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feat(schema): v0.6.0 — PSA backfill migration + Yoast-integrated Drug/MedicalWebPage/FAQ schema

Browse Source 
Piece 1 — Backfill migration 0004: copies PSA psa_molecular_formula/weight/aliases
into PR Core _pr_* meta. Idempotent + re-runnable. PubChem REST fallback for 4
posts missing PSA data (MAX_RETRIES=3, exp backoff). All PSA values UNTRUSTED.
PR_CORE_TARGET_SCHEMA_VERSION bumped 3 -> 4.

Piece 2 — Drug node enrichment + stable @id = {permalink}#drug (ratified contract).
Reads _pr_* schema-input meta. molecularWeight in g/mol. Empty-prop guard throughout.

Piece 3 — Yoast-integrated emission via wpseo_schema_graph_pieces (priority 11),
wpseo_schema_webpage_type (MedicalWebPage retype), wpseo_schema_graph (enrichment).
Standalone @graph fallback retained. No duplicate WebPage/BreadcrumbList.
FAQPage emitted only when _pr_faq_items populated.

Supporting: PR_Core_Schema_Sanitizers, PR_Core_Pubchem_Client, CONTEXT.md,
ARCHITECTURE.md, CONVENTIONS.md, CHANGELOG.md, uninstall.php purge.
Tests: test-migration-0004.php (20 assertions), test-jsonld.php (29 assertions).

Agent-Session: peptide-schema-backfill v0.6.0
This commit is contained in:
peptiderepo
2026-06-13 05:01:59 +00:00
parent cc5d06b970
commit 1e5999e663
17 changed files with 1919 additions and 117 deletions
Download Patch File Download Diff File Expand all files Collapse all files

