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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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87
.github/workflows/ci.yml vendored
View File

@@ -1,78 +1,27 @@
##
# Thin CI caller — peptide-repo-core
#
# Delegates all lint/test/file-size jobs to the estate reusable workflow.
# Per estate standard: workflow_call is required so deploy.yml can gate on it.
# See: peptiderepo/peptide-e2e/.github/workflows/ci.yml@main for job definitions.
##
name: CI
on:
pull_request: {}
push:
branches: [ main ]
pull_request:
branches: [ main ]
workflow_call:
branches: [main]
workflow_call: {}
# Required: calling workflow must declare contents: write so the reusable
# phpcs job can commit phpcbf auto-fixes back to the PR branch.
permissions:
contents: read
contents: write
jobs:
# ── PHP Syntax Check ─────────────────────────────────────────────
lint-php:
name: PHP Lint (${{ matrix.php }})
runs-on: ubuntu-latest
strategy:
matrix:
php: [ '8.1', '8.2', '8.3' ]
steps:
- uses: actions/checkout@v4
- name: Set up PHP ${{ matrix.php }}
uses: shivammathur/setup-php@v2
ci:
uses: peptiderepo/peptide-e2e/.github/workflows/ci.yml@main
with:
php-version: ${{ matrix.php }}
- name: Syntax check all PHP files
run: find . -name "*.php" -not -path "./vendor/*" | xargs -n 1 php -l
- name: Unit tests (lightweight, no PHPUnit)
run: |
for test in tests/unit/test-*.php; do
echo "=== Running $test ==="
php "$test"
done
# ── WordPress Coding Standards (PHP CodeSniffer) ──────────────────
lint-phpcs:
name: WordPress Coding Standards
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up PHP
uses: shivammathur/setup-php@v2
with:
php-version: '8.1'
- name: Install Composer dependencies
run: composer install --no-interaction --prefer-dist --no-progress
- name: Run PHPCS
run: composer run lint
continue-on-error: true
# ── 300-line file check ──────────────────────────────────────────
file-size:
name: 300-line file check
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Check no PHP file exceeds 300 lines
run: |
violations=0
while IFS= read -r file; do
lines=$(wc -l < "$file")
if [ "$lines" -gt 300 ]; then
echo "VIOLATION: $file ($lines lines)"
violations=$((violations + 1))
fi
done < <(find . -name "*.php" -not -path "./vendor/*" -not -path "./tests/*")
if [ "$violations" -gt 0 ]; then
echo "$violations file(s) exceed 300 lines"
exit 1
fi
echo "All PHP files are 300 lines or fewer."
tests: stubs
has_js: false
secrets: inherit

4
.github/workflows/deploy.yml vendored
View File

@@ -4,8 +4,10 @@ on:
push:
branches: [ main ]
# contents: write required so the ci.yml caller can pass write permission
# through to the phpcbf auto-commit step in the reusable workflow.
permissions:
contents: read
contents: write
concurrency:
group: deploy-peptide-repo-core

10
CHANGELOG.md
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@@ -3,6 +3,16 @@
All notable changes to Peptide Repo Core are documented here.
Format: [Semantic Versioning](https://semver.org/).
## [0.7.0] - 2026-06-16
### Changed
- CI: adopt estate reusable workflow (thin caller, tests: stubs, has_js: false).
- PHPUnit test suite: 7 hand-rolled test scripts converted to 7 TestCase classes.
- Added phpunit/phpunit ^9.6, yoast/phpunit-polyfills ^2.0 to require-dev.
- Added phpunit.xml.dist and composer test script.
- deploy.yml: added permissions: contents: write.
## [0.6.2] — 2026-06-13
### Fixed

11
composer.json
View File

@@ -10,7 +10,9 @@
"squizlabs/php_codesniffer": "^3.13",
"wp-coding-standards/wpcs": "^3.0",
"phpcsstandards/phpcsutils": "^1.0",
"dealerdirect/phpcodesniffer-composer-installer": "^1.0"
"dealerdirect/phpcodesniffer-composer-installer": "^1.0",
"phpunit/phpunit": "^9.6",
"yoast/phpunit-polyfills": "^2.0"
},
"config": {
"allow-plugins": {
@@ -19,6 +21,11 @@
},
"scripts": {
"lint": "phpcs",
"lint:fix": "phpcbf"
"lint:fix": "phpcbf",
"test": "vendor/bin/phpunit --configuration phpunit.xml.dist",
"check": [
"@lint",
"@test"
]
}
}

18
includes/admin/class-pr-core-admin-columns.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Admin Columns.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Adds evidence strength, editorial status, and dosing count columns
*
* @package Peptide_Repo_Core
*/
/**
* Custom admin list-table columns for the peptide CPT.
*
@@ -19,7 +31,7 @@ class PR_Core_Admin_Columns {
* @return array<string, string> Modified columns.
*/
public function add_columns( array $columns ): array {
$new = [];
$new = array();
foreach ( $columns as $key => $label ) {
$new[ $key ] = $label;
@@ -44,13 +56,13 @@ class PR_Core_Admin_Columns {
public function render_column( string $column, int $post_id ): void {
switch ( $column ) {
case 'pr_evidence':
$strength = get_post_meta( $post_id, 'evidence_strength', true ) ?: 'preclinical';
$strength = get_post_meta( $post_id, 'evidence_strength', true ) ?: 'preclinical'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$label = apply_filters( 'pr_core_evidence_strength_label', $strength, $strength );
echo esc_html( $label );
break;
case 'pr_editorial':
$status = get_post_meta( $post_id, 'editorial_review_status', true ) ?: 'draft';
$status = get_post_meta( $post_id, 'editorial_review_status', true ) ?: 'draft'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo esc_html( ucfirst( str_replace( '-', ' ', $status ) ) );
break;

34
includes/admin/class-pr-core-admin.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Admin.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Registers admin menu pages, meta boxes, and custom columns for peptides
*
* @package Peptide_Repo_Core
*/
/**
* Admin initialization and hook registration.
*
@@ -25,22 +37,22 @@ class PR_Core_Admin {
*/
public function register_hooks(): void {
$metaboxes = new PR_Core_Peptide_Metaboxes();
add_action( 'add_meta_boxes', [ $metaboxes, 'add_meta_boxes' ] );
add_action( 'save_post_' . PR_Core_Peptide_CPT::POST_TYPE, [ $metaboxes, 'save_meta' ], 10, 2 );
add_action( 'add_meta_boxes', array( $metaboxes, 'add_meta_boxes' ) );
add_action( 'save_post_' . PR_Core_Peptide_CPT::POST_TYPE, array( $metaboxes, 'save_meta' ), 10, 2 );
add_action( 'add_meta_boxes', [ PR_Core_Verification_Metabox::class, 'register' ] );
add_action( 'add_meta_boxes', array( PR_Core_Verification_Metabox::class, 'register' ) );
$columns = new PR_Core_Admin_Columns();
add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', [ $columns, 'add_columns' ] );
add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', [ $columns, 'render_column' ], 10, 2 );
add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', array( $columns, 'add_columns' ) );
add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', array( $columns, 'render_column' ), 10, 2 );
// Repo Daily meta boxes.
$repo_daily_metaboxes = new PR_Core_Repo_Daily_Metaboxes();
add_action( 'add_meta_boxes', [ $repo_daily_metaboxes, 'add_meta_boxes' ] );
add_action( 'save_post_' . PR_Core_Repo_Daily_CPT::POST_TYPE, [ $repo_daily_metaboxes, 'save_meta' ], 10, 2 );
add_action( 'add_meta_boxes', array( $repo_daily_metaboxes, 'add_meta_boxes' ) );
add_action( 'save_post_' . PR_Core_Repo_Daily_CPT::POST_TYPE, array( $repo_daily_metaboxes, 'save_meta' ), 10, 2 );
add_action( 'admin_menu', [ $this, 'add_admin_pages' ] );
add_action( 'admin_enqueue_scripts', [ $this, 'enqueue_admin_styles' ] );
add_action( 'admin_menu', array( $this, 'add_admin_pages' ) );
add_action( 'admin_enqueue_scripts', array( $this, 'enqueue_admin_styles' ) );
}
/**
@@ -60,7 +72,7 @@ class PR_Core_Admin {
__( 'Candidate Queue', 'peptide-repo-core' ) . $badge,
PR_Core_Peptide_CPT::CAPABILITY,
'pr-core-candidates',
[ new PR_Core_Candidate_Queue_Page(), 'render' ]
array( new PR_Core_Candidate_Queue_Page(), 'render' )
);
}
@@ -79,7 +91,7 @@ class PR_Core_Admin {
wp_enqueue_style(
'pr-core-admin',
PR_CORE_PLUGIN_URL . 'assets/css/admin.css',
[],
array(),
PR_CORE_VERSION
);
}

16
includes/admin/class-pr-core-ajax-handlers.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Ajax Handlers.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Handles mark-verified and scan-now admin-ajax actions
*
* @package Peptide_Repo_Core
*/
/**
* AJAX handlers for verification scanner actions.
*
@@ -47,7 +59,7 @@ class PR_Core_Ajax_Handlers {
// Recompute status to 'current'.
update_post_meta( $post_id, '_pr_verification_status', 'current' );
wp_send_json_success( [ 'message' => 'Marked verified' ] );
wp_send_json_success( array( 'message' => 'Marked verified' ) );
}
/**
@@ -74,6 +86,6 @@ class PR_Core_Ajax_Handlers {
// Run scan.
PR_Core_Verification_Scanner::run_scan();
wp_send_json_success( [ 'message' => 'Scan complete' ] );
wp_send_json_success( array( 'message' => 'Scan complete' ) );
}
}

52
includes/admin/class-pr-core-candidate-queue-page.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Candidate Queue Page.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders a review screen for AI-extracted dosing candidates
*
* @package Peptide_Repo_Core
*/
/**
* Admin page for the AI Candidate Queue.
*
@@ -58,8 +70,8 @@ class PR_Core_Candidate_Queue_Page {
$peptide = $pep_repo->find_by_id( $c->peptide_id );
$name = $peptide ? $peptide->title : '#' . $c->peptide_id;
$dose = $c->dose_min !== null ? number_format( $c->dose_min, 2 ) : '?';
if ( $c->dose_max !== null && $c->dose_max !== $c->dose_min ) {
$dose = null !== $c->dose_min ? number_format( $c->dose_min, 2 ) : '?';
if ( null !== $c->dose_max && $c->dose_max !== $c->dose_min ) {
$dose .= ' – ' . number_format( $c->dose_max, 2 );
}
$dose .= ' ' . esc_html( $c->dose_unit );
@@ -71,11 +83,21 @@ class PR_Core_Candidate_Queue_Page {
$confidence_pct = number_format( $c->extraction_confidence * 100, 0 ) . '%';
$approve_url = wp_nonce_url(
add_query_arg( [ 'action' => 'pr_core_approve', 'candidate_id' => $c->id ] ),
add_query_arg(
array(
'action' => 'pr_core_approve',
'candidate_id' => $c->id,
)
),
'pr_core_queue_action'
);
$reject_url = wp_nonce_url(
add_query_arg( [ 'action' => 'pr_core_reject', 'candidate_id' => $c->id ] ),
add_query_arg(
array(
'action' => 'pr_core_reject',
'candidate_id' => $c->id,
)
),
'pr_core_queue_action'
);
@@ -84,7 +106,7 @@ class PR_Core_Candidate_Queue_Page {
printf( '<td>%s</td>', esc_html( $c->route ) );
printf( '<td>%s</td>', esc_html( $dose ) );
printf( '<td>%s</td>', esc_html( $c->population ) );
printf( '<td>%s</td>', $study ); // Contains escaped HTML + link.
printf( '<td>%s</td>', $study ); // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- $study is pre-escaped HTML.
printf( '<td>%s</td>', esc_html( $confidence_pct ) );
printf(
'<td><a href="%s" class="button button-primary button-small">%s</a> <a href="%s" class="button button-small">%s</a></td>',
@@ -107,9 +129,9 @@ class PR_Core_Candidate_Queue_Page {
* @return void
*/
private function handle_actions(): void {
$action = sanitize_text_field( $_GET['action'] ?? '' );
$action = sanitize_text_field( wp_unslash( $_GET['action'] ?? '' ) ); // phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotValidated
if ( ! in_array( $action, [ 'pr_core_approve', 'pr_core_reject' ], true ) ) {
if ( ! in_array( $action, array( 'pr_core_approve', 'pr_core_reject' ), true ) ) {
return;
}
@@ -117,7 +139,7 @@ class PR_Core_Candidate_Queue_Page {
return;
}
$candidate_id = absint( $_GET['candidate_id'] ?? 0 );
$candidate_id = absint( wp_unslash( $_GET['candidate_id'] ?? 0 ) );
if ( 0 === $candidate_id ) {
return;
}
@@ -128,15 +150,21 @@ class PR_Core_Candidate_Queue_Page {
if ( 'pr_core_approve' === $action ) {
$dosing_id = $repo->approve( $candidate_id, $reviewer_id );
if ( $dosing_id > 0 ) {
add_action( 'admin_notices', static function () {
add_action(
'admin_notices',
static function () {
echo '<div class="notice notice-success is-dismissible"><p>' . esc_html__( 'Candidate approved and added to dosing data.', 'peptide-repo-core' ) . '</p></div>';
} );
}
);
}
} else {
$repo->reject( $candidate_id, $reviewer_id );
add_action( 'admin_notices', static function () {
add_action(
'admin_notices',
static function () {
echo '<div class="notice notice-warning is-dismissible"><p>' . esc_html__( 'Candidate rejected.', 'peptide-repo-core' ) . '</p></div>';
} );
}
);
}
}
}

40
includes/admin/class-pr-core-peptide-metaboxes.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Peptide Metaboxes.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders and saves three meta boxes on the peptide edit screen
*
* @package Peptide_Repo_Core
*/
/**
* Meta boxes for the peptide edit screen: scientific identifiers, dosing, and legal.
*
@@ -22,7 +34,7 @@ class PR_Core_Peptide_Metaboxes {
add_meta_box(
'pr-core-identifiers',
__( 'Scientific Identifiers', 'peptide-repo-core' ),
[ $this, 'render_identifiers_box' ],
array( $this, 'render_identifiers_box' ),
PR_Core_Peptide_CPT::POST_TYPE,
'normal',
'high'
@@ -31,7 +43,7 @@ class PR_Core_Peptide_Metaboxes {
add_meta_box(
'pr-core-dosing',
__( 'Dosing Data', 'peptide-repo-core' ),
[ $this, 'render_dosing_box' ],
array( $this, 'render_dosing_box' ),
PR_Core_Peptide_CPT::POST_TYPE,
'normal',
'default'
@@ -40,7 +52,7 @@ class PR_Core_Peptide_Metaboxes {
add_meta_box(
'pr-core-legal',
__( 'Legal Status by Country', 'peptide-repo-core' ),
[ $this, 'render_legal_box' ],
array( $this, 'render_legal_box' ),
PR_Core_Peptide_CPT::POST_TYPE,
'normal',
'default'
@@ -56,7 +68,7 @@ class PR_Core_Peptide_Metaboxes {
public function render_identifiers_box( \WP_Post $post ): void {
wp_nonce_field( 'pr_core_save_meta', 'pr_core_meta_nonce' );
$fields = [
$fields = array(
'display_name' => __( 'Display Name', 'peptide-repo-core' ),
'aliases' => __( 'Aliases (JSON array)', 'peptide-repo-core' ),
'molecular_formula' => __( 'Molecular Formula', 'peptide-repo-core' ),
@@ -64,7 +76,7 @@ class PR_Core_Peptide_Metaboxes {
'cas_number' => __( 'CAS Number', 'peptide-repo-core' ),
'drugbank_id' => __( 'DrugBank ID', 'peptide-repo-core' ),
'chembl_id' => __( 'ChEMBL ID', 'peptide-repo-core' ),
];
);
echo '<table class="form-table pr-core-meta-table">';
foreach ( $fields as $key => $label ) {
@@ -73,12 +85,12 @@ class PR_Core_Peptide_Metaboxes {
'<tr><th><label for="pr_core_%1$s">%2$s</label></th><td><input type="text" id="pr_core_%1$s" name="pr_core_%1$s" value="%3$s" class="regular-text" /></td></tr>',
esc_attr( $key ),
esc_html( $label ),
$value
$value // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- esc_attr applied on assignment
);
}
// Evidence strength dropdown.
$current_strength = get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical';
$current_strength = get_post_meta( $post->ID, 'evidence_strength', true ) ?: 'preclinical'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<tr><th><label for="pr_core_evidence_strength">' . esc_html__( 'Evidence Strength', 'peptide-repo-core' ) . '</label></th><td><select id="pr_core_evidence_strength" name="pr_core_evidence_strength">';
foreach ( PR_Core_Peptide_CPT::EVIDENCE_STRENGTHS as $strength ) {
$label = apply_filters( 'pr_core_evidence_strength_label', $strength, $strength );
@@ -92,7 +104,7 @@ class PR_Core_Peptide_Metaboxes {
echo '</select></td></tr>';
// Editorial review status.
$current_review = get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft';
$current_review = get_post_meta( $post->ID, 'editorial_review_status', true ) ?: 'draft'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<tr><th><label for="pr_core_editorial_review_status">' . esc_html__( 'Editorial Status', 'peptide-repo-core' ) . '</label></th><td><select id="pr_core_editorial_review_status" name="pr_core_editorial_review_status">';
foreach ( PR_Core_Peptide_CPT::REVIEW_STATUSES as $status ) {
printf(
@@ -134,8 +146,8 @@ class PR_Core_Peptide_Metaboxes {
echo '</tr></thead><tbody>';
foreach ( $rows as $row ) {
$dose = $row->dose_min !== null ? number_format( $row->dose_min, 2 ) : '?';
if ( $row->dose_max !== null && $row->dose_max !== $row->dose_min ) {
$dose = null !== $row->dose_min ? number_format( $row->dose_min, 2 ) : '?';
if ( null !== $row->dose_max && $row->dose_max !== $row->dose_min ) {
$dose .= ' – ' . number_format( $row->dose_max, 2 );
}
$dose .= ' ' . esc_html( $row->dose_unit );
@@ -233,11 +245,11 @@ class PR_Core_Peptide_Metaboxes {
foreach ( $meta_fields as $key => $config ) {
$input_key = 'pr_core_' . $key;
if ( ! isset( $_POST[ $input_key ] ) ) {
if ( ! isset( $_POST[ $input_key ] ) ) { // phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotSanitized -- existence check only; unslash+sanitize below
continue;
}
$raw = wp_unslash( $_POST[ $input_key ] );
$raw = wp_unslash( $_POST[ $input_key ] ); // phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotSanitized -- sanitized via config['sanitize'] callback on next line
$clean = is_callable( $config['sanitize'] )
? call_user_func( $config['sanitize'], $raw )
: sanitize_text_field( (string) $raw );
@@ -246,10 +258,10 @@ class PR_Core_Peptide_Metaboxes {
}
// Set last_editorial_review_at when status changes to published.
$new_review_status = sanitize_text_field( $_POST['pr_core_editorial_review_status'] ?? '' );
$new_review_status = sanitize_text_field( wp_unslash( $_POST['pr_core_editorial_review_status'] ?? '' ) );
if ( 'published' === $new_review_status ) {
$old_status = get_post_meta( $post_id, 'editorial_review_status', true );
if ( $old_status !== 'published' ) {
if ( 'published' !== $old_status ) {
update_post_meta( $post_id, 'last_editorial_review_at', current_time( 'mysql' ) );
update_post_meta( $post_id, 'medical_editor_id', get_current_user_id() );
}

22
includes/admin/class-pr-core-repo-daily-metaboxes.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Repo Daily Metaboxes.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders and saves two meta fields on the repo_daily edit screen
*
* @package Peptide_Repo_Core
*/
/**
* Meta boxes for Repo Daily edit screen: author and clinical review flag.
*
@@ -17,7 +29,11 @@ declare(strict_types=1);
*/
class PR_Core_Repo_Daily_Metaboxes {
/** @var string Default author byline for Repo Daily articles. */
/**
* Default author byline for Repo Daily articles.
*
* @var string Default author byline for Repo Daily articles.
*/
private const DEFAULT_AUTHOR = 'Boo Sheeran';
/**
@@ -29,7 +45,7 @@ class PR_Core_Repo_Daily_Metaboxes {
add_meta_box(
'pr-core-repo-daily-meta',
__( 'Article Settings', 'peptide-repo-core' ),
[ $this, 'render_meta_box' ],
array( $this, 'render_meta_box' ),
PR_Core_Repo_Daily_CPT::POST_TYPE,
'normal',
'default'
@@ -46,7 +62,7 @@ class PR_Core_Repo_Daily_Metaboxes {
wp_nonce_field( 'pr_core_repo_daily_meta', 'pr_core_repo_daily_nonce' );
$author = sanitize_text_field(
get_post_meta( $post->ID, '_repo_daily_author', true ) ?: self::DEFAULT_AUTHOR
get_post_meta( $post->ID, '_repo_daily_author', true ) ?: self::DEFAULT_AUTHOR // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
);
$requires_review = get_post_meta( $post->ID, '_repo_daily_clinical_review_required', true );

134
includes/admin/class-pr-core-settings-renderer.php Normal file
View File

@@ -0,0 +1,134 @@
<?php
/**
* Settings Renderer.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Static methods that output HTML for each settings field on the PR Core settings page
*
* @package Peptide_Repo_Core
*/
/**
* Render methods for the PR Core settings admin page.
*
* What: Static methods that output HTML for each settings field on the PR Core settings page.
* Who calls it: PR_Core_Settings — register_*_section() methods reference these via add_settings_field().
* Dependencies: PR_Core_Settings (for option key constants).
*
* @see admin/class-pr-core-settings.php — Settings registration and sanitization.
*/
class PR_Core_Settings_Renderer {
/**
* Render the settings page form.
*
* @return void
*/
public static function render_page(): void {
?>
<div class="wrap">
<h1><?php esc_html_e( 'PR Core Settings', 'peptide-repo-core' ); ?></h1>
<form method="post" action="options.php">
<?php
settings_fields( self::OPTION_GROUP );
do_settings_sections( self::OPTION_GROUP );
submit_button();
?>
</form>
</div>
<?php
}
/**
* Render output.
*
* @return void
*/
public static function render_enabled_field(): void {
$enabled = (bool) get_option( self::RELATED_ENABLED, true );
printf(
'<input type="checkbox" name="%s" value="1"%s /> %s',
esc_attr( self::RELATED_ENABLED ),
checked( $enabled, true, false ),
esc_html__( 'Show related monographs on single peptide pages', 'peptide-repo-core' )
);
}
/**
* Render output.
*
* @return void
*/
public static function render_limit_field(): void {
printf(
'<input type="number" name="%s" value="%d" min="1" max="6" />',
esc_attr( self::RELATED_LIMIT ),
absint( get_option( self::RELATED_LIMIT, 3 ) )
);
echo '<p class="description">' . esc_html__( 'Number of articles to display (1-6). Default: 3.', 'peptide-repo-core' ) . '</p>';
}
/**
* Render output.
*
* @return void
*/
public static function render_verification_section(): void {
echo '<p>' . esc_html__( 'Configure automatic staleness scanning and digest notifications.', 'peptide-repo-core' ) . '</p>';
}
/**
* Render output.
*
* @return void
*/
public static function render_cadence_field(): void {
$current = get_option( self::SCAN_CADENCE, 'weekly' );
echo '<select name="' . esc_attr( self::SCAN_CADENCE ) . '">';
foreach ( array(
'daily' => 'Daily',
'weekly' => 'Weekly',
'monthly' => 'Monthly',
) as $val => $label ) {
printf( '<option value="%s"%s>%s</option>', esc_attr( $val ), selected( $current, $val, false ), esc_html( $label ) );
}
echo '</select>';
}
/**
* Render output.
*
* @return void
*/
public static function render_threshold_field(): void {
printf( '<input type="number" name="%s" value="%d" min="1" />', esc_attr( self::DEFAULT_THRESHOLD ), absint( get_option( self::DEFAULT_THRESHOLD, 180 ) ) );
}
/**
* Render output.
*
* @return void
*/
public static function render_high_velocity_field(): void {
printf( '<input type="number" name="%s" value="%d" min="1" />', esc_attr( self::HIGH_VELOCITY_THRESHOLD ), absint( get_option( self::HIGH_VELOCITY_THRESHOLD, 60 ) ) );
}
/**
* Render output.
*
* @return void
*/
public static function render_email_field(): void {
printf(
'<input type="text" name="%s" value="%s" class="regular-text" placeholder="admin@example.com" />',
esc_attr( self::VERIFICATION_EMAIL ),
esc_attr( (string) get_option( self::VERIFICATION_EMAIL, '' ) )
);
echo '<p class="description">' . esc_html__( 'Comma-separated. Leave blank to disable email digests.', 'peptide-repo-core' ) . '</p>';
}
}

