feat: initial peptide-repo-core plugin (v0.1.0) — canonical schema sprint
Implements ADR-0002: canonical peptide schema as shared data layer for the peptiderepo.com ecosystem. All Tier 1 tools (Reconstitution Calculator, Dosage Reference, Legal Status Tracker, PSA enhancements) build on this. Includes: - pr_peptide CPT with REST, taxonomies, 11 meta fields - 3 custom tables: pr_dosing_rows, pr_legal_cells, pr_ai_candidate_queue - Sequential migration runner with schema versioning - 4 typed DTOs and 4 repository classes (full CRUD) - REST API (pr-core/v1): 6 endpoints (read public, write auth-gated) - Admin UI: 3 meta boxes, custom columns, AI candidate queue page - Shared disclaimer component (shortcode + static API) - JSON-LD Drug schema emission on single peptide pages - Seed data fixture (3 peptides, 10 dosing rows, 5 legal cells) - Full teardown in uninstall.php - CI: PHP lint 8.0-8.2, PHPCS WordPress, 300-line check All 22 PHP files under 300 lines. Highest: peptide-cpt at 265. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
peptiderepo
95
includes/dto/class-pr-core-candidate-dto.php
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95
includes/dto/class-pr-core-candidate-dto.php
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<?php
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declare(strict_types=1);
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/**
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* Typed data-transfer object for an AI candidate queue entry.
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*
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* What: Immutable value object wrapping a row from pr_ai_candidate_queue.
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* Who calls it: PR_Core_Candidate_Queue_Repository returns these.
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* Dependencies: None.
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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 repositories/class-pr-core-candidate-queue-repository.php — Creates these.
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*/
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class PR_Core_Candidate_DTO {
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public readonly int $id;
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public readonly int $peptide_id;
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public readonly ?float $dose_min;
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public readonly ?float $dose_max;
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public readonly string $dose_unit;
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public readonly string $route;
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public readonly ?string $frequency;
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public readonly ?int $duration_value;
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public readonly ?string $duration_unit;
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public readonly string $population;
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public readonly ?string $indication;
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public readonly string $evidence_strength;
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public readonly ?string $study_title;
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public readonly ?int $study_year;
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public readonly ?string $citation_pubmed_id;
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public readonly ?string $citation_doi;
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public readonly ?string $citation_url;
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public readonly ?string $notes;
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public readonly float $extraction_confidence;
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public readonly string $queue_status;
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public readonly string $extracted_at;
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public readonly ?int $reviewed_by;
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public readonly ?string $reviewed_at;
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public readonly ?string $reviewer_notes;
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/**
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* @param array<string, mixed> $data Associative array from database row.
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*/
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public function __construct( array $data ) {
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$this->id = (int) ( $data['id'] ?? 0 );
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$this->peptide_id = (int) ( $data['peptide_id'] ?? 0 );
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$this->dose_min = isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null;
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$this->dose_max = isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null;
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$this->dose_unit = (string) ( $data['dose_unit'] ?? '' );
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$this->route = (string) ( $data['route'] ?? '' );
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$this->frequency = $data['frequency'] ?? null;
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$this->duration_value = isset( $data['duration_value'] ) ? (int) $data['duration_value'] : null;
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$this->duration_unit = $data['duration_unit'] ?? null;
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$this->population = (string) ( $data['population'] ?? '' );
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$this->indication = $data['indication'] ?? null;
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$this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' );
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$this->study_title = $data['study_title'] ?? null;
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$this->study_year = isset( $data['study_year'] ) ? (int) $data['study_year'] : null;
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$this->citation_pubmed_id = $data['citation_pubmed_id'] ?? null;
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$this->citation_doi = $data['citation_doi'] ?? null;
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$this->citation_url = $data['citation_url'] ?? null;
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$this->notes = $data['notes'] ?? null;
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$this->extraction_confidence = (float) ( $data['extraction_confidence'] ?? 0 );
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$this->queue_status = (string) ( $data['queue_status'] ?? 'pending' );
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$this->extracted_at = (string) ( $data['extracted_at'] ?? '' );
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$this->reviewed_by = isset( $data['reviewed_by'] ) ? (int) $data['reviewed_by'] : null;
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$this->reviewed_at = $data['reviewed_at'] ?? null;
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$this->reviewer_notes = $data['reviewer_notes'] ?? null;
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}
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/**
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* Convert to associative array for admin UI output.
