08d7696444
- Replace hand-rolled ci.yml jobs with thin caller to reusable estate workflow
(peptiderepo/peptide-e2e/.github/workflows/ci.yml@main); tests: stubs; has_js: false.
workflow_call + permissions: contents: write added per estate standard so deploy.yml
can gate on it and phpcbf auto-commit step has required token scope.
- Convert 7 hand-rolled test-*.php scripts to PHPUnit TestCase classes:
PeptideCptTest <- test-peptide-cpt.php
VerificationScannerTest <- test-verification-scanner.php
VerificationSettingsTest <- test-verification-settings.php
Migration0004Test <- test-migration-0004.php
JsonldTest <- test-jsonld.php
JsonldWebpageTest <- test-jsonld-webpage.php
JsonldPeptidePieceTest <- test-jsonld-peptide-piece.php
All assertions preserved; old scripts remain in tests/unit/ but CI no longer
runs them (PHPUnit discovery matches *Test.php only).
- Rewrite tests/bootstrap.php: full WP stub library for PHPUnit (WP_Post, WP_Error,
all option/cron/CPT/taxonomy/permalink stubs); registers PR_Core_Autoloader.
- Add phpunit.xml.dist (bootstrap, unit suite, includes/ coverage).
- Add phpunit/phpunit ^9.6 + yoast/phpunit-polyfills ^2.0 to require-dev.
- Add composer test script (vendor/bin/phpunit --configuration phpunit.xml.dist).
- deploy.yml: add permissions: contents: write.
- Version bump 0.6.2 -> 0.7.0.
Agent-Session: claude-adopt-ci-20260616
240 lines
10 KiB
PHP
240 lines
10 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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* Ported from tests/unit/test-migration-0004.php.
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*
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* Coverage:
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* - parse_weight(): strips "Da"/"DA"/"da" suffix, handles plain float,
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* empty string → 0.0, suffix-only → 0.0.
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* - parse_aliases_string(): splits CSV, trims, drops empty, returns '[]' for empty.
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* - PR_Core_Schema_Sanitizers::sanitize_molecular_formula(): valid, HTML, groups,
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* injection, fully-invalid, empty.
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* - Idempotency: backfill_post() returns 'skipped' when all three keys populated.
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* - PSA source path: copies and transforms psa_* → _pr_* keys.
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* - PubChem skip path: 'pubchem_skip' when PubChem network fails.
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*
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* @package PeptideRepoCore\Tests
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*/
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use PHPUnit\Framework\TestCase;
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/**
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* Tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
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*/
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class Migration0004Test extends TestCase {
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/** @var PR_Core_Migration_0004_Backfill_Peptide_Meta */
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private $migration;
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protected function setUp(): void {
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$GLOBALS['pr_test_postmeta'] = [];
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$GLOBALS['pr_test_updated_meta'] = [];
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$GLOBALS['pr_test_posts'] = [];
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$GLOBALS['pr_core_test_state'] = [
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'existing_post_types' => [],
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'existing_taxonomies' => [],
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'registered_post_types' => [],
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'registered_taxonomies' => [],
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'registered_meta' => [],
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'added_actions' => [],
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'added_filters' => [],
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];
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require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
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require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
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require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-pubchem-client.php';
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require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php';
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$this->migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
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}
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// ── Helper: call private method via reflection ────────────────────
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/**
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* @param mixed[] $args
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* @return mixed
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*/
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private 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, $args );
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}
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// ── parse_weight() ────────────────────────────────────────────────
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public function test_parse_weight_strips_da_suffix(): void {
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$this->assertSame( 1419.5, $this->call_private( $this->migration, 'parse_weight', [ '1419.5 Da' ] ) );
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}
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public function test_parse_weight_strips_uppercase_da(): void {
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$this->assertSame( 1419.5, $this->call_private( $this->migration, 'parse_weight', [ '1419.5 DA' ] ) );
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}
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public function test_parse_weight_plain_float(): void {
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$this->assertSame( 1419.5, $this->call_private( $this->migration, 'parse_weight', [ '1419.5' ] ) );
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}
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public function test_parse_weight_empty_returns_zero(): void {
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$this->assertSame( 0.0, $this->call_private( $this->migration, 'parse_weight', [ '' ] ) );
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}
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public function test_parse_weight_suffix_only_returns_zero(): void {
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$this->assertSame( 0.0, $this->call_private( $this->migration, 'parse_weight', [ ' Da ' ] ) );
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}
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public function test_parse_weight_lowercase_da_with_whitespace(): void {
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$this->assertSame( 800.123, $this->call_private( $this->migration, 'parse_weight', [ ' 800.123 da ' ] ) );
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}
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// ── parse_aliases_string() ────────────────────────────────────────
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public function test_parse_aliases_string_splits_csv(): void {
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$result = json_decode(
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$this->call_private( $this->migration, 'parse_aliases_string', [ 'Body Protection Compound-157, PL 14736, PL-10, Bepecin' ] ),
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true
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);
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$this->assertIsArray( $result );
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$this->assertCount( 4, $result );
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$this->assertSame( 'Body Protection Compound-157', $result[0] );
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$this->assertSame( 'PL 14736', $result[1] );
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}
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public function test_parse_aliases_string_empty_returns_json_empty_array(): void {
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$this->assertSame( '[]', $this->call_private( $this->migration, 'parse_aliases_string', [ '' ] ) );
