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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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138
includes/dto/class-pr-core-candidate-dto.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Candidate Dto.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Immutable value object wrapping a row from pr_ai_candidate_queue
*
* @package Peptide_Repo_Core
*/
/**
* Typed data-transfer object for an AI candidate queue entry.
*
@@ -13,32 +25,154 @@ declare(strict_types=1);
*/
class PR_Core_Candidate_DTO {
/**
* Int.
*
* @var int
*/
public readonly int $id;
/**
* Int.
*
* @var int
*/
public readonly int $peptide_id;
/**
* ?float.
*
* @var ?float
*/
public readonly ?float $dose_min;
/**
* ?float.
*
* @var ?float
*/
public readonly ?float $dose_max;
/**
* String.
*
* @var string
*/
public readonly string $dose_unit;
/**
* String.
*
* @var string
*/
public readonly string $route;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $frequency;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $duration_value;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $duration_unit;
/**
* String.
*
* @var string
*/
public readonly string $population;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $indication;
/**
* String.
*
* @var string
*/
public readonly string $evidence_strength;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $study_title;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $study_year;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $citation_pubmed_id;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $citation_doi;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $citation_url;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $notes;
/**
* Float.
*
* @var float
*/
public readonly float $extraction_confidence;
/**
* String.
*
* @var string
*/
public readonly string $queue_status;
/**
* String.
*
* @var string
*/
public readonly string $extracted_at;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $reviewed_by;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $reviewed_at;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $reviewer_notes;
/**
* Construct.
*
* @param array<string, mixed> $data Associative array from database row.
*/
public function __construct( array $data ) {
@@ -74,7 +208,7 @@ class PR_Core_Candidate_DTO {
* @return array<string, mixed>
*/
public function to_array(): array {
return [
return array(
'id' => $this->id,
'peptide_id' => $this->peptide_id,
'dose_min' => $this->dose_min,
@@ -90,6 +224,6 @@ class PR_Core_Candidate_DTO {
'extraction_confidence' => $this->extraction_confidence,
'queue_status' => $this->queue_status,
'extracted_at' => $this->extracted_at,
];
);
}
}

240
includes/dto/class-pr-core-dosing-row-dto.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Dosing Row Dto.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Immutable value object wrapping a row from pr_dosing_rows
*
* @package Peptide_Repo_Core
*/
/**
* Typed data-transfer object for a dosing row.
*
@@ -13,63 +25,195 @@ declare(strict_types=1);
*/
class PR_Core_Dosing_Row_DTO {
/**
* Int.
*
* @var int
*/
public readonly int $id;
/**
* Int.
*
* @var int
*/
public readonly int $peptide_id;
/**
* ?float.
*
* @var ?float
*/
public readonly ?float $dose_min;
/**
* ?float.
*
* @var ?float
*/
public readonly ?float $dose_max;
/**
* String.
*
* @var string
*/
public readonly string $dose_unit;
/**
* String.
*
* @var string
*/
public readonly string $route;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $frequency;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $duration_value;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $duration_unit;
/**
* String.
*
* @var string
*/
public readonly string $population;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $indication;
/**
* String.
*
* @var string
*/
public readonly string $evidence_strength;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $study_title;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $study_year;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $citation_pubmed_id;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $citation_doi;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $citation_url;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $notes;
/**
* Int.
*
* @var int
*/
public readonly int $schema_version;
/**
* String.
*
* @var string
*/
public readonly string $source;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $ai_candidate_id;
/**
* Int.
*
* @var int
*/
public readonly int $added_by;
/**
* String.
*
* @var string
*/
public readonly string $added_at;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $reviewed_by;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $reviewed_at;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $superseded_by_id;
/**
* Construct.
*
* @param array<string, mixed> $data Associative array from database row.
