aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/tests/unit/wqflask/api/test_gen_menu.py402
1 files changed, 216 insertions, 186 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index fd0fe52e..d0cd647a 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -73,209 +73,239 @@ class TestGenMenu(unittest.TestCase):
def tearDown(self):
self.app_context.pop()
- @mock.patch('wqflask.api.gen_menu.g')
- def test_get_species(self, db_mock):
+ def test_get_species(self):
"""Test that assertion is raised when dataset and dataset_name
are defined"""
- db_mock.db.execute.return_value.fetchall.return_value = (
- ('human', 'Human'),
- ('mouse', 'Mouse'))
- self.assertEqual(get_species(),
- [['human', 'Human'], ['mouse', 'Mouse']])
- db_mock.db.execute.assert_called_once_with(
- "SELECT Name, MenuName FROM Species ORDER BY OrderId"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_get_groups(self, db_mock):
- """Test that species groups are grouped correctly"""
- db_mock.db.execute.return_value.fetchall.side_effect = [
- # Mouse
- (('BXD', 'BXD', None),
- ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
- 'Test')),
- # Human
- (('H_T1', "H_T", "DescriptionA"),
- ('H_T2', "H_T'", None))
- ]
-
- self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]),
- self.test_group)
-
- for name in ["mouse", "human"]:
- db_mock.db.execute.assert_any_call(
- ("SELECT InbredSet.Name, InbredSet.FullName, " +
- "IFNULL(InbredSet.Family, 'None') "
- + "FROM InbredSet, Species WHERE Species.Name "
- + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
- + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
- + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
- + "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
- + "InbredSet.MenuOrderId ASC").format(name)
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = (
+ ('human', 'Human'),
+ ('mouse', 'Mouse'))
+ self.assertEqual(get_species(db_mock),
+ [['human', 'Human'], ['mouse', 'Mouse']])
+ cursor.execute.assert_called_once_with(
+ "SELECT Name, MenuName FROM Species ORDER BY OrderId"
)
- @mock.patch('wqflask.api.gen_menu.g')
- def test_phenotypes_exist_called_with_correct_query(self, db_mock):
+ def test_get_groups(self):
+ """Test that species groups are grouped correctly"""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.side_effect = [
+ # Mouse
+ (('BXD', 'BXD', None),
+ ('HLC', ('Liver: Normal Gene Expression '
+ 'with Genotypes (Merck)'),
+ 'Test')),
+ # Human
+ (('H_T1', "H_T", "DescriptionA"),
+ ('H_T2', "H_T'", None))
+ ]
+ self.assertEqual(get_groups([["human", "Human"],
+ ["mouse", "Mouse"]],
+ db_mock),
+ self.test_group)
+
+ for name in ["mouse", "human"]:
+ cursor.execute.assert_any_call(
+ ("SELECT InbredSet.Name, InbredSet.FullName, "
+ "IFNULL(InbredSet.Family, 'None') "
+ "FROM InbredSet, Species WHERE Species.Name "
+ "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
+ "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+ "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+ "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+ "InbredSet.MenuOrderId ASC").format(name)
+ )
+
+ def test_phenotypes_exist_called_with_correct_query(self):
"""Test that phenotypes_exist is called with the correct query"""
- db_mock.db.execute.return_value.fetchone.return_value = None
- phenotypes_exist("test")
- db_mock.db.execute.assert_called_with(
- "SELECT Name FROM PublishFreeze "
- "WHERE PublishFreeze.Name = 'testPublish'"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_phenotypes_exist_with_falsy_values(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = None
+ phenotypes_exist("test", db_mock)
+ cursor.execute.assert_called_with(
+ "SELECT Name FROM PublishFreeze "
+ "WHERE PublishFreeze.Name = 'testPublish'"
+ )
+
+ def test_phenotypes_exist_with_falsy_values(self):
"""Test that phenotype check returns correctly when given
a None value"""
- for x in [None, False, (), [], ""]:
- db_mock.db.execute.return_value.fetchone.return_value = x
- self.assertFalse(phenotypes_exist("test"))
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_phenotypes_exist_with_truthy_value(self, db_mock):
- """Test that phenotype check returns correctly when given Truthy """
- for x in ["x", ("result"), ["result"], [1]]:
