53c71dca12
PHPCS Squiz.Commenting.FileComment requires the file docblock to be the FIRST token after the opening <?php tag. Having declare(strict_types=1) before the docblock means PHPCS sees no file docblock at all. Fix: in every includes/*.php file, insert a minimal /** @package ... */ docblock immediately after <?php (no blank line = satisfies SpacingAfterOpen) with a blank line after it (satisfies SpacingAfterComment), then declare() then the class docblock. Also fixes peptide-repo-core.php SpacingAfterOpen/SpacingAfterComment by removing the blank line between <?php and the existing file docblock and ensuring one blank line after it. Agent-Session: claude-adopt-ci-20260616
253 lines
8.9 KiB
PHP
253 lines
8.9 KiB
PHP
<?php
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/**
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* @package Peptide_Repo_Core
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*/
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declare(strict_types=1);
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/**
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* CRUD for AI-extracted dosing candidates awaiting human review
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*
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* @package Peptide_Repo_Core
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*/
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/**
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* Repository for AI candidate queue (pr_ai_candidate_queue table).
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*
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* What: CRUD for AI-extracted dosing candidates awaiting human review.
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* Who calls it: Admin candidate queue page, extraction pipeline (stub).
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* Dependencies: WordPress $wpdb, PR_Core_Candidate_DTO, PR_Core_Dosing_Repository.
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*
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* Flow: Extract (pending) -> Review (approve/reject) -> Merge into dosing rows.
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*
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* @see migrations/class-pr-core-migration-0003-candidate-queue.php — Table schema.
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* @see dto/class-pr-core-candidate-dto.php — Return type.
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* @see admin/class-pr-core-candidate-queue-page.php — Admin UI.
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*/
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class PR_Core_Candidate_Queue_Repository {
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/**
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* Find a single candidate by ID.
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*
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* @param int $id Row ID.
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* @return PR_Core_Candidate_DTO|null
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*/
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public function find_by_id( int $id ): ?PR_Core_Candidate_DTO {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_ai_candidate_queue';
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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$row = $wpdb->get_row(
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$wpdb->prepare( "SELECT * FROM {$table} WHERE id = %d", $id ), // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
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ARRAY_A
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);
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return $row ? new PR_Core_Candidate_DTO( $row ) : null;
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}
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/**
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* Find candidates by status, optionally filtered by peptide.
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*
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* @param string $status Queue status: pending, approved, rejected, merged.
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* @param int $peptide_id Optional peptide filter (0 = all).
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* @param int $limit Max results.
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* @return PR_Core_Candidate_DTO[]
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*/
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public function find_by_status( string $status = 'pending', int $peptide_id = 0, int $limit = 50 ): array {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_ai_candidate_queue';
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$where = array( 'queue_status = %s' );
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$params = array( sanitize_text_field( $status ) );
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if ( $peptide_id > 0 ) {
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$where[] = 'peptide_id = %d';
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$params[] = $peptide_id;
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}
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$params[] = $limit;
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$where_sql = implode( ' AND ', $where );
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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$rows = $wpdb->get_results(
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$wpdb->prepare(
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"SELECT * FROM {$table} WHERE {$where_sql} ORDER BY extraction_confidence DESC LIMIT %d", // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
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...$params
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),
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ARRAY_A
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) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
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return array_map(
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static fn( array $row ) => new PR_Core_Candidate_DTO( $row ),
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$rows
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);
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}
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/**
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* Insert a new candidate into the queue.
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*
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* Side effects: database insert.
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*
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* @param array<string, mixed> $data Candidate data.
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* @return int Inserted row ID, or 0 on failure.
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*/
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public function insert( array $data ): int {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_ai_candidate_queue';
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$row = array(
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'peptide_id' => absint( $data['peptide_id'] ?? 0 ),
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'dose_min' => isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null,
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'dose_max' => isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null,
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'dose_unit' => sanitize_text_field( $data['dose_unit'] ?? '' ),
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'route' => sanitize_text_field( $data['route'] ?? '' ),
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'frequency' => isset( $data['frequency'] ) ? sanitize_text_field( $data['frequency'] ) : null,
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'duration_value' => isset( $data['duration_value'] ) ? absint( $data['duration_value'] ) : null,
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'duration_unit' => isset( $data['duration_unit'] ) ? sanitize_text_field( $data['duration_unit'] ) : null,
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'population' => sanitize_text_field( $data['population'] ?? '' ),
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'indication' => isset( $data['indication'] ) ? sanitize_text_field( $data['indication'] ) : null,
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'evidence_strength' => PR_Core_Peptide_CPT::sanitize_evidence_strength( $data['evidence_strength'] ?? '' ),
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'study_title' => isset( $data['study_title'] ) ? sanitize_text_field( $data['study_title'] ) : null,
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'study_year' => isset( $data['study_year'] ) ? absint( $data['study_year'] ) : null,
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'citation_pubmed_id' => isset( $data['citation_pubmed_id'] ) ? sanitize_text_field( $data['citation_pubmed_id'] ) : null,
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'citation_doi' => isset( $data['citation_doi'] ) ? sanitize_text_field( $data['citation_doi'] ) : null,
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'citation_url' => isset( $data['citation_url'] ) ? esc_url_raw( $data['citation_url'] ) : null,
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'notes' => isset( $data['notes'] ) ? sanitize_textarea_field( $data['notes'] ) : null,
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'extraction_confidence' => (float) ( $data['extraction_confidence'] ?? 0 ),
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'queue_status' => 'pending',
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'extracted_at' => current_time( 'mysql' ),
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);
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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$result = $wpdb->insert( $table, $row );
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return false !== $result ? (int) $wpdb->insert_id : 0;
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}
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/**
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* Approve a candidate: copy to dosing rows, mark as merged.
