peptide-repo-core

peptide-repo/peptide-repo-core

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Author	SHA1	Message	Date
peptiderepo	817690c1b6	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	2026-06-13 05:42:13 +00:00
peptiderepo	1e5999e663	feat(schema): v0.6.0 — PSA backfill migration + Yoast-integrated Drug/MedicalWebPage/FAQ schema 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	2026-06-13 05:01:59 +00:00

Author

SHA1

Message

Date

peptiderepo

817690c1b6

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

2026-06-13 05:42:13 +00:00

peptiderepo

1e5999e663

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

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

2026-06-13 05:01:59 +00:00

2 Commits