226
includes/admin/class-pr-core-settings.php
View File

@@ -1,4 +1,10 @@
<?php
/**
* Settings.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
@@ -13,25 +19,25 @@ declare(strict_types=1);
*/
class PR_Core_Settings {
/** @var string Option group shared by all PR Core settings. */
/** @var string Option group shared by all PR Core settings. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
public const OPTION_GROUP = 'pr_core_settings';
/** @var string Option key: enable/disable related articles. */
/** @var string Option key: enable/disable related articles. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const RELATED_ENABLED = 'pr_core_related_posts_enabled';
/** @var string Option key: related articles limit (1-6). */
/** @var string Option key: related articles limit (1-6). */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const RELATED_LIMIT = 'pr_core_related_posts_limit';
/** @var string Option key: WP-cron scan cadence. */
/** @var string Option key: WP-cron scan cadence. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const SCAN_CADENCE = 'pr_core_scan_cadence';
/** @var string Option key: default staleness threshold in days. */
/** @var string Option key: default staleness threshold in days. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const DEFAULT_THRESHOLD = 'pr_core_default_threshold';
/** @var string Option key: high-velocity staleness threshold in days. */
/** @var string Option key: high-velocity staleness threshold in days. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const HIGH_VELOCITY_THRESHOLD = 'pr_core_high_velocity_threshold';
/** @var string Option key: comma-separated notification email list. */
/** @var string Option key: comma-separated notification email list. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const VERIFICATION_EMAIL = 'pr_core_verification_email';
/**
@@ -48,28 +54,17 @@ class PR_Core_Settings {
__( 'Settings', 'peptide-repo-core' ),
'manage_options',
'pr-core-settings',
[ __CLASS__, 'render_page' ]
array( __CLASS__, 'render_page' )
);
}
/**
* Render the settings page form.
* Render the settings page HTML. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_page(): void {
?>
<div class="wrap">
<h1><?php esc_html_e( 'PR Core Settings', 'peptide-repo-core' ); ?></h1>
<form method="post" action="options.php">
<?php
settings_fields( self::OPTION_GROUP );
do_settings_sections( self::OPTION_GROUP );
submit_button();
?>
</form>
</div>
<?php
PR_Core_Settings_Renderer::render_page();
}
/**
@@ -83,10 +78,10 @@ class PR_Core_Settings {
public static function register_settings(): void {
self::register_related_articles_section();
self::register_verification_section();
add_action( 'update_option_' . self::SCAN_CADENCE, [ __CLASS__, 'reschedule_cron' ], 10, 2 );
add_action( 'update_option_' . self::SCAN_CADENCE, array( __CLASS__, 'reschedule_cron' ), 10, 2 );
}
// ── Related Articles ─────────────────────────────────────────────────
// ── Related Articles ─────────────────────────────────────────────────.
/**
* Register Related Articles settings.
@@ -94,33 +89,46 @@ class PR_Core_Settings {
* @return void
*/
private static function register_related_articles_section(): void {
register_setting( self::OPTION_GROUP, self::RELATED_ENABLED, [ 'type' => 'boolean', 'default' => true, 'sanitize_callback' => 'rest_sanitize_boolean' ] );
register_setting( self::OPTION_GROUP, self::RELATED_LIMIT, [ 'type' => 'integer', 'default' => 3, 'sanitize_callback' => [ __CLASS__, 'sanitize_limit' ] ] );
register_setting(
self::OPTION_GROUP,
self::RELATED_ENABLED,
array(
'type' => 'boolean',
'default' => true,
'sanitize_callback' => 'rest_sanitize_boolean',
)
);
register_setting(
self::OPTION_GROUP,
self::RELATED_LIMIT,
array(
'type' => 'integer',
'default' => 3,
'sanitize_callback' => array( __CLASS__, 'sanitize_limit' ),
)
);
add_settings_section( 'pr_core_related_articles', __( 'Related Articles', 'peptide-repo-core' ), '__return_false', self::OPTION_GROUP );
add_settings_field( self::RELATED_ENABLED, __( 'Enable Related Articles', 'peptide-repo-core' ), [ __CLASS__, 'render_enabled_field' ], self::OPTION_GROUP, 'pr_core_related_articles' );
add_settings_field( self::RELATED_LIMIT, __( 'Number of Articles', 'peptide-repo-core' ), [ __CLASS__, 'render_limit_field' ], self::OPTION_GROUP, 'pr_core_related_articles' );
add_settings_field( self::RELATED_ENABLED, __( 'Enable Related Articles', 'peptide-repo-core' ), array( __CLASS__, 'render_enabled_field' ), self::OPTION_GROUP, 'pr_core_related_articles' );
add_settings_field( self::RELATED_LIMIT, __( 'Number of Articles', 'peptide-repo-core' ), array( __CLASS__, 'render_limit_field' ), self::OPTION_GROUP, 'pr_core_related_articles' );
}
/** @return void */
/**
* Render the enable/disable checkbox field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_enabled_field(): void {
$enabled = (bool) get_option( self::RELATED_ENABLED, true );
printf(
'<input type="checkbox" name="%s" value="1"%s /> %s',
esc_attr( self::RELATED_ENABLED ),
checked( $enabled, true, false ),
esc_html__( 'Show related monographs on single peptide pages', 'peptide-repo-core' )
);
PR_Core_Settings_Renderer::render_enabled_field();
}
/** @return void */
/**
* Render the article count limit field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_limit_field(): void {
printf(
'<input type="number" name="%s" value="%d" min="1" max="6" />',
esc_attr( self::RELATED_LIMIT ),
absint( get_option( self::RELATED_LIMIT, 3 ) )
);
echo '<p class="description">' . esc_html__( 'Number of articles to display (1-6). Default: 3.', 'peptide-repo-core' ) . '</p>';
PR_Core_Settings_Renderer::render_limit_field();
}
/**
@@ -133,7 +141,7 @@ class PR_Core_Settings {
return min( 6, max( 1, (int) $value ) );
}
// ── Verification ─────────────────────────────────────────────────────
// ── Verification ─────────────────────────────────────────────────────.
/**
* Register Verification settings.
@@ -141,51 +149,93 @@ class PR_Core_Settings {
* @return void
*/
private static function register_verification_section(): void {
register_setting( self::OPTION_GROUP, self::SCAN_CADENCE, [ 'type' => 'string', 'default' => 'weekly', 'sanitize_callback' => [ __CLASS__, 'sanitize_cadence' ] ] );
register_setting( self::OPTION_GROUP, self::DEFAULT_THRESHOLD, [ 'type' => 'integer', 'default' => 180, 'sanitize_callback' => 'absint' ] );
register_setting( self::OPTION_GROUP, self::HIGH_VELOCITY_THRESHOLD, [ 'type' => 'integer', 'default' => 60, 'sanitize_callback' => 'absint' ] );
register_setting( self::OPTION_GROUP, self::VERIFICATION_EMAIL, [ 'type' => 'string', 'default' => '', 'sanitize_callback' => [ __CLASS__, 'sanitize_emails' ] ] );
add_settings_section( 'pr_core_verification', __( 'Verification', 'peptide-repo-core' ), [ __CLASS__, 'render_verification_section' ], self::OPTION_GROUP );
add_settings_field( self::SCAN_CADENCE, __( 'Scan cadence', 'peptide-repo-core' ), [ __CLASS__, 'render_cadence_field' ], self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::DEFAULT_THRESHOLD, __( 'Default staleness threshold (days)', 'peptide-repo-core' ), [ __CLASS__, 'render_threshold_field' ], self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::HIGH_VELOCITY_THRESHOLD, __( 'High-velocity threshold (days)', 'peptide-repo-core' ), [ __CLASS__, 'render_high_velocity_field' ], self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::VERIFICATION_EMAIL, __( 'Notification email(s)', 'peptide-repo-core' ), [ __CLASS__, 'render_email_field' ], self::OPTION_GROUP, 'pr_core_verification' );
}
/** @return void */
public static function render_verification_section(): void {
echo '<p>' . esc_html__( 'Configure automatic staleness scanning and digest notifications.', 'peptide-repo-core' ) . '</p>';
}
/** @return void */
public static function render_cadence_field(): void {
$current = get_option( self::SCAN_CADENCE, 'weekly' );
echo '<select name="' . esc_attr( self::SCAN_CADENCE ) . '">';
foreach ( [ 'daily' => 'Daily', 'weekly' => 'Weekly', 'monthly' => 'Monthly' ] as $val => $label ) {
printf( '<option value="%s"%s>%s</option>', esc_attr( $val ), selected( $current, $val, false ), esc_html( $label ) );
}
echo '</select>';
}
/** @return void */
public static function render_threshold_field(): void {
printf( '<input type="number" name="%s" value="%d" min="1" />', esc_attr( self::DEFAULT_THRESHOLD ), absint( get_option( self::DEFAULT_THRESHOLD, 180 ) ) );
}
/** @return void */
public static function render_high_velocity_field(): void {
printf( '<input type="number" name="%s" value="%d" min="1" />', esc_attr( self::HIGH_VELOCITY_THRESHOLD ), absint( get_option( self::HIGH_VELOCITY_THRESHOLD, 60 ) ) );
}
/** @return void */
public static function render_email_field(): void {
printf(
'<input type="text" name="%s" value="%s" class="regular-text" placeholder="admin@example.com" />',
esc_attr( self::VERIFICATION_EMAIL ),
esc_attr( (string) get_option( self::VERIFICATION_EMAIL, '' ) )
register_setting(
self::OPTION_GROUP,
self::SCAN_CADENCE,
array(
'type' => 'string',
'default' => 'weekly',
'sanitize_callback' => array( __CLASS__, 'sanitize_cadence' ),
)
);
echo '<p class="description">' . esc_html__( 'Comma-separated. Leave blank to disable email digests.', 'peptide-repo-core' ) . '</p>';
register_setting(
self::OPTION_GROUP,
self::DEFAULT_THRESHOLD,
array(
'type' => 'integer',
'default' => 180,
'sanitize_callback' => 'absint',
)
);
register_setting(
self::OPTION_GROUP,
self::HIGH_VELOCITY_THRESHOLD,
array(
'type' => 'integer',
'default' => 60,
'sanitize_callback' => 'absint',
)
);
register_setting(
self::OPTION_GROUP,
self::VERIFICATION_EMAIL,
array(
'type' => 'string',
'default' => '',
'sanitize_callback' => array( __CLASS__, 'sanitize_emails' ),
)
);
add_settings_section( 'pr_core_verification', __( 'Verification', 'peptide-repo-core' ), array( __CLASS__, 'render_verification_section' ), self::OPTION_GROUP );
add_settings_field( self::SCAN_CADENCE, __( 'Scan cadence', 'peptide-repo-core' ), array( __CLASS__, 'render_cadence_field' ), self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::DEFAULT_THRESHOLD, __( 'Default staleness threshold (days)', 'peptide-repo-core' ), array( __CLASS__, 'render_threshold_field' ), self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::HIGH_VELOCITY_THRESHOLD, __( 'High-velocity threshold (days)', 'peptide-repo-core' ), array( __CLASS__, 'render_high_velocity_field' ), self::OPTION_GROUP, 'pr_core_verification' );
add_settings_field( self::VERIFICATION_EMAIL, __( 'Notification email(s)', 'peptide-repo-core' ), array( __CLASS__, 'render_email_field' ), self::OPTION_GROUP, 'pr_core_verification' );
}
/**
* Render the verification section header. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_verification_section(): void {
PR_Core_Settings_Renderer::render_verification_section();
}
/**
* Render the scan cadence select field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_cadence_field(): void {
PR_Core_Settings_Renderer::render_cadence_field();
}
/**
* Render the score threshold input field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_threshold_field(): void {
PR_Core_Settings_Renderer::render_threshold_field();
}
/**
* Render the high-velocity scan toggle field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_high_velocity_field(): void {
PR_Core_Settings_Renderer::render_high_velocity_field();
}
/**
* Render the alert email input field. Delegates to PR_Core_Settings_Renderer.
*
* @return void
*/
public static function render_email_field(): void {
PR_Core_Settings_Renderer::render_email_field();
}
/**
@@ -195,7 +245,7 @@ class PR_Core_Settings {
* @return string
*/
public static function sanitize_cadence( string $value ): string {
return in_array( $value, [ 'daily', 'weekly', 'monthly' ], true ) ? $value : 'weekly';
return in_array( $value, array( 'daily', 'weekly', 'monthly' ), true ) ? $value : 'weekly';
}
/**

32
includes/admin/class-pr-core-verification-metabox.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Metabox.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Renders and saves verification status sidebar meta box
*
* @package Peptide_Repo_Core
*/
/**
* Verification status meta box for peptide edit screen.
*
@@ -21,7 +33,7 @@ class PR_Core_Verification_Metabox {
add_meta_box(
'pr-core-verification',
__( 'Verification Status', 'peptide-repo-core' ),
[ __CLASS__, 'render' ],
array( __CLASS__, 'render' ),
PR_Core_Peptide_CPT::POST_TYPE,
'side',
'default'
@@ -38,16 +50,20 @@ class PR_Core_Verification_Metabox {
wp_nonce_field( 'pr_core_verification_nonce', 'pr_core_verification_nonce' );
$last_verified = get_post_meta( $post->ID, '_pr_last_source_verified', true );
$velocity = get_post_meta( $post->ID, '_pr_verification_velocity', true ) ?: 'medium';
$status = get_post_meta( $post->ID, '_pr_verification_status', true ) ?: 'current';
$notes = get_post_meta( $post->ID, '_pr_verification_notes', true ) ?: '';
$velocity = get_post_meta( $post->ID, '_pr_verification_velocity', true ) ?: 'medium'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$status = get_post_meta( $post->ID, '_pr_verification_status', true ) ?: 'current'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$notes = get_post_meta( $post->ID, '_pr_verification_notes', true ) ?: ''; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<p><strong>' . esc_html__( 'Last Verified', 'peptide-repo-core' ) . ':</strong><br />';
echo '<code style="color: #666;">' . esc_html( $last_verified ?: '—' ) . '</code></p>';
echo '<code style="color: #666;">' . esc_html( $last_verified ?: '—' ) . '</code></p>'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
echo '<p><strong>' . esc_html__( 'Verification Velocity', 'peptide-repo-core' ) . ':</strong><br />';
echo '<select name="pr_core__pr_verification_velocity" style="width:100%;">';
foreach ( [ 'low' => 'Low', 'medium' => 'Medium', 'high' => 'High' ] as $val => $label ) {
foreach ( array(
'low' => 'Low',
'medium' => 'Medium',
'high' => 'High',
) as $val => $label ) {
printf(
'<option value="%s"%s>%s</option>',
esc_attr( $val ),
@@ -58,12 +74,12 @@ class PR_Core_Verification_Metabox {
echo '</select></p>';
echo '<p><strong>' . esc_html__( 'Status', 'peptide-repo-core' ) . ':</strong><br />';
$badge_class = match( $status ) {
$badge_class = match ( $status ) {
'due' => 'style="background:#ff9800;color:white;padding:4px 8px;border-radius:3px;"',
'overdue' => 'style="background:#f44336;color:white;padding:4px 8px;border-radius:3px;"',
default => 'style="background:#4caf50;color:white;padding:4px 8px;border-radius:3px;"',
};
echo '<span ' . $badge_class . '>' . esc_html( ucfirst( $status ) ) . '</span></p>';
echo '<span ' . $badge_class . '>' . esc_html( ucfirst( $status ) ) . '</span></p>'; // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- badge_class is a hardcoded match expression
echo '<p><strong>' . esc_html__( 'Verification Notes', 'peptide-repo-core' ) . ':</strong><br />';
printf(

37
includes/admin/class-pr-core-verification-widget.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Widget.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* WordPress dashboard widget showing peptides needing review (due/overdue)
*
* @package Peptide_Repo_Core
*/
/**
* Dashboard widget for verification status overview.
*
@@ -23,7 +35,7 @@ class PR_Core_Verification_Widget {
wp_add_dashboard_widget(
'pr_core_verification_status',
__( 'Monographs Needing Review', 'peptide-repo-core' ),
[ __CLASS__, 'render' ]
array( __CLASS__, 'render' )
);
}
@@ -34,34 +46,37 @@ class PR_Core_Verification_Widget {
*/
public static function render(): void {
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( [ 'status' => 'publish' ] );
$peptides = $repo->find_all( array( 'status' => 'publish' ) );
$due_overdue = [];
$due_overdue = array();
foreach ( $peptides as $dto ) {
$status = get_post_meta( $dto->id, '_pr_verification_status', true ) ?: 'current';
$status = get_post_meta( $dto->id, '_pr_verification_status', true ) ?: 'current'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
if ( in_array( $status, [ 'due', 'overdue' ], true ) ) {
if ( in_array( $status, array( 'due', 'overdue' ), true ) ) {
$last_verified = get_post_meta( $dto->id, '_pr_last_source_verified', true );
$days_since = $last_verified
? (int) ( ( time() - strtotime( $last_verified ) ) / DAY_IN_SECONDS )
: 999;
$due_overdue[] = [
$due_overdue[] = array(
'id' => $dto->id,
'title' => $dto->title,
'status' => $status,
'velocity' => get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium',
'velocity' => get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium', // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'last_verified' => $last_verified,
'days_since' => $days_since,
];
);
}
}
// Sort by days_since descending (most overdue first).
usort( $due_overdue, static function ( $a, $b ) {
usort(
$due_overdue,
static function ( $a, $b ) {
return $b['days_since'] <=> $a['days_since'];
} );
}
);
if ( empty( $due_overdue ) ) {
echo '<p>' . esc_html__( 'All monographs are current. ', 'peptide-repo-core' );
@@ -93,7 +108,7 @@ class PR_Core_Verification_Widget {
esc_html( ucfirst( $item['status'] ) ),
esc_html( ucfirst( $item['velocity'] ) ),
esc_html( $item['last_verified'] ?? '—' ),
$item['days_since'],
(int) $item['days_since'], // phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- cast to int, safe
esc_url( $edit_url )
);
}

160
includes/api/class-pr-core-rest-controller.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Rest Controller.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Exposes peptides, dosing rows, and legal cells via REST endpoints
*
* @package Peptide_Repo_Core
*/
/**
* REST API controller for peptide data (read-only public, write requires capability).
*
@@ -22,7 +34,7 @@ declare(strict_types=1);
*/
class PR_Core_Rest_Controller {
/** @var string REST namespace. */
/** @var string REST namespace. */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
private const REST_NAMESPACE = 'pr-core/v1';
/**
@@ -31,7 +43,7 @@ class PR_Core_Rest_Controller {
* @return void
*/
public function register_hooks(): void {
add_action( 'rest_api_init', [ $this, 'register_routes' ] );
add_action( 'rest_api_init', array( $this, 'register_routes' ) );
}
/**
@@ -42,58 +54,106 @@ class PR_Core_Rest_Controller {
* @return void
*/
public function register_routes(): void {
// GET /peptides
register_rest_route( self::REST_NAMESPACE, '/peptides', [
// GET /peptides.
register_rest_route(
self::REST_NAMESPACE,
'/peptides',
array(
'methods' => 'GET',
'callback' => [ $this, 'list_peptides' ],
'callback' => array( $this, 'list_peptides' ),
'permission_callback' => '__return_true',
'args' => [
'category' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ],
'evidence_strength' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ],
'search' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ],
'per_page' => [ 'type' => 'integer', 'default' => 25, 'minimum' => 1, 'maximum' => 100 ],
'page' => [ 'type' => 'integer', 'default' => 1, 'minimum' => 1 ],
],
] );
'args' => array(
'category' => array(
'type' => 'string',
'sanitize_callback' => 'sanitize_text_field',
),
'evidence_strength' => array(
'type' => 'string',
'sanitize_callback' => 'sanitize_text_field',
),
'search' => array(
'type' => 'string',
'sanitize_callback' => 'sanitize_text_field',
),
'per_page' => array(
'type' => 'integer',
'default' => 25,
'minimum' => 1,
'maximum' => 100,
),
'page' => array(
'type' => 'integer',
'default' => 1,
'minimum' => 1,
),
),
)
);
// GET /peptides/{id}
register_rest_route( self::REST_NAMESPACE, '/peptides/(?P<id>\d+)', [
// GET /peptides/{id}.
register_rest_route(
self::REST_NAMESPACE,
'/peptides/(?P<id>\d+)',
array(
'methods' => 'GET',
'callback' => [ $this, 'get_peptide' ],
'callback' => array( $this, 'get_peptide' ),
'permission_callback' => '__return_true',
] );
)
);
// GET /peptides/{id}/dosing
register_rest_route( self::REST_NAMESPACE, '/peptides/(?P<id>\d+)/dosing', [
// GET /peptides/{id}/dosing.
register_rest_route(
self::REST_NAMESPACE,
'/peptides/(?P<id>\d+)/dosing',
array(
'methods' => 'GET',
'callback' => [ $this, 'list_dosing' ],
'callback' => array( $this, 'list_dosing' ),
'permission_callback' => '__return_true',
'args' => [
'route' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ],
'population' => [ 'type' => 'string', 'sanitize_callback' => 'sanitize_text_field' ],
],
] );
'args' => array(
'route' => array(
'type' => 'string',
'sanitize_callback' => 'sanitize_text_field',
),
'population' => array(
'type' => 'string',
'sanitize_callback' => 'sanitize_text_field',
),
),
)
);
// POST /peptides/{id}/dosing (auth required)
register_rest_route( self::REST_NAMESPACE, '/peptides/(?P<id>\d+)/dosing', [
// POST /peptides/{id}/dosing (auth required).
register_rest_route(
self::REST_NAMESPACE,
'/peptides/(?P<id>\d+)/dosing',
array(
'methods' => 'POST',
'callback' => [ $this, 'create_dosing' ],
'permission_callback' => [ $this, 'check_write_permission' ],
] );
'callback' => array( $this, 'create_dosing' ),
'permission_callback' => array( $this, 'check_write_permission' ),
)
);
// GET /peptides/{id}/legal
register_rest_route( self::REST_NAMESPACE, '/peptides/(?P<id>\d+)/legal', [
// GET /peptides/{id}/legal.
register_rest_route(
self::REST_NAMESPACE,
'/peptides/(?P<id>\d+)/legal',
array(
'methods' => 'GET',
'callback' => [ $this, 'list_legal' ],
'callback' => array( $this, 'list_legal' ),
'permission_callback' => '__return_true',
] );
)
);
// POST /peptides/{id}/legal (auth required)
register_rest_route( self::REST_NAMESPACE, '/peptides/(?P<id>\d+)/legal', [
// POST /peptides/{id}/legal (auth required).
register_rest_route(
self::REST_NAMESPACE,
'/peptides/(?P<id>\d+)/legal',
array(
'methods' => 'POST',
'callback' => [ $this, 'create_legal' ],
'permission_callback' => [ $this, 'check_write_permission' ],
] );
'callback' => array( $this, 'create_legal' ),
'permission_callback' => array( $this, 'check_write_permission' ),
)
);
}
/**
@@ -109,12 +169,14 @@ class PR_Core_Rest_Controller {
if ( $search ) {
$peptides = $repo->search( $search, (int) $request->get_param( 'per_page' ) );
} else {
$peptides = $repo->find_all( [
$peptides = $repo->find_all(
array(
'category' => $request->get_param( 'category' ),
'evidence_strength' => $request->get_param( 'evidence_strength' ),
'per_page' => $request->get_param( 'per_page' ),
'page' => $request->get_param( 'page' ),
] );
)
);
}
$data = array_map( static fn( PR_Core_Peptide_DTO $p ) => $p->to_array(), $peptides );
@@ -133,7 +195,7 @@ class PR_Core_Rest_Controller {
$peptide = $repo->find_by_id( (int) $request->get_param( 'id' ) );
if ( ! $peptide ) {
return new \WP_Error( 'not_found', __( 'Peptide not found.', 'peptide-repo-core' ), [ 'status' => 404 ] );
return new \WP_Error( 'not_found', __( 'Peptide not found.', 'peptide-repo-core' ), array( 'status' => 404 ) );
}
return new \WP_REST_Response( $peptide->to_array(), 200 );
@@ -149,10 +211,12 @@ class PR_Core_Rest_Controller {
$repo = new PR_Core_Dosing_Repository();
$rows = $repo->find_by_peptide(
(int) $request->get_param( 'id' ),
array_filter( [
array_filter(
array(
'route' => $request->get_param( 'route' ),
'population' => $request->get_param( 'population' ),
] )
)
)
);
$data = array_map( static fn( PR_Core_Dosing_Row_DTO $r ) => $r->to_array(), $rows );
@@ -176,12 +240,12 @@ class PR_Core_Rest_Controller {
$id = $repo->insert( $data );
if ( 0 === $id ) {
return new \WP_Error( 'insert_failed', __( 'Failed to insert dosing row.', 'peptide-repo-core' ), [ 'status' => 500 ] );
return new \WP_Error( 'insert_failed', __( 'Failed to insert dosing row.', 'peptide-repo-core' ), array( 'status' => 500 ) );
}
$row = $repo->find_by_id( $id );
return new \WP_REST_Response( $row ? $row->to_array() : [ 'id' => $id ], 201 );
return new \WP_REST_Response( $row ? $row->to_array() : array( 'id' => $id ), 201 );
}
/**
@@ -215,12 +279,12 @@ class PR_Core_Rest_Controller {
$id = $repo->insert( $data );
if ( 0 === $id ) {
return new \WP_Error( 'insert_failed', __( 'Failed to insert legal cell.', 'peptide-repo-core' ), [ 'status' => 500 ] );
return new \WP_Error( 'insert_failed', __( 'Failed to insert legal cell.', 'peptide-repo-core' ), array( 'status' => 500 ) );
}
$cell = $repo->find_by_id( $id );
return new \WP_REST_Response( $cell ? $cell->to_array() : [ 'id' => $id ], 201 );
return new \WP_REST_Response( $cell ? $cell->to_array() : array( 'id' => $id ), 201 );
}
/**

25
includes/class-pr-core-activator.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Activator.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Runs migrations, adds capabilities, flushes rewrite rules
*
* @package Peptide_Repo_Core
*/
/**
* Plugin activation handler.
*
@@ -17,7 +29,11 @@ declare(strict_types=1);
*/
class PR_Core_Activator {
/** @var string Option key storing the last activated/seen plugin version. */
/**
* Option key storing the last activated/seen plugin version.
*
* @var string Option key storing the last activated/seen plugin version.
*/
private const VERSION_OPTION = 'pr_core_version';
/**
@@ -51,8 +67,8 @@ class PR_Core_Activator {
// Flush rewrite rules for the new CPT.
flush_rewrite_rules( false );
// Record the activated version so the init:999 drift handler can
// detect future in-place updates and re-flush without a manual
// Record the activated version so the init:999 drift handler can.
// detect future in-place updates and re-flush without a manual.
// deactivate/reactivate cycle.
update_option( self::VERSION_OPTION, PR_CORE_VERSION, false );
}
@@ -93,7 +109,7 @@ class PR_Core_Activator {
*/
private static function add_capabilities(): void {
$cap = 'manage_peptide_content';
$roles = [ 'administrator', 'editor' ];
$roles = array( 'administrator', 'editor' );
foreach ( $roles as $role_name ) {
$role = get_role( $role_name );
@@ -156,4 +172,3 @@ class PR_Core_Activator {
}
}
}

30
includes/class-pr-core-autoloader.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Autoloader.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Resolves PR_Core_ class names to file paths under includes/
*
* @package Peptide_Repo_Core
*/
/**
* SPL autoloader for PR_Core_ prefixed classes.
*
@@ -15,8 +27,12 @@ declare(strict_types=1);
*/
class PR_Core_Autoloader {
/** @var string[] Directories to scan for class files. */
private static array $dirs = [];
/**
* Directories to scan for class files.
*
* @var string[] Directories to scan for class files.
*/
private static array $dirs = array();
/**
* Register the autoloader with SPL.
@@ -35,22 +51,22 @@ class PR_Core_Autoloader {
self::$dirs[] = trailingslashit( $dir );
}
spl_autoload_register( [ __CLASS__, 'load' ] );
spl_autoload_register( array( __CLASS__, 'load' ) );
}
/**
* Autoload callback. Only handles PR_Core_ prefixed classes.
*
* @param string $class Fully-qualified class name.
* @param string $class_name Fully-qualified class name.
* @return void
*/
public static function load( string $class ): void {
if ( 0 !== strpos( $class, 'PR_Core_' ) ) {
public static function load( string $class_name ): void {
if ( 0 !== strpos( $class_name, 'PR_Core_' ) ) {
return;
}
// PR_Core_Foo_Bar => foo-bar => class-pr-core-foo-bar.php.
$suffix = substr( $class, 8 ); // Strip 'PR_Core_'.
$suffix = substr( $class_name, 8 ); // Strip 'PR_Core_'.
$filename = 'class-pr-core-' . str_replace( '_', '-', strtolower( $suffix ) ) . '.php';
foreach ( self::$dirs as $dir ) {

12
includes/class-pr-core-deactivator.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Deactivator.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Flushes rewrite rules on deactivation (data preserved)
*
* @package Peptide_Repo_Core
*/
/**
* Plugin deactivation handler.
*

125
includes/class-pr-core-seed-data.php
View File

@@ -1,13 +1,27 @@
<?php
/**
* Seed Data.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Seed data fixture for development and testing.
* Creates 3 peptide posts, 10 dosing rows, and 5 legal cells using fixture data
*
* What: Creates 3 peptide posts, 10 dosing rows, and 5 legal cells.
* @package Peptide_Repo_Core
*/
/**
* Seed data orchestrator for development and testing.
*
* What: Creates 3 peptide posts, 10 dosing rows, and 5 legal cells using fixture data.
* Who calls it: WP-CLI command or admin action (manual trigger only).
* Dependencies: PR_Core_Peptide_CPT, PR_Core_Dosing_Repository, PR_Core_Legal_Repository.
* Dependencies: PR_Core_Seed_Fixtures, PR_Core_Peptide_CPT, PR_Core_Dosing_Repository,
* PR_Core_Legal_Repository.
*
* @see class-pr-core-seed-fixtures.php — Static fixture data arrays.
* @see ARCHITECTURE.md — Seed data specification.
*/
class PR_Core_Seed_Data {
@@ -24,89 +38,54 @@ class PR_Core_Seed_Data {
$dosing = self::seed_dosing_rows( $peptide_ids );
$legal = self::seed_legal_cells( $peptide_ids );
return [
return array(
'peptides' => count( $peptide_ids ),
'dosing_rows' => $dosing,
'legal_cells' => $legal,
];
);
}
/**
* Create 3 canonical peptide posts.
* Create 3 canonical peptide posts using fixture data from PR_Core_Seed_Fixtures.
*
* @return array<string, int> Map of slug => post ID.
*/
private static function seed_peptides(): array {
$peptides = [
[
'title' => 'BPC-157',
'slug' => 'bpc-157',
'excerpt' => 'Body Protection Compound-157, a pentadecapeptide derived from human gastric juice.',
'display_name' => 'BPC-157',
'aliases' => '["Body Protection Compound-157","Bepecin","PL 14736","PL-10"]',
'molecular_formula' => 'C62H98N16O22',
'molecular_weight' => 1419.53,
'cas_number' => '137525-51-0',
'drugbank_id' => '',
'chembl_id' => '',
'evidence_strength' => 'observational',
],
[
'title' => 'Semaglutide',
'slug' => 'semaglutide',
'excerpt' => 'A GLP-1 receptor agonist approved for type 2 diabetes and chronic weight management.',
'display_name' => 'Semaglutide',
'aliases' => '["Ozempic","Wegovy","Rybelsus"]',
'molecular_formula' => 'C187H291N45O59',
'molecular_weight' => 4113.58,
'cas_number' => '910463-68-2',
'drugbank_id' => 'DB13928',
'chembl_id' => 'CHEMBL3137309',
'evidence_strength' => 'meta-analysis',
],
[
'title' => 'TB-500',
'slug' => 'tb-500',
'excerpt' => 'Thymosin Beta-4 fragment, a synthetic peptide used in tissue repair research.',
'display_name' => 'TB-500',
'aliases' => '["Thymosin Beta-4","Tβ4"]',
'molecular_formula' => 'C212H350N56O78S',
'molecular_weight' => 4963.44,
'cas_number' => '77591-33-4',
'drugbank_id' => '',
'chembl_id' => '',
'evidence_strength' => 'preclinical',
],
];
$peptides = PR_Core_Seed_Fixtures::get_peptides();
$ids = array();
$ids = [];
foreach ( $peptides as $p ) {
$existing = get_posts( [
$existing = get_posts(
array(
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
'name' => $p['slug'],
'posts_per_page' => 1,
'post_status' => 'any',
] );
)
);
if ( ! empty( $existing ) ) {
$ids[ $p['slug'] ] = $existing[0]->ID;
continue;
}
$post_id = wp_insert_post( [
$post_id = wp_insert_post(
array(
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
'post_title' => $p['title'],
'post_name' => $p['slug'],
'post_excerpt' => $p['excerpt'],
'post_status' => 'publish',
'post_content' => '',
] );
)
);
if ( is_wp_error( $post_id ) ) {
continue;
}
foreach ( [ 'display_name', 'aliases', 'molecular_formula', 'molecular_weight', 'cas_number', 'drugbank_id', 'chembl_id', 'evidence_strength' ] as $key ) {
$meta_keys = array( 'display_name', 'aliases', 'molecular_formula', 'molecular_weight', 'cas_number', 'drugbank_id', 'chembl_id', 'evidence_strength' );
foreach ( $meta_keys as $key ) {
update_post_meta( $post_id, $key, $p[ $key ] );
}
update_post_meta( $post_id, 'editorial_review_status', 'published' );
@@ -119,30 +98,16 @@ class PR_Core_Seed_Data {
}
/**
* Seed 10 dosing rows across the 3 peptides.
* Seed 10 dosing rows across the 3 peptides using fixture data.
*
* @param array<string, int> $peptide_ids Map of slug => post ID.
* @return int Number of rows inserted.
*/
private static function seed_dosing_rows( array $peptide_ids ): int {
$repo = new PR_Core_Dosing_Repository();
$rows = [
// BPC-157 (4 rows).
[ 'peptide' => 'bpc-157', 'dose_min' => 200, 'dose_max' => 300, 'dose_unit' => 'mcg', 'route' => 'subq', 'frequency' => 'twice daily', 'population' => 'healthy', 'evidence_strength' => 'observational', 'study_title' => 'BPC 157 in wound healing review', 'study_year' => 2021, 'citation_pubmed_id' => '34537800' ],
[ 'peptide' => 'bpc-157', 'dose_min' => 500, 'dose_max' => 500, 'dose_unit' => 'mcg', 'route' => 'subq', 'frequency' => 'daily', 'population' => 'healthy', 'evidence_strength' => 'case-series', 'study_title' => 'Subcutaneous BPC-157 in tendon repair', 'study_year' => 2019, 'citation_pubmed_id' => '30915550' ],
[ 'peptide' => 'bpc-157', 'dose_min' => 10, 'dose_max' => 10, 'dose_unit' => 'mcg', 'route' => 'oral', 'frequency' => 'daily', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'Oral BPC-157 in rat gastric ulcer model', 'study_year' => 2018, 'citation_pubmed_id' => '29869189' ],
[ 'peptide' => 'bpc-157', 'dose_min' => 250, 'dose_max' => 750, 'dose_unit' => 'mcg', 'route' => 'im', 'frequency' => 'daily', 'population' => 'clinical', 'evidence_strength' => 'case-series', 'study_title' => 'Intramuscular BPC-157 for muscle injuries', 'study_year' => 2020, 'citation_pubmed_id' => '33312000' ],
// Semaglutide (4 rows).
[ 'peptide' => 'semaglutide', 'dose_min' => 0.25, 'dose_max' => 0.25, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'SUSTAIN 1: Semaglutide in T2DM', 'study_year' => 2017, 'citation_pubmed_id' => '28930514', 'indication' => 'Type 2 diabetes — initiation dose' ],
[ 'peptide' => 'semaglutide', 'dose_min' => 1.0, 'dose_max' => 1.0, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'SUSTAIN 6: CV outcomes with semaglutide', 'study_year' => 2016, 'citation_pubmed_id' => '27633186', 'indication' => 'Type 2 diabetes — maintenance' ],
[ 'peptide' => 'semaglutide', 'dose_min' => 2.4, 'dose_max' => 2.4, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'STEP 1: Semaglutide 2.4mg for obesity', 'study_year' => 2021, 'citation_pubmed_id' => '33567185', 'indication' => 'Chronic weight management' ],
[ 'peptide' => 'semaglutide', 'dose_min' => 14, 'dose_max' => 14, 'dose_unit' => 'mg', 'route' => 'oral', 'frequency' => 'daily', 'population' => 'clinical', 'evidence_strength' => 'rct-large', 'study_title' => 'PIONEER 1: Oral semaglutide in T2DM', 'study_year' => 2019, 'citation_pubmed_id' => '30924169', 'indication' => 'Type 2 diabetes — oral formulation' ],
// TB-500 (2 rows).
[ 'peptide' => 'tb-500', 'dose_min' => 2, 'dose_max' => 2.5, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'twice weekly', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'Thymosin beta-4 promotes dermal healing in rats', 'study_year' => 2007, 'citation_pubmed_id' => '17584560' ],
[ 'peptide' => 'tb-500', 'dose_min' => 5, 'dose_max' => 5, 'dose_unit' => 'mg', 'route' => 'subq', 'frequency' => 'weekly', 'population' => 'animal', 'evidence_strength' => 'preclinical', 'study_title' => 'TB4 cardiac repair in murine MI model', 'study_year' => 2012, 'citation_pubmed_id' => '22561753' ],
];
$rows = PR_Core_Seed_Fixtures::get_dosing_rows();
$count = 0;
foreach ( $rows as $row ) {
$slug = $row['peptide'];
unset( $row['peptide'] );
@@ -153,10 +118,10 @@ class PR_Core_Seed_Data {
$row['peptide_id'] = $peptide_ids[ $slug ];
$row['source'] = 'manual';
$row['added_by'] = get_current_user_id() ?: 1;
$row['added_by'] = get_current_user_id() !== 0 ? get_current_user_id() : 1;
if ( $repo->insert( $row ) > 0 ) {
$count++;
++$count;
}
}
@@ -164,22 +129,16 @@ class PR_Core_Seed_Data {
}
/**
* Seed 5 legal cells across BPC-157 and Semaglutide.
* Seed 5 legal cells across BPC-157 and Semaglutide using fixture data.
*
* @param array<string, int> $peptide_ids Map of slug => post ID.
* @return int Number of cells inserted.
*/
private static function seed_legal_cells( array $peptide_ids ): int {
$repo = new PR_Core_Legal_Repository();
$cells = [
[ 'peptide' => 'bpc-157', 'country_code' => 'US', 'status' => 'ruo', 'regulatory_framework' => 'Not FDA-approved; available as Research Use Only', 'notes' => 'Compounding pharmacies may dispense under FDA 503A/503B exemptions.' ],
[ 'peptide' => 'bpc-157', 'country_code' => 'GB', 'status' => 'unclear', 'regulatory_framework' => 'Not listed by MHRA', 'notes' => 'No specific scheduling; import for personal use is a grey area.' ],
[ 'peptide' => 'semaglutide', 'country_code' => 'US', 'status' => 'prescription', 'regulatory_framework' => 'FDA-approved (Ozempic, Wegovy, Rybelsus)', 'regulatory_text_url' => 'https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/209637s020lbl.pdf', 'notes' => 'Schedule IV not applicable; requires valid prescription.' ],
[ 'peptide' => 'semaglutide', 'country_code' => 'GB', 'status' => 'prescription', 'regulatory_framework' => 'MHRA-approved (Ozempic, Wegovy)', 'notes' => 'Available via NHS and private prescription.' ],
[ 'peptide' => 'semaglutide', 'country_code' => 'AU', 'status' => 'prescription', 'regulatory_framework' => 'TGA-approved (Ozempic)', 'notes' => 'PBS-listed for type 2 diabetes; Wegovy approval pending as of 2025.' ],
];
$cells = PR_Core_Seed_Fixtures::get_legal_cells();
$count = 0;
foreach ( $cells as $cell ) {
$slug = $cell['peptide'];
unset( $cell['peptide'] );
@@ -189,10 +148,10 @@ class PR_Core_Seed_Data {
}
$cell['peptide_id'] = $peptide_ids[ $slug ];
$cell['reviewer_id'] = get_current_user_id() ?: 1;
$cell['reviewer_id'] = get_current_user_id() !== 0 ? get_current_user_id() : 1;
if ( $repo->insert( $cell ) > 0 ) {
$count++;
++$count;
}
}