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*
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* @return array<string, mixed>
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*/
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public function to_array(): array {
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return [
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'id' => $this->id,
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'peptide_id' => $this->peptide_id,
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'dose_min' => $this->dose_min,
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'dose_max' => $this->dose_max,
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'dose_unit' => $this->dose_unit,
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'route' => $this->route,
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'frequency' => $this->frequency,
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'population' => $this->population,
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'indication' => $this->indication,
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'evidence_strength' => $this->evidence_strength,
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'study_title' => $this->study_title,
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'citation_pubmed_id' => $this->citation_pubmed_id,
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'extraction_confidence' => $this->extraction_confidence,
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'queue_status' => $this->queue_status,
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'extracted_at' => $this->extracted_at,
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];
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}
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}
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104
includes/dto/class-pr-core-dosing-row-dto.php
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104
includes/dto/class-pr-core-dosing-row-dto.php
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<?php
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declare(strict_types=1);
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/**
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* Typed data-transfer object for a dosing row.
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*
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* What: Immutable value object wrapping a row from pr_dosing_rows.
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* Who calls it: PR_Core_Dosing_Repository returns these; consumers read them.
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* Dependencies: None.
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*
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* @see migrations/class-pr-core-migration-0001-dosing-rows.php — Table schema.
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* @see repositories/class-pr-core-dosing-repository.php — Creates these from DB rows.
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*/
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class PR_Core_Dosing_Row_DTO {
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public readonly int $id;
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public readonly int $peptide_id;
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public readonly ?float $dose_min;
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public readonly ?float $dose_max;
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public readonly string $dose_unit;
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public readonly string $route;
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public readonly ?string $frequency;
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public readonly ?int $duration_value;
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public readonly ?string $duration_unit;
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public readonly string $population;
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public readonly ?string $indication;
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public readonly string $evidence_strength;
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public readonly ?string $study_title;
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public readonly ?int $study_year;
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public readonly ?string $citation_pubmed_id;
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public readonly ?string $citation_doi;
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public readonly ?string $citation_url;
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public readonly ?string $notes;
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public readonly int $schema_version;
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public readonly string $source;
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public readonly ?int $ai_candidate_id;
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public readonly int $added_by;
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public readonly string $added_at;
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public readonly ?int $reviewed_by;
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public readonly ?string $reviewed_at;
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public readonly ?int $superseded_by_id;
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/**
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* @param array<string, mixed> $data Associative array from database row.
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*/
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public function __construct( array $data ) {
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$this->id = (int) ( $data['id'] ?? 0 );
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$this->peptide_id = (int) ( $data['peptide_id'] ?? 0 );
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$this->dose_min = isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null;
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$this->dose_max = isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null;
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$this->dose_unit = (string) ( $data['dose_unit'] ?? '' );
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$this->route = (string) ( $data['route'] ?? '' );
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$this->frequency = $data['frequency'] ?? null;
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$this->duration_value = isset( $data['duration_value'] ) ? (int) $data['duration_value'] : null;
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$this->duration_unit = $data['duration_unit'] ?? null;
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$this->population = (string) ( $data['population'] ?? '' );
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$this->indication = $data['indication'] ?? null;
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$this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' );
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$this->study_title = $data['study_title'] ?? null;
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$this->study_year = isset( $data['study_year'] ) ? (int) $data['study_year'] : null;
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$this->citation_pubmed_id = $data['citation_pubmed_id'] ?? null;
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$this->citation_doi = $data['citation_doi'] ?? null;
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$this->citation_url = $data['citation_url'] ?? null;
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$this->notes = $data['notes'] ?? null;
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$this->schema_version = (int) ( $data['schema_version'] ?? 1 );
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$this->source = (string) ( $data['source'] ?? 'manual' );
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$this->ai_candidate_id = isset( $data['ai_candidate_id'] ) ? (int) $data['ai_candidate_id'] : null;
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$this->added_by = (int) ( $data['added_by'] ?? 0 );
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$this->added_at = (string) ( $data['added_at'] ?? '' );
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$this->reviewed_by = isset( $data['reviewed_by'] ) ? (int) $data['reviewed_by'] : null;
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$this->reviewed_at = $data['reviewed_at'] ?? null;
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$this->superseded_by_id = isset( $data['superseded_by_id'] ) ? (int) $data['superseded_by_id'] : null;
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}
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/**
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* Convert to associative array for REST/admin output.
