def test_comples_genes_empty_complexes(self, caplog):
df = pd.DataFrame()
with caplog.at_level(logging.WARNING):
res = Complexes.complex_genes("foo", complexes=df)
assert res is df
assert "Complexes are empty" in caplog.text
def test_complexes_no_total_match(self, complexes: pd.DataFrame):
res = Complexes.complex_genes(
["bar", "baz", "bar"], complexes=complexes, total_match=False
)
assert res.shape == (3, 2)
assert all(
any(v in ("bar", "baz") for v in vs.split("_"))
for vs in res["components_genesymbols"]
)
def test_complexes_complexes_specified(self, complexes: pd.DataFrame):
res = Complexes.complex_genes("foo", complexes=complexes, total_match=False)
assert isinstance(res, pd.DataFrame)
assert res.shape == (2, 2)
assert set(res.columns) == {"components_genesymbols", "dummy"}
assert all(
any(v in "foo" for v in vs.split("_"))
for vs in res["components_genesymbols"]
)
def test_complex_genes_complexes_not_specified(
self, cache_backup, requests_mock, tsv_data: bytes
):
url = urljoin(options.url, Complexes._query_type.endpoint)
df = pd.read_csv(StringIO(tsv_data.decode("utf-8")), sep="\t")
requests_mock.register_uri("GET", f"{url}?format=tsv", content=tsv_data)
res = Complexes.complex_genes("fooo")
np.testing.assert_array_equal(res.columns, df.columns)
assert res.empty
def test_complex_genes_no_genes(self):
with pytest.raises(ValueError, match=r"No genes have been selected."):
Complexes.complex_genes([], complexes=None)
def test_complex_genes_no_column(self):
with pytest.raises(KeyError):
Complexes.complex_genes("foo", complexes=pd.DataFrame({"foo": range(10)}))
def test_complex_genes_wrong_dtype(self):
with pytest.raises(TypeError):
Complexes.complex_genes("foo", complexes=42)