265
includes/class-pr-core-seed-fixtures.php Normal file
View File

@@ -0,0 +1,265 @@
<?php
/**
* Seed Fixtures.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Provides hard-coded peptide, dosing, and legal data used by PR_Core_Seed_Data
*
* @package Peptide_Repo_Core
*/
/**
* Static seed data fixtures for development and testing.
*
* What: Provides hard-coded peptide, dosing, and legal data used by PR_Core_Seed_Data.
* Who calls it: PR_Core_Seed_Data — calls get_peptides(), get_dosing_rows(), get_legal_cells().
* Dependencies: None.
*
* @see class-pr-core-seed-data.php — Orchestrator that consumes these fixtures.
*/
class PR_Core_Seed_Fixtures {
/**
* Return the canonical list of peptide fixture definitions.
*
* @return array<int, array<string, mixed>>
*/
public static function get_peptides(): array {
return array(
array(
'title' => 'BPC-157',
'slug' => 'bpc-157',
'excerpt' => 'Body Protection Compound-157, a pentadecapeptide derived from human gastric juice.',
'display_name' => 'BPC-157',
'aliases' => '["Body Protection Compound-157","Bepecin","PL 14736","PL-10"]',
'molecular_formula' => 'C62H98N16O22',
'molecular_weight' => 1419.53,
'cas_number' => '137525-51-0',
'drugbank_id' => '',
'chembl_id' => '',
'evidence_strength' => 'observational',
),
array(
'title' => 'Semaglutide',
'slug' => 'semaglutide',
'excerpt' => 'A GLP-1 receptor agonist approved for type 2 diabetes and chronic weight management.',
'display_name' => 'Semaglutide',
'aliases' => '["Ozempic","Wegovy","Rybelsus"]',
'molecular_formula' => 'C187H291N45O59',
'molecular_weight' => 4113.58,
'cas_number' => '910463-68-2',
'drugbank_id' => 'DB13928',
'chembl_id' => 'CHEMBL3137309',
'evidence_strength' => 'meta-analysis',
),
array(
'title' => 'TB-500',
'slug' => 'tb-500',
'excerpt' => 'Thymosin Beta-4 fragment, a synthetic peptide used in tissue repair research.',
'display_name' => 'TB-500',
'aliases' => '["Thymosin Beta-4","T\u03b24"]',
'molecular_formula' => 'C212H350N56O78S',
'molecular_weight' => 4963.44,
'cas_number' => '77591-33-4',
'drugbank_id' => '',
'chembl_id' => '',
'evidence_strength' => 'preclinical',
),
);
}
/**
* Return the canonical list of dosing row fixture definitions.
*
* @return array<int, array<string, mixed>>
*/
public static function get_dosing_rows(): array {
return array(
array(
'peptide' => 'bpc-157',
'dose_min' => 200,
'dose_max' => 300,
'dose_unit' => 'mcg',
'route' => 'subq',
'frequency' => 'twice daily',
'population' => 'healthy',
'evidence_strength' => 'observational',
'study_title' => 'BPC 157 in wound healing review',
'study_year' => 2021,
'citation_pubmed_id' => '34537800',
),
array(
'peptide' => 'bpc-157',
'dose_min' => 500,
'dose_max' => 500,
'dose_unit' => 'mcg',
'route' => 'subq',
'frequency' => 'daily',
'population' => 'healthy',
'evidence_strength' => 'case-series',
'study_title' => 'Subcutaneous BPC-157 in tendon repair',
'study_year' => 2019,
'citation_pubmed_id' => '30915550',
),
array(
'peptide' => 'bpc-157',
'dose_min' => 10,
'dose_max' => 10,
'dose_unit' => 'mcg',
'route' => 'oral',
'frequency' => 'daily',
'population' => 'animal',
'evidence_strength' => 'preclinical',
'study_title' => 'Oral BPC-157 in rat gastric ulcer model',
'study_year' => 2018,
'citation_pubmed_id' => '29869189',
),
array(
'peptide' => 'bpc-157',
'dose_min' => 250,
'dose_max' => 750,
'dose_unit' => 'mcg',
'route' => 'im',
'frequency' => 'daily',
'population' => 'clinical',
'evidence_strength' => 'case-series',
'study_title' => 'Intramuscular BPC-157 for muscle injuries',
'study_year' => 2020,
'citation_pubmed_id' => '33312000',
),
array(
'peptide' => 'semaglutide',
'dose_min' => 0.25,
'dose_max' => 0.25,
'dose_unit' => 'mg',
'route' => 'subq',
'frequency' => 'weekly',
'population' => 'clinical',
'evidence_strength' => 'rct-large',
'study_title' => 'SUSTAIN 1: Semaglutide in T2DM',
'study_year' => 2017,
'citation_pubmed_id' => '28930514',
'indication' => 'Type 2 diabetes initiation dose',
),
array(
'peptide' => 'semaglutide',
'dose_min' => 1.0,
'dose_max' => 1.0,
'dose_unit' => 'mg',
'route' => 'subq',
'frequency' => 'weekly',
'population' => 'clinical',
'evidence_strength' => 'rct-large',
'study_title' => 'SUSTAIN 6: CV outcomes with semaglutide',
'study_year' => 2016,
'citation_pubmed_id' => '27633186',
'indication' => 'Type 2 diabetes maintenance',
),
array(
'peptide' => 'semaglutide',
'dose_min' => 2.4,
'dose_max' => 2.4,
'dose_unit' => 'mg',
'route' => 'subq',
'frequency' => 'weekly',
'population' => 'clinical',
'evidence_strength' => 'rct-large',
'study_title' => 'STEP 1: Semaglutide 2.4mg for obesity',
'study_year' => 2021,
'citation_pubmed_id' => '33567185',
'indication' => 'Chronic weight management',
),
array(
'peptide' => 'semaglutide',
'dose_min' => 14,
'dose_max' => 14,
'dose_unit' => 'mg',
'route' => 'oral',
'frequency' => 'daily',
'population' => 'clinical',
'evidence_strength' => 'rct-large',
'study_title' => 'PIONEER 1: Oral semaglutide in T2DM',
'study_year' => 2019,
'citation_pubmed_id' => '30924169',
'indication' => 'Type 2 diabetes oral formulation',
),
array(
'peptide' => 'tb-500',
'dose_min' => 2,
'dose_max' => 2.5,
'dose_unit' => 'mg',
'route' => 'subq',
'frequency' => 'twice weekly',
'population' => 'animal',
'evidence_strength' => 'preclinical',
'study_title' => 'Thymosin beta-4 promotes dermal healing in rats',
'study_year' => 2007,
'citation_pubmed_id' => '17584560',
),
array(
'peptide' => 'tb-500',
'dose_min' => 5,
'dose_max' => 5,
'dose_unit' => 'mg',
'route' => 'subq',
'frequency' => 'weekly',
'population' => 'animal',
'evidence_strength' => 'preclinical',
'study_title' => 'TB4 cardiac repair in murine MI model',
'study_year' => 2012,
'citation_pubmed_id' => '22561753',
),
);
}
/**
* Return the canonical list of legal cell fixture definitions.
*
* @return array<int, array<string, mixed>>
*/
public static function get_legal_cells(): array {
return array(
array(
'peptide' => 'bpc-157',
'country_code' => 'US',
'status' => 'ruo',
'regulatory_framework' => 'Not FDA-approved; available as Research Use Only',
'notes' => 'Compounding pharmacies may dispense under FDA 503A/503B exemptions.',
),
array(
'peptide' => 'bpc-157',
'country_code' => 'GB',
'status' => 'unclear',
'regulatory_framework' => 'Not listed by MHRA',
'notes' => 'No specific scheduling; import for personal use is a grey area.',
),
array(
'peptide' => 'semaglutide',
'country_code' => 'US',
'status' => 'prescription',
'regulatory_framework' => 'FDA-approved (Ozempic, Wegovy, Rybelsus)',
'regulatory_text_url' => 'https://www.accessdata.fda.gov/drugsatfda_docs/label/2023/209637s020lbl.pdf',
'notes' => 'Schedule IV not applicable; requires valid prescription.',
),
array(
'peptide' => 'semaglutide',
'country_code' => 'GB',
'status' => 'prescription',
'regulatory_framework' => 'MHRA-approved (Ozempic, Wegovy)',
'notes' => 'Available via NHS and private prescription.',
),
array(
'peptide' => 'semaglutide',
'country_code' => 'AU',
'status' => 'prescription',
'regulatory_framework' => 'TGA-approved (Ozempic)',
'notes' => 'PBS-listed for type 2 diabetes; Wegovy approval pending as of 2025.',
),
);
}
}

54
includes/class-pr-core.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Class Pr Core.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Registers all hooks, runs migrations, boots subsystems
*
* @package Peptide_Repo_Core
*/
/**
* Main orchestrator for the Peptide Repo Core plugin.
*
@@ -43,28 +55,28 @@ class PR_Core {
$repo_daily_tax = new PR_Core_Repo_Daily_Taxonomy();
$repo_daily_tax->register_hooks();
// One-shot rewrite flush on in-place version bumps. Runs at the very
// end of init (priority 999) so all CPTs/taxonomies — ours and
// anyone else's — are registered first. Handles updates deployed
// One-shot rewrite flush on in-place version bumps. Runs at the very.
// end of init (priority 999) so all CPTs/taxonomies — ours and.
// anyone else's — are registered first. Handles updates deployed.
// without a deactivate/reactivate cycle (e.g., SCP/rsync pushes).
add_action( 'init', [ PR_Core_Activator::class, 'maybe_flush_on_version_change' ], 999 );
add_action( 'init', array( PR_Core_Activator::class, 'maybe_flush_on_version_change' ), 999 );
// Verification scanner: register cron hook and schedule if not already scheduled.
if ( ! wp_next_scheduled( 'pr_core_verification_scan' ) ) {
wp_schedule_event( time(), get_option( 'pr_core_scan_cadence', 'weekly' ), 'pr_core_verification_scan' );
}
add_action( 'pr_core_verification_scan', [ PR_Core_Verification_Scanner::class, 'run_scan' ] );
add_action( 'pr_core_verification_scan', array( PR_Core_Verification_Scanner::class, 'run_scan' ) );
// Ajax handlers must be registered outside is_admin() — admin-ajax.php
// Ajax handlers must be registered outside is_admin() — admin-ajax.php.
// does not define WP_ADMIN, so is_admin() returns false for ajax requests.
add_action( 'wp_ajax_pr_core_mark_verified', [ PR_Core_Ajax_Handlers::class, 'handle_mark_verified' ] );
add_action( 'wp_ajax_pr_core_scan_now', [ PR_Core_Ajax_Handlers::class, 'handle_scan_now' ] );
add_action( 'wp_ajax_pr_core_mark_verified', array( PR_Core_Ajax_Handlers::class, 'handle_mark_verified' ) );
add_action( 'wp_ajax_pr_core_scan_now', array( PR_Core_Ajax_Handlers::class, 'handle_scan_now' ) );
// Admin UI (fires on admin_init, admin_menu).
if ( is_admin() ) {
add_action( 'admin_menu', [ PR_Core_Settings::class, 'add_settings_page' ] );
add_action( 'admin_init', [ PR_Core_Settings::class, 'register_settings' ] );
add_action( 'wp_dashboard_setup', [ PR_Core_Verification_Widget::class, 'register' ] );
add_action( 'admin_menu', array( PR_Core_Settings::class, 'add_settings_page' ) );
add_action( 'admin_init', array( PR_Core_Settings::class, 'register_settings' ) );
add_action( 'wp_dashboard_setup', array( PR_Core_Verification_Widget::class, 'register' ) );
$admin = new PR_Core_Admin();
$admin->register_hooks();
@@ -86,7 +98,7 @@ class PR_Core {
$related_posts->register_hooks();
// Enqueue related-posts CSS on single peptide pages.
add_action( 'wp_enqueue_scripts', [ $this, 'enqueue_frontend_styles' ] );
add_action( 'wp_enqueue_scripts', array( $this, 'enqueue_frontend_styles' ) );
// REST API.
$rest = new PR_Core_Rest_Controller();
@@ -109,7 +121,7 @@ class PR_Core {
wp_enqueue_style(
'pr-core-related-posts',
PR_CORE_PLUGIN_URL . 'assets/css/related-posts.css',
[],
array(),
PR_CORE_VERSION
);
}
@@ -125,9 +137,9 @@ class PR_Core {
* @return void
*/
private function register_public_filters(): void {
add_filter( 'pr_core_get_indexable_corpus', [ $this, 'filter_indexable_corpus' ] );
add_filter( 'pr_core_disclaimer_for_surface', [ $this, 'filter_disclaimer_for_surface' ], 10, 2 );
add_filter( 'pr_core_evidence_strength_label', [ $this, 'filter_evidence_label' ], 10, 2 );
add_filter( 'pr_core_get_indexable_corpus', array( $this, 'filter_indexable_corpus' ) );
add_filter( 'pr_core_disclaimer_for_surface', array( $this, 'filter_disclaimer_for_surface' ), 10, 2 );
add_filter( 'pr_core_evidence_strength_label', array( $this, 'filter_evidence_label' ), 10, 2 );
}
/**
@@ -140,16 +152,16 @@ class PR_Core {
*/
public function filter_indexable_corpus( array $entries ): array {
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( [ 'status' => 'publish' ] );
$peptides = $repo->find_all( array( 'status' => 'publish' ) );
foreach ( $peptides as $dto ) {
$entries[] = [
$entries[] = array(
'id' => $dto->id,
'url' => get_permalink( $dto->id ),
'title' => $dto->title,
'body' => $dto->excerpt . "\n" . $dto->content,
'type' => 'peptide_monograph',
];
);
}
return $entries;
@@ -174,14 +186,14 @@ class PR_Core {
* @return string Localized label.
*/
public function filter_evidence_label( string $label, string $strength ): string {
$map = [
$map = array(
'preclinical' => __( 'Preclinical', 'peptide-repo-core' ),
'case-series' => __( 'Case Series', 'peptide-repo-core' ),
'observational' => __( 'Observational', 'peptide-repo-core' ),
'rct-small' => __( 'Small RCT', 'peptide-repo-core' ),
'rct-large' => __( 'Large RCT', 'peptide-repo-core' ),
'meta-analysis' => __( 'Meta-Analysis', 'peptide-repo-core' ),
];
);
return $map[ $strength ] ?? $strength;
}

38
includes/core/class-pr-core-internal-posts-provider.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Internal Posts Provider.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Implements PR_Core_Related_Posts_Provider by querying posts tagged
*
* @package Peptide_Repo_Core
*/
/**
* Fetches posts related to a peptide via taxonomy and fallback text search.
*
@@ -33,7 +45,7 @@ class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider
public function get_posts( int $peptide_id, int $limit ): array {
$peptide = get_post( $peptide_id );
if ( ! $peptide || 'peptide' !== $peptide->post_type ) {
return [];
return array();
}
$cache_key = 'pr_core_related_' . $peptide_id;
@@ -64,21 +76,23 @@ class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider
* @return array<int, \WP_Post>
*/
private function query_by_taxonomy( string $peptide_slug, int $limit ): array {
$query = new WP_Query( [
$query = new WP_Query(
array(
'post_type' => 'post',
'posts_per_page' => $limit,
'orderby' => 'date',
'order' => 'DESC',
'tax_query' => [
[
'tax_query' => array(
array(
'taxonomy' => 'peptide_topic',
'field' => 'slug',
'terms' => $peptide_slug,
],
],
] );
),
),
)
);
return $query->posts ?: [];
return $query->posts ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
}
/**
@@ -89,14 +103,16 @@ class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider
* @return array<int, \WP_Post>
*/
private function query_by_search( string $search_term, int $limit ): array {
$query = new WP_Query( [
$query = new WP_Query(
array(
'post_type' => 'post',
'posts_per_page' => $limit,
'orderby' => 'date',
'order' => 'DESC',
's' => $search_term,
] );
)
);
return $query->posts ?: [];
return $query->posts ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
}
}

12
includes/core/class-pr-core-related-posts-provider.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Related Posts Provider.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Interface defining the get_posts() contract for related-post providers
*
* @package Peptide_Repo_Core
*/
/**
* Contract for any provider that retrieves posts related to a peptide.
*

25
includes/core/class-pr-core-related-posts-section.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Related Posts Section.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Hooks into pr_core_after_peptide_content and renders a card grid
*
* @package Peptide_Repo_Core
*/
/**
* Renders the related articles section on peptide single pages.
*
@@ -15,7 +27,11 @@ declare(strict_types=1);
*/
class PR_Core_Related_Posts_Section {
/** @var PR_Core_Related_Posts_Provider */
/**
* PR_Core_Related_Posts_Provider.
*
* @var PR_Core_Related_Posts_Provider
*/
private $provider;
/**
@@ -33,8 +49,8 @@ class PR_Core_Related_Posts_Section {
* @return void
*/
public function register_hooks(): void {
add_action( 'pr_core_after_peptide_content', [ $this, 'render' ] );
add_action( 'save_post_post', [ $this, 'invalidate_caches' ] );
add_action( 'pr_core_after_peptide_content', array( $this, 'render' ) );
add_action( 'save_post_post', array( $this, 'invalidate_caches' ) );
}
/**
@@ -72,7 +88,7 @@ class PR_Core_Related_Posts_Section {
break;
}
setup_postdata( $post );
get_template_part( 'template-parts/related-posts/card', null, [ 'post' => $post ] );
get_template_part( 'template-parts/related-posts/card', null, array( 'post' => $post ) );
++$count;
}
wp_reset_postdata();
@@ -90,6 +106,7 @@ class PR_Core_Related_Posts_Section {
<?php
echo wp_kses_post(
sprintf(
// translators: %s: peptide display name.
__( 'View all %s articles &rarr;', 'peptide-repo-core' ),
esc_html( $peptide->post_title )
)

214
includes/cpt/class-pr-core-peptide-cpt.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Peptide Cpt.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Defines peptide CPT with REST support, archive, and meta fields
*
* @package Peptide_Repo_Core
*/
/**
* Registers the peptide custom post type and associated taxonomy.
*
@@ -17,13 +29,25 @@ declare(strict_types=1);
*/
class PR_Core_Peptide_CPT {
/** @var string Post type slug (owned by PR Core since v0.2.0; PSA previously registered this). */
/**
* Post type slug (owned by PR Core since v0.2.0; PSA previously registered this).
*
* @var string Post type slug (owned by PR Core since v0.2.0; PSA previously registered this).
*/
public const POST_TYPE = 'peptide';
/** @var string Taxonomy: category (e.g., GLP-1 agonist). */
/**
* Taxonomy: category (e.g., GLP-1 agonist).
*
* @var string Taxonomy: category (e.g., GLP-1 agonist).
*/
public const TAX_CATEGORY = 'peptide_category';
/** @var string Capability required for editing peptide data. */
/**
* Capability required for editing peptide data.
*
* @var string Capability required for editing peptide data.
*/
public const CAPABILITY = 'manage_peptide_content';
/**
@@ -31,26 +55,26 @@ class PR_Core_Peptide_CPT {
*
* @var string[]
*/
public const EVIDENCE_STRENGTHS = [
public const EVIDENCE_STRENGTHS = array(
'preclinical',
'case-series',
'observational',
'rct-small',
'rct-large',
'meta-analysis',
];
);
/**
* Editorial review status enum values.
*
* @var string[]
*/
public const REVIEW_STATUSES = [
public const REVIEW_STATUSES = array(
'draft',
'in-review',
'published',
'retired',
];
);
/**
* Post-meta field definitions (1:1 with peptide).
@@ -59,115 +83,7 @@ class PR_Core_Peptide_CPT {
* @return array<string, array<string, mixed>>
*/
public static function get_meta_fields(): array {
return [
'display_name' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'aliases' => [
'type' => 'string',
'default' => '[]',
'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
],
'molecular_formula' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'molecular_weight' => [
'type' => 'number',
'default' => 0,
'sanitize' => 'floatval',
],
'cas_number' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'drugbank_id' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'chembl_id' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'evidence_strength' => [
'type' => 'string',
'default' => 'preclinical',
'sanitize' => [ __CLASS__, 'sanitize_evidence_strength' ],
],
'editorial_review_status' => [
'type' => 'string',
'default' => 'draft',
'sanitize' => [ __CLASS__, 'sanitize_review_status' ],
],
'last_editorial_review_at' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'medical_editor_id' => [
'type' => 'integer',
'default' => 0,
'sanitize' => 'absint',
],
'_pr_last_source_verified' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'_pr_last_reviewed' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'_pr_next_review_by' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
],
'_pr_verification_velocity' => [
'type' => 'string',
'default' => 'medium',
'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_velocity' ],
],
'_pr_verification_notes' => [
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_textarea_field',
],
'_pr_verification_status' => [
'type' => 'string',
'default' => 'current',
'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_status' ],
],
// Schema-input meta (v0.6.0): molecular data sourced from PSA psa_* keys via migration 0004.
'_pr_molecular_formula' => [
'type' => 'string',
'default' => '',
'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ],
],
'_pr_molecular_weight' => [
'type' => 'string',
'default' => '',
'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ],
],
'_pr_aliases' => [
'type' => 'string',
'default' => '[]',
'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
],
// FAQ items (v0.6.0): [{question, answer}] JSON for FAQPage schema. Populated by CMO content sprint.
'_pr_faq_items' => [
'type' => 'string',
'default' => '[]',
'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ],
],
];
return PR_Core_Peptide_Meta_Schema::get_fields();
}
/**
@@ -176,9 +92,9 @@ class PR_Core_Peptide_CPT {
* @return void
*/
public function register_hooks(): void {
add_action( 'init', [ __CLASS__, 'register_peptide_post_type' ] );
add_action( 'init', [ __CLASS__, 'register_taxonomies' ] );
add_action( 'init', [ __CLASS__, 'register_meta_fields' ] );
add_action( 'init', array( __CLASS__, 'register_peptide_post_type' ) );
add_action( 'init', array( __CLASS__, 'register_taxonomies' ) );
add_action( 'init', array( __CLASS__, 'register_meta_fields' ) );
}
/**
@@ -193,7 +109,7 @@ class PR_Core_Peptide_CPT {
return;
}
$labels = [
$labels = array(
'name' => __( 'Peptides', 'peptide-repo-core' ),
'singular_name' => __( 'Peptide', 'peptide-repo-core' ),
'add_new_item' => __( 'Add New Peptide', 'peptide-repo-core' ),
@@ -205,11 +121,11 @@ class PR_Core_Peptide_CPT {
'not_found_in_trash' => __( 'No peptides found in trash', 'peptide-repo-core' ),
'all_items' => __( 'All Peptides', 'peptide-repo-core' ),
'menu_name' => __( 'Peptides', 'peptide-repo-core' ),
];
);
// Args harmonized superset of PR Core + PSA for 89 existing posts.
// Supports union, capability/role perms preserved, slugs unchanged.
$args = [
$args = array(
'labels' => $labels,
'public' => true,
'publicly_queryable' => true,
@@ -218,9 +134,9 @@ class PR_Core_Peptide_CPT {
'show_in_nav_menus' => true,
'show_in_rest' => true,
'rest_base' => 'peptides',
// Note: 'rest_namespace' is deliberately omitted. Custom namespaces prevent
// Gutenberg's block editor from loading posts for editing (it fetches the
// hardcoded wp/v2 REST route). WordPress defaults to wp/v2 — appropriate for
// Note: 'rest_namespace' is deliberately omitted. Custom namespaces prevent.
// Gutenberg's block editor from loading posts for editing (it fetches the.
// hardcoded wp/v2 REST route). WordPress defaults to wp/v2 — appropriate for.
// this CPT — and keeps the REST endpoint at /wp-json/wp/v2/peptides/.
'menu_position' => 25,
'menu_icon' => 'dashicons-database',
@@ -228,9 +144,12 @@ class PR_Core_Peptide_CPT {
'map_meta_cap' => true,
'hierarchical' => false,
'has_archive' => true,
'rewrite' => [ 'slug' => 'peptides', 'with_front' => false ],
'supports' => [ 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ],
];
'rewrite' => array(
'slug' => 'peptides',
'with_front' => false,
),
'supports' => array( 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ),
);
register_post_type( self::POST_TYPE, $args );
}
@@ -246,19 +165,26 @@ class PR_Core_Peptide_CPT {
return;
}
register_taxonomy( self::TAX_CATEGORY, self::POST_TYPE, [
'labels' => [
register_taxonomy(
self::TAX_CATEGORY,
self::POST_TYPE,
array(
'labels' => array(
'name' => __( 'Peptide Categories', 'peptide-repo-core' ),
'singular_name' => __( 'Peptide Category', 'peptide-repo-core' ),
],
),
'public' => true,
'publicly_queryable' => true,
'show_in_rest' => true,
'show_ui' => true,
'show_admin_column' => true,
'hierarchical' => true,
'rewrite' => [ 'slug' => 'peptide-category', 'with_front' => false ],
] );
'rewrite' => array(
'slug' => 'peptide-category',
'with_front' => false,
),
)
);
}
/**
@@ -268,7 +194,10 @@ class PR_Core_Peptide_CPT {
*/
public static function register_meta_fields(): void {
foreach ( self::get_meta_fields() as $key => $config ) {
register_post_meta( self::POST_TYPE, $key, [
register_post_meta(
self::POST_TYPE,
$key,
array(
'type' => $config['type'],
'single' => true,
'default' => $config['default'],
@@ -277,17 +206,28 @@ class PR_Core_Peptide_CPT {
'auth_callback' => static function () {
return current_user_can( self::CAPABILITY );
},
] );
)
);
}
}
/** Sanitize evidence_strength to allowed enum values. */
/**
* Sanitize evidence_strength to allowed enum values.
*
* @param mixed $value Raw input value.
* @return string
*/
public static function sanitize_evidence_strength( $value ): string {
$value = sanitize_text_field( (string) $value );
return in_array( $value, self::EVIDENCE_STRENGTHS, true ) ? $value : 'preclinical';
}
/** Sanitize editorial_review_status to allowed enum values. */
/**
* Sanitize editorial_review_status to allowed enum values.
*
* @param mixed $value Raw input value.
* @return string
*/
public static function sanitize_review_status( $value ): string {
$value = sanitize_text_field( (string) $value );
return in_array( $value, self::REVIEW_STATUSES, true ) ? $value : 'draft';

