peptide-repo/peptide-repo-core
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Adopt reusable CI standard + PHPUnit conversion (#22)

Browse Source 
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
Download Patch File Download Diff File Expand all files Collapse all files

90
includes/repositories/class-pr-core-candidate-queue-repository.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Candidate Queue Repository.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* CRUD for AI-extracted dosing candidates awaiting human review
*
* @package Peptide_Repo_Core
*/
/**
* Repository for AI candidate queue (pr_ai_candidate_queue table).
*
@@ -28,7 +40,7 @@ class PR_Core_Candidate_Queue_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$row = $wpdb->get_row(
$wpdb->prepare( "SELECT * FROM {$table} WHERE id = %d", $id ),
$wpdb->prepare( "SELECT * FROM {$table} WHERE id = %d", $id ), // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
ARRAY_A
);
@@ -47,25 +59,25 @@ class PR_Core_Candidate_Queue_Repository {
global $wpdb;
$table = $wpdb->prefix . 'pr_ai_candidate_queue';
$where = [ 'queue_status = %s' ];
$params = [ sanitize_text_field( $status ) ];
$where = array( 'queue_status = %s' );
$params = array( sanitize_text_field( $status ) );
if ( $peptide_id > 0 ) {
$where[] = 'peptide_id = %d';
$params[] = $peptide_id;
}
$params[] = $limit;
$params[] = $limit;
$where_sql = implode( ' AND ', $where );
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$rows = $wpdb->get_results(
$wpdb->prepare(
"SELECT * FROM {$table} WHERE {$where_sql} ORDER BY extraction_confidence DESC LIMIT %d",
"SELECT * FROM {$table} WHERE {$where_sql} ORDER BY extraction_confidence DESC LIMIT %d", // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
...$params
),
ARRAY_A
) ?: [];
) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
return array_map(
static fn( array $row ) => new PR_Core_Candidate_DTO( $row ),
@@ -85,7 +97,7 @@ class PR_Core_Candidate_Queue_Repository {
global $wpdb;
$table = $wpdb->prefix . 'pr_ai_candidate_queue';
$row = [
$row = array(
'peptide_id' => absint( $data['peptide_id'] ?? 0 ),
'dose_min' => isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null,
'dose_max' => isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null,
@@ -106,7 +118,7 @@ class PR_Core_Candidate_Queue_Repository {
'extraction_confidence' => (float) ( $data['extraction_confidence'] ?? 0 ),
'queue_status' => 'pending',
'extracted_at' => current_time( 'mysql' ),
];
);
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$result = $wpdb->insert( $table, $row );
@@ -134,30 +146,32 @@ class PR_Core_Candidate_Queue_Repository {
// Copy candidate data into a dosing row.
$dosing_repo = new PR_Core_Dosing_Repository();
$dosing_id = $dosing_repo->insert( [
'peptide_id' => $candidate->peptide_id,
'dose_min' => $candidate->dose_min,
'dose_max' => $candidate->dose_max,
'dose_unit' => $candidate->dose_unit,
'route' => $candidate->route,
'frequency' => $candidate->frequency,
'duration_value' => $candidate->duration_value,
'duration_unit' => $candidate->duration_unit,
'population' => $candidate->population,
'indication' => $candidate->indication,
'evidence_strength' => $candidate->evidence_strength,
'study_title' => $candidate->study_title,
'study_year' => $candidate->study_year,
'citation_pubmed_id' => $candidate->citation_pubmed_id,
'citation_doi' => $candidate->citation_doi,
'citation_url' => $candidate->citation_url,
'notes' => $candidate->notes,
'source' => 'ai-candidate-approved',
'ai_candidate_id' => $candidate_id,
'added_by' => $reviewer_id,
'reviewed_by' => $reviewer_id,
'reviewed_at' => current_time( 'mysql' ),
] );
$dosing_id = $dosing_repo->insert(
array(
'peptide_id' => $candidate->peptide_id,
'dose_min' => $candidate->dose_min,
'dose_max' => $candidate->dose_max,
'dose_unit' => $candidate->dose_unit,
'route' => $candidate->route,
'frequency' => $candidate->frequency,
'duration_value' => $candidate->duration_value,
'duration_unit' => $candidate->duration_unit,
'population' => $candidate->population,
'indication' => $candidate->indication,
'evidence_strength' => $candidate->evidence_strength,
'study_title' => $candidate->study_title,
'study_year' => $candidate->study_year,
'citation_pubmed_id' => $candidate->citation_pubmed_id,
'citation_doi' => $candidate->citation_doi,
'citation_url' => $candidate->citation_url,
'notes' => $candidate->notes,
'source' => 'ai-candidate-approved',
'ai_candidate_id' => $candidate_id,
'added_by' => $reviewer_id,
'reviewed_by' => $reviewer_id,
'reviewed_at' => current_time( 'mysql' ),
)
);
if ( 0 === $dosing_id ) {
return 0;
@@ -204,7 +218,7 @@ class PR_Core_Candidate_Queue_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
return (int) $wpdb->get_var(
$wpdb->prepare( "SELECT COUNT(*) FROM {$table} WHERE queue_status = %s", $status )
$wpdb->prepare( "SELECT COUNT(*) FROM {$table} WHERE queue_status = %s", $status ) // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
);
}
@@ -224,15 +238,15 @@ class PR_Core_Candidate_Queue_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$result = $wpdb->update(
$table,
[
array(
'queue_status' => sanitize_text_field( $status ),
'reviewed_by' => $reviewer_id,
'reviewed_at' => current_time( 'mysql' ),
'reviewer_notes' => sanitize_textarea_field( $notes ),
],
[ 'id' => $id ],
[ '%s', '%d', '%s', '%s' ],
[ '%d' ]
),
array( 'id' => $id ),
array( '%s', '%d', '%s', '%s' ),
array( '%d' )
);
return false !== $result;