*/
public function __construct( array $data ) {
$this->id = (int) ( $data['id'] ?? 0 );
$this->peptide_id = (int) ( $data['peptide_id'] ?? 0 );
$this->dose_min = isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null;
$this->dose_max = isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null;
$this->dose_unit = (string) ( $data['dose_unit'] ?? '' );
$this->route = (string) ( $data['route'] ?? '' );
$this->frequency = $data['frequency'] ?? null;
$this->duration_value = isset( $data['duration_value'] ) ? (int) $data['duration_value'] : null;
$this->duration_unit = $data['duration_unit'] ?? null;
$this->population = (string) ( $data['population'] ?? '' );
$this->indication = $data['indication'] ?? null;
$this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' );
$this->study_title = $data['study_title'] ?? null;
$this->study_year = isset( $data['study_year'] ) ? (int) $data['study_year'] : null;
$this->citation_pubmed_id = $data['citation_pubmed_id'] ?? null;
$this->citation_doi = $data['citation_doi'] ?? null;
$this->citation_url = $data['citation_url'] ?? null;
$this->notes = $data['notes'] ?? null;
$this->schema_version = (int) ( $data['schema_version'] ?? 1 );
$this->source = (string) ( $data['source'] ?? 'manual' );
$this->ai_candidate_id = isset( $data['ai_candidate_id'] ) ? (int) $data['ai_candidate_id'] : null;
$this->added_by = (int) ( $data['added_by'] ?? 0 );
$this->added_at = (string) ( $data['added_at'] ?? '' );
$this->reviewed_by = isset( $data['reviewed_by'] ) ? (int) $data['reviewed_by'] : null;
$this->reviewed_at = $data['reviewed_at'] ?? null;
$this->superseded_by_id = isset( $data['superseded_by_id'] ) ? (int) $data['superseded_by_id'] : null;
$this->id = (int) ( $data['id'] ?? 0 );
$this->peptide_id = (int) ( $data['peptide_id'] ?? 0 );
$this->dose_min = isset( $data['dose_min'] ) ? (float) $data['dose_min'] : null;
$this->dose_max = isset( $data['dose_max'] ) ? (float) $data['dose_max'] : null;
$this->dose_unit = (string) ( $data['dose_unit'] ?? '' );
$this->route = (string) ( $data['route'] ?? '' );
$this->frequency = $data['frequency'] ?? null;
$this->duration_value = isset( $data['duration_value'] ) ? (int) $data['duration_value'] : null;
$this->duration_unit = $data['duration_unit'] ?? null;
$this->population = (string) ( $data['population'] ?? '' );
$this->indication = $data['indication'] ?? null;
$this->evidence_strength = (string) ( $data['evidence_strength'] ?? 'preclinical' );
$this->study_title = $data['study_title'] ?? null;
$this->study_year = isset( $data['study_year'] ) ? (int) $data['study_year'] : null;
$this->citation_pubmed_id = $data['citation_pubmed_id'] ?? null;
$this->citation_doi = $data['citation_doi'] ?? null;
$this->citation_url = $data['citation_url'] ?? null;
$this->notes = $data['notes'] ?? null;
$this->schema_version = (int) ( $data['schema_version'] ?? 1 );
$this->source = (string) ( $data['source'] ?? 'manual' );
$this->ai_candidate_id = isset( $data['ai_candidate_id'] ) ? (int) $data['ai_candidate_id'] : null;
$this->added_by = (int) ( $data['added_by'] ?? 0 );
$this->added_at = (string) ( $data['added_at'] ?? '' );
$this->reviewed_by = isset( $data['reviewed_by'] ) ? (int) $data['reviewed_by'] : null;
$this->reviewed_at = $data['reviewed_at'] ?? null;
$this->superseded_by_id = isset( $data['superseded_by_id'] ) ? (int) $data['superseded_by_id'] : null;
}
/**
@@ -78,27 +222,27 @@ class PR_Core_Dosing_Row_DTO {
* @return array<string, mixed>
*/
public function to_array(): array {
return [
'id' => $this->id,
'peptide_id' => $this->peptide_id,
'dose_min' => $this->dose_min,
'dose_max' => $this->dose_max,
'dose_unit' => $this->dose_unit,
'route' => $this->route,
'frequency' => $this->frequency,
'duration_value' => $this->duration_value,
'duration_unit' => $this->duration_unit,
'population' => $this->population,
'indication' => $this->indication,
'evidence_strength' => $this->evidence_strength,
'study_title' => $this->study_title,
'study_year' => $this->study_year,
'citation_pubmed_id' => $this->citation_pubmed_id,
'citation_doi' => $this->citation_doi,
'citation_url' => $this->citation_url,
'notes' => $this->notes,
'source' => $this->source,
'added_at' => $this->added_at,
];
return array(
'id' => $this->id,
'peptide_id' => $this->peptide_id,
'dose_min' => $this->dose_min,
'dose_max' => $this->dose_max,
'dose_unit' => $this->dose_unit,
'route' => $this->route,
'frequency' => $this->frequency,
'duration_value' => $this->duration_value,
'duration_unit' => $this->duration_unit,
'population' => $this->population,
'indication' => $this->indication,
'evidence_strength' => $this->evidence_strength,
'study_title' => $this->study_title,
'study_year' => $this->study_year,
'citation_pubmed_id' => $this->citation_pubmed_id,
'citation_doi' => $this->citation_doi,
'citation_url' => $this->citation_url,
'notes' => $this->notes,
'source' => $this->source,
'added_at' => $this->added_at,
);
}
}

78
includes/dto/class-pr-core-legal-cell-dto.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Legal Cell Dto.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Immutable value object wrapping a row from pr_legal_cells
*
* @package Peptide_Repo_Core
*/
/**
* Typed data-transfer object for a legal status cell.
*
@@ -13,20 +25,82 @@ declare(strict_types=1);
*/
class PR_Core_Legal_Cell_DTO {
/**
* Int.
*
* @var int
*/
public readonly int $id;
/**
* Int.
*
* @var int
*/
public readonly int $peptide_id;
/**
* String.
*
* @var string
*/
public readonly string $country_code;
/**
* String.
