def test_build_datasets_with_type_phenotypes(self):
"""Test that correct dataset is returned for a phenotype type"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchall.return_value = ((602, "BXDPublish",
"BXD Published Phenotypes"), )
self.assertEqual(
build_datasets("Mouse", "BXD", "Phenotypes", db_mock),
[['602', "BXDPublish", "BXD Published Phenotypes"]])
cursor.execute.assert_called_with(
"SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " +
"PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " +
"InbredSet WHERE InbredSet.Name = 'BXD' AND " +
"PublishFreeze.InbredSetId = InbredSet.Id AND " +
"InfoFiles.InfoPageName = PublishFreeze.Name " +
"ORDER BY PublishFreeze.CreateTime ASC")
self.assertEqual(
build_datasets("Mouse", "MDP", "Phenotypes", db_mock),
[['602', "BXDPublish", "Mouse Phenome Database"]])
cursor.fetchall.return_value = ()
cursor.fetchone.return_value = ("BXDPublish",
"Mouse Phenome Database")
self.assertEqual(
build_datasets("Mouse", "MDP", "Phenotypes", db_mock),
[["None", "BXDPublish", "Mouse Phenome Database"]])
def test_build_datasets_with_type_genotypes(self, db_mock):
"""Test that correct dataset is returned for a phenotype type"""
db_mock.db.execute.return_value.fetchone.return_value = (
635, "HLCPublish", "HLC Published Genotypes")
self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
[["635", "HLCGeno", "HLC Genotypes"]])
db_mock.db.execute.assert_called_with(
"SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
"GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
"GenoFreeze.InbredSetId = InbredSet.Id AND "
"InfoFiles.InfoPageName = GenoFreeze.ShortName " +
"ORDER BY GenoFreeze.CreateTime DESC")
db_mock.db.execute.return_value.fetchone.return_value = ()
self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
[["None", "HLCGeno", "HLC Genotypes"]])
def test_build_datasets_with_type_mrna(self):
"""Test that correct dataset is returned for a mRNA
expression/ Probeset"""
db_mock = mock.MagicMock()
with db_mock.cursor() as cursor:
cursor.fetchall.return_value = (
(112, "HC_M2_0606_P",
"Hippocampus Consortium M430v2 (Jun06) PDNN"), )
self.assertEqual(build_datasets("Mouse", "HLC", "mRNA", db_mock),
[[
"112", 'HC_M2_0606_P',
"Hippocampus Consortium M430v2 (Jun06) PDNN"
]])
cursor.execute.assert_called_once_with(
"SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
"ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
"ProbeFreeze, InbredSet, Tissue, Species WHERE "
"Species.Name = 'Mouse' AND Species.Id = "
"InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND "
"ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
"Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = "
"Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
"ProbeSetFreeze.public > 0 "
"ORDER BY -ProbeSetFreeze.OrderList DESC, "
"ProbeSetFreeze.CreateTime DESC")
def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock):
"""Test that correct dataset is returned for a phenotype type with no
results
"""
db_mock.db.execute.return_value.fetchall.return_value = None
db_mock.db.execute.return_value.fetchone.return_value = (121,
"text value")
self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
[["None", "121", "text value"]])
db_mock.db.execute.assert_called_with(
"SELECT PublishFreeze.Name, PublishFreeze.FullName "
"FROM PublishFreeze, InbredSet "
"WHERE InbredSet.Name = 'BXD' AND "
"PublishFreeze.InbredSetId = InbredSet.Id "
"ORDER BY PublishFreeze.CreateTime ASC")
def test_build_datasets_with_type_mrna(self, db_mock):
"""Test that correct dataset is returned for a mRNA
expression/ Probeset"""
db_mock.db.execute.return_value.fetchall.return_value = (
(112, "HC_M2_0606_P",
"Hippocampus Consortium M430v2 (Jun06) PDNN"), )
self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[
"112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"
]])
db_mock.db.execute.assert_called_once_with(
"SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
"ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
"ProbeFreeze, InbredSet, Tissue, Species WHERE " +
"Species.Name = 'Mouse' AND Species.Id = " +
"InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " +
"ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and " +
"Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " +
"Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id " +
"ORDER BY ProbeSetFreeze.OrderList DESC")