def test_efetch_IPGs_error(hits):
with requests_mock.Mocker() as mock, pytest.raises(requests.HTTPError):
mock.post(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?",
status_code=400,
)
context.efetch_IPGs([hit.subject for hit in hits])
def test_efetch_IPGs(hits):
with requests_mock.Mocker() as mock:
mock.post("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?")
context.efetch_IPGs([hit.subject for hit in hits])
assert mock.request_history[0].url == (
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"
"db=protein&rettype=ipg&retmode=text&retmax=10000")
def test_efetch_IPGs_IOError(hits, monkeypatch):
def mock_ioerror(*args, **kwargs):
raise IOError
from Bio import Entrez
monkeypatch.setattr(Entrez, "efetch", mock_ioerror)
with pytest.raises(IOError):
context.efetch_IPGs([hit.subject for hit in hits])
def test_efetch_IPGs_output(tmp_path, monkeypatch):
def mock_output(*args, **kwargs):
text = "testing".encode("utf-8")
return io.BytesIO(text)
from Bio import Entrez
monkeypatch.setattr(Entrez, "efetch", mock_output)
test_out = tmp_path / "out.tsv"
context.efetch_IPGs(["placeholder"], output_file=test_out)
assert test_out.read_text() == "testing"
def test_efetch_IPGs_output(hits, tmp_path):
with requests_mock.Mocker() as mock:
mock.post("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?",
text="test")
test_out = tmp_path / "out.tsv"
with test_out.open("w") as handle:
context.efetch_IPGs([hit.subject for hit in hits],
output_handle=handle)
assert test_out.read_text() == "test"
def test_efetch_IPGs_chunks(monkeypatch):
def mock_chunks(
_,
rettype=None,
retmode=None,
retmax=None,
id=None,
):
text = "\n".join(id).encode("utf-8")
return io.BytesIO(text)
from Bio import Entrez
monkeypatch.setattr(Entrez, "efetch", mock_chunks)
for num in [500, 10001, 1]:
ids = ["id"] * num
table = context.efetch_IPGs(ids)
assert len(table) == num
def test_efetch_IPGs_no_ids():
with pytest.raises(ValueError):
context.efetch_IPGs([])