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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 | """Tests for techspec.md §2 structure-export endpoints."""
import pytest
from fastapi import HTTPException
from app.routers import structure_export as se
# ── Identifier resolution ────────────────────────────────────────────────────
def test_uniprot_accession_routes_to_alphafold():
kind, ident, label = se._resolve_source("P04637")
assert (kind, ident) == ("alphafold", "P04637")
assert label == "AF_P04637"
def test_pdb_id_routes_to_rcsb():
kind, ident, label = se._resolve_source("1ubq")
assert (kind, ident) == ("rcsb", "1UBQ")
assert label == "1UBQ"
def test_garbage_identifier_rejected_with_400():
with pytest.raises(HTTPException) as exc:
se._resolve_source("../../etc/passwd")
assert exc.value.status_code == 400
def test_empty_identifier_rejected():
with pytest.raises(HTTPException) as exc:
se._resolve_source(" ")
assert exc.value.status_code == 400
# ── URL construction ─────────────────────────────────────────────────────────
def test_alphafold_urls_use_canonical_file_pattern():
assert se._source_url("alphafold", "P04637", "pdb") == (
"https://alphafold.ebi.ac.uk/files/AF_P04637-F1-model_v4.pdb"
)
assert se._source_url("alphafold", "P04637", "cif") == (
"https://alphafold.ebi.ac.uk/files/AF_P04637-F1-model_v4.cif"
)
def test_rcsb_urls():
assert se._source_url("rcsb", "1UBQ", "cif") == "https://files.rcsb.org/download/1UBQ.cif"
# ── Format gate + fetch behaviour ────────────────────────────────────────────
@pytest.mark.asyncio
async def test_invalid_format_rejected_before_network():
with pytest.raises(HTTPException) as exc:
await se.export_structure("P04637", format="exe", user_id="u1")
assert exc.value.status_code == 400
class _FakeResp:
def __init__(self, status_code=200, text="ATOM 1 CA ALA A 1"):
self.status_code = status_code
self.text = text
def raise_for_status(self):
if self.status_code >= 400:
import httpx
raise httpx.HTTPStatusError(f"HTTP {self.status_code}", request=None, response=None)
class _FakeClient:
last_url = None
def __init__(self, *a, **k):
pass
async def __aenter__(self):
return self
async def __aexit__(self, *a):
return False
async def get(self, url):
_FakeClient.last_url = url
return _FakeResp()
@pytest.mark.asyncio
async def test_pdb_export_returns_attachment(monkeypatch):
monkeypatch.setattr(se.httpx, "AsyncClient", _FakeClient)
res = await se.export_structure("P04637", format="pdb", user_id="u1")
assert res.media_type == "chemical/x-pdb"
assert "AF_P04637.pdb" in res.headers["content-disposition"]
assert b"ATOM" in res.body
@pytest.mark.asyncio
async def test_upstream_404_maps_to_404(monkeypatch):
class _404Client(_FakeClient):
async def get(self, url):
return _FakeResp(404)
monkeypatch.setattr(se.httpx, "AsyncClient", _404Client)
with pytest.raises(HTTPException) as exc:
await se.export_structure("Q9NZB7", format="cif", user_id="u1") # no AF model
assert exc.value.status_code == 404
# ── PyMOL session path ───────────────────────────────────────────────────────
@pytest.mark.asyncio
async def test_pse_without_pymol2_returns_503(monkeypatch):
async def fake_fetch(url):
return "ATOM 1 CA ALA A 1"
def no_pymol(*a, **k):
raise ImportError("pymol2 not installed")
monkeypatch.setattr(se, "_fetch_text", fake_fetch)
monkeypatch.setattr(se, "_build_pse", no_pymol)
with pytest.raises(HTTPException) as exc:
await se.export_structure("P04637", format="pse", user_id="u1")
assert exc.value.status_code == 503
def test_build_pse_rejects_empty_output(tmp_path, monkeypatch):
"""A pymol2 that produces a stub file must fail loudly, not ship junk."""
import sys, types
from pathlib import Path
fake = types.ModuleType("pymol2")
class _Cmd:
def load(self, *a): pass
def hide(self, *a): pass
def show(self, *a): pass
def spectrum(self, *a, **k): pass
def bg_color(self, *a): pass
def set(self, *a, **k): pass
def save(self, out, *a):
Path(out).write_bytes(b"PSE-stub") # < 100 bytes
class _PyMOL:
cmd = _Cmd()
def __enter__(self): return self
def __exit__(self, *a): return False
fake.PyMOL = _PyMOL
monkeypatch.setitem(sys.modules, "pymol2", fake)
with pytest.raises(RuntimeError, match="empty session"):
se._build_pse("ATOM 1 CA ALA A 1\nEND\n".replace("\n", "\n"), "test")
def test_docking_complex_merges_receptor_and_ligand():
receptor = "ATOM 1 CA ALA A 1\nTER"
ligand = "HETATM 1 C LIG B 1"
merged = receptor.rstrip() + "\n" + ligand.rstrip() + "\nEND\n"
assert merged.count("END") == 1
assert "HETATM" in merged and "ATOM" in merged
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