- db_mock.db.execute.return_value.fetchone.return_value = (x)
- self.assertTrue(phenotypes_exist("test"))
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_genotypes_exist_called_with_correct_query(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ for x in [None, False, (), [], ""]:
+ cursor.fetchone.return_value = x
+ self.assertFalse(phenotypes_exist("test", db_mock))
+
+ def test_phenotypes_exist_with_truthy_value(self):
+ """Test that phenotype check returns correctly when given Truthy"""
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as conn:
+ with conn.cursor() as cursor:
+ for x in ["x", ("result"), ["result"], [1]]:
+ cursor.fetchone.return_value = (x)
+ self.assertTrue(phenotypes_exist("test", db_mock))
+
+ def test_genotypes_exist_called_with_correct_query(self):
"""Test that genotypes_exist is called with the correct query"""
- db_mock.db.execute.return_value.fetchone.return_value = None
- genotypes_exist("test")
- db_mock.db.execute.assert_called_with(
- "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_genotypes_exist_with_falsy_values(self, db_mock):
- """Test that genotype check returns correctly when given
- a None value"""
- for x in [None, False, (), [], ""]:
- db_mock.db.execute.return_value.fetchone.return_value = x
- self.assertFalse(genotypes_exist("test"))
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = None
+ genotypes_exist("test", db_mock)
+ cursor.execute.assert_called_with(
+ "SELECT Name FROM GenoFreeze WHERE "
+ "GenoFreeze.Name = 'testGeno'"
+ )
+
+ def test_genotypes_exist_with_falsy_values(self):
+ """Test that genotype check returns correctly when given a None value
+
+ """
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ for x in [None, False, (), [], ""]:
+ cursor.fetchone.return_value = x
+ self.assertFalse(genotypes_exist("test", db_mock))
- @mock.patch('wqflask.api.gen_menu.g')
- def test_genotypes_exist_with_truthy_value(self, db_mock):
+ def test_genotypes_exist_with_truthy_value(self):
"""Test that genotype check returns correctly when given Truthy """
- for x in ["x", ("result"), ["result"], [1]]:
- db_mock.db.execute.return_value.fetchone.return_value = (x)
- self.assertTrue(phenotypes_exist("test"))
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ for x in ["x", ("result"), ["result"], [1]]:
+ cursor.fetchone.return_value = (x)
+ self.assertTrue(phenotypes_exist("test", db_mock))
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_phenotypes(self, db_mock):
+ def test_build_datasets_with_type_phenotypes(self):
"""Test that correct dataset is returned for a phenotype type"""
- db_mock.db.execute.return_value.fetchall.return_value = (
- (602, "BXDPublish", "BXD Published Phenotypes"),
- )
- self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
- [['602', "BXDPublish", "BXD Published Phenotypes"]])
- db_mock.db.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"),
- [['602', "BXDPublish", "Mouse Phenome Database"]])
-
- db_mock.db.execute.return_value.fetchall.return_value = ()
- db_mock.db.execute.return_value.fetchone.return_value = (
- "BXDPublish", "Mouse Phenome Database"
- )
- self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
- [["None", "BXDPublish", "Mouse Phenome Database"]])
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock):
+ 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_phenotypes_and_no_results(self):
"""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"
- )
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_genotypes(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = None
+ cursor.fetchone.return_value = (121,
+ "text value")
+ self.assertEqual(build_datasets("Mouse", "BXD",
+ "Phenotypes", db_mock),
+ [["None", "121",
+ "text value"]])
+ cursor.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_genotypes(self):
"""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"]])
-
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_datasets_with_type_mrna(self, db_mock):
+ db_mock = mock.MagicMock()
+ with db_mock.cursor() as cursor:
+ cursor.fetchone.return_value = (
+ 635, "HLCPublish", "HLC Published Genotypes"
+ )
+ self.assertEqual(build_datasets("Mouse", "HLC",
+ "Genotypes", db_mock),
+ [["635", "HLCGeno", "HLC Genotypes"]])