299
tests/unit/test-jsonld.php Normal file
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<?php
/**
* Unit tests for v0.6.0 JSON-LD emission: Drug @id, MedicalWebPage type,
* FAQ conditional emission, no duplicate nodes.
*
* Run: php tests/unit/test-jsonld.php
* Exit 0 = all pass, 1 = any failure.
*
* Coverage:
* - Drug node: @id = {permalink}#drug, @type includes 'Drug'.
* - Drug node: molecularFormula present when _pr_molecular_formula set.
* - Drug node: molecularWeight present and uses g/mol when _pr_molecular_weight set.
* - Drug node: alternateName present when _pr_aliases has items.
* - Drug node: molecularFormula OMITTED when meta empty.
* - Drug node: molecularWeight OMITTED when meta empty.
* - Drug node: alternateName OMITTED when _pr_aliases is empty array.
* - FAQPage: present when _pr_faq_items has items.
* - FAQPage: absent when _pr_faq_items is empty or '[]'.
* - FAQPage: @id = {permalink}#faq.
* - MedicalWebPage retype: retype_to_medical_webpage() returns 'MedicalWebPage' on peptide singles.
* - MedicalWebPage retype: passes through unchanged on non-peptide pages.
* - No duplicate WebPage or BreadcrumbList nodes emitted by our code.
* - PR_Core_Schema_Sanitizers::sanitize_faq_items() validation.
*
* @package PeptideRepoCore
*/
declare(strict_types=1);
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs ─────────────────────────────────────────────────────
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
}
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_is_singular'] = false;
$GLOBALS['pr_test_singular_type'] = '';
$GLOBALS['pr_test_the_id'] = 0;
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 ] ?? [] );
}
function get_permalink( $post_id = null ): string {
return 'https://peptiderepo.com/peptides/bpc-157/';
}
function get_the_ID(): int {
return $GLOBALS['pr_test_the_id'];
}
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 );
}
function get_post_modified_time( $format, $gmt, $post_id ) {
return '2026-04-25';
}
function get_post_meta_val( $post_id, $key ) {
return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
}
function get_userdata( int $id ) {
return false;
}
function get_author_posts_url( int $id ): string {
return 'https://peptiderepo.com/author/' . $id;
}
function home_url( string $path = '' ): string {
return 'https://peptiderepo.com' . $path;
}
function apply_filters( string $tag, $value ) {
return $value; // No-op in test context.
}
function esc_html( string $val ): string {
return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
}
function esc_html__( string $text, string $domain = '' ): string {
return $text;
}
function wp_strip_all_tags( $value ): string {
return strip_tags( (string) $value );
}
function sanitize_textarea_field( $value ): string {
return is_scalar( $value ) ? trim( (string) $value ) : '';
}
// 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';
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 ──────────────────────────────────────────────────────────────
/**
* Create a minimal PR_Core_Peptide_DTO for testing.
*
* @param array<string, mixed> $overrides Field overrides.
* @return PR_Core_Peptide_DTO
*/
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 ) );
}
echo "== JSON-LD v0.6.0 unit tests ==\n\n";
// ── Drug @id ─────────────────────────────────────────────────────────────
echo "Drug @id:\n";
$GLOBALS['pr_test_postmeta'][1] = [];
$peptide = make_peptide_dto();
$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
pr_assert( isset( $drug_node['@id'] ), 'Drug node has @id' );
pr_assert_equals(
'https://peptiderepo.com/peptides/bpc-157/#drug',
$drug_node['@id'],
'Drug @id = {permalink}#drug'
);
// ── 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 ─────────────────────────────────────────
echo "\nFields present when _pr_* meta set:\n";
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Body Protection Compound-157","PL 14736"]',
];
$drug_node_populated = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
pr_assert( isset( $drug_node_populated['molecularFormula'] ), 'molecularFormula present when meta set' );
pr_assert_equals( 'C62H98N16O22', $drug_node_populated['molecularFormula'], 'molecularFormula value correct' );
pr_assert( isset( $drug_node_populated['molecularWeight'] ), 'molecularWeight present when meta set' );