144
includes/cpt/class-pr-core-peptide-meta-schema.php Normal file
View File

@@ -0,0 +1,144 @@
<?php
/**
* Peptide Meta Schema.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Returns the complete meta field definition map used by PR_Core_Peptide_CPT
*
* @package Peptide_Repo_Core
*/
/**
* Meta field schema definitions for the peptide CPT.
*
* What: Returns the complete meta field definition map used by PR_Core_Peptide_CPT.
* Who calls it: PR_Core_Peptide_CPT::get_meta_fields() delegates here.
* Dependencies: PR_Core_Peptide_CPT (for sanitize callbacks), PR_Core_Schema_Sanitizers,
* PR_Core_Verification_Sanitizers.
*
* @see cpt/class-pr-core-peptide-cpt.php — Consumer of this schema.
*/
class PR_Core_Peptide_Meta_Schema {
/**
* Return the full meta field definition array for the peptide CPT.
*
* Keys map to meta_key strings; values are arrays with type, default, and sanitize.
*
* @return array<string, array<string, mixed>>
*/
public static function get_fields(): array {
return array(
'display_name' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'aliases' => array(
'type' => 'string',
'default' => '[]',
'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ),
),
'molecular_formula' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'molecular_weight' => array(
'type' => 'number',
'default' => 0,
'sanitize' => 'floatval',
),
'cas_number' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'drugbank_id' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'chembl_id' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'evidence_strength' => array(
'type' => 'string',
'default' => 'preclinical',
'sanitize' => array( PR_Core_Peptide_CPT::class, 'sanitize_evidence_strength' ),
),
'editorial_review_status' => array(
'type' => 'string',
'default' => 'draft',
'sanitize' => array( PR_Core_Peptide_CPT::class, 'sanitize_review_status' ),
),
'last_editorial_review_at' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'medical_editor_id' => array(
'type' => 'integer',
'default' => 0,
'sanitize' => 'absint',
),
'_pr_last_source_verified' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'_pr_last_reviewed' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'_pr_next_review_by' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_text_field',
),
'_pr_verification_velocity' => array(
'type' => 'string',
'default' => 'medium',
'sanitize' => array( PR_Core_Verification_Sanitizers::class, 'sanitize_velocity' ),
),
'_pr_verification_notes' => array(
'type' => 'string',
'default' => '',
'sanitize' => 'sanitize_textarea_field',
),
'_pr_verification_status' => array(
'type' => 'string',
'default' => 'current',
'sanitize' => array( PR_Core_Verification_Sanitizers::class, 'sanitize_status' ),
),
'_pr_molecular_formula' => array(
'type' => 'string',
'default' => '',
'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ),
),
'_pr_molecular_weight' => array(
'type' => 'string',
'default' => '',
'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ),
),
'_pr_aliases' => array(
'type' => 'string',
'default' => '[]',
'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ),
),
'_pr_faq_items' => array(
'type' => 'string',
'default' => '[]',
'sanitize' => array( PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ),
),
);
}
}

35
includes/cpt/class-pr-core-repo-daily-cpt.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Repo Daily Cpt.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Defines the `repo_daily` CPT for articles, guides, comparisons, and news
*
* @package Peptide_Repo_Core
*/
/**
* Registers the repo_daily custom post type for editorial publications.
*
@@ -18,7 +30,11 @@ declare(strict_types=1);
*/
class PR_Core_Repo_Daily_CPT {
/** @var string Post type slug (repo_daily). */
/**
* Post type slug (repo_daily).
*
* @var string Post type slug (repo_daily).
*/
public const POST_TYPE = 'repo_daily';
/**
@@ -27,7 +43,7 @@ class PR_Core_Repo_Daily_CPT {
* @return void
*/
public function register_hooks(): void {
add_action( 'init', [ __CLASS__, 'register_post_type' ] );
add_action( 'init', array( __CLASS__, 'register_post_type' ) );
}
/**
@@ -42,7 +58,7 @@ class PR_Core_Repo_Daily_CPT {
return;
}
$labels = [
$labels = array(
'name' => __( 'Repo Daily', 'peptide-repo-core' ),
'singular_name' => __( 'Repo Daily', 'peptide-repo-core' ),
'add_new_item' => __( 'Add New Article', 'peptide-repo-core' ),
@@ -54,9 +70,9 @@ class PR_Core_Repo_Daily_CPT {
'not_found_in_trash' => __( 'No articles found in trash', 'peptide-repo-core' ),
'all_items' => __( 'All Articles', 'peptide-repo-core' ),
'menu_name' => __( 'Repo Daily', 'peptide-repo-core' ),
];
);
$args = [
$args = array(
'labels' => $labels,
'public' => true,
'publicly_queryable' => true,
@@ -71,9 +87,12 @@ class PR_Core_Repo_Daily_CPT {
'map_meta_cap' => true,
'hierarchical' => false,
'has_archive' => true,
'rewrite' => [ 'slug' => 'daily', 'with_front' => false ],
'supports' => [ 'title', 'editor', 'excerpt', 'thumbnail', 'custom-fields' ],
];
'rewrite' => array(
'slug' => 'daily',
'with_front' => false,
),
'supports' => array( 'title', 'editor', 'excerpt', 'thumbnail', 'custom-fields' ),
);
register_post_type( self::POST_TYPE, $args );
}

22
includes/cpt/class-pr-core-schema-sanitizers.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Schema Sanitizers.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Static sanitizer methods for _pr_molecular_formula, _pr_molecular_weight,
*
* @package Peptide_Repo_Core
*/
/**
* Sanitizers for v0.6.0 schema-input meta fields.
*
@@ -68,7 +80,7 @@ class PR_Core_Schema_Sanitizers {
}
// 3. Extract the maximal leading run of valid element tokens and separators.
// A valid run must start with an element token ([A-Z][a-z]?\d*), not a separator.
$pattern = '/^((?:' . self::FORMULA_TOKEN . '|' . self::FORMULA_SEP . ')+)/u';
$pattern = '/^((?:' . self::FORMULA_TOKEN . '|' . self::FORMULA_SEP . ')+)/u'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
if ( preg_match( $pattern, $value, $m ) ) {
return $m[1];
}
@@ -132,7 +144,7 @@ class PR_Core_Schema_Sanitizers {
return '[]';
}
$clean = [];
$clean = array();
foreach ( $value as $item ) {
if ( ! is_array( $item ) ) {
continue;
@@ -140,13 +152,13 @@ class PR_Core_Schema_Sanitizers {
$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
$answer = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
if ( '' !== $question && '' !== $answer ) {
$clean[] = [
$clean[] = array(
'question' => $question,
'answer' => $answer,
];
);
}
}
return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
}
}

37
includes/cpt/class-pr-core-topic-taxonomy.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Topic Taxonomy.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Defines the `peptide_topic` taxonomy attached to the post CPT
*
* @package Peptide_Repo_Core
*/
/**
* Registers the peptide_topic taxonomy for linking blog posts to peptides.
*
@@ -18,7 +30,11 @@ declare(strict_types=1);
*/
class PR_Core_Topic_Taxonomy {
/** @var string Taxonomy: topic (links blog posts to peptides by slug). */
/**
* Taxonomy: topic (links blog posts to peptides by slug).
*
* @var string Taxonomy: topic (links blog posts to peptides by slug).
*/
public const TAX_TOPIC = 'peptide_topic';
/**
@@ -27,7 +43,7 @@ class PR_Core_Topic_Taxonomy {
* @return void
*/
public function register_hooks(): void {
add_action( 'init', [ __CLASS__, 'register_topic_taxonomy' ] );
add_action( 'init', array( __CLASS__, 'register_topic_taxonomy' ) );
}
/**
@@ -45,18 +61,25 @@ class PR_Core_Topic_Taxonomy {
return;
}
register_taxonomy( self::TAX_TOPIC, 'post', [
'labels' => [
register_taxonomy(
self::TAX_TOPIC,
'post',
array(
'labels' => array(
'name' => __( 'Peptide Topics', 'peptide-repo-core' ),
'singular_name' => __( 'Peptide Topic', 'peptide-repo-core' ),
],
),
'public' => true,
'publicly_queryable' => true,
'show_in_rest' => true,
'show_ui' => true,
'show_admin_column' => true,
'hierarchical' => false,
'rewrite' => [ 'slug' => 'peptide-topic', 'with_front' => false ],
] );
'rewrite' => array(
'slug' => 'peptide-topic',
'with_front' => false,
),
)
);
}
}

16
includes/cpt/class-pr-core-verification-sanitizers.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Sanitizers.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Standalone sanitization functions for verification_velocity and verification_status fields
*
* @package Peptide_Repo_Core
*/
/**
* Sanitizers for verification meta fields.
*
@@ -19,7 +31,7 @@ class PR_Core_Verification_Sanitizers {
* @return string Valid enum value (low, medium, high).
*/
public static function sanitize_velocity( string $value ): string {
return in_array( $value, [ 'low', 'medium', 'high' ], true ) ? $value : 'medium';
return in_array( $value, array( 'low', 'medium', 'high' ), true ) ? $value : 'medium';
}
/**
@@ -29,6 +41,6 @@ class PR_Core_Verification_Sanitizers {
* @return string Valid enum value (current, due, overdue).
*/
public static function sanitize_status( string $value ): string {
return in_array( $value, [ 'current', 'due', 'overdue' ], true ) ? $value : 'current';
return in_array( $value, array( 'current', 'due', 'overdue' ), true ) ? $value : 'current';
}
}

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,
];
);
}
}

148
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.
*
@@ -13,34 +25,166 @@ 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 ) {
@@ -78,7 +222,7 @@ class PR_Core_Dosing_Row_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,
@@ -99,6 +243,6 @@ class PR_Core_Dosing_Row_DTO {
'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 ),
];
);
}
}

36
includes/frontend/class-pr-core-disclaimer.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Disclaimer.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Provides shortcode [pr_disclaimer surface="dosing"] and function
*
* @package Peptide_Repo_Core
*/
/**
* Shared disclaimer component for all peptide data surfaces.
*
@@ -17,10 +29,18 @@ declare(strict_types=1);
*/
class PR_Core_Disclaimer {
/** @var string Option key for disclaimer copy (JSON). */
/**
* Option key for disclaimer copy (JSON).
*
* @var string Option key for disclaimer copy (JSON).
*/
private const COPY_OPTION = 'pr_core_disclaimer_copy';
/** @var string Option key for disclaimer version. */
/**
* Option key for disclaimer version.
*
* @var string Option key for disclaimer version.
*/
private const VERSION_OPTION = 'pr_core_disclaimer_version';
/**
@@ -28,13 +48,13 @@ class PR_Core_Disclaimer {
*
* @var array<string, string>
*/
private const DEFAULTS = [
private const DEFAULTS = array(
'dosing' => 'The dosing information presented here is compiled from published peer-reviewed literature and is provided for educational and research purposes only. It does not constitute medical advice, diagnosis, or treatment recommendations. Always consult a licensed healthcare professional before making any decisions based on this information.',
'legal' => 'Legal status information is compiled from publicly available regulatory texts and is current as of the last-verified date shown. Regulatory frameworks change frequently. This information does not constitute legal advice. Verify current regulations with the relevant regulatory authority in your jurisdiction before taking any action.',
'reconstitution' => 'This calculator is provided for educational purposes only. Always verify your calculations independently and consult a licensed healthcare professional. The results are based on the inputs you provide and standard reconstitution mathematics.',
'ai-answer' => 'This response was generated by an AI system and may contain errors or omissions. All claims are grounded in the Peptide Repo corpus and cited sources where possible. This is not medical advice. Always verify information with primary sources and consult a licensed healthcare professional.',
'general' => 'The information on this site is for educational and research purposes only. It is not intended as medical advice, diagnosis, or treatment. Always consult a licensed healthcare professional.',
];
);
/**
* Register shortcode and any frontend hooks.
@@ -42,7 +62,7 @@ class PR_Core_Disclaimer {
* @return void
*/
public function register_hooks(): void {
add_shortcode( 'pr_disclaimer', [ $this, 'shortcode_handler' ] );
add_shortcode( 'pr_disclaimer', array( $this, 'shortcode_handler' ) );
}
/**
@@ -52,7 +72,7 @@ class PR_Core_Disclaimer {
* @return string Disclaimer HTML.
*/
public function shortcode_handler( $atts ): string {
$atts = shortcode_atts( [ 'surface' => 'general' ], $atts, 'pr_disclaimer' );
$atts = shortcode_atts( array( 'surface' => 'general' ), $atts, 'pr_disclaimer' );
return self::render( sanitize_text_field( $atts['surface'] ) );
}
@@ -81,7 +101,7 @@ class PR_Core_Disclaimer {
*/
public static function get_disclaimer_text( string $surface ): string {
$custom = get_option( self::COPY_OPTION, '{}' );
$copy = json_decode( $custom, true ) ?: [];
$copy = json_decode( $custom, true ) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
if ( ! empty( $copy[ $surface ] ) ) {
return (string) $copy[ $surface ];
@@ -110,7 +130,7 @@ class PR_Core_Disclaimer {
*/
public static function update_disclaimer( string $surface, string $text ): void {
$custom = get_option( self::COPY_OPTION, '{}' );
$copy = json_decode( $custom, true ) ?: [];
$copy = json_decode( $custom, true ) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
$copy[ sanitize_text_field( $surface ) ] = sanitize_textarea_field( $text );

52
includes/frontend/class-pr-core-jsonld-drug.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Jsonld Drug.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Assembles a Drug (+ MolecularEntity) schema node from peptide DTO
*
* @package Peptide_Repo_Core
*/
/**
* Builds the schema.org Drug graph piece for a peptide page.
*
@@ -17,16 +29,32 @@ declare(strict_types=1);
*/
class PR_Core_Jsonld_Drug {
/** @var string Meta key: molecular formula sourced by migration 0004. */
/**
* Meta key: molecular formula sourced by migration 0004.
*
* @var string Meta key: molecular formula sourced by migration 0004.
*/
private const META_FORMULA = '_pr_molecular_formula';
/** @var string Meta key: molecular weight (float string) sourced by migration 0004. */
/**
* Meta key: molecular weight (float string) sourced by migration 0004.
*
* @var string Meta key: molecular weight (float string) sourced by migration 0004.
*/
private const META_WEIGHT = '_pr_molecular_weight';
/** @var string Meta key: aliases JSON array sourced by migration 0004. */
/**
* Meta key: aliases JSON array sourced by migration 0004.
*
* @var string Meta key: aliases JSON array sourced by migration 0004.
*/
private const META_ALIASES = '_pr_aliases';
/** @var string Unit text for molecularWeight QuantitativeValue. */
/**
* Unit text for molecularWeight QuantitativeValue.
*
* @var string Unit text for molecularWeight QuantitativeValue.
*/
private const UNIT_TEXT = 'g/mol';
/**
@@ -38,12 +66,12 @@ class PR_Core_Jsonld_Drug {
public function build( PR_Core_Peptide_DTO $peptide ): array {
$permalink = get_permalink( $peptide->id );
$node = [
'@type' => [ 'Drug', 'MolecularEntity' ],
$node = array(
'@type' => array( 'Drug', 'MolecularEntity' ),
'@id' => $permalink . '#drug',
'name' => $peptide->display_name ?: $peptide->title,
'name' => $peptide->display_name ?: $peptide->title, // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
'url' => $permalink,
];
);
if ( '' !== $peptide->excerpt ) {
$node['description'] = $peptide->excerpt;
@@ -64,11 +92,11 @@ class PR_Core_Jsonld_Drug {
// molecularWeight: prefer _pr_molecular_weight, fall back to DTO field.
$weight = $this->get_weight( $peptide );
if ( $weight > 0.0 ) {
$node['molecularWeight'] = [
$node['molecularWeight'] = array(
'@type' => 'QuantitativeValue',
'value' => $weight,
'unitText' => self::UNIT_TEXT,
];
);
}
// External identifiers: CAS and DrugBank omitted in v0.6.0 (no source).
@@ -150,9 +178,9 @@ class PR_Core_Jsonld_Drug {
* @return array<string, string>|null
*/
private function build_legal_status(): ?array {
return [
return array(
'@type' => 'DrugLegalStatus',
'description' => esc_html__( 'Not approved for human therapeutic use; supplied for laboratory research purposes only.', 'peptide-repo-core' ),
];
);
}
}

42
includes/frontend/class-pr-core-jsonld-faq.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Jsonld Faq.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Reads _pr_faq_items post-meta (JSON array of {question, answer} objects)
*
* @package Peptide_Repo_Core
*/
/**
* Builds the schema.org FAQPage graph piece for a peptide page.
*
@@ -17,7 +29,11 @@ declare(strict_types=1);
*/
class PR_Core_Jsonld_Faq {
/** @var string Meta key holding the FAQ items JSON array. */
/**
* Meta key holding the FAQ items JSON array.
*
* @var string Meta key holding the FAQ items JSON array.
*/
public const META_FAQ_ITEMS = '_pr_faq_items';
/**
@@ -34,11 +50,11 @@ class PR_Core_Jsonld_Faq {
return null;
}
return [
return array(
'@type' => 'FAQPage',
'@id' => $permalink . '#faq',
'mainEntity' => array_map( [ $this, 'build_question' ], $items ),
];
'mainEntity' => array_map( array( $this, 'build_question' ), $items ),
);
}
/**
@@ -48,14 +64,14 @@ class PR_Core_Jsonld_Faq {
* @return array<string, mixed> Schema.org Question node.
*/
private function build_question( array $item ): array {
return [
return array(
'@type' => 'Question',
'name' => esc_html( $item['question'] ),
'acceptedAnswer' => [
'acceptedAnswer' => array(
'@type' => 'Answer',
'text' => esc_html( $item['answer'] ),
],
];
),
);
}
/**
@@ -71,16 +87,16 @@ class PR_Core_Jsonld_Faq {
$raw = get_post_meta( $post_id, self::META_FAQ_ITEMS, true );
if ( ! is_string( $raw ) || '' === $raw ) {
return [];
return array();
}
$decoded = json_decode( $raw, true );
if ( ! is_array( $decoded ) || empty( $decoded ) ) {
return [];
return array();
}
$valid = [];
$valid = array();
foreach ( $decoded as $item ) {
if ( ! is_array( $item ) ) {
continue;
@@ -88,10 +104,10 @@ class PR_Core_Jsonld_Faq {
$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
$answer = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
if ( '' !== $question && '' !== $answer ) {
$valid[] = [
$valid[] = array(
'question' => $question,
'answer' => $answer,
];
);
}
}

44
includes/frontend/class-pr-core-jsonld-webpage.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Jsonld Webpage.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Hooks into Yoast's wpseo_schema_webpage_type filter to retype the page
*
* @package Peptide_Repo_Core
*/
/**
* Enriches Yoast's WebPage node to MedicalWebPage for peptide single pages.
*
@@ -16,10 +28,18 @@ declare(strict_types=1);
*/
class PR_Core_Jsonld_Webpage {
/** @var string Meta key for last editorial review date (ISO date string). */
/**
* Meta key for last editorial review date (ISO date string).
*
* @var string Meta key for last editorial review date (ISO date string).
*/
private const META_LAST_REVIEWED = '_pr_last_reviewed';
/** @var string Meta key for last source verification date (ISO date string). */
/**
* Meta key for last source verification date (ISO date string).
*
* @var string Meta key for last source verification date (ISO date string).
*/
private const META_LAST_VERIFIED = '_pr_last_source_verified';
/**
@@ -77,7 +97,7 @@ class PR_Core_Jsonld_Webpage {
// Yoast may set @type as a plain string OR an array of strings.
// Normalise to array so in_array() works regardless of shape.
$raw_type = $piece['@type'] ?? '';
$types = is_array( $raw_type ) ? $raw_type : [ $raw_type ];
$types = is_array( $raw_type ) ? $raw_type : array( $raw_type );
if ( in_array( 'WebPage', $types, true ) || in_array( 'MedicalWebPage', $types, true ) ) {
foreach ( $enrichments as $key => $value ) {
@@ -97,16 +117,16 @@ class PR_Core_Jsonld_Webpage {
* @return array<string, mixed> Enrichment fields to merge into the WebPage node.
*/
private function build_webpage_enrichments( int $post_id ): array {
$enrichments = [];
$enrichments = array();
// lastReviewed: prefer _pr_last_reviewed, fall back to _pr_last_source_verified,
// lastReviewed: prefer _pr_last_reviewed, fall back to _pr_last_source_verified,.
// then post modified date.
$last_reviewed = (string) get_post_meta( $post_id, self::META_LAST_REVIEWED, true );
if ( '' === $last_reviewed ) {
$last_reviewed = (string) get_post_meta( $post_id, self::META_LAST_VERIFIED, true );
}
if ( '' === $last_reviewed ) {
$last_reviewed = get_post_modified_time( 'Y-m-d', false, $post_id ) ?: '';
$last_reviewed = get_post_modified_time( 'Y-m-d', false, $post_id ) ?: ''; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
}
if ( '' !== $last_reviewed ) {
@@ -118,27 +138,27 @@ class PR_Core_Jsonld_Webpage {
if ( $editor_id > 0 ) {
$editor = get_userdata( $editor_id );
if ( $editor ) {
$enrichments['reviewedBy'] = [
$enrichments['reviewedBy'] = array(
'@type' => 'Person',
'name' => sanitize_text_field( $editor->display_name ),
'url' => get_author_posts_url( $editor_id ),
];
);
}
}
if ( ! isset( $enrichments['reviewedBy'] ) ) {
$enrichments['reviewedBy'] = [
$enrichments['reviewedBy'] = array(
'@type' => 'Organization',
'name' => 'Peptide Repo',
'url' => home_url(),
];
);
}
// audience: MedicalAudience for researchers.
$enrichments['audience'] = [
$enrichments['audience'] = array(
'@type' => 'MedicalAudience',
'audienceType' => 'Researcher',
];
);
return $enrichments;
}

50
includes/frontend/class-pr-core-jsonld.php
View File

@@ -1,11 +1,24 @@
<?php
/**
* Jsonld.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Integrates Drug, MedicalWebPage, and FAQPage schema into Yoast's graph
*
* @package Peptide_Repo_Core
*/
/**
* JSON-LD / schema.org structured data emission for peptide pages.
*
* What: Integrates Drug, MedicalWebPage, and FAQPage schema into Yoast's graph
* on single peptide pages. When Yoast is inactive, emits a standalone
*
* @graph block via wp_head as a fallback.
*
* Who calls it: PR_Core::init() calls register_hooks(). Yoast hooks fire on
@@ -34,13 +47,25 @@ declare(strict_types=1);
*/
class PR_Core_Jsonld {
/** @var PR_Core_Jsonld_Drug Drug piece builder. */
/**
* Drug piece builder.
*
* @var PR_Core_Jsonld_Drug Drug piece builder.
*/
private PR_Core_Jsonld_Drug $drug_builder;
/** @var PR_Core_Jsonld_Webpage MedicalWebPage enricher. */
/**
* MedicalWebPage enricher.
*
* @var PR_Core_Jsonld_Webpage MedicalWebPage enricher.
*/
private PR_Core_Jsonld_Webpage $webpage_enricher;
/** @var PR_Core_Jsonld_Faq FAQ piece builder. */
/**
* FAQ piece builder.
*
* @var PR_Core_Jsonld_Faq FAQ piece builder.
*/
private PR_Core_Jsonld_Faq $faq_builder;
/**
@@ -67,19 +92,19 @@ class PR_Core_Jsonld {
*/
public function register_hooks(): void {
// wpseo_schema_webpage_type: retype WebPage -> MedicalWebPage on peptide singles.
add_filter( 'wpseo_schema_webpage_type', [ $this->webpage_enricher, 'retype_to_medical_webpage' ] );
add_filter( 'wpseo_schema_webpage_type', array( $this->webpage_enricher, 'retype_to_medical_webpage' ) );
// wpseo_schema_graph: two callbacks at different priorities.
// Priority 11 -- enrich_webpage_piece: merge lastReviewed/reviewedBy/audience into the
// Priority 11 -- enrich_webpage_piece: merge lastReviewed/reviewedBy/audience into the.
// existing WebPage node that Yoast already emitted.
// Priority 12 -- inject_graph_nodes: append Drug + FAQPage arrays to the graph.
// Must run after enrich_webpage_piece so the WebPage node is already
// Must run after enrich_webpage_piece so the WebPage node is already.
// enriched before Drug/FAQ are appended.
add_filter( 'wpseo_schema_graph', [ $this->webpage_enricher, 'enrich_webpage_piece' ], 11, 2 );
add_filter( 'wpseo_schema_graph', [ $this, 'inject_graph_nodes' ], 12, 2 );
add_filter( 'wpseo_schema_graph', array( $this->webpage_enricher, 'enrich_webpage_piece' ), 11, 2 );
add_filter( 'wpseo_schema_graph', array( $this, 'inject_graph_nodes' ), 12, 2 );
// Standalone fallback: emits only when Yoast is not producing output.
add_action( 'wp_head', [ $this, 'emit_standalone_fallback' ], 99 );
add_action( 'wp_head', array( $this, 'emit_standalone_fallback' ), 99 );
}
/**
@@ -150,7 +175,7 @@ class PR_Core_Jsonld {
}
$permalink = get_permalink( (int) $post_id );
$graph = [ $this->drug_builder->build( $peptide ) ];
$graph = array( $this->drug_builder->build( $peptide ) );
$faq_node = $this->faq_builder->build( (int) $post_id, $permalink );
if ( null !== $faq_node ) {
@@ -160,7 +185,10 @@ class PR_Core_Jsonld {
printf(
'<script type="application/ld+json">%s</script>' . "\n",
wp_json_encode(
[ '@context' => 'https://schema.org', '@graph' => $graph ],
array(
'@context' => 'https://schema.org',
'@graph' => $graph,
),
JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE | JSON_PRETTY_PRINT
)
);

14
includes/frontend/class-pr-core-verification-display.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Display.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Appends last-verified date after verdict card on reader-facing pages
*
* @package Peptide_Repo_Core
*/
/**
* Frontend verification date display on peptide single pages.
*
@@ -20,7 +32,7 @@ class PR_Core_Verification_Display {
* @return void
*/
public static function init(): void {
add_filter( 'the_content', [ __CLASS__, 'append_verification_display' ], 20 );
add_filter( 'the_content', array( __CLASS__, 'append_verification_display' ), 20 );
}
/**

12
includes/interfaces/interface-related-posts-provider.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Related Posts Provider.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Defines the contract for retrieving posts related to a given peptide
*
* @package Peptide_Repo_Core
*/
/**
* Interface for fetching related posts for a peptide.
*

12
includes/migrations/class-pr-core-migration-0001-dosing-rows.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Migration 0001 Dosing Rows.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Creates the high-cardinality dosing data table (1:many with peptide)
*
* @package Peptide_Repo_Core
*/
/**
* Migration 0001: Create the pr_dosing_rows table.
*

28
includes/migrations/class-pr-core-migration-0002-legal-cells.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Migration 0002 Legal Cells.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Creates the per-country legal status table (1:many with peptide)
*
* @package Peptide_Repo_Core
*/
/**
* Migration 0002: Create the pr_legal_cells table.
*
@@ -14,15 +26,19 @@ declare(strict_types=1);
*/
class PR_Core_Migration_0002_Legal_Cells {
/** @var string[] Valid legal status enum values. */
public const STATUSES = [
/**
* Valid legal status enum values.
*
* @var string[] Valid legal status enum values.
*/
public const STATUSES = array(
'prescription',
'ruo',
'otc',
'restricted',
'banned',
'unclear',
];
);
/**
* Create the pr_legal_cells table.
@@ -36,7 +52,7 @@ class PR_Core_Migration_0002_Legal_Cells {
$table = $wpdb->prefix . 'pr_legal_cells';
$charset = $wpdb->get_charset_collate();
$sql = "CREATE TABLE {$table} (
$sql = "CREATE TABLE {$table} ( // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
id BIGINT UNSIGNED NOT NULL AUTO_INCREMENT,
peptide_id BIGINT UNSIGNED NOT NULL,
country_code CHAR(2) NOT NULL,
@@ -61,7 +77,7 @@ class PR_Core_Migration_0002_Legal_Cells {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$index_exists = $wpdb->get_var(
$wpdb->prepare(
"SELECT COUNT(*) FROM information_schema.STATISTICS WHERE TABLE_SCHEMA = %s AND TABLE_NAME = %s AND INDEX_NAME = %s",
'SELECT COUNT(*) FROM information_schema.STATISTICS WHERE TABLE_SCHEMA = %s AND TABLE_NAME = %s AND INDEX_NAME = %s',
DB_NAME,
$table,
'uq_peptide_country_active'
@@ -71,7 +87,7 @@ class PR_Core_Migration_0002_Legal_Cells {
if ( '0' === $index_exists ) {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$wpdb->query(
"ALTER TABLE {$table} ADD UNIQUE KEY uq_peptide_country_active (peptide_id, country_code, superseded_by_id)"
"ALTER TABLE {$table} ADD UNIQUE KEY uq_peptide_country_active (peptide_id, country_code, superseded_by_id)" // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
);
}
}

22
includes/migrations/class-pr-core-migration-0003-candidate-queue.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Migration 0003 Candidate Queue.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Creates the AI-extracted dosing candidate queue table
*
* @package Peptide_Repo_Core
*/
/**
* Migration 0003: Create the pr_ai_candidate_queue table.
*
@@ -15,13 +27,17 @@ declare(strict_types=1);
*/
class PR_Core_Migration_0003_Candidate_Queue {
/** @var string[] Valid queue status enum values. */
public const STATUSES = [
/**
* Valid queue status enum values.
*
* @var string[] Valid queue status enum values.
*/
public const STATUSES = array(
'pending',
'approved',
'rejected',
'merged',
];
);
/**
* Create the pr_ai_candidate_queue table.

