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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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132
includes/repositories/class-pr-core-peptide-repository.php
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@@ -1,6 +1,18 @@
<?php
/**
* Peptide Repository.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* CRUD operations over peptide posts, returning typed DTOs
*
* @package Peptide_Repo_Core
*/
/**
* Repository for peptide CPT records.
*
@@ -36,12 +48,14 @@ class PR_Core_Peptide_Repository {
* @return PR_Core_Peptide_DTO|null
*/
public function find_by_slug( string $slug ): ?PR_Core_Peptide_DTO {
$posts = get_posts( [
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
'name' => sanitize_title( $slug ),
'posts_per_page' => 1,
'post_status' => 'any',
] );
$posts = get_posts(
array(
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
'name' => sanitize_title( $slug ),
'posts_per_page' => 1,
'post_status' => 'any',
)
);
return ! empty( $posts ) ? $this->post_to_dto( $posts[0] ) : null;
}
@@ -56,14 +70,16 @@ class PR_Core_Peptide_Repository {
public function search( string $query, int $limit = 20 ): array {
$query = sanitize_text_field( $query );
$posts = get_posts( [
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
's' => $query,
'posts_per_page' => $limit,
'post_status' => 'publish',
] );
$posts = get_posts(
array(
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
's' => $query,
'posts_per_page' => $limit,
'post_status' => 'publish',
)
);
return array_map( [ $this, 'post_to_dto' ], $posts );
return array_map( array( $this, 'post_to_dto' ), $posts );
}
/**
@@ -73,40 +89,44 @@ class PR_Core_Peptide_Repository {
* evidence_strength, per_page, page.
* @return PR_Core_Peptide_DTO[]
*/
public function find_all( array $filters = [] ): array {
$args = [
public function find_all( array $filters = array() ): array {
$args = array(
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
'posts_per_page' => (int) ( $filters['per_page'] ?? 100 ),
'paged' => (int) ( $filters['page'] ?? 1 ),
'orderby' => 'title',
'order' => 'ASC',
];
);
$args['post_status'] = $filters['status'] ?? 'publish';
if ( ! empty( $filters['category'] ) ) {
$args['tax_query'] = [ [
'taxonomy' => PR_Core_Peptide_CPT::TAX_CATEGORY,
'field' => 'slug',
'terms' => sanitize_text_field( $filters['category'] ),
] ];
$args['tax_query'] = array(
array(
'taxonomy' => PR_Core_Peptide_CPT::TAX_CATEGORY,
'field' => 'slug',
'terms' => sanitize_text_field( $filters['category'] ),
),
);
}
// v0.2.0: `family` filter silently ignored — `pr_peptide_family` taxonomy
// was removed with the CPT consolidation. Callers passing `family` get
// all-category results rather than a fatal. Remove this key from the
// v0.2.0: `family` filter silently ignored — `pr_peptide_family` taxonomy.
// was removed with the CPT consolidation. Callers passing `family` get.
// all-category results rather than a fatal. Remove this key from the.
// REST schema in a future minor bump.
if ( ! empty( $filters['evidence_strength'] ) ) {
$args['meta_query'] = [ [
'key' => 'evidence_strength',
'value' => sanitize_text_field( $filters['evidence_strength'] ),
] ];
$args['meta_query'] = array(
array(
'key' => 'evidence_strength',
'value' => sanitize_text_field( $filters['evidence_strength'] ),
),
);
}
$posts = get_posts( $args );
return array_map( [ $this, 'post_to_dto' ], $posts );
return array_map( array( $this, 'post_to_dto' ), $posts );
}
/**
@@ -128,34 +148,36 @@ class PR_Core_Peptide_Repository {
*/
private function post_to_dto( \WP_Post $post ): PR_Core_Peptide_DTO {
$aliases_raw = get_post_meta( $post->ID, 'aliases', true );
$aliases = json_decode( $aliases_raw ?: '[]', true ) ?: [];
$aliases = json_decode( $aliases_raw ?: '[]', true ) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$categories = wp_get_post_terms( $post->ID, PR_Core_Peptide_CPT::TAX_CATEGORY, [ 'fields' => 'names' ] );
// v0.2.0: `pr_peptide_family` taxonomy removed. DTO `families` field
// preserved as empty array to keep the REST response shape stable for
$categories = wp_get_post_terms( $post->ID, PR_Core_Peptide_CPT::TAX_CATEGORY, array( 'fields' => 'names' ) );
// v0.2.0: `pr_peptide_family` taxonomy removed. DTO `families` field.
// preserved as empty array to keep the REST response shape stable for.
// clients; will be dropped in a future minor bump with a release note.
$families = [];
$families = array();
return new PR_Core_Peptide_DTO( [
'id' => $post->ID,
'title' => $post->post_title,
'slug' => $post->post_name,
'content' => $post->post_content,
'excerpt' => $post->post_excerpt,
'status' => $post->post_status,
'display_name' => get_post_meta( $post->ID, 'display_name', true ) ?: '',
'aliases' => $aliases,
'molecular_formula' => get_post_meta( $post->ID, 'molecular_formula', true ) ?: '',
'molecular_weight' => (float) get_post_meta( $post->ID, 'molecular_weight', true ),
'cas_number' => get_post_meta( $post->ID, 'cas_number', true ) ?: '',
'drugbank_id' => get_post_meta( $post->ID, 'drugbank_id', true ) ?: '',
'chembl_id' => get_post_meta( $post->ID, 'chembl_id', true ) ?: '',
'evidence_strength' => get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical',
'editorial_review_status' => get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft',
'last_editorial_review_at' => get_post_meta( $post->ID, 'last_editorial_review_at', true ) ?: '',
'medical_editor_id' => (int) get_post_meta( $post->ID, 'medical_editor_id', true ),
'categories' => is_array( $categories ) ? $categories : [],
'families' => $families,
] );
return new PR_Core_Peptide_DTO(
array(
'id' => $post->ID,
'title' => $post->post_title,
'slug' => $post->post_name,
'content' => $post->post_content,
'excerpt' => $post->post_excerpt,
'status' => $post->post_status,
'display_name' => get_post_meta( $post->ID, 'display_name', true ) ?: '', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'aliases' => $aliases,
'molecular_formula' => get_post_meta( $post->ID, 'molecular_formula', true ) ?: '', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'molecular_weight' => (float) get_post_meta( $post->ID, 'molecular_weight', true ),
'cas_number' => get_post_meta( $post->ID, 'cas_number', true ) ?: '', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'drugbank_id' => get_post_meta( $post->ID, 'drugbank_id', true ) ?: '', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'chembl_id' => get_post_meta( $post->ID, 'chembl_id', true ) ?: '', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'evidence_strength' => get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'editorial_review_status' => get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'last_editorial_review_at' => get_post_meta( $post->ID, 'last_editorial_review_at', true ) ?: '', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'medical_editor_id' => (int) get_post_meta( $post->ID, 'medical_editor_id', true ),
'categories' => is_array( $categories ) ? $categories : array(),
'families' => $families,
)
);
}
}