pr_assert_equals( 'QuantitativeValue', $drug_node_populated['molecularWeight']['@type'], 'molecularWeight @type is QuantitativeValue' );
pr_assert_equals( 1419.5, $drug_node_populated['molecularWeight']['value'], 'molecularWeight value correct' );
pr_assert_equals( 'g/mol', $drug_node_populated['molecularWeight']['unitText'], 'molecularWeight unitText = g/mol' );
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 ───────────────────────────────────────
echo "\nFields OMITTED when meta empty:\n";
$GLOBALS['pr_test_postmeta'][1] = [];
$drug_node_empty = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
pr_assert( ! isset( $drug_node_empty['molecularFormula'] ), 'molecularFormula OMITTED when meta empty' );
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 ─────────────────────────
echo "\nFAQPage emission:\n";
$faq_builder = new PR_Core_Jsonld_Faq();
$permalink = 'https://peptiderepo.com/peptides/bpc-157/';
$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 = $faq_builder->build( 1, $permalink );
pr_assert( null !== $faq_piece, 'FAQPage piece not null when items present' );
pr_assert_equals( 'FAQPage', $faq_piece['@type'], 'FAQPage @type correct' );
pr_assert_equals( $permalink . '#faq', $faq_piece['@id'], 'FAQPage @id = {permalink}#faq' );
pr_assert( isset( $faq_piece['mainEntity'] ), 'FAQPage has mainEntity' );
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 ──────────────────────────────
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => '[]' ];
$faq_empty = $faq_builder->build( 1, $permalink );
pr_assert( null === $faq_empty, 'FAQPage piece IS null when _pr_faq_items is "[]"' );
$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 ────────────────────────────────────────────────
echo "\nMedicalWebPage retype:\n";
$webpage_enricher = new PR_Core_Jsonld_Webpage();
$GLOBALS['pr_test_is_singular'] = true;
$GLOBALS['pr_test_singular_type'] = 'peptide';
$result = $webpage_enricher->retype_to_medical_webpage( 'WebPage' );
pr_assert_equals( 'MedicalWebPage', $result, 'returns MedicalWebPage on peptide single' );
$GLOBALS['pr_test_is_singular'] = false;
$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 ───────────────────────────
echo "\nNo duplicate WebPage/BreadcrumbList nodes:\n";
// Verify our builders only produce Drug and FAQPage — never WebPage or BreadcrumbList.
$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q', 'answer' => 'A' ] ] ) ];
$types_from_builders = [];
foreach ( [ $drug_node_populated, $faq_piece ] as $piece ) {
if ( null === $piece ) { continue; }
$t = $piece['@type'] ?? '';
foreach ( ( is_array( $t ) ? $t : [ $t ] ) as $type ) {
$types_from_builders[] = $type;
}
}
pr_assert( ! in_array( 'WebPage', $types_from_builders, true ), 'WebPage NOT in our emitted pieces' );
pr_assert( ! in_array( 'MedicalWebPage', $types_from_builders, true ), 'MedicalWebPage NOT in injected pieces (Yoast owns node)' );
pr_assert( ! in_array( 'BreadcrumbList', $types_from_builders, true ), 'BreadcrumbList NOT in our emitted pieces' );
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() ──────────────────────
echo "\nPR_Core_Schema_Sanitizers::sanitize_faq_items():\n";
$valid_input = wp_json_encode( [
[ 'question' => 'What is BPC-157?', 'answer' => 'A peptide.' ],
] );
$result = PR_Core_Schema_Sanitizers::sanitize_faq_items( $valid_input );
$decoded = json_decode( $result, true );
pr_assert( is_array( $decoded ), 'sanitize_faq_items returns JSON-decodable string' );
pr_assert_equals( 1, count( $decoded ), 'correct count after sanitize' );
$result_empty = PR_Core_Schema_Sanitizers::sanitize_faq_items( '[]' );
pr_assert_equals( '[]', $result_empty, 'empty JSON array returns "[]"' );
$result_malformed = PR_Core_Schema_Sanitizers::sanitize_faq_items( 'not-json' );
pr_assert_equals( '[]', $result_malformed, 'malformed JSON returns "[]"' );
// Item missing 'answer' key: should be dropped.
$incomplete_input = wp_json_encode( [ [ 'question' => 'No answer here?' ] ] );
$result_incomplete = PR_Core_Schema_Sanitizers::sanitize_faq_items( $incomplete_input );
$decoded_incomplete = json_decode( $result_incomplete, true );
pr_assert_equals( 0, count( $decoded_incomplete ), 'item without answer field dropped' );
// ── Summary ──────────────────────────────────────────────────────────────
exit( pr_test_summary() );

