1e5999e663
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
297 lines
11 KiB
PHP
297 lines
11 KiB
PHP
<?php
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/**
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* Unit tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
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*
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* Run: php tests/unit/test-migration-0004.php
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* Exit 0 = all pass, 1 = any failure.
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*
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* Coverage:
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* - parse_weight(): strips "Da" suffix, strips "DA" variant, handles plain float,
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* handles empty string (returns 0.0), handles zero-value string.
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* - parse_aliases_string(): splits comma-separated string, trims whitespace,
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* drops empty segments, returns '[]' for empty input.
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* - PR_Core_Schema_Sanitizers::sanitize_molecular_formula(): valid chars, strips HTML, strips invalid.
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* - Idempotency: backfill_post() returns 'skipped' when all three PR Core keys populated.
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* - PSA source path: copies and transforms psa_* values to _pr_* keys.
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* - Empty PSA data: skips to pubchem path, returns 'pubchem_skip' on no data.
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*
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* Not covered here (require live WP + DB or network):
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* - PubChem HTTP round-trip (mocked at the http_get_once level in integration tests).
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* - Actual update_post_meta() persistence.
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*
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* @package PeptideRepoCore
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*/
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declare(strict_types=1);
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// Bootstrap the lightweight WP stubs.
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require_once __DIR__ . '/../bootstrap.php';
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// ── Additional stubs needed for migration 0004 ──────────────────────────
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if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
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define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
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}
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// Post meta store for testing.
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$GLOBALS['pr_test_postmeta'] = [];
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$GLOBALS['pr_test_updated_meta'] = [];
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function get_post_meta( int $post_id, string $key, bool $single = false ) {
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$store = $GLOBALS['pr_test_postmeta'][ $post_id ] ?? [];
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return $single ? ( $store[ $key ] ?? '' ) : array_values( $store );
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}
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function update_post_meta( int $post_id, string $key, $value ): bool {
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$GLOBALS['pr_test_postmeta'][ $post_id ][ $key ] = $value;
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$GLOBALS['pr_test_updated_meta'][] = [ 'post_id' => $post_id, 'key' => $key, 'value' => $value ];
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return true;
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}
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function get_post( int $id ) {
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if ( isset( $GLOBALS['pr_test_posts'][ $id ] ) ) {
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return $GLOBALS['pr_test_posts'][ $id ];
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}
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return null;
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}
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function get_posts( array $args = [] ): array {
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return $GLOBALS['pr_test_all_post_ids'] ?? [];
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}
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function is_wp_error( $value ): bool {
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return false;
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}
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function wp_strip_all_tags( $value ): string {
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return strip_tags( (string) $value );
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}
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function esc_html( string $val ): string {
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return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
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}
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function error_log( string $msg ): bool {
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// Suppress during tests.
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return true;
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}
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// Load dependencies.
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require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
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require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
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require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-pubchem-client.php';
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// Load migration class under test.
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require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php';
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// ── Expose private methods via reflection ────────────────────────────────
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/**
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* Call a private/protected method on an object via reflection.
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*
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* @param object $obj Instance.
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* @param string $method Method name.
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* @param array $args Arguments.
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* @return mixed Return value.
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*/
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function call_private( object $obj, string $method, array $args = [] ) {
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$ref = new ReflectionMethod( $obj, $method );
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$ref->setAccessible( true );
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return $ref->invokeArgs( $obj, $args );
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}
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$migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
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echo "== PR_Core_Migration_0004 unit tests ==\n\n";
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// ── parse_weight() ───────────────────────────────────────────────────────
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echo "parse_weight():\n";
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pr_assert_equals(
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1419.5,
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$migration->parse_weight( '1419.5 Da' ),
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'strips " Da" suffix and parses float'
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);
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pr_assert_equals(
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1419.5,
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$migration->parse_weight( '1419.5 DA' ),
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'strips uppercase " DA" suffix'
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);
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pr_assert_equals(
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1419.5,
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$migration->parse_weight( '1419.5' ),
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'parses plain float string without suffix'
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);
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pr_assert_equals(
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0.0,
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$migration->parse_weight( '' ),
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'returns 0.0 for empty string'
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);
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pr_assert_equals(
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0.0,
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$migration->parse_weight( ' Da ' ),
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'returns 0.0 for suffix-only string'
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);
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pr_assert_equals(
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800.123,
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$migration->parse_weight( ' 800.123 da ' ),
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'strips whitespace and lowercase "da"'
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);
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// ── parse_aliases_string() ───────────────────────────────────────────────
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echo "\nparse_aliases_string():\n";
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$result = json_decode(
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$migration->parse_aliases_string( 'Body Protection Compound-157, PL 14736, PL-10, Bepecin' ),
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true
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);
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pr_assert( is_array( $result ), 'returns a JSON-decodable array' );
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pr_assert_equals( 4, count( $result ), 'correct count: 4 aliases' );
