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4939f56 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 | """Tests for structure-prep input validation and integrity tagging (pre-work A1/A4/A5)."""
import pytest
from fastapi import HTTPException
from app.tools.structure_prep import (
PDB_ID_RE,
TEMPLATE_RE,
fetch_pdb_text,
swissmodel_fetch_pdb,
swissmodel_fetch_structures,
validate_pdb_id,
validate_template,
validate_uniprot_accession,
)
from app.routers.structure_prep import PipelineRequest, _validate_request
class TestPdbIdValidation:
def test_accepts_valid_ids(self):
assert validate_pdb_id("1crn") == "1CRN"
assert validate_pdb_id(" 4HHB ") == "4HHB"
@pytest.mark.parametrize("bad", ["", "123", "12345", "1CR!", "../etc/passwd", "1CRN; rm -rf"])
def test_rejects_invalid_ids(self, bad):
with pytest.raises(ValueError):
validate_pdb_id(bad)
class TestUniprotAccessionValidation:
def test_accepts_valid_accessions(self):
assert validate_uniprot_accession("p04637") == "P04637"
assert validate_uniprot_accession("A0A1234567") == "A0A1234567"
@pytest.mark.parametrize("bad", ["", "not-an-accession", "ZZ9999", "P04637 OR 1=1"])
def test_rejects_invalid_accessions(self, bad):
with pytest.raises(ValueError):
validate_uniprot_accession(bad)
class TestTemplateValidation:
def test_accepts_alnum_hyphen(self):
assert validate_template("SMR-p00120-1") == "SMR-p00120-1"
def test_rejects_path_traversal(self):
with pytest.raises(ValueError):
validate_template("../../secret")
with pytest.raises(ValueError):
validate_template("")
with pytest.raises(ValueError):
validate_template("a b/c")
class TestRequestValidation:
def test_rejects_empty_request(self):
with pytest.raises(HTTPException) as exc:
_validate_request(PipelineRequest())
assert exc.value.status_code == 400
def test_rejects_multiple_inputs(self):
with pytest.raises(HTTPException) as exc:
_validate_request(PipelineRequest(pdb_id="1CRN", sequence="ACDEFGHIKLM"))
assert exc.value.status_code == 400
def test_rejects_bad_pdb_id_before_network(self):
with pytest.raises(HTTPException) as exc:
_validate_request(PipelineRequest(pdb_id="DROP TABLE jobs"))
assert exc.value.status_code == 400
def test_rejects_bad_sequence_length_and_charset(self):
with pytest.raises(HTTPException):
_validate_request(PipelineRequest(sequence="ACDEF")) # too short
with pytest.raises(HTTPException):
_validate_request(PipelineRequest(sequence="ACDEFGHIK1")) # digit
def test_normalizes_valid_inputs(self):
body = _validate_request(
PipelineRequest(pdb_id="1crn", probe_radius=1.4)
)
assert body.pdb_id == "1CRN"
class TestSsrfRouting:
"""A5: outbound URLs must be validated before requests are made."""
@pytest.mark.asyncio
async def test_fetch_pdb_text_rejects_injection_without_network_call(self):
# Path-traversal-style ID must be rejected locally, never fetched.
with pytest.raises(ValueError):
await fetch_pdb_text("../../admin")
@pytest.mark.asyncio
async def test_swissmodel_fetch_structures_rejects_bad_accession(self):
with pytest.raises(ValueError):
await swissmodel_fetch_structures("x'; DROP TABLE x")
@pytest.mark.asyncio
async def test_swissmodel_fetch_pdb_rejects_bad_template(self):
with pytest.raises(ValueError):
await swissmodel_fetch_pdb("../nope")
def test_allowlist_contains_pipeline_hosts(self):
from app.services.ssrf import ALLOWED_HOSTS
for host in ("swissmodel.expasy.org", "cfold.bme.uic.edu",
"files.rcsb.org", "api-inference.huggingface.co"):
assert host in ALLOWED_HOSTS
class TestRegexes:
def test_pdb_id_regex_shape(self):
assert PDB_ID_RE.match("9FED") # numeric-leading IDs exist
assert not PDB_ID_RE.match("9FEDD")
def test_template_regex_shape(self):
assert TEMPLATE_RE.match("AF-P04637-F1-model_v4")
assert not TEMPLATE_RE.match("-leading-hyphen")
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