avoigt1121
Claude Opus 5.5
feat: governed ToolUniverse core for the knowledge specialist (s1)
377417d | """What may leave the Space: identifiers only (ADR-0001 §6). Refusals are data.""" | |
| from __future__ import annotations | |
| import pytest | |
| from src.identifiers import MAX_IDENTIFIERS, parse_disease, parse_gene_list, parse_nct | |
| # Real HGNC symbols chosen to exercise the edges of the pattern and of the sample-id prefixes. | |
| VALID_SYMBOLS = [ | |
| "KRAS", | |
| "TP53", | |
| "ELAVL1", | |
| "C1orf112", | |
| "HLA-DRB1", | |
| "NKX2-1", | |
| "IGHV1-69-2", | |
| "CPT1A", | |
| "ERRFI1", | |
| "DOK1", | |
| "SAA1", | |
| "SORD2P", | |
| ] | |
| def test_real_symbols_pass(symbol): | |
| parsed = parse_gene_list(symbol) | |
| assert parsed.ok, parsed.message | |
| assert parsed.identifiers[0].kind == "symbol" | |
| def test_a_list_splits_on_commas_spaces_and_semicolons_and_keeps_order(): | |
| parsed = parse_gene_list("JAK1, JAK2;STAT1 jak1") | |
| assert parsed.ok | |
| assert [i.value for i in parsed.identifiers] == ["JAK1", "JAK2", "STAT1"] | |
| assert parsed.duplicates_dropped == 1 | |
| def test_ensembl_ids_are_genes_and_uniprot_only_when_allowed(): | |
| assert parse_gene_list("ENSG00000133703").identifiers[0].kind == "ensembl" | |
| assert parse_gene_list("P05161", allow_uniprot=True).identifiers[0].kind == "uniprot" | |
| assert parse_gene_list("P05161").identifiers[0].kind == "symbol" | |
| def test_free_text_sample_ids_and_numbers_are_refused(raw): | |
| parsed = parse_gene_list(raw) | |
| assert not parsed.ok | |
| assert parsed.reason == "invalid_identifier" | |
| assert "free text, sample ids and numbers are not" in parsed.message | |
| def test_an_empty_list_is_refused(): | |
| assert parse_gene_list(" ").reason == "invalid_identifier" | |
| assert parse_gene_list([]).reason == "invalid_identifier" | |
| def test_more_than_the_cap_is_refused_with_the_cap(): | |
| raw = ",".join(f"GENE{i}" for i in range(MAX_IDENTIFIERS + 1)) | |
| parsed = parse_gene_list(raw) | |
| assert parsed.reason == "too_many_identifiers" | |
| assert str(MAX_IDENTIFIERS) in parsed.message | |
| assert parse_gene_list(",".join(f"GENE{i}" for i in range(MAX_IDENTIFIERS))).ok | |
| def test_a_refusal_never_echoes_a_long_token(): | |
| parsed = parse_gene_list("x" * 200 + "!") | |
| assert len(parsed.message) < 250 | |
| assert "x" * 30 not in parsed.message | |
| def test_diseases(raw, kind): | |
| parsed = parse_disease(raw) | |
| assert parsed.ok and parsed.identifiers[0].kind == kind | |
| def test_bad_diseases_are_refused(raw): | |
| assert parse_disease(raw).reason == "invalid_identifier" | |
| def test_nct_ids(): | |
| assert parse_nct("nct04635059").identifiers[0].value == "NCT04635059" | |
| assert parse_nct("NCT123").reason == "invalid_identifier" | |