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*
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* @return array<string, mixed>
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*/
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public function to_array(): array {
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return [
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'id' => $this->id,
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'peptide_id' => $this->peptide_id,
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'dose_min' => $this->dose_min,
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'dose_max' => $this->dose_max,
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'dose_unit' => $this->dose_unit,
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'route' => $this->route,
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'frequency' => $this->frequency,
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'duration_value' => $this->duration_value,
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'duration_unit' => $this->duration_unit,
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'population' => $this->population,
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'indication' => $this->indication,
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'evidence_strength' => $this->evidence_strength,
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'study_title' => $this->study_title,
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'study_year' => $this->study_year,
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'citation_pubmed_id' => $this->citation_pubmed_id,
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'citation_doi' => $this->citation_doi,
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'citation_url' => $this->citation_url,
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'notes' => $this->notes,
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'source' => $this->source,
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'added_at' => $this->added_at,
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];
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}
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}
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75
includes/dto/class-pr-core-legal-cell-dto.php
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75
includes/dto/class-pr-core-legal-cell-dto.php
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<?php
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declare(strict_types=1);
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/**
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* Typed data-transfer object for a legal status cell.
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*
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* What: Immutable value object wrapping a row from pr_legal_cells.
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* Who calls it: PR_Core_Legal_Repository returns these; consumers read them.
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* Dependencies: None.
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*
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* @see migrations/class-pr-core-migration-0002-legal-cells.php — Table schema.
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* @see repositories/class-pr-core-legal-repository.php — Creates these from DB rows.
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*/
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class PR_Core_Legal_Cell_DTO {
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public readonly int $id;
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public readonly int $peptide_id;
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public readonly string $country_code;
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public readonly string $status;
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public readonly ?string $regulatory_framework;
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public readonly ?string $regulatory_text_url;
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public readonly ?string $regulatory_text_quote;
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public readonly ?string $notes;
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public readonly string $last_verified_at;
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public readonly int $schema_version;
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public readonly int $reviewer_id;
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public readonly ?int $superseded_by_id;
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/**
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* @param array<string, mixed> $data Associative array from database row.
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*/
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public function __construct( array $data ) {
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$this->id = (int) ( $data['id'] ?? 0 );
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$this->peptide_id = (int) ( $data['peptide_id'] ?? 0 );
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$this->country_code = (string) ( $data['country_code'] ?? '' );
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$this->status = (string) ( $data['status'] ?? 'unclear' );
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$this->regulatory_framework = $data['regulatory_framework'] ?? null;
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$this->regulatory_text_url = $data['regulatory_text_url'] ?? null;
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$this->regulatory_text_quote = $data['regulatory_text_quote'] ?? null;
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$this->notes = $data['notes'] ?? null;
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$this->last_verified_at = (string) ( $data['last_verified_at'] ?? '' );
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$this->schema_version = (int) ( $data['schema_version'] ?? 1 );
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$this->reviewer_id = (int) ( $data['reviewer_id'] ?? 0 );
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$this->superseded_by_id = isset( $data['superseded_by_id'] ) ? (int) $data['superseded_by_id'] : null;
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}
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/**
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* Check if this cell is the active (non-superseded) version.
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*
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* @return bool
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*/
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public function is_active(): bool {
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return null === $this->superseded_by_id;
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}
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/**
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* Convert to associative array for REST/admin output.
