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from unittest import mock, TestCase
class TestDatasetsDBFunctions(TestCase):
def test_retrieve_trait_dataset_name(self):
"""Test that the function is called correctly."""
for trait_type, thresh, trait_dataset_name, columns, table in [
["ProbeSet", 9, "testName",
"Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"],
["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName",
"GenoFreeze"],
["Publish", 6, "publishTraitName",
"Id, Name, FullName, ShortName", "PublishFreeze"],
["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName",
"TempFreeze"]]:
db_mock = mock.MagicMock()
with self.subTest(trait_type=trait_type):
with db_mock.cursor() as cursor:
cursor.fetchone.return_value = (
"testName", "testNameFull", "testNameShort",
"dataScale")
self.assertEqual(
retrieve_trait_dataset_name(
trait_type, thresh, trait_dataset_name, db_mock),
("testName", "testNameFull", "testNameShort",
"dataScale"))
cursor.execute.assert_called_once_with(
"SELECT %(columns)s "
"FROM %(table)s "
"WHERE public > %(threshold)s AND "
"(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format(
cols=columns, ttype=trait_type),
{"threshold": thresh, "name": trait_dataset_name,
"table": table, "columns": columns})
def test_set_probeset_riset_fields(self):
"""
Test that the `riset` and `riset_id` fields are retrieved appropriately
for the 'ProbeSet' trait type.
"""
for trait_name, expected in [
["testProbeSetName", ()]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
set_probeset_riset_fields(trait_name, db_mock), expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, ProbeSetFreeze, ProbeFreeze"
" WHERE ProbeFreeze.InbredSetId = InbredSet.Id"
" AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId"
" AND ProbeSetFreeze.Name = %(name)s"),
{"name": trait_name})
def test_set_riset_fields(self):
"""
Test that the riset fields are set up correctly for the different trait
types.
"""
for trait_info, expected in [
[{}, {}],
[{"haveinfo": 0, "type": "Publish"},
{"haveinfo": 0, "type": "Publish"}],
[{"haveinfo": 0, "type": "ProbeSet"},
{"haveinfo": 0, "type": "ProbeSet"}],
[{"haveinfo": 0, "type": "Geno"},
{"haveinfo": 0, "type": "Geno"}],
[{"haveinfo": 0, "type": "Temp"},
{"haveinfo": 0, "type": "Temp"}],
[{"haveinfo": 1, "type": "Publish", "name": "test"},
{"haveinfo": 1, "type": "Publish", "name": "test",
"riset": "riset_name", "risetid": 0}],
[{"haveinfo": 1, "type": "ProbeSet", "name": "test"},
{"haveinfo": 1, "type": "ProbeSet", "name": "test",
"riset": "riset_name", "risetid": 0}],
[{"haveinfo": 1, "type": "Geno", "name": "test"},
{"haveinfo": 1, "type": "Geno", "name": "test",
"riset": "riset_name", "risetid": 0}],
[{"haveinfo": 1, "type": "Temp", "name": "test"},
{"haveinfo": 1, "type": "Temp", "name": "test", "riset": None,
"risetid": None}]
]:
db_mock = mock.MagicMock()
with self.subTest(trait_info=trait_info, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ("riset_name", 0)
self.assertEqual(
set_riset_fields(trait_info, db_mock), expected)
def test_set_publish_riset_fields(self):
"""
Test that the `riset` and `riset_id` fields are retrieved appropriately
for the 'Publish' trait type.
"""
for trait_name, expected in [
["testPublishName", ()]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
set_publish_riset_fields(trait_name, db_mock), expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, PublishFreeze"
" WHERE PublishFreeze.InbredSetId = InbredSet.Id"
" AND PublishFreeze.Name = %(name)s"),
{"name": trait_name})
def test_set_geno_riset_fields(self):
"""
Test that the `riset` and `riset_id` fields are retrieved appropriately
for the 'Geno' trait type.
"""
for trait_name, expected in [
["testGenoName", ()]]:
db_mock = mock.MagicMock()
with self.subTest(trait_name=trait_name, expected=expected):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
set_geno_riset_fields(trait_name, db_mock), expected)
cursor.execute.assert_called_once_with(
(
"SELECT InbredSet.Name, InbredSet.Id"
" FROM InbredSet, GenoFreeze"
" WHERE GenoFreeze.InbredSetId = InbredSet.Id"
" AND GenoFreeze.Name = %(name)s"),
{"name": trait_name})
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