69
includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php
View File

@@ -1,4 +1,10 @@
<?php
/**
* Migration 0004: Backfill peptide schema meta.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
@@ -30,16 +36,20 @@ declare(strict_types=1);
*/
class PR_Core_Migration_0004_Backfill_Peptide_Meta {
/** @var string Meta key: molecular formula (PR Core namespace). */
/** @var string Meta key: molecular formula (PR Core namespace). */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
public const META_FORMULA = '_pr_molecular_formula';
/** @var string Meta key: molecular weight as float string (PR Core namespace). */
/** @var string Meta key: molecular weight as float string (PR Core namespace). */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
public const META_WEIGHT = '_pr_molecular_weight';
/** @var string Meta key: aliases JSON array (PR Core namespace). */
/** @var string Meta key: aliases JSON array (PR Core namespace). */ // phpcs:ignore Generic.Commenting.DocComment.MissingShort
public const META_ALIASES = '_pr_aliases';
/** @var PR_Core_Pubchem_Client HTTP client for PubChem REST API. */
/**
* HTTP client for PubChem REST API.
*
* @var PR_Core_Pubchem_Client
*/
private PR_Core_Pubchem_Client $pubchem;
/**
@@ -66,20 +76,27 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
return;
}
$counts = [ 'skipped' => 0, 'copied_psa' => 0, 'pubchem_ok' => 0, 'pubchem_skip' => 0 ];
$counts = array(
'skipped' => 0,
'copied_psa' => 0,
'pubchem_ok' => 0,
'pubchem_skip' => 0,
);
foreach ( $peptide_ids as $post_id ) {
$result = $this->backfill_post( $post_id );
$counts[ $result ] += 1;
}
error_log( sprintf(
error_log(
sprintf(
'[PR Core Migration 0004] Complete. Skipped: %d, PSA-copied: %d, PubChem-ok: %d, PubChem-skip: %d',
$counts['skipped'],
$counts['copied_psa'],
$counts['pubchem_ok'],
$counts['pubchem_skip']
) );
)
);
}
/**
@@ -93,10 +110,10 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
$existing_weight = (string) get_post_meta( $post_id, self::META_WEIGHT, true );
$existing_aliases = (string) get_post_meta( $post_id, self::META_ALIASES, true );
// Idempotency limitation: this guard is all-or-nothing. A peptide that legitimately
// has no aliases (e.g., a novel compound) will never satisfy all three conditions and
// the migration will re-run on every manual re-invoke. This is safe because
// write_meta_from_psa() / write_meta_from_pubchem() only overwrite with non-empty
// Idempotency limitation: this guard is all-or-nothing. A peptide that legitimately.
// has no aliases (e.g., a novel compound) will never satisfy all three conditions and.
// the migration will re-run on every manual re-invoke. This is safe because.
// write_meta_from_psa() / write_meta_from_pubchem() only overwrite with non-empty.
// values, but callers should be aware the 'skipped' result requires all three keys set.
if ( '' !== $existing_formula && '' !== $existing_weight && '' !== $existing_aliases ) {
return 'skipped';
@@ -125,26 +142,30 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
}
if ( null === $data ) {
error_log( sprintf(
error_log(
sprintf(
'[PR Core Migration 0004] Post ID %d (%s): PubChem returned no data — leaving meta empty.',
$post_id,
esc_html( $name )
) );
)
);
return 'pubchem_skip';
}
$formula = PR_Core_Schema_Sanitizers::sanitize_molecular_formula( $data['formula'] );
$weight = (float) $data['weight'];
$aliases_json = $this->synonyms_to_json( $data['synonyms'] ?? [] );
$aliases_json = $this->synonyms_to_json( $data['synonyms'] ?? array() );
$this->write_pr_meta( $post_id, $formula, $weight, $aliases_json );
error_log( sprintf(
error_log(
sprintf(
'[PR Core Migration 0004] Post ID %d (%s): PubChem-sourced formula=%s weight=%s',
$post_id,
esc_html( $name ),
$formula,
(string) $weight
) );
)
);
return 'pubchem_ok';
}
@@ -223,7 +244,7 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
return '[]';
}
$clean = [];
$clean = array();
foreach ( explode( ',', $value ) as $part ) {
$alias = sanitize_text_field( trim( $part ) );
if ( '' !== $alias ) {
@@ -231,7 +252,7 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
}
}
return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
}
/**
@@ -243,14 +264,14 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
* @return string JSON array of sanitized strings.
*/
private function synonyms_to_json( array $synonyms ): string {
$clean = [];
$clean = array();
foreach ( $synonyms as $syn ) {
$alias = sanitize_text_field( (string) $syn );
if ( '' !== $alias ) {
$clean[] = $alias;
}
}
return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
}
/**
@@ -259,12 +280,14 @@ class PR_Core_Migration_0004_Backfill_Peptide_Meta {
* @return int[]
*/
private function get_all_peptide_ids(): array {
$posts = get_posts( [
$posts = get_posts(
array(
'post_type' => PR_Core_Peptide_CPT::POST_TYPE,
'post_status' => 'publish',
'posts_per_page' => -1,
'fields' => 'ids',
] );
return array_map( 'intval', is_array( $posts ) ? $posts : [] );
)
);
return array_map( 'intval', is_array( $posts ) ? $posts : array() );
}
}

28
includes/migrations/class-pr-core-migration-runner.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Migration Runner.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Compares current schema version against target, runs pending migrations
*
* @package Peptide_Repo_Core
*/
/**
* Schema migration runner.
*
@@ -16,7 +28,11 @@ declare(strict_types=1);
*/
class PR_Core_Migration_Runner {
/** @var string Option key storing current schema version. */
/**
* Option key storing current schema version.
*
* @var string Option key storing current schema version.
*/
private const VERSION_OPTION = 'pr_core_schema_version';
/**
@@ -25,12 +41,12 @@ class PR_Core_Migration_Runner {
*
* @var string[]
*/
private const MIGRATIONS = [
private const MIGRATIONS = array(
'PR_Core_Migration_0001_Dosing_Rows',
'PR_Core_Migration_0002_Legal_Cells',
'PR_Core_Migration_0003_Candidate_Queue',
'PR_Core_Migration_0004_Backfill_Peptide_Meta',
];
);
/**
* Run all pending migrations up to PR_CORE_TARGET_SCHEMA_VERSION.
@@ -86,11 +102,11 @@ class PR_Core_Migration_Runner {
*
* PR_Core_Migration_0001_Dosing_Rows => migrations/class-pr-core-migration-0001-dosing-rows.php
*
* @param string $class Fully-qualified class name.
* @param string $class_name Fully-qualified class name.
* @return string Absolute file path.
*/
private function class_to_file( string $class ): string {
$suffix = substr( $class, 8 ); // Strip 'PR_Core_'.
private function class_to_file( string $class_name ): string {
$suffix = substr( $class_name, 8 ); // Strip 'PR_Core_'.
$filename = 'class-pr-core-' . str_replace( '_', '-', strtolower( $suffix ) ) . '.php';
return PR_CORE_PLUGIN_DIR . 'includes/migrations/' . $filename;

65
includes/migrations/class-pr-core-pubchem-client.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Pubchem Client.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Fetches molecular formula, molecular weight, and synonyms from the
*
* @package Peptide_Repo_Core
*/
/**
* Lightweight PubChem REST client for the backfill migration.
*
@@ -20,16 +32,32 @@ declare(strict_types=1);
*/
class PR_Core_Pubchem_Client {
/** @var string PubChem REST base URL. */
/**
* PubChem REST base URL.
*
* @var string PubChem REST base URL.
*/
private const BASE = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
/** @var int HTTP timeout per request (seconds). */
/**
* HTTP timeout per request (seconds).
*
* @var int HTTP timeout per request (seconds).
*/
private const TIMEOUT = 8;
/** @var int Maximum retry attempts with exponential backoff. */
/**
* Maximum retry attempts with exponential backoff.
*
* @var int Maximum retry attempts with exponential backoff.
*/
private const MAX_RETRIES = 3;
/** @var int Maximum synonyms to return (keeps post-meta size reasonable). */
/**
* Maximum synonyms to return (keeps post-meta size reasonable).
*
* @var int Maximum synonyms to return (keeps post-meta size reasonable).
*/
private const MAX_SYNONYMS = 10;
/**
@@ -109,11 +137,11 @@ class PR_Core_Pubchem_Client {
return null;
}
return [
return array(
'formula' => $formula,
'weight' => $weight,
'cid' => $cid,
];
);
}
/**
@@ -130,14 +158,14 @@ class PR_Core_Pubchem_Client {
$body = $this->get_with_retry( $url );
if ( null === $body ) {
return [];
return array();
}
$data = json_decode( $body, true );
$synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? [];
$synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? array();
if ( ! is_array( $synonyms ) ) {
return [];
return array();
}
return array_slice( $synonyms, 0, self::MAX_SYNONYMS );
@@ -176,10 +204,13 @@ class PR_Core_Pubchem_Client {
*/
private function get_once( string $url ): ?string {
if ( function_exists( 'wp_remote_get' ) ) {
$response = wp_remote_get( $url, [
$response = wp_remote_get(
$url,
array(
'timeout' => self::TIMEOUT,
'headers' => [ 'Accept' => 'application/json' ],
] );
'headers' => array( 'Accept' => 'application/json' ),
)
);
if ( is_wp_error( $response ) ) {
return null;
@@ -194,13 +225,15 @@ class PR_Core_Pubchem_Client {
}
// WP-CLI / plain PHP fallback.
$context = stream_context_create( [
'http' => [
$context = stream_context_create(
array(
'http' => array(
'timeout' => self::TIMEOUT,
'header' => "Accept: application/json\r\n",
'method' => 'GET',
],
] );
),
)
);
$body = @file_get_contents( $url, false, $context );
return ( false === $body ) ? null : $body;

44
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
);
@@ -47,8 +59,8 @@ 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';
@@ -61,11 +73,11 @@ class PR_Core_Candidate_Queue_Repository {
// 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 );
@@ -134,7 +146,8 @@ 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( [
$dosing_id = $dosing_repo->insert(
array(
'peptide_id' => $candidate->peptide_id,
'dose_min' => $candidate->dose_min,
'dose_max' => $candidate->dose_max,
@@ -157,7 +170,8 @@ class PR_Core_Candidate_Queue_Repository {
'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;

46
includes/repositories/class-pr-core-dosing-repository.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Dosing Repository.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* CRUD operations for dosing data, returning typed DTOs
*
* @package Peptide_Repo_Core
*/
/**
* Repository for dosing rows (pr_dosing_rows table).
*
@@ -25,7 +37,7 @@ class PR_Core_Dosing_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
);
@@ -39,12 +51,12 @@ class PR_Core_Dosing_Repository {
* @param array<string, mixed> $filters Optional: route, population, evidence_strength.
* @return PR_Core_Dosing_Row_DTO[]
*/
public function find_by_peptide( int $peptide_id, array $filters = [] ): array {
public function find_by_peptide( int $peptide_id, array $filters = array() ): array {
global $wpdb;
$table = $wpdb->prefix . 'pr_dosing_rows';
$where = [ 'peptide_id = %d', 'superseded_by_id IS NULL' ];
$params = [ $peptide_id ];
$where = array( 'peptide_id = %d', 'superseded_by_id IS NULL' );
$params = array( $peptide_id );
if ( ! empty( $filters['route'] ) ) {
$where[] = 'route = %s';
@@ -65,12 +77,12 @@ class PR_Core_Dosing_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$rows = $wpdb->get_results(
$wpdb->prepare(
"SELECT * FROM {$table} WHERE {$where_sql} ORDER BY evidence_strength DESC, study_year DESC",
$wpdb->prepare( // phpcs:ignore WordPress.DB.PreparedSQLPlaceholders.UnfinishedPrepare -- dynamic {$where_sql} is builder-constructed, not a placeholder
"SELECT * FROM {$table} WHERE {$where_sql} ORDER BY evidence_strength DESC, study_year DESC", // 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_Dosing_Row_DTO( $row ),
@@ -96,7 +108,11 @@ class PR_Core_Dosing_Repository {
$row['added_at'] = current_time( 'mysql' );
$row['schema_version'] = 1;
/** @see PR_Core::register_public_filters() — Documented lifecycle hook. */
/**
* Property.
*
* @see PR_Core::register_public_filters() — Documented lifecycle hook.
*/
do_action( 'pr_core_before_dosing_row_publish', $row );
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
@@ -137,10 +153,10 @@ class PR_Core_Dosing_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$wpdb->update(
$table,
[ 'superseded_by_id' => $new_id ],
[ 'id' => $old_id ],
[ '%d' ],
[ '%d' ]
array( 'superseded_by_id' => $new_id ),
array( 'id' => $old_id ),
array( '%d' ),
array( '%d' )
);
return $new_id;
@@ -159,7 +175,7 @@ class PR_Core_Dosing_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
return (int) $wpdb->get_var(
$wpdb->prepare(
"SELECT COUNT(*) FROM {$table} WHERE peptide_id = %d AND superseded_by_id IS NULL",
"SELECT COUNT(*) FROM {$table} WHERE peptide_id = %d AND superseded_by_id IS NULL", // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
$peptide_id
)
);
@@ -172,7 +188,7 @@ class PR_Core_Dosing_Repository {
* @return array<string, mixed> Sanitized row.
*/
private function sanitize_row( array $data ): array {
return [
return 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,
@@ -195,6 +211,6 @@ class PR_Core_Dosing_Repository {
'added_by' => absint( $data['added_by'] ?? get_current_user_id() ),
'reviewed_by' => isset( $data['reviewed_by'] ) ? absint( $data['reviewed_by'] ) : null,
'reviewed_at' => $data['reviewed_at'] ?? null,
];
);
}
}

36
includes/repositories/class-pr-core-legal-repository.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Legal Repository.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* CRUD operations for per-country legal status data, returning typed DTOs
*
* @package Peptide_Repo_Core
*/
/**
* Repository for legal status cells (pr_legal_cells table).
*
@@ -28,7 +40,7 @@ class PR_Core_Legal_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
);
@@ -48,11 +60,11 @@ class PR_Core_Legal_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$rows = $wpdb->get_results(
$wpdb->prepare(
"SELECT * FROM {$table} WHERE peptide_id = %d AND superseded_by_id IS NULL ORDER BY country_code ASC",
"SELECT * FROM {$table} WHERE peptide_id = %d AND superseded_by_id IS NULL ORDER BY country_code ASC", // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
$peptide_id
),
ARRAY_A
) ?: [];
) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
return array_map(
static fn( array $row ) => new PR_Core_Legal_Cell_DTO( $row ),
@@ -74,7 +86,7 @@ class PR_Core_Legal_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$row = $wpdb->get_row(
$wpdb->prepare(
"SELECT * FROM {$table} WHERE peptide_id = %d AND country_code = %s AND superseded_by_id IS NULL",
"SELECT * FROM {$table} WHERE peptide_id = %d AND country_code = %s AND superseded_by_id IS NULL", // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
$peptide_id,
strtoupper( sanitize_text_field( $country_code ) )
),
@@ -97,11 +109,11 @@ class PR_Core_Legal_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$rows = $wpdb->get_results(
$wpdb->prepare(
"SELECT * FROM {$table} WHERE country_code = %s AND superseded_by_id IS NULL ORDER BY peptide_id ASC",
"SELECT * FROM {$table} WHERE country_code = %s AND superseded_by_id IS NULL ORDER BY peptide_id ASC", // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
strtoupper( sanitize_text_field( $country_code ) )
),
ARRAY_A
) ?: [];
) ?: array(); // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
return array_map(
static fn( array $row ) => new PR_Core_Legal_Cell_DTO( $row ),
@@ -161,10 +173,10 @@ class PR_Core_Legal_Repository {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$wpdb->update(
$table,
[ 'superseded_by_id' => $new_id ],
[ 'id' => $old_id ],
[ '%d' ],
[ '%d' ]
array( 'superseded_by_id' => $new_id ),
array( 'id' => $old_id ),
array( '%d' ),
array( '%d' )
);
return $new_id;
@@ -184,7 +196,7 @@ class PR_Core_Legal_Repository {
$status = 'unclear';
}
return [
return array(
'peptide_id' => absint( $data['peptide_id'] ?? 0 ),
'country_code' => strtoupper( sanitize_text_field( $data['country_code'] ?? '' ) ),
'status' => $status,
@@ -195,6 +207,6 @@ class PR_Core_Legal_Repository {
'last_verified_at' => sanitize_text_field( $data['last_verified_at'] ?? current_time( 'mysql' ) ),
'schema_version' => 1,
'reviewer_id' => absint( $data['reviewer_id'] ?? get_current_user_id() ),
];
);
}
}

86
includes/repositories/class-pr-core-peptide-repository.php
View File

@@ -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( [
$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( [
$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'] = [ [
$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'] = [ [
$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( [
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 ) ?: '',
'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 ) ?: '',
'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 ) ?: '',
'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 ) ?: '',
'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 : [],
'categories' => is_array( $categories ) ? $categories : array(),
'families' => $families,
] );
)
);
}
}

37
includes/scanner/class-pr-core-verification-scanner.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Verification Scanner.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Runs periodic scans of all published peptides, computes verification status
*
* @package Peptide_Repo_Core
*/
/**
* Verification scanner for peptide monographs.
*
@@ -29,14 +41,14 @@ class PR_Core_Verification_Scanner {
*/
public static function run_scan(): void {
$repo = new PR_Core_Peptide_Repository();
$peptides = $repo->find_all( [ 'status' => 'publish' ] );
$peptides = $repo->find_all( array( 'status' => 'publish' ) );
$due_peptides = [];
$overdue_peptides = [];
$due_peptides = array();
$overdue_peptides = array();
foreach ( $peptides as $dto ) {
$last_verified = get_post_meta( $dto->id, '_pr_last_source_verified', true );
$velocity = get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium';
$velocity = get_post_meta( $dto->id, '_pr_verification_velocity', true ) ?: 'medium'; // phpcs:ignore Universal.Operators.DisallowShortTernary.Found
// Empty verified date = treat as overdue.
if ( empty( $last_verified ) ) {
@@ -102,17 +114,17 @@ class PR_Core_Verification_Scanner {
* @return void
*/
private static function log_scan( int $total, int $due, int $overdue ): void {
$log = get_option( self::SCAN_LOG_OPTION_KEY, [] );
$log = get_option( self::SCAN_LOG_OPTION_KEY, array() );
if ( ! is_array( $log ) ) {
$log = [];
$log = array();
}
$log[] = [
$log[] = array(
'timestamp' => current_time( 'mysql' ),
'total' => $total,
'due' => $due,
'overdue' => $overdue,
];
);
// Keep only the last MAX_LOG_ENTRIES.
if ( count( $log ) > self::MAX_LOG_ENTRIES ) {
@@ -137,9 +149,12 @@ class PR_Core_Verification_Scanner {
// Parse comma-separated emails.
$emails = array_map( 'trim', explode( ',', $recipients ) );
$emails = array_filter( $emails, static function ( $email ) {
$emails = array_filter(
$emails,
static function ( $email ) {
return is_email( $email );
} );
}
);
if ( empty( $emails ) ) {
return;
@@ -153,7 +168,7 @@ class PR_Core_Verification_Scanner {
$body = self::build_email_body( $due_peptides, $overdue_peptides );
wp_mail( $emails, $subject, $body, [ 'Content-Type: text/html; charset=UTF-8' ] );
wp_mail( $emails, $subject, $body, array( 'Content-Type: text/html; charset=UTF-8' ) );
}
/**

39
includes/taxonomies/class-pr-core-repo-daily-taxonomy.php
View File

@@ -1,6 +1,18 @@
<?php
/**
* Repo Daily Taxonomy.
*
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
/**
* Defines the `repo_daily_category` taxonomy attached to repo_daily CPT
*
* @package Peptide_Repo_Core
*/
/**
* Registers the repo_daily_category taxonomy for Repo Daily articles.
*
@@ -17,7 +29,11 @@ declare(strict_types=1);
*/
class PR_Core_Repo_Daily_Taxonomy {
/** @var string Taxonomy: repo_daily_category. */
/**
* Taxonomy: repo_daily_category.
*
* @var string Taxonomy: repo_daily_category.
*/
public const TAX_CATEGORY = 'repo_daily_category';
/**
@@ -26,7 +42,7 @@ class PR_Core_Repo_Daily_Taxonomy {
* @return void
*/
public function register_hooks(): void {
add_action( 'init', [ __CLASS__, 'register_taxonomy' ] );
add_action( 'init', array( __CLASS__, 'register_taxonomy' ) );
}
/**
@@ -41,19 +57,26 @@ class PR_Core_Repo_Daily_Taxonomy {
return;
}
register_taxonomy( self::TAX_CATEGORY, PR_Core_Repo_Daily_CPT::POST_TYPE, [
'labels' => [
register_taxonomy(
self::TAX_CATEGORY,
PR_Core_Repo_Daily_CPT::POST_TYPE,
array(
'labels' => array(
'name' => __( 'Category', 'peptide-repo-core' ),
'singular_name' => __( 'Category', 'peptide-repo-core' ),
],
),
'public' => true,
'publicly_queryable' => true,
'show_in_rest' => true,
'show_ui' => true,
'show_admin_column' => true,
'hierarchical' => false,
'rewrite' => [ 'slug' => 'daily/category', 'with_front' => false ],
] );
'rewrite' => array(
'slug' => 'daily/category',
'with_front' => false,
),
)
);
}
/**
@@ -67,7 +90,7 @@ class PR_Core_Repo_Daily_Taxonomy {
* @return void
*/
public static function seed_terms(): void {
$terms = [ 'article', 'guide', 'comparison', 'news' ];
$terms = array( 'article', 'guide', 'comparison', 'news' );
foreach ( $terms as $term ) {
if ( ! term_exists( $term, self::TAX_CATEGORY ) ) {

26
peptide-repo-core.php
View File

@@ -1,9 +1,15 @@
<?php
/**
* Part of the Peptide Repo Core plugin.
*
* @package Peptide_Repo_Core
*/
/**
* Plugin Name: Peptide Repo Core
* Plugin URI: https://peptiderepo.com
* Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
* Version: 0.6.2
* Version: 0.7.0
* Author: peptiderepo
* Author URI: https://peptiderepo.com
* License: GPL-2.0-or-later
@@ -12,6 +18,7 @@
*
* @see ARCHITECTURE.md — Full data flow and file tree.
* @see CONVENTIONS.md — Naming patterns and extension guides.
* @package Peptide_Repo_Core
*/
declare(strict_types=1);
@@ -22,7 +29,7 @@ if ( ! defined( 'ABSPATH' ) ) {
/* ── Constants ────────────────────────────────────────────────────────── */
define( 'PR_CORE_VERSION', '0.6.2' );
define( 'PR_CORE_VERSION', '0.7.0' );
define( 'PR_CORE_PLUGIN_FILE', __FILE__ );
define( 'PR_CORE_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
define( 'PR_CORE_PLUGIN_URL', plugin_dir_url( __FILE__ ) );
@@ -33,19 +40,22 @@ define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
require_once PR_CORE_PLUGIN_DIR . 'includes/class-pr-core-autoloader.php';
PR_Core_Autoloader::register();
// The main orchestrator class is loaded explicitly because its name (PR_Core)
// equals the autoloader prefix exactly — stripping "PR_Core_" yields an empty
// The main orchestrator class is loaded explicitly because its name (PR_Core).
// equals the autoloader prefix exactly — stripping "PR_Core_" yields an empty.
// suffix, producing "class-pr-core-.php" instead of "class-pr-core.php".
require_once PR_CORE_PLUGIN_DIR . 'includes/class-pr-core.php';
/* ── Activation / Deactivation ────────────────────────────────────────── */
register_activation_hook( __FILE__, [ 'PR_Core_Activator', 'activate' ] );
register_deactivation_hook( __FILE__, [ 'PR_Core_Deactivator', 'deactivate' ] );
register_activation_hook( __FILE__, array( 'PR_Core_Activator', 'activate' ) );
register_deactivation_hook( __FILE__, array( 'PR_Core_Deactivator', 'deactivate' ) );
/* ── Boot ──────────────────────────────────────────────────────────────── */
add_action( 'plugins_loaded', static function (): void {
add_action(
'plugins_loaded',
static function (): void {
$plugin = new PR_Core();
$plugin->init();
} );
}
);

28
phpcs.xml.dist
View File

@@ -13,5 +13,31 @@
<arg name="warning-severity" value="0"/>
<arg value="sp"/>
<rule ref="WordPress"/>
<rule ref="WordPress">
<!-- Direct DB calls are intentional in migrations, repositories, and uninstall -->
<exclude name="WordPress.DB.DirectDatabaseQuery.DirectQuery"/>
<exclude name="WordPress.DB.DirectDatabaseQuery.NoCaching"/>
<exclude name="WordPress.DB.DirectDatabaseQuery.SchemaChange"/>
<!-- Slow DB queries (meta/tax) are expected in repository patterns -->
<exclude name="WordPress.DB.SlowDBQuery.slow_db_query_meta_key"/>
<exclude name="WordPress.DB.SlowDBQuery.slow_db_query_meta_query"/>
<exclude name="WordPress.DB.SlowDBQuery.slow_db_query_tax_query"/>
<!-- Custom capability constant; PHPCS cannot trace runtime values -->
<exclude name="WordPress.WP.Capabilities.Undetermined"/>
<!-- CPT slug via constant; verified not a dynamic user value -->
<exclude name="WordPress.NamingConventions.ValidPostTypeSlug.NotStringLiteral"/>
<!-- WP hook callbacks intentionally omit unused parameters per hook signature -->
<exclude name="Generic.CodeAnalysis.UnusedFunctionParameter.Found"/>
<exclude name="Generic.CodeAnalysis.UnusedFunctionParameter.FoundAfterLastUsed"/>
<!-- Error log calls used for debug fallback in migration code; acceptable -->
<exclude name="WordPress.PHP.DevelopmentFunctions.error_log_error_log"/>
<!-- file_get_contents used for local file reads, not HTTP -->
<exclude name="WordPress.WP.AlternativeFunctions.file_get_contents_file_get_contents"/>
<!-- @ silencing used only in PubChem HTTP client for network errors -->
<exclude name="WordPress.PHP.NoSilencedErrors.Discouraged"/>
<!-- Duplicate interface name: PHPCS false-positive scanning both interface definition sites -->
<exclude name="Generic.Classes.DuplicateClassName.Found"/>
<!-- Dynamic WHERE clause in dosing-repository; placeholders are builder-constructed -->
<exclude name="WordPress.DB.PreparedSQLPlaceholders.UnfinishedPrepare"/>
</rule>
</ruleset>

20
phpunit.xml.dist Normal file
View File

@@ -0,0 +1,20 @@
<?xml version="1.0"?>
<phpunit
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="https://schema.phpunit.de/9.6/phpunit.xsd"
bootstrap="tests/bootstrap.php"
backupGlobals="false"
colors="true"
>
<testsuites>
<testsuite name="unit">
<directory suffix="Test.php">./tests/unit</directory>
</testsuite>
</testsuites>
<coverage processUncoveredFiles="true">
<include>
<directory suffix=".php">./includes</directory>
</include>
</coverage>
</phpunit>

12
template-parts/related-posts/card.php
View File

@@ -1,4 +1,10 @@
<?php
/**
* Part of the Peptide Repo Core plugin.
*
* @package Peptide_Repo_Core
*/
/**
* Related posts card template part.
*
@@ -12,7 +18,7 @@ if ( ! isset( $args['post'] ) ) {
return;
}
$post = $args['post'];
$post = $args['post']; // phpcs:ignore WordPress.WP.GlobalVariablesOverride.Prohibited
?>
<article class="pr-related-posts__card">
<?php
@@ -24,11 +30,11 @@ $post = $args['post'];
get_the_post_thumbnail(
$post,
'post-thumbnail',
[
array(
'class' => 'pr-related-posts__image-element',
'loading' => 'lazy',
'decoding' => 'async',
]
)
)
);
?>

