tests/test_plasmid_api.py

"""Endpoint tests for Plasmid Studio (Flask test client; auth stubbed, no DB).
Covers the sign-in gate + import / restriction / digest / export wiring."""
import types

import pytest

from dee import server

SEQ = ("TAATACGACTCACTATAG" + "GAATTC" + "AAAAGGGGAAAAGGGGAAAA"
       + "GAATTC" + "CCCCTTTTCCCCTTTTCCCC")


@pytest.fixture
def client():
    app = server.create_app()
    app.config.update(TESTING=True)
    return app.test_client()


def _signed_in(monkeypatch):
    monkeypatch.setattr(server._auth, "get_auth",
                        lambda: types.SimpleNamespace(anonymous=False, user_id="u1",
                                                      email="x@y.z", plan="free"))


def _anon(monkeypatch):
    monkeypatch.setattr(server._auth, "get_auth",
                        lambda: types.SimpleNamespace(anonymous=True, user_id=None,
                                                      email=None, plan="anon"))


def test_import_requires_signin(client, monkeypatch):
    _anon(monkeypatch)
    r = client.post("/api/plasmid/import", json={"text": SEQ})
    assert r.status_code == 403
    assert r.get_json()["kind"] == "signin_required"


def test_import_raw_dna_annotates(client, monkeypatch):
    _signed_in(monkeypatch)
    r = client.post("/api/plasmid/import", json={"text": SEQ})
    assert r.status_code == 200
    p = r.get_json()["plasmid"]
    assert p["length"] == len(SEQ)
    assert p["topology"] == "circular"
    assert any(f["name"] == "T7 promoter" for f in p["features"])


def test_import_bad_input_400(client, monkeypatch):
    _signed_in(monkeypatch)
    r = client.post("/api/plasmid/import", json={"text": "this is not dna @@@"})
    assert r.status_code == 400
    assert "error" in r.get_json()


def test_restriction(client, monkeypatch):
    _signed_in(monkeypatch)
    r = client.post("/api/plasmid/restriction",
                    json={"sequence": SEQ, "topology": "circular", "enzymes": ["EcoRI", "BamHI"]})
    assert r.status_code == 200
    a = r.get_json()["analysis"]
    assert "EcoRI" in a["double_cutters"]
    assert "BamHI" in a["non_cutters"]


def test_digest_fragments(client, monkeypatch):
    _signed_in(monkeypatch)
    r = client.post("/api/plasmid/digest",
                    json={"sequence": SEQ, "topology": "circular", "enzymes": ["EcoRI"]})
    assert r.status_code == 200
    d = r.get_json()["digest"]
    assert d["n_fragments"] == 2
    assert sum(d["fragments"]) == len(SEQ)


def test_digest_requires_enzyme(client, monkeypatch):
    _signed_in(monkeypatch)
    r = client.post("/api/plasmid/digest",
                    json={"sequence": SEQ, "topology": "circular", "enzymes": []})
    assert r.status_code == 400


def test_import_rejects_oversize_text(client, monkeypatch):
    _signed_in(monkeypatch)
    from dee.core import plasmid as PL
    monkeypatch.setattr(PL, "MAX_INPUT_TEXT", 2000)
    r = client.post("/api/plasmid/import", json={"text": "A" * 5000})
    assert r.status_code == 400


def test_export_sanitizes_malicious_features(client, monkeypatch):
    _signed_in(monkeypatch)
    # injection-laden colour + out-of-range coords + a flood of features:
    # must not crash, must produce a valid GenBank (sanitized server-side).
    feats = [{"name": "evil", "type": "cds", "start": 0, "end": 18,
              "color": '#fff" onload="alert(1)'}]
    feats += [{"name": "f", "type": "misc", "start": 0, "end": 3} for _ in range(20000)]
    r = client.post("/api/plasmid/export", json={
        "sequence": SEQ, "topology": "circular", "name": "pX", "features": feats, "format": "genbank"})
    assert r.status_code == 200
    body = r.data.decode("utf-8", "replace")
    assert "LOCUS" in body
    assert "onload=" not in body            # injection scrubbed out of the export


def test_export_genbank_and_fasta(client, monkeypatch):
    _signed_in(monkeypatch)
    gb = client.post("/api/plasmid/export", json={
        "sequence": SEQ, "topology": "circular", "name": "pTEST",
        "features": [{"name": "T7 promoter", "type": "promoter", "start": 0, "end": 18, "strand": 1}],
        "format": "genbank"})
    assert gb.status_code == 200
    assert b"LOCUS" in gb.data and b"promoter" in gb.data
    fa = client.post("/api/plasmid/export",
                     json={"sequence": SEQ, "topology": "circular", "name": "pTEST", "format": "fasta"})
    assert fa.status_code == 200
    assert fa.data.startswith(b">")