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*
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* Fires pr_core_candidate_approved action.
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*
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* Side effects: database insert (dosing row) + update (queue row).
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*
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* @param int $candidate_id Queue row ID.
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* @param int $reviewer_id User ID of the reviewer.
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* @param string $notes Optional reviewer notes.
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* @return int New dosing row ID, or 0 on failure.
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*/
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public function approve( int $candidate_id, int $reviewer_id, string $notes = '' ): int {
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$candidate = $this->find_by_id( $candidate_id );
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if ( ! $candidate || 'pending' !== $candidate->queue_status ) {
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return 0;
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}
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// Copy candidate data into a dosing row.
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$dosing_repo = new PR_Core_Dosing_Repository();
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$dosing_id = $dosing_repo->insert(
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array(
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'peptide_id' => $candidate->peptide_id,
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'dose_min' => $candidate->dose_min,
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'dose_max' => $candidate->dose_max,
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'dose_unit' => $candidate->dose_unit,
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'route' => $candidate->route,
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'frequency' => $candidate->frequency,
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'duration_value' => $candidate->duration_value,
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'duration_unit' => $candidate->duration_unit,
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'population' => $candidate->population,
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'indication' => $candidate->indication,
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'evidence_strength' => $candidate->evidence_strength,
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'study_title' => $candidate->study_title,
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'study_year' => $candidate->study_year,
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'citation_pubmed_id' => $candidate->citation_pubmed_id,
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'citation_doi' => $candidate->citation_doi,
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'citation_url' => $candidate->citation_url,
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'notes' => $candidate->notes,
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'source' => 'ai-candidate-approved',
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'ai_candidate_id' => $candidate_id,
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'added_by' => $reviewer_id,
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'reviewed_by' => $reviewer_id,
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'reviewed_at' => current_time( 'mysql' ),
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)
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);
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if ( 0 === $dosing_id ) {
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return 0;
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}
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$this->update_status( $candidate_id, 'merged', $reviewer_id, $notes );
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do_action( 'pr_core_candidate_approved', $candidate_id, $dosing_id );
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return $dosing_id;
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}
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/**
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* Reject a candidate.
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*
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* Fires pr_core_candidate_rejected action.
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*
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* Side effects: database update.
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*
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* @param int $candidate_id Queue row ID.
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* @param int $reviewer_id User ID.
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* @param string $notes Rejection reason.
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* @return bool
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*/
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public function reject( int $candidate_id, int $reviewer_id, string $notes = '' ): bool {
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$result = $this->update_status( $candidate_id, 'rejected', $reviewer_id, $notes );
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if ( $result ) {
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do_action( 'pr_core_candidate_rejected', $candidate_id );
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}
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return $result;
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}
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/**
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* Count candidates by status.
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*
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* @param string $status Queue status.
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* @return int
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*/
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public function count_by_status( string $status = 'pending' ): int {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_ai_candidate_queue';
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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return (int) $wpdb->get_var(
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$wpdb->prepare( "SELECT COUNT(*) FROM {$table} WHERE queue_status = %s", $status ) // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
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);
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}
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/**
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* Update a candidate's queue status.
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*
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* @param int $id Row ID.
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* @param string $status New status.
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* @param int $reviewer_id Reviewer user ID.
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* @param string $notes Optional notes.
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* @return bool
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*/
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private function update_status( int $id, string $status, int $reviewer_id, string $notes ): bool {
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global $wpdb;
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$table = $wpdb->prefix . 'pr_ai_candidate_queue';
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// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
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$result = $wpdb->update(
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$table,
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array(
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'queue_status' => sanitize_text_field( $status ),
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'reviewed_by' => $reviewer_id,
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'reviewed_at' => current_time( 'mysql' ),
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'reviewer_notes' => sanitize_textarea_field( $notes ),
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),
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array( 'id' => $id ),
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array( '%s', '%d', '%s', '%s' ),
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array( '%d' )
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);
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return false !== $result;
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}
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}
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