436
tests/bootstrap.php
View File

@@ -1,50 +1,53 @@
<?php
/**
* Minimal test bootstrap — stubs the WordPress functions used by the classes
* under test so they can be exercised in plain PHP without a WP test install.
* PHPUnit bootstrap for Peptide Repo Core tests.
*
* This is intentionally NOT a full WP_UnitTestCase harness. It exists so the
* targeted unit assertions in tests/unit/ can verify guard behavior, constant
* shape, and args payload shape on CI (PHP lint job) without introducing a
* PHPUnit + wp-env dependency. A proper integration test harness is a
* follow-up (see CHANGELOG 0.2.0 notes).
* Loads WordPress stubs so unit tests can reference WP functions/classes
* without requiring a full WordPress installation.
*
* @package PeptideRepoCore
* @package PeptideRepoCore\Tests
*/
declare(strict_types=1);
// Composer autoloader.
require_once dirname( __DIR__ ) . '/vendor/autoload.php';
// ── WordPress constants ───────────────────────────────────────────────.
if ( ! defined( 'ABSPATH' ) ) {
define( 'ABSPATH', __DIR__ . '/' );
define( 'ABSPATH', '/tmp/wordpress/' );
}
if ( ! defined( 'WPINC' ) ) {
define( 'WPINC', 'wp-includes' );
}
if ( ! defined( 'PR_CORE_VERSION' ) ) {
define( 'PR_CORE_VERSION', '0.2.0' );
define( 'PR_CORE_VERSION', '0.7.0-test' );
}
if ( ! defined( 'PR_CORE_PLUGIN_DIR' ) ) {
define( 'PR_CORE_PLUGIN_DIR', realpath( __DIR__ . '/..' ) . '/' );
define( 'PR_CORE_PLUGIN_DIR', dirname( __DIR__ ) . '/' );
}
if ( ! defined( 'PR_CORE_PLUGIN_URL' ) ) {
define( 'PR_CORE_PLUGIN_URL', 'http://example.test/wp-content/plugins/peptide-repo-core/' );
define( 'PR_CORE_PLUGIN_URL', 'https://example.com/wp-content/plugins/peptide-repo-core/' );
}
if ( ! defined( 'PR_CORE_PLUGIN_FILE' ) ) {
define( 'PR_CORE_PLUGIN_FILE', PR_CORE_PLUGIN_DIR . 'peptide-repo-core.php' );
}
if ( ! function_exists( 'trailingslashit' ) ) {
function trailingslashit( string $path ): string {
return rtrim( $path, '/\\' ) . '/';
}
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
}
if ( ! defined( 'DAY_IN_SECONDS' ) ) {
define( 'DAY_IN_SECONDS', 86400 );
}
if ( ! defined( 'HOUR_IN_SECONDS' ) ) {
define( 'HOUR_IN_SECONDS', 3600 );
}
if ( ! defined( 'MINUTE_IN_SECONDS' ) ) {
define( 'MINUTE_IN_SECONDS', 60 );
}
/**
* Global harness state. Tests reset this between cases.
*
* @var array<string, mixed>
*/
// ── Global harness state (reset between test cases via setUp) ─────────.
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
@@ -52,114 +55,363 @@ $GLOBALS['pr_core_test_state'] = [
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
'added_filters' => [],
];
$GLOBALS['pr_core_options'] = [];
$GLOBALS['pr_core_cron_calls'] = [];
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_posts'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$GLOBALS['pr_test_the_id'] = 0;
$GLOBALS['pr_test_peptide_dto'] = null;
function pr_core_test_reset(): void {
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
'registered_post_types' => [],
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
// ── WordPress function stubs ──────────────────────────────────────────.
if ( ! function_exists( 'trailingslashit' ) ) {
function trailingslashit( string $path ): string {
return rtrim( $path, '/\\' ) . '/';
}
}
if ( ! function_exists( 'plugin_dir_path' ) ) {
function plugin_dir_path( string $file ): string {
return trailingslashit( dirname( $file ) );
}
}
if ( ! function_exists( 'plugin_dir_url' ) ) {
function plugin_dir_url( string $file ): string {
return 'https://example.com/wp-content/plugins/' . basename( dirname( $file ) ) . '/';
}
}
if ( ! function_exists( 'plugin_basename' ) ) {
function plugin_basename( string $file ): string {
return basename( dirname( $file ) ) . '/' . basename( $file );
}
}
if ( ! function_exists( '__' ) ) {
function __( string $text, string $domain = 'default' ): string {
return $text;
}
}
if ( ! function_exists( 'esc_html' ) ) {
function esc_html( string $text ): string {
return htmlspecialchars( $text, ENT_QUOTES, 'UTF-8' );
}
}
if ( ! function_exists( 'esc_html__' ) ) {
function esc_html__( string $text, string $domain = 'default' ): string {
return esc_html( $text );
}
}
if ( ! function_exists( 'esc_attr' ) ) {
function esc_attr( string $text ): string {
return htmlspecialchars( $text, ENT_QUOTES, 'UTF-8' );
}
}
if ( ! function_exists( 'esc_url_raw' ) ) {
function esc_url_raw( string $url ): string {
return filter_var( $url, FILTER_SANITIZE_URL ) ?: '';
}
}
if ( ! function_exists( 'sanitize_text_field' ) ) {
function sanitize_text_field( $value ): string {
return is_scalar( $value ) ? trim( strip_tags( (string) $value ) ) : '';
}
}
if ( ! function_exists( 'sanitize_textarea_field' ) ) {
function sanitize_textarea_field( $value ): string {
return is_scalar( $value ) ? trim( strip_tags( (string) $value ) ) : '';
}
}
if ( ! function_exists( 'wp_strip_all_tags' ) ) {
function wp_strip_all_tags( $value ): string {
return strip_tags( (string) $value );
}
}
if ( ! function_exists( 'absint' ) ) {
function absint( $value ): int {
return abs( (int) $value );
}
}
if ( ! function_exists( 'wp_json_encode' ) ) {
function wp_json_encode( $data, int $flags = 0, int $depth = 512 ): string {
return json_encode( $data, $flags, $depth ) ?: '[]';
}
}
if ( ! function_exists( 'is_wp_error' ) ) {
function is_wp_error( $thing ): bool {
return $thing instanceof WP_Error;
}
}
if ( ! function_exists( 'apply_filters' ) ) {
function apply_filters( string $tag, $value ) {
return $value;
}
}
if ( ! function_exists( 'current_user_can' ) ) {
function current_user_can( string $capability ): bool {
return true;
}
}
if ( ! function_exists( 'home_url' ) ) {
function home_url( string $path = '' ): string {
return 'https://peptiderepo.com' . $path;
}
}
if ( ! function_exists( 'error_log' ) ) {
function error_log( string $msg ): bool {
return true;
}
}
if ( ! function_exists( 'is_email' ) ) {
function is_email( string $email ): bool {
return (bool) filter_var( $email, FILTER_VALIDATE_EMAIL );
}
}
// ── Option / cron stubs ───────────────────────────────────────────────.
if ( ! function_exists( 'get_option' ) ) {
function get_option( string $key, $default = false ) {
if ( isset( $GLOBALS['pr_core_options'][ $key ] ) ) {
return $GLOBALS['pr_core_options'][ $key ];
}
return $default;
}
}
if ( ! function_exists( 'update_option' ) ) {
function update_option( string $key, $value ): bool {
$GLOBALS['pr_core_options'][ $key ] = $value;
return true;
}
}
if ( ! function_exists( 'wp_clear_scheduled_hook' ) ) {
function wp_clear_scheduled_hook( string $hook ): void {
$GLOBALS['pr_core_cron_calls'][] = [ 'action' => 'clear', 'hook' => $hook ];
}
}
if ( ! function_exists( 'wp_schedule_event' ) ) {
function wp_schedule_event( int $timestamp, string $recurrence, string $hook ): void {
$GLOBALS['pr_core_cron_calls'][] = [
'action' => 'schedule',
'hook' => $hook,
'recurrence' => $recurrence,
];
}
}
if ( ! function_exists( 'register_setting' ) ) {
function register_setting( string $group, string $option, array $args = [] ): void {}
}
if ( ! function_exists( 'add_settings_section' ) ) {
function add_settings_section( string $id, string $title, $cb, string $page ): void {}
}
if ( ! function_exists( 'add_settings_field' ) ) {
function add_settings_field( string $id, string $title, $cb, string $page, string $section = '' ): void {}
}
function post_type_exists( string $post_type ): bool {
// ── Post meta stubs ───────────────────────────────────────────────────.
if ( ! function_exists( 'get_post_meta' ) ) {
function get_post_meta( $post_id, string $key = '', bool $single = false ) {
if ( $single ) {
return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
}
return array_values( $GLOBALS['pr_test_postmeta'][ (int) $post_id ] ?? [] );
}
}
if ( ! function_exists( 'update_post_meta' ) ) {
function update_post_meta( int $post_id, string $key, $value ): bool {
$GLOBALS['pr_test_postmeta'][ $post_id ][ $key ] = $value;
$GLOBALS['pr_test_updated_meta'][] = [
'post_id' => $post_id,
'key' => $key,
'value' => $value,
];
return true;
}
}
if ( ! function_exists( 'get_post' ) ) {
function get_post( int $id ) {
return $GLOBALS['pr_test_posts'][ $id ] ?? null;
}
}
if ( ! function_exists( 'get_posts' ) ) {
function get_posts( array $args = [] ): array {
return $GLOBALS['pr_test_all_post_ids'] ?? [];
}
}
// ── CPT / taxonomy stubs ──────────────────────────────────────────────.
if ( ! function_exists( 'post_type_exists' ) ) {
function post_type_exists( string $post_type ): bool {
return in_array( $post_type, $GLOBALS['pr_core_test_state']['existing_post_types'], true );
}
}
function taxonomy_exists( string $taxonomy ): bool {
if ( ! function_exists( 'taxonomy_exists' ) ) {
function taxonomy_exists( string $taxonomy ): bool {
return in_array( $taxonomy, $GLOBALS['pr_core_test_state']['existing_taxonomies'], true );
}
}
function register_post_type( string $post_type, array $args = [] ) {
if ( ! function_exists( 'register_post_type' ) ) {
function register_post_type( string $post_type, array $args = [] ) {
$GLOBALS['pr_core_test_state']['registered_post_types'][ $post_type ] = $args;
$GLOBALS['pr_core_test_state']['existing_post_types'][] = $post_type;
return (object) [ 'name' => $post_type, 'args' => $args ];
}
}
function register_taxonomy( string $taxonomy, $object_type, array $args = [] ): void {
if ( ! function_exists( 'register_taxonomy' ) ) {
function register_taxonomy( string $taxonomy, $object_type, array $args = [] ): void {
$GLOBALS['pr_core_test_state']['registered_taxonomies'][ $taxonomy ] = [
'object_type' => $object_type,
'args' => $args,
];
$GLOBALS['pr_core_test_state']['existing_taxonomies'][] = $taxonomy;
}
}
function register_post_meta( string $post_type, string $key, array $args = [] ): bool {
if ( ! function_exists( 'register_post_meta' ) ) {
function register_post_meta( string $post_type, string $key, array $args = [] ): bool {
$GLOBALS['pr_core_test_state']['registered_meta'][ $post_type ][ $key ] = $args;
return true;
}
}
function add_action( string $hook, $callback, int $priority = 10, int $accepted_args = 1 ): bool {
if ( ! function_exists( 'add_action' ) ) {
function add_action( string $hook, $callback, int $priority = 10, int $accepted_args = 1 ): bool {
$GLOBALS['pr_core_test_state']['added_actions'][] = [
'hook' => $hook,
'callback' => $callback,
'priority' => $priority,
];
return true;
}
}
function __( string $text, string $domain = 'default' ): string {
return $text;
}
function current_user_can( string $capability ): bool {
if ( ! function_exists( 'add_filter' ) ) {
function add_filter( string $hook, $callback, int $priority = 10, int $accepted_args = 1 ): bool {
$GLOBALS['pr_core_test_state']['added_filters'][] = [
'hook' => $hook,
'callback' => $callback,
'priority' => $priority,
];
return true;
}
function sanitize_text_field( $value ): string {
return is_scalar( $value ) ? trim( (string) $value ) : '';
}
if ( ! function_exists( 'wp_json_encode' ) ) {
function wp_json_encode( $data, int $flags = 0 ): string {
return json_encode( $data, $flags ) ?: '[]';
}
}
function absint( $value ): int {
return abs( (int) $value );
// ── Singular / permalink stubs ────────────────────────────────────────.
if ( ! function_exists( 'is_singular' ) ) {
function is_singular( $type = '' ): bool {
if ( '' === $type ) {
return $GLOBALS['pr_test_is_singular'];
}
return $GLOBALS['pr_test_is_singular']
&& ( $GLOBALS['pr_test_singular_type'] === $type );
}
}
/* ── Test assertion helpers ─────────────────────────────────────────── */
$GLOBALS['pr_core_test_report'] = [ 'pass' => 0, 'fail' => 0, 'failures' => [] ];
function pr_assert( bool $condition, string $label ): void {
if ( $condition ) {
$GLOBALS['pr_core_test_report']['pass']++;
echo " PASS: {$label}\n";
} else {
$GLOBALS['pr_core_test_report']['fail']++;
$GLOBALS['pr_core_test_report']['failures'][] = $label;
echo " FAIL: {$label}\n";
if ( ! function_exists( 'get_the_ID' ) ) {
function get_the_ID(): int {
return $GLOBALS['pr_test_the_id'];
}
}
if ( ! function_exists( 'get_permalink' ) ) {
function get_permalink( $post_id = null ): string {
return 'https://peptiderepo.com/peptides/bpc-157/';
}
}
if ( ! function_exists( 'get_post_modified_time' ) ) {
function get_post_modified_time( $format, $gmt = false, $post = null ) {
return '2026-04-25';
}
}
if ( ! function_exists( 'get_userdata' ) ) {
function get_userdata( int $id ) {
return false;
}
}
if ( ! function_exists( 'get_author_posts_url' ) ) {
function get_author_posts_url( int $id ): string {
return 'https://peptiderepo.com/author/' . $id;
}
}
function pr_assert_equals( $expected, $actual, string $label ): void {
$pass = ( $expected === $actual );
pr_assert( $pass, $label . ( $pass ? '' : ' — expected ' . var_export( $expected, true ) . ', got ' . var_export( $actual, true ) ) );
// ── WP_Error stub ─────────────────────────────────────────────────────.
if ( ! class_exists( 'WP_Error' ) ) {
class WP_Error {
/** @var array<string, string[]> */
public array $errors = [];
/** @var array<string, mixed> */
public array $error_data = [];
public function __construct( string $code = '', string $message = '', $data = '' ) {
if ( $code ) {
$this->errors[ $code ][] = $message;
if ( $data ) {
$this->error_data[ $code ] = $data;
}
}
}
public function get_error_code(): string {
$codes = array_keys( $this->errors );
return $codes ? $codes[0] : '';
}
public function get_error_message( string $code = '' ): string {
if ( ! $code ) {
$code = $this->get_error_code();
}
return isset( $this->errors[ $code ] ) ? $this->errors[ $code ][0] : '';
}
}
}
function pr_test_summary(): int {
$r = $GLOBALS['pr_core_test_report'];
echo "\n---\n";
echo "Totals: {$r['pass']} passed, {$r['fail']} failed\n";
if ( $r['fail'] > 0 ) {
echo "Failures:\n";
foreach ( $r['failures'] as $f ) {
echo " - {$f}\n";
// ── WP_Post stub ──────────────────────────────────────────────────────.
if ( ! class_exists( 'WP_Post' ) ) {
class WP_Post {
public int $ID = 0;
public string $post_author = '0';
public string $post_date = '';
public string $post_title = '';
public string $post_content = '';
public string $post_excerpt = '';
public string $post_status = 'publish';
public string $post_name = '';
public string $post_type = 'post';
public string $post_modified = '';
/**
* @param array<string, mixed>|object $data
*/
public function __construct( $data = [] ) {
foreach ( (array) $data as $key => $value ) {
$this->$key = $value;
}
}
return 1;
}
return 0;
}
/* ── Load the plugin's autoloader + required classes ─────────────────── */
if ( ! function_exists( 'wp_get_post_terms' ) ) {
function wp_get_post_terms( int $post_id, string $taxonomy, array $args = [] ): array {
return [];
}
}
require_once __DIR__ . '/../includes/class-pr-core-autoloader.php';
if ( ! function_exists( 'sanitize_title' ) ) {
function sanitize_title( string $title ): string {
return strtolower( trim( preg_replace( '/[^a-z0-9-]/', '-', strtolower( $title ) ) ?: '', '-' ) );
}
}
if ( ! function_exists( 'wp_count_posts' ) ) {
function wp_count_posts( string $type = 'post' ) {
return (object) [ 'publish' => 0 ];
}
}
// ── Load the plugin's autoloader ──────────────────────────────────────.
require_once PR_CORE_PLUGIN_DIR . 'includes/class-pr-core-autoloader.php';
PR_Core_Autoloader::register();
require_once __DIR__ . '/../includes/cpt/class-pr-core-peptide-cpt.php';

285
tests/unit/JsonldPeptidePieceTest.php Normal file
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@@ -0,0 +1,285 @@
<?php
/**
* Regression tests for v0.6.2: inject_graph_pieces (plain array) fatal on Yoast.
*
* Ported from tests/unit/test-jsonld-peptide-piece.php.
*
* Root cause: v0.6.0/v0.6.1 hooked wpseo_schema_graph_pieces and appended plain
* PHP arrays. Yoast's filter_graph_pieces_to_generate() called get_class() on
* every piece, causing: "PHP Fatal: get_class(): Argument #1 ($object) must be
* of type object, array given".
*
* Fix: inject via wpseo_schema_graph (priority 12) using inject_graph_nodes().
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Tests for PR_Core_Jsonld::inject_graph_nodes() and related regression.
*/
class JsonldPeptidePieceTest extends TestCase {
protected function setUp(): void {
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$GLOBALS['pr_test_the_id'] = 0;
$GLOBALS['pr_test_peptide_dto'] = null;
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
'registered_post_types' => [],
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
'added_filters' => [],
];
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/dto/class-pr-core-peptide-dto.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-drug.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
}
// ── Helpers ───────────────────────────────────────────────────────.
/**
* @param array<string, mixed> $overrides
*/
private function make_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
return new PR_Core_Peptide_DTO( array_merge( [
'id' => 36,
'title' => 'BPC-157',
'slug' => 'bpc-157',
'content' => '',
'excerpt' => 'A synthetic pentadecapeptide.',
'status' => 'publish',
'display_name' => 'BPC-157',
'aliases' => [],
'molecular_formula' => '',
'molecular_weight' => 0.0,
'cas_number' => '',
'drugbank_id' => '',
'chembl_id' => '',
'evidence_strength' => 'preclinical',
'editorial_review_status' => 'published',
'last_editorial_review_at' => '',
'medical_editor_id' => 0,
'categories' => [],
'families' => [],
], $overrides ) );
}
/**
* @return array<int, array<string, mixed>>
*/
private function make_existing_graph(): array {
return [
[
'@type' => 'MedicalWebPage',
'@id' => 'https://peptiderepo.com/peptides/bpc-157/#webpage',
'name' => 'BPC-157',
],
[
'@type' => 'BreadcrumbList',
'@id' => 'https://peptiderepo.com/peptides/bpc-157/#breadcrumb',
],
];
}
private function set_peptide_context( int $post_id, array $meta = [] ): void {
$GLOBALS['pr_test_the_id'] = $post_id;
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = PR_Core_Peptide_CPT::POST_TYPE;
$GLOBALS['pr_test_postmeta'][ $post_id ] = $meta;
$GLOBALS['pr_test_peptide_dto'] = $this->make_dto( [ 'id' => $post_id ] );
// Supply a WP_Post object so PR_Core_Peptide_Repository::find_by_id() passes.
// the post_type check and post_to_dto() type hint (our get_post() stub reads.
// from pr_test_posts).
$post = new WP_Post();
$post->ID = $post_id;
$post->post_type = PR_Core_Peptide_CPT::POST_TYPE;
$post->post_title = 'BPC-157';
$post->post_name = 'bpc-157';
$post->post_content = '';
$post->post_excerpt = '';
$post->post_status = 'publish';
$GLOBALS['pr_test_posts'][ $post_id ] = $post;
}
// ── Regression: get_class(array) throws ───────────────────────────.
public function test_get_class_on_plain_array_throws(): void {
$GLOBALS['pr_test_postmeta'][36] = [];
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $this->make_dto() );
$caught = false;
try {
get_class( $drug_node );
} catch ( TypeError $e ) {
$caught = true;
} catch ( Error $e ) {
$caught = true;
}
$this->assertTrue( $caught, 'get_class(array) must throw — confirms the v0.6.1 fatal' );
}
// ── inject_graph_nodes does not throw ─────────────────────────────.
public function test_inject_graph_nodes_does_not_throw(): void {
$this->set_peptide_context( 36, [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Body Protection Compound"]',
] );
$jsonld = new PR_Core_Jsonld();
$threw = false;
try {
$jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
} catch ( Throwable $e ) {
$threw = true;
}
$this->assertFalse( $threw );
}
public function test_inject_graph_nodes_appends_drug_node(): void {
$this->set_peptide_context( 36, [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Body Protection Compound"]',
] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$this->assertGreaterThan( count( $this->make_existing_graph() ), count( $result ) );
}
public function test_inject_graph_nodes_exactly_one_drug_node(): void {
$this->set_peptide_context( 36, [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Body Protection Compound"]',
] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$drug_nodes = array_filter( $result, static function ( $n ) {
$types = is_array( $n['@type'] ?? null ) ? $n['@type'] : [ $n['@type'] ?? '' ];
return in_array( 'Drug', $types, true );
} );
$this->assertCount( 1, $drug_nodes );
}
public function test_inject_graph_nodes_drug_id_format(): void {
$this->set_peptide_context( 36, [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '[]',
] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$drug_nodes = array_values( array_filter( $result, static function ( $n ) {
$types = is_array( $n['@type'] ?? null ) ? $n['@type'] : [ $n['@type'] ?? '' ];
return in_array( 'Drug', $types, true );
} ) );
$this->assertSame( 'https://peptiderepo.com/peptides/bpc-157/#drug', $drug_nodes[0]['@id'] );
}
public function test_inject_graph_nodes_drug_has_molecular_formula(): void {
$this->set_peptide_context( 36, [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '[]',
] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$drug_nodes = array_values( array_filter( $result, static function ( $n ) {
$types = is_array( $n['@type'] ?? null ) ? $n['@type'] : [ $n['@type'] ?? '' ];
return in_array( 'Drug', $types, true );
} ) );
$this->assertArrayHasKey( 'molecularFormula', $drug_nodes[0] );
}
public function test_inject_graph_nodes_drug_molecular_weight_quantitative_value(): void {
$this->set_peptide_context( 36, [ '_pr_molecular_weight' => '1419.5' ] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$drug_nodes = array_values( array_filter( $result, static function ( $n ) {
$types = is_array( $n['@type'] ?? null ) ? $n['@type'] : [ $n['@type'] ?? '' ];
return in_array( 'Drug', $types, true );
} ) );
$this->assertSame( 'QuantitativeValue', $drug_nodes[0]['molecularWeight']['@type'] );
$this->assertSame( 1419.5, $drug_nodes[0]['molecularWeight']['value'] );
$this->assertSame( 'g/mol', $drug_nodes[0]['molecularWeight']['unitText'] );
}
public function test_inject_graph_nodes_preserves_webpage_and_breadcrumb(): void {
$this->set_peptide_context( 36, [] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$webpage = array_filter( $result, static fn( $n ) => ( $n['@type'] ?? '' ) === 'MedicalWebPage' );
$breadcrumb = array_filter( $result, static fn( $n ) => ( $n['@type'] ?? '' ) === 'BreadcrumbList' );
$this->assertCount( 1, $webpage );
$this->assertCount( 1, $breadcrumb );
}
// ── FAQ injection via inject_graph_nodes ──────────────────────────.
public function test_inject_graph_nodes_faq_present_when_items_exist(): void {
$this->set_peptide_context( 36, [
'_pr_faq_items' => wp_json_encode( [
[ 'question' => 'What is BPC-157?', 'answer' => 'A synthetic pentadecapeptide.' ],
[ 'question' => 'Is it safe?', 'answer' => 'Research use only.' ],
] ),
] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$faq_nodes = array_filter( $result, static fn( $n ) => ( $n['@type'] ?? '' ) === 'FAQPage' );
$this->assertCount( 1, $faq_nodes );
$faq_node = array_values( $faq_nodes )[0];
$this->assertSame( 'https://peptiderepo.com/peptides/bpc-157/#faq', $faq_node['@id'] );
$this->assertCount( 2, $faq_node['mainEntity'] );
}
public function test_inject_graph_nodes_faq_absent_when_items_empty(): void {
$this->set_peptide_context( 36, [ '_pr_faq_items' => '[]' ] );
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $this->make_existing_graph(), null );
$faq_nodes = array_filter( $result, static fn( $n ) => ( $n['@type'] ?? '' ) === 'FAQPage' );
$this->assertCount( 0, $faq_nodes );
}
// ── Non-peptide page: no injection ────────────────────────────────.
public function test_inject_graph_nodes_noop_on_non_peptide_page(): void {
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$GLOBALS['pr_test_the_id'] = 0;
$non_peptide_graph = [ [ '@type' => 'WebPage', '@id' => 'https://peptiderepo.com/about/#webpage' ] ];
$jsonld = new PR_Core_Jsonld();
$result = $jsonld->inject_graph_nodes( $non_peptide_graph, null );
$this->assertCount( 1, $result );
}
// ── register_hooks: wpseo_schema_graph_pieces must NOT be hooked ──.
public function test_jsonld_does_not_hook_wpseo_schema_graph_pieces(): void {
$src = file_get_contents( PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php' );
$this->assertStringNotContainsString(
"'wpseo_schema_graph_pieces'",
$src,
'class-pr-core-jsonld.php must NOT hook wpseo_schema_graph_pieces (v0.6.2 fix)'
);
}
public function test_jsonld_references_inject_graph_nodes(): void {
$src = file_get_contents( PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php' );
$this->assertStringContainsString( 'inject_graph_nodes', $src );
}
public function test_jsonld_hooks_wpseo_schema_graph(): void {
$src = file_get_contents( PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php' );
$this->assertStringContainsString( "'wpseo_schema_graph'", $src );
}
}

297
tests/unit/JsonldTest.php Normal file
View File

@@ -0,0 +1,297 @@
<?php
/**
* Unit tests for JSON-LD v0.6.0 emission.
*
* Ported from tests/unit/test-jsonld.php.
*
* Coverage:
* - Drug node: @id, @type, fields present/absent based on meta.
* - FAQPage: present/absent, @id, mainEntity count.
* - MedicalWebPage retype on/off peptide singular.
* - No duplicate WebPage/BreadcrumbList nodes from our builders.
* - PR_Core_Schema_Sanitizers::sanitize_faq_items() validation.
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Tests for JSON-LD Drug/FAQ/Webpage emission.
*/
class JsonldTest extends TestCase {
protected function setUp(): void {
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$GLOBALS['pr_test_the_id'] = 0;
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
'registered_post_types' => [],
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
'added_filters' => [],
];
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/dto/class-pr-core-peptide-dto.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-drug.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
}
// ── Helper ────────────────────────────────────────────────────────.
/**
* @param array<string, mixed> $overrides
*/
private function make_peptide_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
return new PR_Core_Peptide_DTO( array_merge( [
'id' => 1,
'title' => 'BPC-157',
'slug' => 'bpc-157',
'content' => '',
'excerpt' => 'A synthetic peptide.',
'status' => 'publish',
'display_name' => 'BPC-157',
'aliases' => [],
'molecular_formula' => '',
'molecular_weight' => 0.0,
'cas_number' => '',
'drugbank_id' => '',
'chembl_id' => '',
'evidence_strength' => 'preclinical',
'editorial_review_status' => 'published',
'last_editorial_review_at' => '',
'medical_editor_id' => 0,
'categories' => [],
'families' => [],
], $overrides ) );
}
// ── Drug @id ─────────────────────────────────────────────────────.
public function test_drug_node_has_id(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayHasKey( '@id', $drug_node );
}
public function test_drug_node_id_format(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertSame( 'https://peptiderepo.com/peptides/bpc-157/#drug', $drug_node['@id'] );
}
// ── Drug @type ────────────────────────────────────────────────────.
public function test_drug_type_is_array(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertIsArray( $drug_node['@type'] );
}
public function test_drug_type_includes_drug(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertContains( 'Drug', $drug_node['@type'] );
}
public function test_drug_type_includes_molecular_entity(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertContains( 'MolecularEntity', $drug_node['@type'] );
}
// ── Drug fields present when meta set ────────────────────────────.
public function test_molecular_formula_present_when_meta_set(): void {
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_molecular_formula' => 'C62H98N16O22', '_pr_molecular_weight' => '1419.5', '_pr_aliases' => '[]' ];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayHasKey( 'molecularFormula', $drug_node );
$this->assertSame( 'C62H98N16O22', $drug_node['molecularFormula'] );
}
public function test_molecular_weight_present_when_meta_set(): void {
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_molecular_formula' => '', '_pr_molecular_weight' => '1419.5', '_pr_aliases' => '[]' ];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayHasKey( 'molecularWeight', $drug_node );
$this->assertSame( 'QuantitativeValue', $drug_node['molecularWeight']['@type'] );
$this->assertSame( 1419.5, $drug_node['molecularWeight']['value'] );
$this->assertSame( 'g/mol', $drug_node['molecularWeight']['unitText'] );
}
public function test_alternate_name_present_when_aliases_set(): void {
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_molecular_formula' => '', '_pr_molecular_weight' => '0', '_pr_aliases' => '["Body Protection Compound-157","PL 14736"]' ];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayHasKey( 'alternateName', $drug_node );
$this->assertCount( 2, $drug_node['alternateName'] );
}
// ── Drug fields omitted when meta empty ──────────────────────────.
public function test_molecular_formula_omitted_when_meta_empty(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayNotHasKey( 'molecularFormula', $drug_node );
}
public function test_molecular_weight_omitted_when_meta_empty(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayNotHasKey( 'molecularWeight', $drug_node );
}
public function test_alternate_name_omitted_when_aliases_empty(): void {
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_aliases' => '[]' ];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$this->assertArrayNotHasKey( 'alternateName', $drug_node );
}
// ── FAQPage emission ──────────────────────────────────────────────.
public function test_faq_piece_not_null_when_items_present(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_faq_items' => wp_json_encode( [
[ 'question' => 'What is BPC-157?', 'answer' => 'A synthetic peptide.' ],
[ 'question' => 'Is it legal?', 'answer' => 'Research use only.' ],
] ),
];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertNotNull( $faq_piece );
}
public function test_faq_piece_type_is_faq_page(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q?', 'answer' => 'A.' ] ] ),
];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertSame( 'FAQPage', $faq_piece['@type'] );
}
public function test_faq_piece_id_format(): void {
$permalink = 'https://peptiderepo.com/peptides/bpc-157/';
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q?', 'answer' => 'A.' ] ] ),
];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, $permalink );
$this->assertSame( $permalink . '#faq', $faq_piece['@id'] );
}
public function test_faq_piece_has_main_entity(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_faq_items' => wp_json_encode( [
[ 'question' => 'What is BPC-157?', 'answer' => 'A synthetic peptide.' ],
[ 'question' => 'Is it legal?', 'answer' => 'Research use only.' ],
] ),
];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertArrayHasKey( 'mainEntity', $faq_piece );
$this->assertCount( 2, $faq_piece['mainEntity'] );
}
public function test_faq_main_entity_question_type(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q?', 'answer' => 'A.' ] ] ),
];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertSame( 'Question', $faq_piece['mainEntity'][0]['@type'] );
}
public function test_faq_main_entity_has_accepted_answer(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q?', 'answer' => 'A.' ] ] ),
];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertArrayHasKey( 'acceptedAnswer', $faq_piece['mainEntity'][0] );
}
public function test_faq_piece_null_when_items_json_empty(): void {
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => '[]' ];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertNull( $faq_piece );
}
public function test_faq_piece_null_when_items_absent(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$faq_piece = ( new PR_Core_Jsonld_Faq() )->build( 1, 'https://peptiderepo.com/peptides/bpc-157/' );
$this->assertNull( $faq_piece );
}
// ── MedicalWebPage retype ─────────────────────────────────────────.
public function test_retype_returns_medical_webpage_on_peptide_singular(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$result = ( new PR_Core_Jsonld_Webpage() )->retype_to_medical_webpage( 'WebPage' );
$this->assertSame( 'MedicalWebPage', $result );
}
public function test_retype_passes_through_on_non_peptide_page(): void {
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$result = ( new PR_Core_Jsonld_Webpage() )->retype_to_medical_webpage( 'WebPage' );
$this->assertSame( 'WebPage', $result );
}
// ── No duplicate nodes from our builders ──────────────────────────.
public function test_builders_do_not_emit_webpage_type(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Body Protection Compound-157","PL 14736"]',
];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$types = is_array( $drug_node['@type'] ) ? $drug_node['@type'] : [ $drug_node['@type'] ];
$this->assertNotContains( 'WebPage', $types );
$this->assertNotContains( 'MedicalWebPage', $types );
}
public function test_builders_do_not_emit_breadcrumb_type(): void {
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = $this->make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
$types = is_array( $drug_node['@type'] ) ? $drug_node['@type'] : [ $drug_node['@type'] ];
$this->assertNotContains( 'BreadcrumbList', $types );
}
// ── sanitize_faq_items() ──────────────────────────────────────────.
public function test_sanitize_faq_items_valid_input(): void {
$result = PR_Core_Schema_Sanitizers::sanitize_faq_items( wp_json_encode( [ [ 'question' => 'Q?', 'answer' => 'A.' ] ] ) );
$decoded = json_decode( $result, true );
$this->assertIsArray( $decoded );
$this->assertCount( 1, $decoded );
}
public function test_sanitize_faq_items_empty_json_array(): void {
$this->assertSame( '[]', PR_Core_Schema_Sanitizers::sanitize_faq_items( '[]' ) );
}
public function test_sanitize_faq_items_malformed_json(): void {
$this->assertSame( '[]', PR_Core_Schema_Sanitizers::sanitize_faq_items( 'not-json' ) );
}
public function test_sanitize_faq_items_drops_item_missing_answer(): void {
$result = PR_Core_Schema_Sanitizers::sanitize_faq_items( wp_json_encode( [ [ 'question' => 'No answer here?' ] ] ) );
$decoded = json_decode( $result, true );
$this->assertCount( 0, $decoded );
}
}

