fix(schema): rewrite sanitize_molecular_formula() with element-grammar (Option B)

Replace character-allowlist regex with an element-token grammar validator.
Strip control characters first, then extract the maximal leading run of
valid element tokens ([A-Z][a-z]?\d*) and group separators (()[]·.).

Fixes: 'C10H12\ninjection' now returns 'C10H12' (was 'C10H12injection').
New:   fully invalid inputs (e.g. '<script>alert(1)</script>') return ''.
Keep:  parenthesised formulas (e.g. 'C2H5(OH)') pass unchanged.

Unit tests expanded from 4 to 7 formula cases covering all five DoD
requirements plus whitespace-only edge case.

PHP not installable in sandbox; all 7 test inputs hand-traced
against the regex and confirmed correct via Python simulation.

Agent-Session: peptide-schema-backfill v0.6.0 formula-validator
This commit is contained in:
peptiderepo
2026-06-13 05:42:13 +00:00
parent 1880d1db1f
commit 817690c1b6
3 changed files with 75 additions and 6 deletions

View File

@@ -168,6 +168,12 @@ $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):
// 1. Valid formula unchanged.
// 2. Parenthesised formula preserved.
// 3. Newline-injected payload — "injection" stripped, formula kept.
// 4. Fully invalid string (script tag contents) → empty.
// 5. Empty / whitespace-only → empty.
echo "\nPR_Core_Schema_Sanitizers::sanitize_molecular_formula():\n";
@@ -183,10 +189,22 @@ pr_assert_equals(
'HTML tags stripped from formula'
);
pr_assert_equals(
'C2H5(OH)',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C2H5(OH)' ),
'parenthesised formula preserved unchanged'
);
pr_assert_equals(
'C10H12',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ),
'non-formula characters removed'
'non-formula characters removed — newline+word stripped, formula kept'
);
pr_assert_equals(
'',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<script>alert(1)</script>' ),
'fully invalid string returns empty string'
);
pr_assert_equals(
@@ -195,6 +213,12 @@ pr_assert_equals(
'empty string returns empty string'
);
pr_assert_equals(
'',
PR_Core_Schema_Sanitizers::sanitize_molecular_formula( ' ' ),
'whitespace-only returns empty string'
);
// ── Idempotency: skips when all three PR Core keys populated ─────────────
echo "\nIdempotency (all _pr_* keys populated):\n";