*
* @var string
*/
public readonly string $status;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $regulatory_framework;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $regulatory_text_url;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $regulatory_text_quote;
/**
* ?string.
*
* @var ?string
*/
public readonly ?string $notes;
/**
* String.
*
* @var string
*/
public readonly string $last_verified_at;
/**
* Int.
*
* @var int
*/
public readonly int $schema_version;
/**
* Int.
*
* @var int
*/
public readonly int $reviewer_id;
/**
* ?int.
*
* @var ?int
*/
public readonly ?int $superseded_by_id;
/**
* Construct.
*
* @param array<string, mixed> $data Associative array from database row.
*/
public function __construct( array $data ) {
@@ -59,7 +133,7 @@ class PR_Core_Legal_Cell_DTO {
* @return array<string, mixed>
*/
public function to_array(): array {
return [
return array(
'id' => $this->id,
'peptide_id' => $this->peptide_id,
'country_code' => $this->country_code,
@@ -70,6 +144,6 @@ class PR_Core_Legal_Cell_DTO {
'notes' => $this->notes,
'last_verified_at' => $this->last_verified_at,
'is_active' => $this->is_active(),
];
);
}
}

122
includes/dto/class-pr-core-peptide-dto.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Peptide Dto.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Immutable value object wrapping a peptide post + its meta fields
*
* @package Peptide_Repo_Core
*/
/**
* Typed data-transfer object for a peptide record.
*
@@ -13,30 +25,124 @@ declare(strict_types=1);
*/
class PR_Core_Peptide_DTO {
/**
* Int.
*
* @var int
*/
public readonly int $id;
/**
* String.
*
* @var string
*/
public readonly string $title;
/**
* String.
*
* @var string
*/
public readonly string $slug;
/**
* String.
*
* @var string
*/
public readonly string $content;
/**
* String.
*
* @var string
*/
public readonly string $excerpt;
/**
* String.
*
* @var string
*/
public readonly string $status;
/**
* String.
*
* @var string
*/
public readonly string $display_name;
/** @var string[] */
/**
* String[].
*
* @var string[]
*/
public readonly array $aliases;
/**
* String.
*
* @var string
*/
public readonly string $molecular_formula;
/**
* Float.
*
* @var float
*/
public readonly float $molecular_weight;
/**
* String.
*
* @var string
*/
public readonly string $cas_number;
/**
* String.
*
* @var string
*/
public readonly string $drugbank_id;
/**
* String.
*
* @var string
*/
public readonly string $chembl_id;
/**
* String.
*
* @var string
*/
public readonly string $evidence_strength;
/**
* String.
*
* @var string
*/
public readonly string $editorial_review_status;
/**
* String.
*
* @var string
*/
public readonly string $last_editorial_review_at;
/**
* Int.
*
* @var int
*/
public readonly int $medical_editor_id;
/** @var string[] Category term names. */
/**
* Category term names.
*
* @var string[] Category term names.
*/
public readonly array $categories;
/** @var string[] Family term names. */
/**
* Family term names.
*
* @var string[] Family term names.
*/
public readonly array $families;
/**
* Construct.
*
* @param array<string, mixed> $data Associative array of peptide fields.
*/
public function __construct( array $data ) {
@@ -47,7 +153,7 @@ class PR_Core_Peptide_DTO {
$this->excerpt = (string) ( $data['excerpt'] ?? '' );
$this->status = (string) ( $data['status'] ?? 'draft' );
$this->display_name = (string) ( $data['display_name'] ?? '' );
$this->aliases = (array) ( $data['aliases'] ?? [] );
$this->aliases = (array) ( $data['aliases'] ?? array() );
$this->molecular_formula = (string) ( $data['molecular_formula'] ?? '' );
$this->molecular_weight = (float) ( $data['molecular_weight'] ?? 0 );
$this->cas_number = (string) ( $data['cas_number'] ?? '' );
@@ -57,8 +163,8 @@ class PR_Core_Peptide_DTO {
$this->editorial_review_status = (string) ( $data['editorial_review_status'] ?? 'draft' );
$this->last_editorial_review_at = (string) ( $data['last_editorial_review_at'] ?? '' );
$this->medical_editor_id = (int) ( $data['medical_editor_id'] ?? 0 );
$this->categories = (array) ( $data['categories'] ?? [] );
$this->families = (array) ( $data['families'] ?? [] );
$this->categories = (array) ( $data['categories'] ?? array() );
$this->families = (array) ( $data['families'] ?? array() );
}
/**
@@ -67,7 +173,7 @@ class PR_Core_Peptide_DTO {
* @return array<string, mixed>
*/
public function to_array(): array {
return [
return array(
'id' => $this->id,
'title' => $this->title,
'slug' => $this->slug,
@@ -86,6 +192,6 @@ class PR_Core_Peptide_DTO {
'categories' => $this->categories,
'families' => $this->families,
'url' => get_permalink( $this->id ),
];
);
}
}