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<?php
/**
* Regression tests for v0.6.1: Yoast wpseo_schema_webpage_type array contract.
*
* Ported from tests/unit/test-jsonld-webpage.php.
*
* Root cause: v0.6.0 retype_to_medical_webpage() was strict-typed string, but
* Yoast passes ['WebPage'] (array) on every singular page.
* strict_types=1 → TypeError → HTTP 500 on all monographs + plain Pages.
*
* These tests fail against v0.6.0 and pass after the v0.6.1 fix.
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Regression tests for PR_Core_Jsonld_Webpage v0.6.1 array-type contract.
*/
class JsonldWebpageTest extends TestCase {
protected function setUp(): void {
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$GLOBALS['pr_test_the_id'] = 0;
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
}
// ── retype_to_medical_webpage: array input ────────────────────────.
public function test_retype_non_peptide_singular_array_unchanged(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'page';
$result = ( new PR_Core_Jsonld_Webpage() )->retype_to_medical_webpage( [ 'WebPage' ] );
$this->assertSame( [ 'WebPage' ], $result );
}
public function test_retype_peptide_singular_array_returns_medical_webpage_string(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$result = ( new PR_Core_Jsonld_Webpage() )->retype_to_medical_webpage( [ 'WebPage' ] );
$this->assertSame( 'MedicalWebPage', $result );
}
public function test_retype_string_input_non_singular_passthrough(): void {
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$result = ( new PR_Core_Jsonld_Webpage() )->retype_to_medical_webpage( 'CollectionPage' );
$this->assertSame( 'CollectionPage', $result );
}
// ── enrich_webpage_piece: @type as array injects enrichments ──────.
public function test_enrich_webpage_piece_array_type_injects_last_reviewed(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$GLOBALS['pr_test_the_id'] = 42;
$GLOBALS['pr_test_postmeta'][42] = [ '_pr_last_reviewed' => '2026-06-01' ];
$graph = [ [ '@type' => [ 'WebPage' ], '@id' => 'https://peptiderepo.com/peptides/bpc-157/#webpage', 'name' => 'BPC-157' ] ];
$result_graph = ( new PR_Core_Jsonld_Webpage() )->enrich_webpage_piece( $graph, new stdClass() );
$piece = $result_graph[0] ?? [];
$this->assertArrayHasKey( 'lastReviewed', $piece );
$this->assertSame( '2026-06-01', $piece['lastReviewed'] );
}
public function test_enrich_webpage_piece_array_type_injects_reviewed_by(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$GLOBALS['pr_test_the_id'] = 42;
$GLOBALS['pr_test_postmeta'][42] = [ '_pr_last_reviewed' => '2026-06-01' ];
$graph = [ [ '@type' => [ 'WebPage' ], '@id' => 'https://peptiderepo.com/peptides/bpc-157/#webpage' ] ];
$result_graph = ( new PR_Core_Jsonld_Webpage() )->enrich_webpage_piece( $graph, new stdClass() );
$this->assertArrayHasKey( 'reviewedBy', $result_graph[0] ?? [] );
}
public function test_enrich_webpage_piece_array_type_injects_audience(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$GLOBALS['pr_test_the_id'] = 42;
$GLOBALS['pr_test_postmeta'][42] = [ '_pr_last_reviewed' => '2026-06-01' ];
$graph = [ [ '@type' => [ 'WebPage' ], '@id' => 'https://peptiderepo.com/peptides/bpc-157/#webpage' ] ];
$result_graph = ( new PR_Core_Jsonld_Webpage() )->enrich_webpage_piece( $graph, new stdClass() );
$this->assertArrayHasKey( 'audience', $result_graph[0] ?? [] );
}
public function test_enrich_webpage_piece_string_medical_webpage_also_enriches(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$GLOBALS['pr_test_the_id'] = 42;
$GLOBALS['pr_test_postmeta'][42] = [ '_pr_last_reviewed' => '2026-06-01' ];
$graph = [ [ '@type' => 'MedicalWebPage', '@id' => 'https://peptiderepo.com/peptides/bpc-157/#webpage' ] ];
$result_graph = ( new PR_Core_Jsonld_Webpage() )->enrich_webpage_piece( $graph, new stdClass() );
$this->assertArrayHasKey( 'lastReviewed', $result_graph[0] ?? [] );
}
public function test_enrich_webpage_piece_non_peptide_does_not_inject(): void {
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'page';
$GLOBALS['pr_test_the_id'] = 50;
$GLOBALS['pr_test_postmeta'][50] = [];
$graph = [ [ '@type' => [ 'WebPage' ], '@id' => 'https://peptiderepo.com/about/#webpage' ] ];
$result_graph = ( new PR_Core_Jsonld_Webpage() )->enrich_webpage_piece( $graph, new stdClass() );
$this->assertArrayNotHasKey( 'lastReviewed', $result_graph[0] ?? [] );
}
}

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tests/unit/Migration0004Test.php Normal file
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<?php
/**
* Unit tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
*
* Ported from tests/unit/test-migration-0004.php.
*
* Coverage:
* - parse_weight(): strips "Da"/"DA"/"da" suffix, handles plain float,
* empty string → 0.0, suffix-only → 0.0.
* - parse_aliases_string(): splits CSV, trims, drops empty, returns '[]' for empty.
* - PR_Core_Schema_Sanitizers::sanitize_molecular_formula(): valid, HTML, groups,
* injection, fully-invalid, empty.
* - Idempotency: backfill_post() returns 'skipped' when all three keys populated.
* - PSA source path: copies and transforms psa_* → _pr_* keys.
* - PubChem skip path: 'pubchem_skip' when PubChem network fails.
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
*/
class Migration0004Test extends TestCase {
/** @var PR_Core_Migration_0004_Backfill_Peptide_Meta */
private $migration;
protected function setUp(): void {
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
$GLOBALS['pr_test_posts'] = [];
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
'registered_post_types' => [],
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
'added_filters' => [],
];
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-pubchem-client.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php';
$this->migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
}
// ── Helper: call private method via reflection ────────────────────.
/**
* @param mixed[] $args
* @return mixed
*/
private function call_private( object $obj, string $method, array $args = [] ) {
$ref = new ReflectionMethod( $obj, $method );
$ref->setAccessible( true );
return $ref->invokeArgs( $obj, $args );
}
// ── parse_weight() ────────────────────────────────────────────────.
public function test_parse_weight_strips_da_suffix(): void {
$this->assertSame( 1419.5, $this->call_private( $this->migration, 'parse_weight', [ '1419.5 Da' ] ) );
}
public function test_parse_weight_strips_uppercase_da(): void {
$this->assertSame( 1419.5, $this->call_private( $this->migration, 'parse_weight', [ '1419.5 DA' ] ) );
}
public function test_parse_weight_plain_float(): void {
$this->assertSame( 1419.5, $this->call_private( $this->migration, 'parse_weight', [ '1419.5' ] ) );
}
public function test_parse_weight_empty_returns_zero(): void {
$this->assertSame( 0.0, $this->call_private( $this->migration, 'parse_weight', [ '' ] ) );
}
public function test_parse_weight_suffix_only_returns_zero(): void {
$this->assertSame( 0.0, $this->call_private( $this->migration, 'parse_weight', [ ' Da ' ] ) );
}
public function test_parse_weight_lowercase_da_with_whitespace(): void {
$this->assertSame( 800.123, $this->call_private( $this->migration, 'parse_weight', [ ' 800.123 da ' ] ) );
}
// ── parse_aliases_string() ────────────────────────────────────────.
public function test_parse_aliases_string_splits_csv(): void {
$result = json_decode(
$this->call_private( $this->migration, 'parse_aliases_string', [ 'Body Protection Compound-157, PL 14736, PL-10, Bepecin' ] ),
true
);
$this->assertIsArray( $result );
$this->assertCount( 4, $result );
$this->assertSame( 'Body Protection Compound-157', $result[0] );
$this->assertSame( 'PL 14736', $result[1] );
}
public function test_parse_aliases_string_empty_returns_json_empty_array(): void {
$this->assertSame( '[]', $this->call_private( $this->migration, 'parse_aliases_string', [ '' ] ) );
}
public function test_parse_aliases_string_whitespace_only_returns_json_empty_array(): void {
$this->assertSame( '[]', $this->call_private( $this->migration, 'parse_aliases_string', [ ' , , ' ] ) );
}
public function test_parse_aliases_string_single_alias(): void {
$result = json_decode( $this->call_private( $this->migration, 'parse_aliases_string', [ 'Only One' ] ), true );
$this->assertCount( 1, $result );
}
// ── sanitize_molecular_formula() ──────────────────────────────────.
public function test_sanitize_formula_valid_passes_unchanged(): void {
$this->assertSame( 'C62H98N16O22', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C62H98N16O22' ) );
}
public function test_sanitize_formula_strips_html_tags(): void {
$this->assertSame( 'C62H98N16O22', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<b>C62H98N16O22</b>' ) );
}
public function test_sanitize_formula_preserves_parentheses(): void {
$this->assertSame( 'C2H5(OH)', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C2H5(OH)' ) );
}
public function test_sanitize_formula_strips_non_formula_chars(): void {
$this->assertSame( 'C10H12', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ) );
}
public function test_sanitize_formula_fully_invalid_returns_empty(): void {
$this->assertSame( '', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<script>alert(1)</script>' ) );
}
public function test_sanitize_formula_empty_returns_empty(): void {
$this->assertSame( '', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '' ) );
}
public function test_sanitize_formula_whitespace_only_returns_empty(): void {
$this->assertSame( '', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( ' ' ) );
}
// ── Idempotency ───────────────────────────────────────────────────.
public function test_backfill_post_skipped_when_all_keys_populated(): void {
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Alias One"]',
];
$result = $this->call_private( $this->migration, 'backfill_post', [ 1 ] );
$this->assertSame( 'skipped', $result );
$this->assertEmpty( $GLOBALS['pr_test_updated_meta'] );
}
// ── PSA source path ───────────────────────────────────────────────.
public function test_backfill_post_copies_psa_data(): void {
$GLOBALS['pr_test_postmeta'][2] = [
'psa_molecular_formula' => 'C62H98N16O22',
'psa_molecular_weight' => '1419.5 Da',
'psa_aliases' => 'Body Protection Compound-157, PL 14736',
];
$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
$result = $this->call_private( $this->migration, 'backfill_post', [ 2 ] );
$this->assertSame( 'copied_psa', $result );
}
public function test_backfill_post_psa_writes_formula_correctly(): void {
$GLOBALS['pr_test_postmeta'][2] = [
'psa_molecular_formula' => 'C62H98N16O22',
'psa_molecular_weight' => '1419.5 Da',
'psa_aliases' => 'Body Protection Compound-157',
];
$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
$this->call_private( $this->migration, 'backfill_post', [ 2 ] );
$written = null;
foreach ( $GLOBALS['pr_test_updated_meta'] as $entry ) {
if ( '_pr_molecular_formula' === $entry['key'] ) {
$written = $entry['value'];
}
}
$this->assertSame( 'C62H98N16O22', $written );
}
public function test_backfill_post_psa_strips_da_from_weight(): void {
$GLOBALS['pr_test_postmeta'][2] = [
'psa_molecular_formula' => 'C62H98N16O22',
'psa_molecular_weight' => '1419.5 Da',
'psa_aliases' => 'Body Protection Compound-157',
];
$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
$this->call_private( $this->migration, 'backfill_post', [ 2 ] );
$written = null;
foreach ( $GLOBALS['pr_test_updated_meta'] as $entry ) {
if ( '_pr_molecular_weight' === $entry['key'] ) {
$written = $entry['value'];
}
}
$this->assertSame( '1419.5', $written );
}
public function test_backfill_post_psa_writes_aliases_as_json_array(): void {
$GLOBALS['pr_test_postmeta'][2] = [
'psa_molecular_formula' => 'C62H98N16O22',
'psa_molecular_weight' => '1419.5 Da',
'psa_aliases' => 'Body Protection Compound-157, PL 14736',
];
$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
$this->call_private( $this->migration, 'backfill_post', [ 2 ] );
$written = null;
foreach ( $GLOBALS['pr_test_updated_meta'] as $entry ) {
if ( '_pr_aliases' === $entry['key'] ) {
$written = $entry['value'];
}
}
$aliases = json_decode( $written, true );
$this->assertIsArray( $aliases );
$this->assertCount( 2, $aliases );
}
// ── PubChem skip path ─────────────────────────────────────────────.
public function test_backfill_post_returns_pubchem_skip_when_network_fails(): void {
$mock_pubchem = new class extends PR_Core_Pubchem_Client {
public function fetch_by_cid( string $cid ): ?array { return null; }
public function fetch_by_name( string $name ): ?array { return null; }
};
$mock_migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta( $mock_pubchem );
$GLOBALS['pr_test_postmeta'][10] = [];
$GLOBALS['pr_test_posts'][10] = (object) [ 'post_title' => 'IGF-1 LR3', 'ID' => 10 ];
$result = $this->call_private( $mock_migration, 'backfill_post', [ 10 ] );
$this->assertSame( 'pubchem_skip', $result );
$this->assertEmpty( $GLOBALS['pr_test_updated_meta'] );
}
}

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<?php
/**
* Unit tests for PR_Core_Peptide_CPT (v0.2.0 CPT consolidation).
*
* Ported from tests/unit/test-peptide-cpt.php.
*
* Coverage:
* - Constants match the v0.2.0 consolidated contract.
* - TAX_FAMILY constant is removed.
* - register_peptide_post_type() guard: no-op when post_type_exists.
* - register_peptide_post_type() payload: args match contract.
* - register_taxonomies() guard: no-op when taxonomy_exists.
* - register_taxonomies() only registers peptide_category.
* - register_hooks() adds action on 'init'.
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Tests for PR_Core_Peptide_CPT.
*/
class PeptideCptTest extends TestCase {
/**
* Reset global WP state before each test.
*/
protected function setUp(): void {
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
'registered_post_types' => [],
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
'added_filters' => [],
];
// Ensure CPT class is loaded.
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
}
// ── Constants ─────────────────────────────────────────────────────.
public function test_post_type_constant(): void {
$this->assertSame( 'peptide', PR_Core_Peptide_CPT::POST_TYPE );
}
public function test_tax_category_constant(): void {
$this->assertSame( 'peptide_category', PR_Core_Peptide_CPT::TAX_CATEGORY );
}
public function test_capability_constant(): void {
$this->assertSame( 'manage_peptide_content', PR_Core_Peptide_CPT::CAPABILITY );
}
public function test_tax_family_constant_removed(): void {
$reflection = new ReflectionClass( PR_Core_Peptide_CPT::class );
$this->assertFalse(
$reflection->hasConstant( 'TAX_FAMILY' ),
'TAX_FAMILY constant should have been removed in v0.2.0'
);
}
// ── CPT registration guard ────────────────────────────────────────.
public function test_register_post_type_noop_when_already_exists(): void {
$GLOBALS['pr_core_test_state']['existing_post_types'] = [ 'peptide' ];
PR_Core_Peptide_CPT::register_peptide_post_type();
$this->assertEmpty(
$GLOBALS['pr_core_test_state']['registered_post_types'],
'register_peptide_post_type() must no-op when post_type_exists("peptide") is true'
);
}
// ── CPT registration payload ──────────────────────────────────────.
public function test_register_post_type_registers_peptide_slug(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$this->assertArrayHasKey(
'peptide',
$GLOBALS['pr_core_test_state']['registered_post_types']
);
}
public function test_register_post_type_args_public(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertTrue( $args['public'] ?? null );
}
public function test_register_post_type_args_publicly_queryable(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertTrue( $args['publicly_queryable'] ?? null );
}
public function test_register_post_type_args_show_in_rest(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertTrue( $args['show_in_rest'] ?? null );
}
public function test_register_post_type_args_rest_base(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertSame( 'peptides', $args['rest_base'] ?? null );
}
public function test_register_post_type_args_no_rest_namespace(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertArrayNotHasKey(
'rest_namespace',
$args,
'rest_namespace must be absent — defaults to wp/v2 for Gutenberg compatibility'
);
}
public function test_register_post_type_args_capability_type(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertSame( 'post', $args['capability_type'] ?? null );
}
public function test_register_post_type_args_map_meta_cap(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertTrue( $args['map_meta_cap'] ?? null );
}
public function test_register_post_type_args_not_hierarchical(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertFalse( $args['hierarchical'] ?? null );
}
public function test_register_post_type_args_has_archive(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertTrue( $args['has_archive'] ?? null );
}
public function test_register_post_type_args_rewrite_slug(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertSame( 'peptides', $args['rewrite']['slug'] ?? null );
}
public function test_register_post_type_args_rewrite_with_front(): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$this->assertFalse( $args['rewrite']['with_front'] ?? null );
}
/**
* @dataProvider supports_provider
*/
public function test_register_post_type_supports_feature( string $feature ): void {
PR_Core_Peptide_CPT::register_peptide_post_type();
$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'];
$supports = $args['supports'] ?? [];
$this->assertContains( $feature, $supports );
}
/**
* @return array<array<string>>
*/
public static function supports_provider(): array {
return [
[ 'title' ],
[ 'editor' ],
[ 'thumbnail' ],
[ 'excerpt' ],
[ 'revisions' ],
[ 'custom-fields' ],
];
}
// ── Taxonomy guard ────────────────────────────────────────────────.
public function test_register_taxonomies_noop_when_already_exists(): void {
$GLOBALS['pr_core_test_state']['existing_taxonomies'] = [ 'peptide_category' ];
PR_Core_Peptide_CPT::register_taxonomies();
$this->assertEmpty( $GLOBALS['pr_core_test_state']['registered_taxonomies'] );
}
// ── Taxonomy registration payload ─────────────────────────────────.
public function test_register_taxonomies_registers_peptide_category(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$this->assertArrayHasKey(
'peptide_category',
$GLOBALS['pr_core_test_state']['registered_taxonomies']
);
}
public function test_register_taxonomies_does_not_register_pr_peptide_family(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$this->assertArrayNotHasKey(
'pr_peptide_family',
$GLOBALS['pr_core_test_state']['registered_taxonomies'],
'pr_peptide_family taxonomy must not be registered (removed in v0.2.0)'
);
}
public function test_register_taxonomies_does_not_register_peptide_family(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$this->assertArrayNotHasKey(
'peptide_family',
$GLOBALS['pr_core_test_state']['registered_taxonomies']
);
}
public function test_register_taxonomies_attached_to_peptide_cpt(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$tax = $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_category'];
$this->assertSame( 'peptide', $tax['object_type'] ?? null );
}
public function test_register_taxonomies_is_hierarchical(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$tax = $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_category'];
$this->assertTrue( $tax['args']['hierarchical'] ?? null );
}
public function test_register_taxonomies_show_in_rest(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$tax = $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_category'];
$this->assertTrue( $tax['args']['show_in_rest'] ?? null );
}
public function test_register_taxonomies_rewrite_slug(): void {
PR_Core_Peptide_CPT::register_taxonomies();
$tax = $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_category'];
$this->assertSame( 'peptide-category', $tax['args']['rewrite']['slug'] ?? null );
}
// ── Hook registration ─────────────────────────────────────────────.
public function test_register_hooks_adds_init_action(): void {
$cpt = new PR_Core_Peptide_CPT();
$cpt->register_hooks();
$hooks = array_column( $GLOBALS['pr_core_test_state']['added_actions'], 'hook' );
$this->assertContains( 'init', $hooks );
}
}

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<?php
/**
* Unit tests for PR_Core_Verification_Scanner::compute_status().
*
* Ported from tests/unit/test-verification-scanner.php.
*
* Coverage:
* - Empty last_verified → overdue.
* - Days < 90% of threshold → current.
* - Days >= 90% and < 100% → due.
* - Days >= threshold → overdue.
* - Boundary at exactly 90% → due.
* - high velocity applies 60-day threshold from option.
* - low velocity applies 365-day constant (ignores option).
* - medium/default applies 180-day threshold from option.
* - Unknown velocity falls to medium/default.
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Tests for PR_Core_Verification_Scanner::compute_status().
*/
class VerificationScannerTest extends TestCase {
protected function setUp(): void {
$GLOBALS['pr_core_options'] = [];
require_once PR_CORE_PLUGIN_DIR . 'includes/scanner/class-pr-core-verification-scanner.php';
}
// ── Helper ────────────────────────────────────────────────────────.
private function days_ago( int $days ): string {
return gmdate( 'Y-m-d', time() - ( $days * DAY_IN_SECONDS ) );
}
// ── Empty last_verified ───────────────────────────────────────────.
public function test_empty_last_verified_returns_overdue(): void {
$this->assertSame(
'overdue',
PR_Core_Verification_Scanner::compute_status( '', 'medium' )
);
}
// ── Medium velocity (default 180-day threshold) ───────────────────.
public function test_medium_160_days_is_current(): void {
$this->assertSame( 'current', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 160 ), 'medium' ) );
}
public function test_medium_163_days_is_due(): void {
$this->assertSame( 'due', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 163 ), 'medium' ) );
}
public function test_medium_180_days_is_overdue(): void {
$this->assertSame( 'overdue', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 180 ), 'medium' ) );
}
public function test_medium_200_days_is_overdue(): void {
$this->assertSame( 'overdue', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 200 ), 'medium' ) );
}
// ── 90% boundary exactness ────────────────────────────────────────.
public function test_boundary_89_days_threshold_100_is_current(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 100 ];
$this->assertSame( 'current', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 89 ), 'medium' ) );
}
public function test_boundary_90_days_threshold_100_is_due(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 100 ];
$this->assertSame( 'due', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 90 ), 'medium' ) );
}
public function test_boundary_100_days_threshold_100_is_overdue(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 100 ];
$this->assertSame( 'overdue', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 100 ), 'medium' ) );
}
// ── High velocity (60-day threshold from option) ──────────────────.
public function test_high_50_days_is_current(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_high_velocity_threshold' => 60 ];
$this->assertSame( 'current', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 50 ), 'high' ) );
}
public function test_high_55_days_is_due(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_high_velocity_threshold' => 60 ];
$this->assertSame( 'due', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 55 ), 'high' ) );
}
public function test_high_61_days_is_overdue(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_high_velocity_threshold' => 60 ];
$this->assertSame( 'overdue', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 61 ), 'high' ) );
}
// ── Low velocity (365-day constant — ignores option) ──────────────.
public function test_low_300_days_is_current(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 999 ];
$this->assertSame( 'current', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 300 ), 'low' ) );
}
public function test_low_340_days_is_due(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 999 ];
$this->assertSame( 'due', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 340 ), 'low' ) );
}
public function test_low_366_days_is_overdue(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 999 ];
$this->assertSame( 'overdue', PR_Core_Verification_Scanner::compute_status( $this->days_ago( 366 ), 'low' ) );
}
// ── Unknown velocity falls to medium/default ──────────────────────.
public function test_unknown_velocity_uses_default_threshold(): void {
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 180 ];
$this->assertSame(
'current',
PR_Core_Verification_Scanner::compute_status( $this->days_ago( 100 ), 'unknown' )
);
}
}

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<?php
/**
* Unit tests for PR_Core_Settings verification methods.
*
* Ported from tests/unit/test-verification-settings.php.
*
* Coverage:
* - sanitize_cadence() accepts valid values, rejects invalid → 'weekly'.
* - sanitize_emails() filters invalid addresses, preserves valid ones.
* - reschedule_cron() no-ops when old === new value.
* - reschedule_cron() clears + reschedules when value changes.
*
* @package PeptideRepoCore\Tests
*/
use PHPUnit\Framework\TestCase;
/**
* Tests for PR_Core_Settings verification methods.
*/
class VerificationSettingsTest extends TestCase {
protected function setUp(): void {
$GLOBALS['pr_core_options'] = [];
$GLOBALS['pr_core_cron_calls'] = [];
$GLOBALS['pr_core_test_state'] = [
'existing_post_types' => [],
'existing_taxonomies' => [],
'registered_post_types' => [],
'registered_taxonomies' => [],
'registered_meta' => [],
'added_actions' => [],
'added_filters' => [],
];
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/admin/class-pr-core-settings.php';
}
// ── sanitize_cadence() ────────────────────────────────────────────.
public function test_sanitize_cadence_daily(): void {
$this->assertSame( 'daily', PR_Core_Settings::sanitize_cadence( 'daily' ) );
}
public function test_sanitize_cadence_weekly(): void {
$this->assertSame( 'weekly', PR_Core_Settings::sanitize_cadence( 'weekly' ) );
}
public function test_sanitize_cadence_monthly(): void {
$this->assertSame( 'monthly', PR_Core_Settings::sanitize_cadence( 'monthly' ) );
}
public function test_sanitize_cadence_invalid_defaults_to_weekly(): void {
$this->assertSame( 'weekly', PR_Core_Settings::sanitize_cadence( 'hourly' ) );
}
public function test_sanitize_cadence_empty_defaults_to_weekly(): void {
$this->assertSame( 'weekly', PR_Core_Settings::sanitize_cadence( '' ) );
}
public function test_sanitize_cadence_uppercase_defaults_to_weekly(): void {
$this->assertSame( 'weekly', PR_Core_Settings::sanitize_cadence( 'DAILY' ) );
}
// ── sanitize_emails() ─────────────────────────────────────────────.
public function test_sanitize_emails_empty_returns_empty(): void {
$this->assertSame( '', PR_Core_Settings::sanitize_emails( '' ) );
}
public function test_sanitize_emails_valid_single_kept(): void {
$this->assertSame( 'admin@example.com', PR_Core_Settings::sanitize_emails( 'admin@example.com' ) );
}
public function test_sanitize_emails_invalid_single_returns_empty(): void {
$this->assertSame( '', PR_Core_Settings::sanitize_emails( 'not-an-email' ) );
}
public function test_sanitize_emails_valid_pair_both_kept(): void {
$this->assertSame( 'a@test.com, b@test.com', PR_Core_Settings::sanitize_emails( 'a@test.com, b@test.com' ) );
}
public function test_sanitize_emails_mixed_only_valid_kept(): void {
$this->assertSame( 'good@test.com', PR_Core_Settings::sanitize_emails( 'good@test.com, bad-email' ) );
}
public function test_sanitize_emails_whitespace_trimmed(): void {
$this->assertSame( 'trimmed@test.com', PR_Core_Settings::sanitize_emails( ' trimmed@test.com ' ) );
}
// ── reschedule_cron(): no-op when same value ──────────────────────.
public function test_reschedule_cron_noop_when_value_unchanged(): void {
PR_Core_Settings::reschedule_cron( 'weekly', 'weekly' );
$this->assertEmpty( $GLOBALS['pr_core_cron_calls'] );
}
// ── reschedule_cron(): clears + reschedules on change ─────────────.
public function test_reschedule_cron_calls_clear_when_changed(): void {
PR_Core_Settings::reschedule_cron( 'weekly', 'daily' );
$actions = array_column( $GLOBALS['pr_core_cron_calls'], 'action' );
$this->assertContains( 'clear', $actions );
}
public function test_reschedule_cron_calls_schedule_when_changed(): void {
PR_Core_Settings::reschedule_cron( 'weekly', 'daily' );
$actions = array_column( $GLOBALS['pr_core_cron_calls'], 'action' );
$this->assertContains( 'schedule', $actions );
}
public function test_reschedule_cron_schedules_correct_hook(): void {
PR_Core_Settings::reschedule_cron( 'weekly', 'daily' );
$schedule_call = null;
foreach ( $GLOBALS['pr_core_cron_calls'] as $call ) {
if ( 'schedule' === $call['action'] ) {
$schedule_call = $call;
break;
}
}
$this->assertNotNull( $schedule_call );
$this->assertSame( 'pr_core_verification_scan', $schedule_call['hook'] ?? '' );
}
public function test_reschedule_cron_schedules_new_cadence(): void {
PR_Core_Settings::reschedule_cron( 'weekly', 'daily' );
$schedule_call = null;
foreach ( $GLOBALS['pr_core_cron_calls'] as $call ) {
if ( 'schedule' === $call['action'] ) {
$schedule_call = $call;
break;
}
}
$this->assertSame( 'daily', $schedule_call['recurrence'] ?? '' );
}
public function test_reschedule_cron_clear_fires_before_schedule(): void {
PR_Core_Settings::reschedule_cron( 'weekly', 'daily' );
$actions = array_column( $GLOBALS['pr_core_cron_calls'], 'action' );
$clear_idx = array_search( 'clear', $actions, true );
$schedule_idx = array_search( 'schedule', $actions, true );
$this->assertLessThan( $schedule_idx, $clear_idx );
}
}

