def test_invalid_organism(self, cache_backup, requests_mock, tsv_data: bytes):
url = urljoin(options.url, Enzsub._query_type.endpoint)
requests_mock.register_uri(
"GET",
f"{url}?fields=curation_effort%2Creferences%2Csources&format=tsv",
content=tsv_data,
)
with pytest.raises(
ValueError,
match=r"Invalid value `foobarbaz` for `Organism`. Valid options are:",
):
Enzsub.get(organism="foobarbaz")
assert not requests_mock.called_once
def test_resources(self, cache_backup, requests_mock, resources: bytes):
url = urljoin(options.url, Endpoint.RESOURCES.s)
requests_mock.register_uri("GET", f"{url}?format=json", content=resources)
res = Enzsub.resources()
assert res == ("quux",)
assert requests_mock.called_once
def test_no_dtype_conversion(self, cache_backup, requests_mock, tsv_data: bytes):
url = urljoin(options.url, Enzsub._query_type.endpoint)
options.convert_dtypes = False
requests_mock.register_uri(
"GET",
f"{url}?fields=curation_effort%2Creferences%2Csources&format=tsv",
content=tsv_data,
)
res = Enzsub.get()
assert is_object_dtype(res["modification"])
options.convert_dtypes = True
res = Enzsub.get()
assert is_categorical_dtype(res["modification"])
assert requests_mock.called_once
def test_field_injection(self, cache_backup, requests_mock, tsv_data: bytes):
url = urljoin(options.url, Enzsub._query_type.endpoint)
requests_mock.register_uri(
"GET",
f"{url}?fields=Alpha%2Cbeta%2Ccuration_effort%2Creferences%2Csources&format=tsv",
content=tsv_data,
)
_ = Enzsub.get(fields=("beta", "Alpha", "Alpha"))
assert requests_mock.called_once
def test_genesymbols_dont_matter(
self, cache_backup, requests_mock, tsv_data: bytes
):
url = urljoin(options.url, Enzsub._query_type.endpoint)
requests_mock.register_uri(
"GET",
f"{url}?fields=curation_effort%2Creferences%2Csources&format=tsv",
content=tsv_data,
)
_ = Enzsub.get(genesymbol=True)
assert requests_mock.called_once
def test_params_no_org_genesymbol(self):
params = Enzsub.params()
assert Key.ORGANISM.value not in params
assert Key.GENESYMBOLS.value in params
for k, valid in params.items():
if isinstance(valid, Iterable):
np.testing.assert_array_equal(
list(set(valid)), list(set(EnzsubQuery(k).valid))
)
else:
assert valid == EnzsubQuery(k).valid
def get(
cls,
ptms: Optional[pd.DataFrame] = None,
interactions: Optional[pd.DataFrame] = None,
) -> pd.DataFrame:
"""
Get signs for enzyme-PTM interactions.
Parameters
----------
ptms
Data generated by :meth:`omnipath.requests.Enzsub.get`. If `None`, a new request will be performed.
interactions
Data generated by :meth:`omnipath.interactions.OmniPath.get`. If `None`, a new request will be performed.
Returns
-------
:class:`pandas.DataFrame`
The signed PTMs with columns **'is_inhibition'** and **'is_stimulation'**.
"""
from omnipath.requests import Enzsub
from omnipath.interactions import OmniPath
ptms = Enzsub.get() if ptms is None else ptms
interactions = OmniPath.get() if interactions is None else interactions
if not isinstance(ptms, pd.DataFrame):
raise TypeError(
f"Expected `ptms` to be of type `pandas.DataFrame`, found `{type(ptms).__name__}`."
)
if not isinstance(interactions, pd.DataFrame):
raise TypeError(
f"Expected `interactions` to be of type `pandas.DataFrame`, found `{type(ptms).__name__}`."
)
if ptms.empty:
raise ValueError(_ERROR_EMPTY_FMT.format(obj="PTMs"))
if interactions.empty:
raise ValueError(_ERROR_EMPTY_FMT.format(obj="interactions"))
return pd.merge(
ptms,
interactions[[
"source", "target", "is_stimulation", "is_inhibition"
]],
left_on=["enzyme", "substrate"],
right_on=["source", "target"],
how="left",
)
def test_valid_params(self, cache_backup, requests_mock, tsv_data: bytes, caplog):
url = urljoin(options.url, Enzsub._query_type.endpoint)
df = pd.read_csv(StringIO(tsv_data.decode("utf-8")), sep="\t")
requests_mock.register_uri(
"GET",
f"{url}?fields=curation_effort%2Creferences%2Csources&format=tsv&license=academic",
content=tsv_data,
)
with caplog.at_level(logging.WARNING):
res = Enzsub.get(license="academic", format="text")
assert f"Invalid `{Key.FORMAT.s}='text'`" in caplog.text
np.testing.assert_array_equal(res.index, df.index)
np.testing.assert_array_equal(res.columns, df.columns)
np.testing.assert_array_equal(res.values, df.values)
assert requests_mock.called_once
def test_docs(self):
assert set(Enzsub._docs().keys()) == {e.param for e in EnzsubQuery}
assert all(d is None for d in Enzsub._docs().values())
def test_annotations(self):
assert set(Enzsub._annotations().keys()) == {e.param for e in EnzsubQuery}
assert all(
isinstance(a, (_GenericAlias, type)) for a in Enzsub._annotations().values()
)
def test_invalid_format(self):
with pytest.raises(ValueError, match=r"Invalid value `bar` for `Format`."):
Enzsub.get(format="bar")
def test_invalid_license(self):
with pytest.raises(ValueError, match=r"Invalid value `bar` for `License`."):
Enzsub.get(license="bar")
def test_invalid_params(self):
with pytest.raises(ValueError, match=r"Invalid value `foo` for `EnzsubQuery`."):
Enzsub.get(foo="bar")
def test_str_repr(self):
assert str(Enzsub()) == f"<{Enzsub().__class__.__name__}>"
assert repr(Enzsub()) == f"<{Enzsub().__class__.__name__}>"