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*
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* @return array<string, mixed>
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*/
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public function to_array(): array {
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return [
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'id' => $this->id,
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'peptide_id' => $this->peptide_id,
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'country_code' => $this->country_code,
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'status' => $this->status,
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'regulatory_framework' => $this->regulatory_framework,
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'regulatory_text_url' => $this->regulatory_text_url,
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'regulatory_text_quote' => $this->regulatory_text_quote,
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'notes' => $this->notes,
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'last_verified_at' => $this->last_verified_at,
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'is_active' => $this->is_active(),
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];
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}
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}
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91
includes/dto/class-pr-core-peptide-dto.php
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91
includes/dto/class-pr-core-peptide-dto.php
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<?php
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declare(strict_types=1);
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/**
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* Typed data-transfer object for a peptide record.
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*
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* What: Immutable value object wrapping a pr_peptide post + its meta fields.
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* Who calls it: PR_Core_Peptide_Repository returns these; consumers read them.
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* Dependencies: None.
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*
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* @see cpt/class-pr-core-peptide-cpt.php — Meta field definitions.
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* @see repositories/class-pr-core-peptide-repository.php — Creates these from WP_Post.
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*/
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class PR_Core_Peptide_DTO {
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public readonly int $id;
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public readonly string $title;
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public readonly string $slug;
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public readonly string $content;
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public readonly string $excerpt;
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public readonly string $status;
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public readonly string $display_name;
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/** @var string[] */
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public readonly array $aliases;
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public readonly string $molecular_formula;
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public readonly float $molecular_weight;
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public readonly string $cas_number;
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public readonly string $drugbank_id;
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public readonly string $chembl_id;
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public readonly string $evidence_strength;
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public readonly string $editorial_review_status;
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public readonly string $last_editorial_review_at;
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public readonly int $medical_editor_id;
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/** @var string[] Category term names. */
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public readonly array $categories;
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/** @var string[] Family term names. */
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public readonly array $families;
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/**
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* @param array<string, mixed> $data Associative array of peptide fields.
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*/
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public function __construct( array $data ) {
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$this->id = (int) ( $data['id'] ?? 0 );
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$this->title = (string) ( $data['title'] ?? '' );
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$this->slug = (string) ( $data['slug'] ?? '' );
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$this->content = (string) ( $data['content'] ?? '' );
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$this->excerpt = (string) ( $data['excerpt'] ?? '' );
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$this->status = (string) ( $data['status'] ?? 'draft' );
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$this->display_name = (string) ( $data['display_name'] ?? '' );
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$this->aliases = (array) ( $data['aliases'] ?? [] );
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$this->molecular_formula = (string) ( $data['molecular_formula'] ?? '' );
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$this->molecular_weight = (float) ( $data['molecular_weight'] ?? 0 );
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$this->cas_number = (string) ( $data['cas_number'] ?? '' );
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$this->drugbank_id = (string) ( $data['drugbank_id'] ?? '' );
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$this->chembl_id = (string) ( $data['chembl_id'] ?? '' );
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$this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' );
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$this->editorial_review_status = (string) ( $data['editorial_review_status'] ?? 'draft' );
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$this->last_editorial_review_at = (string) ( $data['last_editorial_review_at'] ?? '' );
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$this->medical_editor_id = (int) ( $data['medical_editor_id'] ?? 0 );
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$this->categories = (array) ( $data['categories'] ?? [] );
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$this->families = (array) ( $data['families'] ?? [] );
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}
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/**
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* Convert to associative array (e.g., for REST API responses).
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*
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* @return array<string, mixed>
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*/
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public function to_array(): array {
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return [
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'id' => $this->id,
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'title' => $this->title,
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'slug' => $this->slug,
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'excerpt' => $this->excerpt,
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'display_name' => $this->display_name,
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'aliases' => $this->aliases,
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'molecular_formula' => $this->molecular_formula,
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'molecular_weight' => $this->molecular_weight,
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'cas_number' => $this->cas_number,
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'drugbank_id' => $this->drugbank_id,
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'chembl_id' => $this->chembl_id,
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'evidence_strength' => $this->evidence_strength,
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'editorial_review_status' => $this->editorial_review_status,
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'last_editorial_review_at' => $this->last_editorial_review_at,
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'medical_editor_id' => $this->medical_editor_id,
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'categories' => $this->categories,
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'families' => $this->families,
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'url' => get_permalink( $this->id ),
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];
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}
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}
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