34
tests/unit/test-jsonld-peptide-piece.php
View File

@@ -31,7 +31,7 @@ declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs ─────────────────────────────────────────────────────
// ── Additional stubs ─────────────────────────────────────────────────────.
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
@@ -129,7 +129,7 @@ if ( ! function_exists( 'sanitize_textarea_field' ) ) {
}
}
// ── Stub PR_Core_Peptide_Repository ──────────────────────────────────────
// ── Stub PR_Core_Peptide_Repository ──────────────────────────────────────.
/**
* Minimal repository stub — returns whatever is in $GLOBALS['pr_test_peptide_dto'].
@@ -140,7 +140,7 @@ class PR_Core_Peptide_Repository {
}
}
// ── Load classes under test ───────────────────────────────────────────────
// ── Load classes under test ───────────────────────────────────────────────.
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
@@ -150,7 +150,7 @@ require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.ph
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
// ── Helper ────────────────────────────────────────────────────────────────
// ── Helper ────────────────────────────────────────────────────────────────.
/**
* Create a minimal PR_Core_Peptide_DTO for testing.
@@ -184,7 +184,7 @@ function make_peptide_piece_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
echo "== JSON-LD peptide-piece regression tests (v0.6.2) ==\n\n";
// ── Setup ─────────────────────────────────────────────────────────────────
// ── Setup ─────────────────────────────────────────────────────────────────.
$GLOBALS['pr_test_the_id'] = 36;
$GLOBALS['pr_test_is_singular'] = true;
@@ -198,11 +198,11 @@ $GLOBALS['pr_test_peptide_dto'] = make_peptide_piece_dto();
$jsonld = new PR_Core_Jsonld();
// ── Regression: inject_graph_pieces fatal reproduced against old contract ─
// ── Regression: inject_graph_pieces fatal reproduced against old contract ─.
echo "Regression: inject_graph_pieces (OLD hook) with plain array fatal:\n";
// Simulate what Yoast's filter_graph_pieces_to_generate does:
// Simulate what Yoast's filter_graph_pieces_to_generate does:.
// it calls get_class($piece) on every item. A plain array causes a fatal.
$drug_builder = new PR_Core_Jsonld_Drug();
$drug_array = $drug_builder->build( $GLOBALS['pr_test_peptide_dto'] );
@@ -210,8 +210,8 @@ $drug_array = $drug_builder->build( $GLOBALS['pr_test_peptide_dto'] );
$caught_fatal = false;
try {
// This is the exact operation Yoast does in filter_graph_pieces_to_generate().
// Against the old v0.6.1 code (inject via wpseo_schema_graph_pieces), this would
// produce: "get_class(): Argument #1 ($object) must be of type object, array given"
// Against the old v0.6.1 code (inject via wpseo_schema_graph_pieces), this would.
// produce: "get_class(): Argument #1 ($object) must be of type object, array given".
$class_result = get_class( $drug_array );
} catch ( TypeError $e ) {
$caught_fatal = true;
@@ -220,7 +220,7 @@ try {
}
pr_assert( $caught_fatal, 'get_class(array) throws TypeError/Error — confirms the v0.6.1 fatal' );
// ── Fix: inject_graph_nodes (NEW hook) works without fatal ────────────────
// ── Fix: inject_graph_nodes (NEW hook) works without fatal ────────────────.
echo "\nFix: inject_graph_nodes via wpseo_schema_graph (plain array graph):\n";
@@ -279,7 +279,7 @@ pr_assert( count( $webpage_nodes ) === 1, 'MedicalWebPage node preserved (no dup
$breadcrumb_nodes = array_filter( $result_graph, static fn( $n ) => ( $n['@type'] ?? '' ) === 'BreadcrumbList' );
pr_assert( count( $breadcrumb_nodes ) === 1, 'BreadcrumbList node preserved (no duplicate)' );
// ── FAQ: present when _pr_faq_items has items ─────────────────────────────
// ── FAQ: present when _pr_faq_items has items ─────────────────────────────.
echo "\nFAQ injection via inject_graph_nodes:\n";
@@ -301,7 +301,7 @@ pr_assert_equals( 'https://peptiderepo.com/peptides/bpc-157/#faq', $faq_node['@i
pr_assert( isset( $faq_node['mainEntity'] ), 'FAQPage has mainEntity' );
pr_assert_equals( 2, count( $faq_node['mainEntity'] ), 'FAQPage has 2 questions' );
// ── FAQ: absent when _pr_faq_items empty ─────────────────────────────────
// ── FAQ: absent when _pr_faq_items empty ─────────────────────────────────.
$GLOBALS['pr_test_postmeta'][36]['_pr_faq_items'] = '[]';
@@ -312,7 +312,7 @@ $faq_nodes_empty = array_filter(
);
pr_assert( count( $faq_nodes_empty ) === 0, 'FAQPage NOT injected when _pr_faq_items is empty array' );
// ── Non-peptide page: no injection ───────────────────────────────────────
// ── Non-peptide page: no injection ───────────────────────────────────────.
echo "\nNon-peptide page: no injection:\n";
@@ -332,7 +332,7 @@ pr_assert( count( $result_non_peptide ) === 1, 'inject_graph_nodes no-ops on non
$drug_nodes_np = array_filter( $result_non_peptide, static fn( $n ) => ( is_array( $n['@type'] ?? null ) ? in_array( 'Drug', $n['@type'], true ) : ( $n['@type'] ?? '' ) === 'Drug' ) );
pr_assert( count( $drug_nodes_np ) === 0, 'Drug NOT injected on non-peptide page' );
// ── register_hooks: does NOT hook wpseo_schema_graph_pieces ──────────────
// ── register_hooks: does NOT hook wpseo_schema_graph_pieces ──────────────.
echo "\nregister_hooks: wpseo_schema_graph_pieces must NOT be hooked:\n";
@@ -341,11 +341,11 @@ $GLOBALS['pr_core_test_state']['added_filters'] = [];
$filters_added = [];
// Override add_filter in the bootstrap to capture calls.
// (bootstrap only stubs add_action; we check via a fresh parse of register_hooks.)
// (bootstrap only stubs add_action; we check via a fresh parse of register_hooks.).
$jsonld2 = new PR_Core_Jsonld();
// Use Reflection to inspect what hooks register_hooks would call.
// Instead: inspect the class source for the string — if inject_graph_pieces is
// Instead: inspect the class source for the string — if inject_graph_pieces is.
// still registered on wpseo_schema_graph_pieces, the bug is NOT fixed.
$src = file_get_contents( PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php' );
pr_assert(
@@ -361,6 +361,6 @@ pr_assert(
'class-pr-core-jsonld.php hooks wpseo_schema_graph for injection'
);
// ── Summary ───────────────────────────────────────────────────────────────
// ── Summary ───────────────────────────────────────────────────────────────.
exit( pr_test_summary() );

8
tests/unit/test-jsonld-webpage.php
View File

@@ -21,7 +21,7 @@ declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs ─────────────────────────────────────────────────────
// ── Additional stubs ─────────────────────────────────────────────────────.
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
@@ -81,7 +81,7 @@ echo "== JSON-LD WebPage v0.6.1 regression tests ==\n\n";
$enricher = new PR_Core_Jsonld_Webpage();
// ── retype_to_medical_webpage: array input, non-peptide singular ──────────
// ── retype_to_medical_webpage: array input, non-peptide singular ──────────.
echo "retype_to_medical_webpage — array input:\n";
@@ -106,7 +106,7 @@ $GLOBALS['pr_test_singular_type'] = '';
$result = $enricher->retype_to_medical_webpage( 'CollectionPage' );
pr_assert_equals( 'CollectionPage', $result, 'non-singular string: passes through unchanged' );
// ── enrich_webpage_piece: @type as array injects enrichments ─────────────
// ── enrich_webpage_piece: @type as array injects enrichments ─────────────.
echo "\nenrich_webpage_piece — @type as array:\n";
@@ -160,6 +160,6 @@ $graph_non_peptide = [
$result_non_peptide = $enricher->enrich_webpage_piece( $graph_non_peptide, new stdClass() );
pr_assert( ! isset( $result_non_peptide[0]['lastReviewed'] ), 'non-peptide: lastReviewed NOT injected' );
// ── Summary ──────────────────────────────────────────────────────────────
// ── Summary ──────────────────────────────────────────────────────────────.
exit( pr_test_summary() );

24
tests/unit/test-jsonld.php
View File

@@ -29,7 +29,7 @@ declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs ─────────────────────────────────────────────────────
// ── Additional stubs ─────────────────────────────────────────────────────.
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
@@ -111,7 +111,7 @@ require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.ph
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
// ── Helpers ──────────────────────────────────────────────────────────────
// ── Helpers ──────────────────────────────────────────────────────────────.
/**
* Create a minimal PR_Core_Peptide_DTO for testing.
@@ -145,7 +145,7 @@ function make_peptide_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
echo "== JSON-LD v0.6.0 unit tests ==\n\n";
// ── Drug @id ─────────────────────────────────────────────────────────────
// ── Drug @id ─────────────────────────────────────────────────────────────.
echo "Drug @id:\n";
@@ -160,14 +160,14 @@ pr_assert_equals(
'Drug @id = {permalink}#drug'
);
// ── Drug @type ───────────────────────────────────────────────────────────
// ── Drug @type ───────────────────────────────────────────────────────────.
echo "\nDrug @type:\n";
pr_assert( is_array( $drug_node['@type'] ), 'Drug @type is an array' );
pr_assert( in_array( 'Drug', $drug_node['@type'], true ), '@type includes "Drug"' );
pr_assert( in_array( 'MolecularEntity', $drug_node['@type'], true ), '@type includes "MolecularEntity"' );
// ── Fields present when meta set ─────────────────────────────────────────
// ── Fields present when meta set ─────────────────────────────────────────.
echo "\nFields present when _pr_* meta set:\n";
@@ -190,7 +190,7 @@ pr_assert_equals( 'g/mol', $drug_node_populated['molecularWeight']['unitText'],
pr_assert( isset( $drug_node_populated['alternateName'] ), 'alternateName present when _pr_aliases set' );
pr_assert_equals( 2, count( $drug_node_populated['alternateName'] ), 'alternateName has correct count' );
// ── Fields omitted when meta empty ───────────────────────────────────────
// ── Fields omitted when meta empty ───────────────────────────────────────.
echo "\nFields OMITTED when meta empty:\n";
@@ -201,7 +201,7 @@ pr_assert( ! isset( $drug_node_empty['molecularFormula'] ), 'molecularFormula OM
pr_assert( ! isset( $drug_node_empty['molecularWeight'] ), 'molecularWeight OMITTED when meta empty' );
pr_assert( ! isset( $drug_node_empty['alternateName'] ), 'alternateName OMITTED when _pr_aliases empty' );
// ── FAQPage present when _pr_faq_items has items ─────────────────────────
// ── FAQPage present when _pr_faq_items has items ─────────────────────────.
echo "\nFAQPage emission:\n";
@@ -224,7 +224,7 @@ pr_assert_equals( 2, count( $faq_piece['mainEntity'] ), 'FAQPage has 2 questions
pr_assert_equals( 'Question', $faq_piece['mainEntity'][0]['@type'], 'Question @type correct' );
pr_assert( isset( $faq_piece['mainEntity'][0]['acceptedAnswer'] ), 'Question has acceptedAnswer' );
// ── FAQPage absent when _pr_faq_items empty ──────────────────────────────
// ── FAQPage absent when _pr_faq_items empty ──────────────────────────────.
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => '[]' ];
$faq_empty = $faq_builder->build( 1, $permalink );
@@ -234,7 +234,7 @@ $GLOBALS['pr_test_postmeta'][1] = [];
$faq_absent = $faq_builder->build( 1, $permalink );
pr_assert( null === $faq_absent, 'FAQPage piece IS null when _pr_faq_items absent' );
// ── MedicalWebPage retype ────────────────────────────────────────────────
// ── MedicalWebPage retype ────────────────────────────────────────────────.
echo "\nMedicalWebPage retype:\n";
@@ -250,7 +250,7 @@ $GLOBALS['pr_test_singular_type'] = '';
$result = $webpage_enricher->retype_to_medical_webpage( 'WebPage' );
pr_assert_equals( 'WebPage', $result, 'passes through unchanged on non-peptide pages' );
// ── No duplicate WebPage / BreadcrumbList nodes ───────────────────────────
// ── No duplicate WebPage / BreadcrumbList nodes ───────────────────────────.
echo "\nNo duplicate WebPage/BreadcrumbList nodes:\n";
@@ -270,7 +270,7 @@ pr_assert( ! in_array( 'BreadcrumbList', $types_from_builders, true ), 'Breadcru
pr_assert( in_array( 'Drug', $types_from_builders, true ), 'Drug IS in our emitted pieces' );
pr_assert( in_array( 'FAQPage', $types_from_builders, true ), 'FAQPage IS in our emitted pieces when items present' );
// ── PR_Core_Schema_Sanitizers::sanitize_faq_items() ──────────────────────
// ── PR_Core_Schema_Sanitizers::sanitize_faq_items() ──────────────────────.
echo "\nPR_Core_Schema_Sanitizers::sanitize_faq_items():\n";
@@ -294,6 +294,6 @@ $result_incomplete = PR_Core_Schema_Sanitizers::sanitize_faq_items( $incomplete_
$decoded_incomplete = json_decode( $result_incomplete, true );
pr_assert_equals( 0, count( $decoded_incomplete ), 'item without answer field dropped' );
// ── Summary ──────────────────────────────────────────────────────────────
// ── Summary ──────────────────────────────────────────────────────────────.
exit( pr_test_summary() );

22
tests/unit/test-migration-0004.php
View File

@@ -27,7 +27,7 @@ declare(strict_types=1);
// Bootstrap the lightweight WP stubs.
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs needed for migration 0004 ──────────────────────────
// ── Additional stubs needed for migration 0004 ──────────────────────────.
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
@@ -85,7 +85,7 @@ require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-pubchem-cli
// Load migration class under test.
require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php';
// ── Expose private methods via reflection ────────────────────────────────
// ── Expose private methods via reflection ────────────────────────────────.
/**
* Call a private/protected method on an object via reflection.
@@ -105,7 +105,7 @@ $migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
echo "== PR_Core_Migration_0004 unit tests ==\n\n";
// ── parse_weight() ───────────────────────────────────────────────────────
// ── parse_weight() ───────────────────────────────────────────────────────.
echo "parse_weight():\n";
@@ -145,7 +145,7 @@ pr_assert_equals(
'strips whitespace and lowercase "da"'
);
// ── parse_aliases_string() ───────────────────────────────────────────────
// ── parse_aliases_string() ───────────────────────────────────────────────.
echo "\nparse_aliases_string():\n";
@@ -167,8 +167,8 @@ pr_assert_equals( '[]', $whitespace_result, 'whitespace-only segments dropped, r
$single = json_decode( $migration->parse_aliases_string( 'Only One' ), true );
pr_assert_equals( 1, count( $single ), 'single alias produces array of 1' );
// ── sanitize_formula() ───────────────────────────────────────────────────
// Five required cases (Option B — validate, don't allowlist):
// ── sanitize_formula() ───────────────────────────────────────────────────.
// Five required cases (Option B — validate, don't allowlist):.
// 1. Valid formula unchanged.
// 2. Parenthesised formula preserved.
// 3. Newline-injected payload — "injection" stripped, formula kept.
@@ -219,7 +219,7 @@ pr_assert_equals(
'whitespace-only returns empty string'
);
// ── Idempotency: skips when all three PR Core keys populated ─────────────
// ── Idempotency: skips when all three PR Core keys populated ─────────────.
echo "\nIdempotency (all _pr_* keys populated):\n";
@@ -235,7 +235,7 @@ $result = call_private( $migration, 'backfill_post', [ 1 ] );
pr_assert_equals( 'skipped', $result, 'returns "skipped" when all three keys non-empty' );
pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no update_post_meta calls when skipped' );
// ── PSA source path ──────────────────────────────────────────────────────
// ── PSA source path ──────────────────────────────────────────────────────.
echo "\nPSA source path:\n";
@@ -277,7 +277,7 @@ pr_assert( $formula_written, 'molecular formula meta was written' );
pr_assert( $weight_written, 'molecular weight meta was written' );
pr_assert( $aliases_written, 'aliases meta was written' );
// ── Partial re-run: existing values preserved ────────────────────────────
// ── Partial re-run: existing values preserved ────────────────────────────.
echo "\nIdempotency: only some keys populated (partial re-run):\n";
@@ -297,7 +297,7 @@ $GLOBALS['pr_test_posts'][3] = (object) [ 'post_title' => 'BPC-157', 'ID' => 3 ]
$result = call_private( $migration, 'backfill_post', [ 3 ] );
pr_assert_equals( 'copied_psa', $result, 'runs PSA copy even when only some keys populated' );
// ── PubChem skip path: no PSA data, no network ──────────────────────────
// ── PubChem skip path: no PSA data, no network ──────────────────────────.
echo "\nPubChem skip path (no PSA data, no network in unit tests):\n";
@@ -317,6 +317,6 @@ $result = call_private( $mock_migration, 'backfill_post', [ 10 ] );
pr_assert_equals( 'pubchem_skip', $result, 'returns "pubchem_skip" when PubChem network fails' );
pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no meta written on pubchem_skip' );
// ── Summary ──────────────────────────────────────────────────────────────
// ── Summary ──────────────────────────────────────────────────────────────.
exit( pr_test_summary() );

20
tests/unit/test-verification-scanner.php
View File

@@ -22,7 +22,7 @@ declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs needed by the scanner ──────────────────────────────
// ── Additional stubs needed by the scanner ──────────────────────────────.
if ( ! defined( 'DAY_IN_SECONDS' ) ) {
define( 'DAY_IN_SECONDS', 86400 );
@@ -37,11 +37,11 @@ if ( ! function_exists( 'get_option' ) ) {
}
}
// ── Load the scanner class ──────────────────────────────────────────────
// ── Load the scanner class ──────────────────────────────────────────────.
require_once __DIR__ . '/../../includes/scanner/class-pr-core-verification-scanner.php';
// ── Helper: build a date N days ago ────────────────────────────────────
// ── Helper: build a date N days ago ────────────────────────────────────.
function days_ago( int $days ): string {
return gmdate( 'Y-m-d', time() - ( $days * DAY_IN_SECONDS ) );
@@ -49,7 +49,7 @@ function days_ago( int $days ): string {
echo "== PR_Core_Verification_Scanner::compute_status() unit tests ==\n\n";
// ── Empty last_verified ─────────────────────────────────────────────────
// ── Empty last_verified ─────────────────────────────────────────────────.
echo "Empty last_verified:\n";
pr_assert_equals(
@@ -58,7 +58,7 @@ pr_assert_equals(
'empty string → overdue'
);
// ── Medium velocity (default 180-day threshold) ─────────────────────────
// ── Medium velocity (default 180-day threshold) ─────────────────────────.
echo "\nMedium velocity (threshold=180, option default):\n";
$GLOBALS['pr_core_options'] = [];
@@ -75,7 +75,7 @@ pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_
// 200 days ago → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 200 ), 'medium' ), '200 days → overdue' );
// ── 90% boundary exactness ──────────────────────────────────────────────
// ── 90% boundary exactness ──────────────────────────────────────────────.
echo "\n90% boundary (threshold=100):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 100 ];
@@ -89,7 +89,7 @@ pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago(
// 100 days → 100 >= 100 → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 100 ), 'medium' ), '100 days (threshold 100) → overdue' );
// ── High velocity (60-day threshold from option) ────────────────────────
// ── High velocity (60-day threshold from option) ────────────────────────.
echo "\nHigh velocity (threshold=60 from option):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_high_velocity_threshold' => 60 ];
@@ -103,7 +103,7 @@ pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago(
// 61 days → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 61 ), 'high' ), 'high: 61 days → overdue' );
// ── Low velocity (365-day constant — ignores option) ────────────────────
// ── Low velocity (365-day constant — ignores option) ────────────────────.
echo "\nLow velocity (threshold=365, constant, ignores option):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 999 ]; // Should be ignored for low.
@@ -117,12 +117,12 @@ pr_assert_equals( 'due', PR_Core_Verification_Scanner::compute_status( days_ago(
// 366 days → overdue.
pr_assert_equals( 'overdue', PR_Core_Verification_Scanner::compute_status( days_ago( 366 ), 'low' ), 'low: 366 days → overdue' );
// ── Unknown velocity falls through to medium/default ────────────────────
// ── Unknown velocity falls through to medium/default ────────────────────.
echo "\nUnknown velocity (falls to default/medium):\n";
$GLOBALS['pr_core_options'] = [ 'pr_core_default_threshold' => 180 ];
pr_assert_equals( 'current', PR_Core_Verification_Scanner::compute_status( days_ago( 100 ), 'unknown' ), 'unknown velocity: 100 days → current (uses default 180)' );
// ── Summary ─────────────────────────────────────────────────────────────
// ── Summary ─────────────────────────────────────────────────────────────.
exit( pr_test_summary() );

14
tests/unit/test-verification-settings.php
View File

@@ -18,7 +18,7 @@ declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs needed by the settings class ───────────────────────
// ── Additional stubs needed by the settings class ───────────────────────.
$GLOBALS['pr_core_options'] = [];
$GLOBALS['pr_core_cron_calls'] = [];
@@ -66,14 +66,14 @@ if ( ! function_exists( 'wp_schedule_event' ) ) {
}
}
// ── Load the settings class ─────────────────────────────────────────────
// ── Load the settings class ─────────────────────────────────────────────.
require_once __DIR__ . '/../../includes/cpt/class-pr-core-peptide-cpt.php';
require_once __DIR__ . '/../../includes/admin/class-pr-core-settings.php';
echo "== PR_Core_Settings verification methods unit tests ==\n\n";
// ── sanitize_cadence() ──────────────────────────────────────────────────
// ── sanitize_cadence() ──────────────────────────────────────────────────.
echo "sanitize_cadence():\n";
pr_assert_equals( 'daily', PR_Core_Settings::sanitize_cadence( 'daily' ), 'daily → daily' );
@@ -83,7 +83,7 @@ pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( 'hourly' ), 'h
pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( '' ), 'empty → weekly default' );
pr_assert_equals( 'weekly', PR_Core_Settings::sanitize_cadence( 'DAILY' ), 'uppercase → weekly (case-sensitive)' );
// ── sanitize_emails() ───────────────────────────────────────────────────
// ── sanitize_emails() ───────────────────────────────────────────────────.
echo "\nsanitize_emails():\n";
pr_assert_equals( '', PR_Core_Settings::sanitize_emails( '' ), 'empty → empty' );
@@ -93,14 +93,14 @@ pr_assert_equals( 'a@test.com, b@test.com', PR_Core_Settings::sanitize_emails( '
pr_assert_equals( 'good@test.com', PR_Core_Settings::sanitize_emails( 'good@test.com, bad-email' ), 'mixed → only valid kept' );
pr_assert_equals( 'trimmed@test.com', PR_Core_Settings::sanitize_emails( ' trimmed@test.com ' ), 'whitespace trimmed around valid email' );
// ── reschedule_cron(): no-op when same value ────────────────────────────
// ── reschedule_cron(): no-op when same value ────────────────────────────.
echo "\nreschedule_cron() — no-op when value unchanged:\n";
$GLOBALS['pr_core_cron_calls'] = [];
PR_Core_Settings::reschedule_cron( 'weekly', 'weekly' );
pr_assert( empty( $GLOBALS['pr_core_cron_calls'] ), 'no cron calls when old === new' );
// ── reschedule_cron(): clears + reschedules on change ───────────────────
// ── reschedule_cron(): clears + reschedules on change ───────────────────.
echo "\nreschedule_cron() — reschedules when value changes:\n";
$GLOBALS['pr_core_cron_calls'] = [];
@@ -126,6 +126,6 @@ $clear_idx = array_search( 'clear', $actions, true );
$schedule_idx = array_search( 'schedule', $actions, true );
pr_assert( $clear_idx < $schedule_idx, 'clear fires before schedule' );
// ── Summary ─────────────────────────────────────────────────────────────
// ── Summary ─────────────────────────────────────────────────────────────.
exit( pr_test_summary() );

25
uninstall.php
View File

@@ -8,6 +8,7 @@
* peptide_category taxonomy terms) is preserved.
*
* @see ARCHITECTURE.md — §2.9 Uninstall specification.
* @package Peptide_Repo_Core
*/
if ( ! defined( 'WP_UNINSTALL_PLUGIN' ) ) {
@@ -18,15 +19,16 @@ global $wpdb;
/* ── 1. Drop custom tables ────────────────────────────────────────────── */
$tables = [
$tables = array(
$wpdb->prefix . 'pr_dosing_rows',
$wpdb->prefix . 'pr_legal_cells',
$wpdb->prefix . 'pr_ai_candidate_queue',
];
);
foreach ( $tables as $table ) {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery, WordPress.DB.DirectDatabaseQuery.SchemaChange
$wpdb->query( "DROP TABLE IF EXISTS {$table}" );
// phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared,WordPress.DB.DirectDatabaseQuery.SchemaChange,WordPress.DB.DirectDatabaseQuery.DirectQuery
$wpdb->query( "DROP TABLE IF EXISTS {$table}" ); // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
}
/* ── 2. Delete only peptide posts authored through PR Core's UI ───────── */
@@ -44,7 +46,7 @@ foreach ( $tables as $table ) {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$post_ids = $wpdb->get_col(
$wpdb->prepare(
"SELECT p.ID FROM {$wpdb->posts} p
"SELECT p.ID FROM {$wpdb->posts} p // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
INNER JOIN {$wpdb->postmeta} pm
ON p.ID = pm.post_id AND pm.meta_key = %s AND pm.meta_value = %s
WHERE p.post_type = %s",
@@ -54,7 +56,7 @@ $post_ids = $wpdb->get_col(
)
);
foreach ( $post_ids as $post_id ) {
foreach ( $post_ids as $post_id ) { // phpcs:ignore WordPress.WP.GlobalVariablesOverride.Prohibited
wp_delete_post( (int) $post_id, true );
}
@@ -72,8 +74,9 @@ foreach ( $post_ids as $post_id ) {
/* ── 4. Delete all pr_core_ prefixed options ──────────────────────────── */
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
// phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared,WordPress.DB.DirectDatabaseQuery.NoCaching
$wpdb->query(
"DELETE FROM {$wpdb->options} WHERE option_name LIKE 'pr\_core\_%'"
"DELETE FROM {$wpdb->options} WHERE option_name LIKE 'pr\_core\_%'" // phpcs:ignore WordPress.DB.PreparedSQL.InterpolatedNotPrepared
);
/* ── 4b. Delete v0.6.0 schema-input meta keys from all peptide posts ──── */
@@ -85,19 +88,19 @@ $wpdb->query(
*
* @see ARCHITECTURE.md — §2.9 Uninstall specification.
*/
$schema_meta_keys = [
$schema_meta_keys = array(
'_pr_molecular_formula',
'_pr_molecular_weight',
'_pr_aliases',
'_pr_faq_items',
];
);
foreach ( $schema_meta_keys as $meta_key ) {
// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
$wpdb->delete(
$wpdb->postmeta,
[ 'meta_key' => $meta_key ],
[ '%s' ]
array( 'meta_key' => $meta_key ),
array( '%s' )
);
}
@@ -106,7 +109,7 @@ foreach ( $schema_meta_keys as $meta_key ) {
$editable_roles = wp_roles()->roles;
foreach ( array_keys( $editable_roles ) as $role_name ) {
$role = get_role( $role_name );
$role = get_role( $role_name ); // phpcs:ignore WordPress.WP.GlobalVariablesOverride.Prohibited
if ( $role && $role->has_cap( 'manage_peptide_content' ) ) {
$role->remove_cap( 'manage_peptide_content' );
}