def test_unfound_names_return_0(self, mock_get):
"""If we can't find an NCBI taxonomy ID for an organism name
we can keep things moving for a while without it.
get_taxonomy_id will log an error message which will prompt
a developer to investigate what the organism name that was
unable to be found is. Therefore setting the ID to 0 is the
right thing to do in this case despite not seeming like it.
"""
mock_get.return_value = Mock(ok=True)
mock_get.return_value.text = ESEARCH_NOT_FOUND_XML
taxonomy_id = Organism.get_id_for_name("blah")
self.assertEqual(taxonomy_id, 0)
mock_get.assert_has_calls([
call(ESEARCH_URL, {
"db": "taxonomy",
"field": "scin",
"term": "BLAH"
}),
call(ESEARCH_URL, {
"db": "taxonomy",
"term": "BLAH"
})
])
# The first call should have stored the organism record in the
# database so this call should not make a request.
mock_get.reset_mock()
new_id = Organism.get_id_for_name("BLAH")
self.assertEqual(new_id, 0)
mock_get.assert_not_called()
def test_uncached_other_names_are_found(self, mock_get):
mock_get.side_effect = mocked_requests_get
taxonomy_id = Organism.get_id_for_name("Human")
self.assertEqual(taxonomy_id, 9606)
mock_get.assert_has_calls([
call(ESEARCH_URL, {
"db": "taxonomy",
"field": "scin",
"term": "HUMAN"
}),
call(ESEARCH_URL, {
"db": "taxonomy",
"term": "HUMAN"
})
])
# The first call should have stored the organism record in the
# database so this call should not make a request.
mock_get.reset_mock()
new_id = Organism.get_id_for_name("Human")
self.assertEqual(new_id, 9606)
mock_get.assert_not_called()
def test_unfound_names_raise(self, mock_get):
"""If we can't find the taxonomy id, it's likely a bad organism name.
"""
mock_get.return_value = Mock(ok=True)
mock_get.return_value.text = ESEARCH_NOT_FOUND_XML
with self.assertRaises(UnknownOrganismId):
Organism.get_id_for_name("blah")
mock_get.assert_has_calls(
[
call(
ESEARCH_URL,
{
"db": "taxonomy",
"field": "scin",
"api_key": "3a1f8d818b0aa05d1aa3c334fa2cc9a17e09",
"term": "BLAH",
},
),
call(
ESEARCH_URL,
{
"db": "taxonomy",
"api_key": "3a1f8d818b0aa05d1aa3c334fa2cc9a17e09",
"term": "BLAH",
},
),
]
)
def test_cached_ids_are_found(self, mock_get):
Organism.objects.create(name="HOMO_SAPIENS", taxonomy_id=9606, is_scientific_name=True)
id = Organism.get_id_for_name("H**o Sapiens")
self.assertEqual(id, 9606)
mock_get.assert_not_called()
def test_uncached_scientific_names_are_found(self, mock_get):
mock_get.return_value = Mock(ok=True)
mock_get.return_value.text = ESEARCH_RESPONSE_XML
taxonomy_id = Organism.get_id_for_name("H**o Sapiens")
self.assertEqual(taxonomy_id, 9606)
mock_get.assert_called_once_with(ESEARCH_URL, {
"db": "taxonomy",
"field": "scin",
"term": "HOMO_SAPIENS"
})
# The first call should have stored the organism record in the
# database so this call should not make a request.
mock_get.reset_mock()
new_id = Organism.get_id_for_name("H**o Sapiens")
self.assertEqual(new_id, 9606)
mock_get.assert_not_called()