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"""
Smoke tests for the genenetwork3 REST API.
All tests hit public, unauthenticated endpoints. The gn3 API is proxied
at /api3/ on the gn2 domain; nginx rewrites /api3/<path> → /api/<path>
before forwarding to gn3, so the URL seen by the caller is:
https://cd.genenetwork.org/api3/metadata/species
(→ gn3 internal: /api/metadata/species)
Response format note: gn3 metadata endpoints return JSON-LD, shaped as:
{"@context": {...}, "data": [...]}
The actual payload is always in the "data" key. On the CD environment the
RDF/SPARQL store may be empty, so "data" can be []; production will have
real entries. Content assertions (e.g. "contains mouse") are therefore
skipped when the data list is empty.
Run with:
pytest -m "gn3 and smoke"
Known CD/production bugs (as of 2026-05-27):
- POST /api3/metadata/datasets/edit returns 500 on both CD and production
due to TypeError in privileges_fulfill_specs() — tracked separately.
"""
import pytest
pytestmark = [pytest.mark.gn3, pytest.mark.smoke]
# ---------------------------------------------------------------------------
# Known-good test data (sourced from existing gn2/gn3 test fixtures)
# ---------------------------------------------------------------------------
_KNOWN_DATASET = "HC_M2_0606_P" # Hippocampus Consortium M430v2 Jun06 PDNN
_KNOWN_SPECIES = "mouse"
_KNOWN_GROUP = "BXD"
_KNOWN_PROBESET = "1435395_s_at"
_KNOWN_INBREDSET_ID = 1 # BXD inbredset_id in the database
def _jsonld_data(resp):
"""Return the 'data' list from a JSON-LD gn3 response."""
body = resp.json()
assert isinstance(body, dict), f"Expected JSON object, got: {type(body)}"
assert "data" in body, f"Missing 'data' key in JSON-LD response: {list(body.keys())}"
assert isinstance(body["data"], list), (
f"'data' should be a list, got {type(body['data'])}"
)
return body["data"]
# ---------------------------------------------------------------------------
# GET /api3/metadata/species
# ---------------------------------------------------------------------------
class TestMetadataSpecies:
def test_returns_200(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/species", timeout=30)
assert resp.status_code == 200
def test_response_is_jsonld_with_data_key(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/species", timeout=30)
data = _jsonld_data(resp) # asserts structure internally
assert isinstance(data, list)
def test_contains_mouse_when_data_populated(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/species", timeout=30)
items = _jsonld_data(resp)
if not items:
pytest.skip("Species data is empty in this environment (RDF store not populated)")
all_names = [
s.get("fullName", s.get("name", s.get("shortName", "")))
for s in items
]
assert any("mouse" in n.lower() or "mus" in n.lower() for n in all_names), (
f"Mouse not found in species list: {all_names}"
)
def test_species_entry_schema_when_data_populated(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/species", timeout=30)
items = _jsonld_data(resp)
if not items:
pytest.skip("Species data is empty in this environment")
entry = items[0]
assert any(k in entry for k in ("fullName", "name", "shortName")), (
f"Species entry has no recognisable name field: {entry}"
)
# ---------------------------------------------------------------------------
# GET /api3/metadata/species/<name>
# ---------------------------------------------------------------------------
class TestMetadataSpeciesByName:
def test_known_species_returns_200(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/species/{_KNOWN_SPECIES}", timeout=30)
assert resp.status_code == 200, (
f"Expected 200 for species '{_KNOWN_SPECIES}', "
f"got {resp.status_code}: {resp.text}"
)
def test_unknown_species_does_not_500(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/species/nonexistent_xyz", timeout=30)
assert resp.status_code != 500, (
f"Unknown species caused 500: {resp.text}"
)
# ---------------------------------------------------------------------------
# GET /api3/metadata/groups
# ---------------------------------------------------------------------------
class TestMetadataGroups:
def test_returns_200(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/groups", timeout=30)
assert resp.status_code == 200
def test_response_is_jsonld_with_data_key(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/groups", timeout=30)
data = _jsonld_data(resp)
assert isinstance(data, list)
def test_contains_bxd_when_data_populated(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/groups", timeout=30)
items = _jsonld_data(resp)
if not items:
pytest.skip("Groups data is empty in this environment")
names = [g.get("name", g.get("shortName", "")) for g in items]
assert "BXD" in names, f"BXD not found in groups: {names[:20]}"
# ---------------------------------------------------------------------------
# GET /api3/metadata/datasets/<name>
# ---------------------------------------------------------------------------
class TestMetadataDatasets:
def test_known_dataset_returns_200(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/datasets/{_KNOWN_DATASET}", timeout=30)
assert resp.status_code == 200, (
f"Expected 200 for dataset '{_KNOWN_DATASET}', "
f"got {resp.status_code}: {resp.text}"
)
def test_known_dataset_response_is_jsonld(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/datasets/{_KNOWN_DATASET}", timeout=30)
body = resp.json()
assert isinstance(body, dict), f"Expected JSON object, got {type(body)}"
assert "@context" in body or "data" in body, (
f"Response does not look like JSON-LD: {list(body.keys())}"
)
def test_unknown_dataset_does_not_500(self, gn3_url, http):
resp = http.get(f"{gn3_url}/metadata/datasets/NONEXISTENT_XYZ", timeout=30)
assert resp.status_code != 500, (
f"Unknown dataset caused 500: {resp.text}"
)
# ---------------------------------------------------------------------------
# GET /api3/metadata/probesets/<dataset>/<name>
# ---------------------------------------------------------------------------
class TestMetadataProbesets:
def test_known_probeset_returns_200(self, gn3_url, http):
resp = http.get(
f"{gn3_url}/metadata/probesets/{_KNOWN_DATASET}/{_KNOWN_PROBESET}",
timeout=30,
)
assert resp.status_code == 200, (
f"Expected 200 for probeset '{_KNOWN_DATASET}/{_KNOWN_PROBESET}', "
f"got {resp.status_code}: {resp.text}"
)
# ---------------------------------------------------------------------------
# GET /api3/case-attribute/<inbredset_id>
# ---------------------------------------------------------------------------
class TestCaseAttributes:
def test_known_inbredset_does_not_500(self, gn3_url, http):
resp = http.get(
f"{gn3_url}/case-attribute/{_KNOWN_INBREDSET_ID}",
timeout=30,
)
assert resp.status_code != 500, (
f"case-attribute inbredset_id={_KNOWN_INBREDSET_ID} caused 500: {resp.text}"
)
# ---------------------------------------------------------------------------
# Protected endpoints — known bug
# ---------------------------------------------------------------------------
@pytest.mark.xfail(
reason=(
"BUG: POST /api3/metadata/datasets/edit returns 500 on both CD and "
"production due to TypeError: privileges_fulfill_specs() missing 1 "
"required positional argument: 'system_privileges' "
"(gn3/api/metadata.py:279). Should return 401 without a token."
),
strict=True,
)
def test_metadata_edit_without_token_returns_401(gn3_url, http):
resp = http.post(
f"{gn3_url}/metadata/datasets/edit",
json={},
timeout=30,
)
assert resp.status_code == 401, (
f"Expected 401 on /metadata/datasets/edit without token, "
f"got {resp.status_code}: {resp.text}"
)
|
