_Core_Pubchem_Client {
return null;
}
return [
return array(
'formula' => $formula,
'weight' => $weight,
'cid' => $cid,
];
);
}
/**
@@ -130,14 +158,14 @@ class PR_Core_Pubchem_Client {
$body = $this->get_with_retry( $url );
if ( null === $body ) {
return [];
return array();
}
$data = json_decode( $body, true );
$synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? [];
$synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? array();
if ( ! is_array( $synonyms ) ) {
return [];
return array();
}
return array_slice( $synonyms, 0, self::MAX_SYNONYMS );
@@ -176,10 +204,13 @@ class PR_Core_Pubchem_Client {
*/
private function get_once( string $url ): ?string {
if ( function_exists( 'wp_remote_get' ) ) {
$response = wp_remote_get( $url, [
'timeout' => self::TIMEOUT,
'headers' => [ 'Accept' => 'application/json' ],
] );
$response = wp_remote_get(
$url,
array(
'timeout' => self::TIMEOUT,
'headers' => array( 'Accept' => 'application/json' ),
)
);
if ( is_wp_error( $response ) ) {
return null;
@@ -194,13 +225,15 @@ class PR_Core_Pubchem_Client {
}
// WP-CLI / plain PHP fallback.
$context = stream_context_create( [
'http' => [
'timeout' => self::TIMEOUT,
'header' => "Accept: application/json\r\n",
'method' => 'GET',
],
] );
$context = stream_context_create(
array(
'http' => array(
'timeout' => self::TIMEOUT,
'header' => "Accept: application/json\r\n",
'method' => 'GET',
),
)
);
$body = @file_get_contents( $url, false, $context );
return ( false === $body ) ? null : $body;