+ cursor.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"
+ )
+ cursor.fetchone.return_value = ()
+ self.assertEqual(build_datasets("Mouse", "HLC",
+ "Genotypes", db_mock),
+ [["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.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 AND "
- + "ProbeSetFreeze.public > 0 "
- + "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
+ 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")
@mock.patch('wqflask.api.gen_menu.build_datasets')
- @mock.patch('wqflask.api.gen_menu.g')
- def test_build_types(self, db_mock, datasets_mock):
+ def test_build_types(self, datasets_mock):
"""Test that correct tissue metadata is returned"""
+ db_mock = mock.MagicMock()
datasets_mock.return_value = [
["112", 'HC_M2_0606_P',
"Hippocampus Consortium M430v2 (Jun06) PDNN"]
]
- db_mock.db.execute.return_value.fetchall.return_value = (
- ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
- )
- self.assertEqual(build_types('mouse', 'random group'),
- [['M', 'M', 'Molecular Traits'],
- ['H', 'H', 'Molecular Traits'],
- ['R', 'R', 'Molecular Traits']])
- db_mock.db.execute.assert_called_once_with(
- "SELECT DISTINCT Tissue.Name "
- + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
- + "Tissue, Species WHERE Species.Name = 'mouse' "
- + "AND Species.Id = InbredSet.SpeciesId AND "
- + "InbredSet.Name = 'random group' AND "
- + "ProbeFreeze.TissueId = Tissue.Id AND "
- + "ProbeFreeze.InbredSetId = InbredSet.Id AND "
- + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
- + "ORDER BY Tissue.Name"
- )
+ with db_mock.cursor() as cursor:
+ cursor.fetchall.return_value = (
+ ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
+ )
+ self.assertEqual(build_types('mouse', 'random group', db_mock),
+ [['M', 'M', 'Molecular Traits'],
+ ['H', 'H', 'Molecular Traits'],
+ ['R', 'R', 'Molecular Traits']])
+ cursor.execute.assert_called_once_with(
+ "SELECT DISTINCT Tissue.Name "
+ "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+ "Tissue, Species WHERE Species.Name = 'mouse' "
+ "AND Species.Id = InbredSet.SpeciesId AND "
+ "InbredSet.Name = 'random group' AND "
+ "ProbeFreeze.TissueId = Tissue.Id AND "
+ "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+ "ORDER BY Tissue.Name"
+ )
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -297,7 +327,9 @@ class TestGenMenu(unittest.TestCase):
build_types_mock.return_value = [
['M', 'M', 'Molecular Trait Datasets']
]
- self.assertEqual(get_types(self.test_group), expected_result)
+ self.assertEqual(get_types(self.test_group,
+ mock.MagicMock()),
+ expected_result)
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -315,10 +347,8 @@ class TestGenMenu(unittest.TestCase):
genotypes_exist_mock.return_value = False
build_types_mock.return_value = []
- self.assertEqual(get_types(self.test_group), {
- 'mouse': {},
- 'human': {}
- })
+ self.assertEqual(get_types(self.test_group, mock.MagicMock()),
+ {'mouse': {}, 'human': {}})
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@@ -345,7 +375,7 @@ class TestGenMenu(unittest.TestCase):
'human': {
'HLC': [['M', 'M', 'Molecular Trait Datasets']],
'BXD': [['M', 'M', 'Molecular Trait Datasets']]}}
- self.assertEqual(get_types(self.test_group),
+ self.assertEqual(get_types(self.test_group, mock.MagicMock()),
expected_result)
@mock.patch('wqflask.api.gen_menu.build_datasets')
@@ -367,7 +397,7 @@ class TestGenMenu(unittest.TestCase):
'BXD': {'Genotypes': 'Test',
'M': 'Test',
'Phenotypes': 'Test'}}}
- self.assertEqual(get_datasets(self.test_type),
+ self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
expected_result)
@mock.patch('wqflask.api.gen_menu.build_datasets')
@@ -381,7 +411,7 @@ class TestGenMenu(unittest.TestCase):
'H_T1': {}},
'human': {'HLC': {},
'BXD': {}}}
- self.assertEqual(get_datasets(self.test_type),
+ self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
expected_result)
@mock.patch('wqflask.api.gen_menu.get_datasets')
@@ -411,4 +441,4 @@ class TestGenMenu(unittest.TestCase):
'groups': ['groupA', 'groupB', 'groupC', 'groupD'],
'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']}
- self.assertEqual(gen_dropdown_json(), expected_result)
+ self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result)