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}
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public function test_parse_aliases_string_whitespace_only_returns_json_empty_array(): void {
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$this->assertSame( '[]', $this->call_private( $this->migration, 'parse_aliases_string', [ ' , , ' ] ) );
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}
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public function test_parse_aliases_string_single_alias(): void {
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$result = json_decode( $this->call_private( $this->migration, 'parse_aliases_string', [ 'Only One' ] ), true );
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$this->assertCount( 1, $result );
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}
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// ── sanitize_molecular_formula() ──────────────────────────────────
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public function test_sanitize_formula_valid_passes_unchanged(): void {
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$this->assertSame( 'C62H98N16O22', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C62H98N16O22' ) );
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}
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public function test_sanitize_formula_strips_html_tags(): void {
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$this->assertSame( 'C62H98N16O22', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<b>C62H98N16O22</b>' ) );
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}
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public function test_sanitize_formula_preserves_parentheses(): void {
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$this->assertSame( 'C2H5(OH)', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C2H5(OH)' ) );
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}
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public function test_sanitize_formula_strips_non_formula_chars(): void {
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$this->assertSame( 'C10H12', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ) );
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}
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public function test_sanitize_formula_fully_invalid_returns_empty(): void {
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$this->assertSame( '', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<script>alert(1)</script>' ) );
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}
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public function test_sanitize_formula_empty_returns_empty(): void {
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$this->assertSame( '', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '' ) );
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}
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public function test_sanitize_formula_whitespace_only_returns_empty(): void {
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$this->assertSame( '', PR_Core_Schema_Sanitizers::sanitize_molecular_formula( ' ' ) );
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}
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// ── Idempotency ───────────────────────────────────────────────────
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public function test_backfill_post_skipped_when_all_keys_populated(): void {
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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 = $this->call_private( $this->migration, 'backfill_post', [ 1 ] );
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$this->assertSame( 'skipped', $result );
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$this->assertEmpty( $GLOBALS['pr_test_updated_meta'] );
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}
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// ── PSA source path ───────────────────────────────────────────────
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public function test_backfill_post_copies_psa_data(): void {
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$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 = $this->call_private( $this->migration, 'backfill_post', [ 2 ] );
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$this->assertSame( 'copied_psa', $result );
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}
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public function test_backfill_post_psa_writes_formula_correctly(): void {
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$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',
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];
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$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
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$this->call_private( $this->migration, 'backfill_post', [ 2 ] );
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$written = null;
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foreach ( $GLOBALS['pr_test_updated_meta'] as $entry ) {
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if ( '_pr_molecular_formula' === $entry['key'] ) {
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$written = $entry['value'];
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}
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}
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$this->assertSame( 'C62H98N16O22', $written );
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}
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public function test_backfill_post_psa_strips_da_from_weight(): void {
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$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',
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];
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$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
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$this->call_private( $this->migration, 'backfill_post', [ 2 ] );
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$written = null;
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foreach ( $GLOBALS['pr_test_updated_meta'] as $entry ) {
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if ( '_pr_molecular_weight' === $entry['key'] ) {
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$written = $entry['value'];
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}
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}
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$this->assertSame( '1419.5', $written );
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}
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public function test_backfill_post_psa_writes_aliases_as_json_array(): void {
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$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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$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
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$this->call_private( $this->migration, 'backfill_post', [ 2 ] );
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$written = null;
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foreach ( $GLOBALS['pr_test_updated_meta'] as $entry ) {
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if ( '_pr_aliases' === $entry['key'] ) {
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$written = $entry['value'];
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}
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}
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$aliases = json_decode( $written, true );
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$this->assertIsArray( $aliases );
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$this->assertCount( 2, $aliases );
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}
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// ── PubChem skip path ─────────────────────────────────────────────
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public function test_backfill_post_returns_pubchem_skip_when_network_fails(): void {
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$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'][10] = [];
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$GLOBALS['pr_test_posts'][10] = (object) [ 'post_title' => 'IGF-1 LR3', 'ID' => 10 ];
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$result = $this->call_private( $mock_migration, 'backfill_post', [ 10 ] );
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$this->assertSame( 'pubchem_skip', $result );
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$this->assertEmpty( $GLOBALS['pr_test_updated_meta'] );
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}
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}
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