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pr_assert_equals( 'Body Protection Compound-157', $result[0], 'first alias trimmed correctly' );
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pr_assert_equals( 'PL 14736', $result[1], 'second alias trimmed correctly' );
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$empty_result = $migration->parse_aliases_string( '' );
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pr_assert_equals( '[]', $empty_result, 'empty string returns "[]"' );
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$whitespace_result = $migration->parse_aliases_string( ' , , ' );
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pr_assert_equals( '[]', $whitespace_result, 'whitespace-only segments dropped, returns "[]"' );
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$single = json_decode( $migration->parse_aliases_string( 'Only One' ), true );
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pr_assert_equals( 1, count( $single ), 'single alias produces array of 1' );
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// ── sanitize_formula() ───────────────────────────────────────────────────
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echo "\nPR_Core_Schema_Sanitizers::sanitize_molecular_formula():\n";
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pr_assert_equals(
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'C62H98N16O22',
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PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C62H98N16O22' ),
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'valid formula passes unchanged'
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);
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pr_assert_equals(
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'C62H98N16O22',
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PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<b>C62H98N16O22</b>' ),
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'HTML tags stripped from formula'
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);
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pr_assert_equals(
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'C10H12',
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PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ),
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'non-formula characters removed'
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);
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pr_assert_equals(
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'',
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PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '' ),
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'empty string returns empty string'
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);
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// ── Idempotency: skips when all three PR Core keys populated ─────────────
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echo "\nIdempotency (all _pr_* keys populated):\n";
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$GLOBALS['pr_test_postmeta'] = [];
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$GLOBALS['pr_test_updated_meta'] = [];
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$GLOBALS['pr_test_postmeta'][1] = [
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'_pr_molecular_formula' => 'C62H98N16O22',
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'_pr_molecular_weight' => '1419.5',
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'_pr_aliases' => '["Alias One"]',
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];
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$result = call_private( $migration, 'backfill_post', [ 1 ] );
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pr_assert_equals( 'skipped', $result, 'returns "skipped" when all three keys non-empty' );
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pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no update_post_meta calls when skipped' );
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// ── PSA source path ──────────────────────────────────────────────────────
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echo "\nPSA source path:\n";
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$GLOBALS['pr_test_postmeta'] = [];
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$GLOBALS['pr_test_updated_meta'] = [];
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$GLOBALS['pr_test_postmeta'][2] = [
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'psa_molecular_formula' => 'C62H98N16O22',
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'psa_molecular_weight' => '1419.5 Da',
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'psa_aliases' => 'Body Protection Compound-157, PL 14736',
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];
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$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
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$result = call_private( $migration, 'backfill_post', [ 2 ] );
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pr_assert_equals( 'copied_psa', $result, 'returns "copied_psa" when PSA data present' );
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$updated = $GLOBALS['pr_test_updated_meta'];
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$formula_written = false;
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$weight_written = false;
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$aliases_written = false;
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foreach ( $updated as $entry ) {
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if ( '_pr_molecular_formula' === $entry['key'] ) {
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$formula_written = true;
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pr_assert_equals( 'C62H98N16O22', $entry['value'], 'formula written correctly' );
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}
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if ( '_pr_molecular_weight' === $entry['key'] ) {
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$weight_written = true;
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pr_assert_equals( '1419.5', $entry['value'], 'weight written as float string without Da' );
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}
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if ( '_pr_aliases' === $entry['key'] ) {
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$aliases_written = true;
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$aliases_arr = json_decode( $entry['value'], true );
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pr_assert( is_array( $aliases_arr ), 'aliases stored as JSON array' );
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pr_assert_equals( 2, count( $aliases_arr ), 'correct number of aliases' );
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}
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}
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pr_assert( $formula_written, 'molecular formula meta was written' );
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pr_assert( $weight_written, 'molecular weight meta was written' );
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pr_assert( $aliases_written, 'aliases meta was written' );
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// ── Partial re-run: existing values preserved ────────────────────────────
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echo "\nIdempotency: only some keys populated (partial re-run):\n";
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$GLOBALS['pr_test_postmeta'] = [];
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$GLOBALS['pr_test_updated_meta'] = [];
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// Only formula already set; weight and aliases are empty.
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$GLOBALS['pr_test_postmeta'][3] = [
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'_pr_molecular_formula' => 'C10H12',
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'_pr_molecular_weight' => '',
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'_pr_aliases' => '',
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'psa_molecular_formula' => 'C62H98N16O22',
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'psa_molecular_weight' => '1419.5 Da',
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'psa_aliases' => 'Body Protection Compound-157',
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];
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$GLOBALS['pr_test_posts'][3] = (object) [ 'post_title' => 'BPC-157', 'ID' => 3 ];
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$result = call_private( $migration, 'backfill_post', [ 3 ] );
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pr_assert_equals( 'copied_psa', $result, 'runs PSA copy even when only some keys populated' );
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// ── PubChem skip path: no PSA data, no network ──────────────────────────
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echo "\nPubChem skip path (no PSA data, no network in unit tests):\n";
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// Inject a null-returning PubChem client mock to simulate network failure.
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$mock_pubchem = new class extends PR_Core_Pubchem_Client {
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public function fetch_by_cid( string $cid ): ?array { return null; }
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public function fetch_by_name( string $name ): ?array { return null; }
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};
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$mock_migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta( $mock_pubchem );
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$GLOBALS['pr_test_postmeta'] = [];
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$GLOBALS['pr_test_updated_meta'] = [];
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$GLOBALS['pr_test_postmeta'][10] = []; // No PSA data, no PR Core data.
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$GLOBALS['pr_test_posts'][10] = (object) [ 'post_title' => 'IGF-1 LR3', 'ID' => 10 ];
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$result = call_private( $mock_migration, 'backfill_post', [ 10 ] );
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pr_assert_equals( 'pubchem_skip', $result, 'returns "pubchem_skip" when PubChem network fails' );
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pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no meta written on pubchem_skip' );
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// ── Summary ──────────────────────────────────────────────────────────────
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exit( pr_test_summary() );
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