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tests/unit/test-migration-0004.php Normal file
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<?php
/**
* Unit tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
*
* Run: php tests/unit/test-migration-0004.php
* Exit 0 = all pass, 1 = any failure.
*
* Coverage:
* - parse_weight(): strips "Da" suffix, strips "DA" variant, handles plain float,
* handles empty string (returns 0.0), handles zero-value string.
* - parse_aliases_string(): splits comma-separated string, trims whitespace,
* drops empty segments, returns '[]' for empty input.
* - PR_Core_Schema_Sanitizers::sanitize_molecular_formula(): valid chars, strips HTML, strips invalid.
* - Idempotency: backfill_post() returns 'skipped' when all three PR Core keys populated.
* - PSA source path: copies and transforms psa_* values to _pr_* keys.
* - Empty PSA data: skips to pubchem path, returns 'pubchem_skip' on no data.
*
* Not covered here (require live WP + DB or network):
* - PubChem HTTP round-trip (mocked at the http_get_once level in integration tests).
* - Actual update_post_meta() persistence.
*
* @package PeptideRepoCore
*/
declare(strict_types=1);
// Bootstrap the lightweight WP stubs.
require_once __DIR__ . '/../bootstrap.php';
// ── Additional stubs needed for migration 0004 ──────────────────────────
if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
}
// Post meta store for testing.
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
function get_post_meta( int $post_id, string $key, bool $single = false ) {
$store = $GLOBALS['pr_test_postmeta'][ $post_id ] ?? [];
return $single ? ( $store[ $key ] ?? '' ) : array_values( $store );
}
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;
}
function get_post( int $id ) {
if ( isset( $GLOBALS['pr_test_posts'][ $id ] ) ) {
return $GLOBALS['pr_test_posts'][ $id ];
}
return null;
}
function get_posts( array $args = [] ): array {
return $GLOBALS['pr_test_all_post_ids'] ?? [];
}
function is_wp_error( $value ): bool {
return false;
}
function wp_strip_all_tags( $value ): string {
return strip_tags( (string) $value );
}
function esc_html( string $val ): string {
return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
}
function error_log( string $msg ): bool {
// Suppress during tests.
return true;
}
// Load dependencies.
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';
// 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 ────────────────────────────────
/**
* Call a private/protected method on an object via reflection.
*
* @param object $obj Instance.
* @param string $method Method name.
* @param array $args Arguments.
* @return mixed Return value.
*/
function call_private( object $obj, string $method, array $args = [] ) {
$ref = new ReflectionMethod( $obj, $method );
$ref->setAccessible( true );
return $ref->invokeArgs( $obj, $args );
}
$migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
echo "== PR_Core_Migration_0004 unit tests ==\n\n";
// ── parse_weight() ───────────────────────────────────────────────────────
echo "parse_weight():\n";
pr_assert_equals(
1419.5,
$migration->parse_weight( '1419.5 Da' ),
'strips " Da" suffix and parses float'
);
pr_assert_equals(
1419.5,
$migration->parse_weight( '1419.5 DA' ),
'strips uppercase " DA" suffix'
);
pr_assert_equals(
1419.5,
$migration->parse_weight( '1419.5' ),
'parses plain float string without suffix'
);
pr_assert_equals(
0.0,
$migration->parse_weight( '' ),
'returns 0.0 for empty string'
);
pr_assert_equals(
0.0,
$migration->parse_weight( ' Da ' ),
'returns 0.0 for suffix-only string'
);
pr_assert_equals(
800.123,
$migration->parse_weight( ' 800.123 da ' ),
'strips whitespace and lowercase "da"'
);
// ── parse_aliases_string() ───────────────────────────────────────────────
echo "\nparse_aliases_string():\n";
$result = json_decode(
$migration->parse_aliases_string( 'Body Protection Compound-157, PL 14736, PL-10, Bepecin' ),
true
);
pr_assert( is_array( $result ), 'returns a JSON-decodable array' );
pr_assert_equals( 4, count( $result ), 'correct count: 4 aliases' );
pr_assert_equals( 'Body Protection Compound-157', $result[0], 'first alias trimmed correctly' );
pr_assert_equals( 'PL 14736', $result[1], 'second alias trimmed correctly' );
$empty_result = $migration->parse_aliases_string( '' );
pr_assert_equals( '[]', $empty_result, 'empty string returns "[]"' );
$whitespace_result = $migration->parse_aliases_string( ' , , ' );
pr_assert_equals( '[]', $whitespace_result, 'whitespace-only segments dropped, returns "[]"' );
$single = json_decode( $migration->parse_aliases_string( 'Only One' ), true );
pr_assert_equals( 1, count( $single ), 'single alias produces array of 1' );
// ── sanitize_formula() ───────────────────────────────────────────────────
echo "\nPR_Core_Schema_Sanitizers::sanitize_molecular_formula():\n";
pr_assert_equals(
'C62H98N16O22',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C62H98N16O22' ),
'valid formula passes unchanged'
);
pr_assert_equals(
'C62H98N16O22',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<b>C62H98N16O22</b>' ),
'HTML tags stripped from formula'
);
pr_assert_equals(
'C10H12',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ),
'non-formula characters removed'
);
pr_assert_equals(
'',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '' ),
'empty string returns empty string'
);
// ── Idempotency: skips when all three PR Core keys populated ─────────────
echo "\nIdempotency (all _pr_* keys populated):\n";
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
$GLOBALS['pr_test_postmeta'][1] = [
'_pr_molecular_formula' => 'C62H98N16O22',
'_pr_molecular_weight' => '1419.5',
'_pr_aliases' => '["Alias One"]',
];
$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 ──────────────────────────────────────────────────────
echo "\nPSA source path:\n";
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
$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 = call_private( $migration, 'backfill_post', [ 2 ] );
pr_assert_equals( 'copied_psa', $result, 'returns "copied_psa" when PSA data present' );
$updated = $GLOBALS['pr_test_updated_meta'];
$formula_written = false;
$weight_written = false;
$aliases_written = false;
foreach ( $updated as $entry ) {
if ( '_pr_molecular_formula' === $entry['key'] ) {
$formula_written = true;
pr_assert_equals( 'C62H98N16O22', $entry['value'], 'formula written correctly' );
}
if ( '_pr_molecular_weight' === $entry['key'] ) {
$weight_written = true;
pr_assert_equals( '1419.5', $entry['value'], 'weight written as float string without Da' );
}
if ( '_pr_aliases' === $entry['key'] ) {
$aliases_written = true;
$aliases_arr = json_decode( $entry['value'], true );
pr_assert( is_array( $aliases_arr ), 'aliases stored as JSON array' );
pr_assert_equals( 2, count( $aliases_arr ), 'correct number of aliases' );
}
}
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 ────────────────────────────
echo "\nIdempotency: only some keys populated (partial re-run):\n";
$GLOBALS['pr_test_postmeta'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
// Only formula already set; weight and aliases are empty.
$GLOBALS['pr_test_postmeta'][3] = [
'_pr_molecular_formula' => 'C10H12',
'_pr_molecular_weight' => '',
'_pr_aliases' => '',
'psa_molecular_formula' => 'C62H98N16O22',
'psa_molecular_weight' => '1419.5 Da',
'psa_aliases' => 'Body Protection Compound-157',
];
$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 ──────────────────────────
echo "\nPubChem skip path (no PSA data, no network in unit tests):\n";
// Inject a null-returning PubChem client mock to simulate network failure.
$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'] = [];
$GLOBALS['pr_test_updated_meta'] = [];
$GLOBALS['pr_test_postmeta'][10] = []; // No PSA data, no PR Core data.
$GLOBALS['pr_test_posts'][10] = (object) [ 'post_title' => 'IGF-1 LR3', 'ID' => 10 ];
$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 ──────────────────────────────────────────────────────────────
exit( pr_test_summary() );