"""Test cases for wqflask.api.gen_menu"""
import unittest
from unittest import mock
from gn2.wqflask.api.gen_menu import gen_dropdown_json
from gn2.wqflask.api.gen_menu import get_groups
from gn2.wqflask.api.gen_menu import get_types
from gn2.wqflask.api.gen_menu import get_datasets
from gn2.wqflask.api.gen_menu import phenotypes_exist
from gn2.wqflask.api.gen_menu import genotypes_exist
from gn2.wqflask.api.gen_menu import build_datasets
from gn2.wqflask.api.gen_menu import build_types
class TestGenMenu(unittest.TestCase):
"""Tests for the gen_menu module"""
def setUp(self):
self.test_group = {
'mouse': [
['H_T1',
'H_T',
'Family:DescriptionA'
],
['H_T2', "H_T'", 'Family:None']
],
'human': [
['BXD', 'BXD', 'Family:None'],
['HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
'Family:Test']
]
}
self.test_type = {
'mouse': {
'H_T2': [('Phenotypes',
'Traits and Cofactors',
'Phenotypes'),
('Genotypes',
'DNA Markers and SNPs',
'Genotypes'),
['M', 'M', 'Molecular Trait Datasets']],
'H_T1': [('Phenotypes',
'Traits and Cofactors',
'Phenotypes'),
('Genotypes',
'DNA Markers and SNPs',
'Genotypes'),
['M', 'M', 'Molecular Trait Datasets']]
},
'human': {
'HLC': [('Phenotypes',
'Traits and Cofactors',
'Phenotypes'),
('Genotypes',
'DNA Markers and SNPs',
'Genotypes'),
['M', 'M', 'Molecular Trait Datasets']],
'BXD': [('Phenotypes',
'Traits and Cofactors',
'Phenotypes'),
('Genotypes',
'DNA Markers and SNPs',
'Genotypes'),
['M', 'M', 'Molecular Trait Datasets']]
}
}
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 = 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"""
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 = 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))
def test_genotypes_exist_with_truthy_value(self):
"""Test that genotype check returns correctly when given Truthy """
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))
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_phenotypes_and_no_results(self):
"""Test that correct dataset is returned for a phenotype type with no
results
"""
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 = 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 = 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('gn2.wqflask.api.gen_menu.build_datasets')
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"]
]
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('gn2.wqflask.api.gen_menu.build_types')
@mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
@mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
def test_get_types_with_existing_genotype_and_phenotypes(
self,
phenotypes_exist_mock,
genotypes_exist_mock,
build_types_mock):
"""Test that build types are constructed correctly if phenotypes and genotypes
exist
"""
phenotypes_exist_mock.return_value = True
genotypes_exist_mock.return_value = True
expected_result = self.test_type
build_types_mock.return_value = [
['M', 'M', 'Molecular Trait Datasets']
]
self.assertEqual(get_types(self.test_group,
mock.MagicMock()),
expected_result)
@mock.patch('gn2.wqflask.api.gen_menu.build_types')
@mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
@mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes(
self,
phenotypes_exist_mock,
genotypes_exist_mock,
build_types_mock):
"""Test that build types are constructed correctly if phenotypes_exist and
genotypes_exist are false but build_type is falsy
"""
phenotypes_exist_mock.return_value = False
genotypes_exist_mock.return_value = False
build_types_mock.return_value = []
self.assertEqual(get_types(self.test_group, mock.MagicMock()),
{'mouse': {}, 'human': {}})
@mock.patch('gn2.wqflask.api.gen_menu.build_types')
@mock.patch('gn2.wqflask.api.gen_menu.genotypes_exist')
@mock.patch('gn2.wqflask.api.gen_menu.phenotypes_exist')
def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype(
self,
phenotypes_exist_mock,
genotypes_exist_mock,
build_types_mock):
"""Test that build types are constructed correctly if phenotypes_exist,
genotypes_exist and build_types are truthy
"""
phenotypes_exist_mock.return_value = False
genotypes_exist_mock.return_value = False
build_types_mock.return_value = [
['M', 'M', 'Molecular Trait Datasets']
]
expected_result = {
'mouse': {
'H_T2': [['M', 'M', 'Molecular Trait Datasets']],
'H_T1': [['M', 'M', 'Molecular Trait Datasets']]},
'human': {
'HLC': [['M', 'M', 'Molecular Trait Datasets']],
'BXD': [['M', 'M', 'Molecular Trait Datasets']]}}
self.assertEqual(get_types(self.test_group, mock.MagicMock()),
expected_result)
@mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
def test_get_datasets_with_existent_datasets(self,
build_datasets_mock):
"""Test correct dataset is returned with existent build_datasets"""
build_datasets_mock.return_value = "Test"
expected_result = {
'mouse': {
'H_T2': {'Genotypes': 'Test',
'M': 'Test',
'Phenotypes': 'Test'},
'H_T1': {'Genotypes': 'Test',
'M': 'Test',
'Phenotypes': 'Test'}},
'human': {'HLC': {'Genotypes': 'Test',
'M': 'Test',
'Phenotypes': 'Test'},
'BXD': {'Genotypes': 'Test',
'M': 'Test',
'Phenotypes': 'Test'}}}
self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
expected_result)
@mock.patch('gn2.wqflask.api.gen_menu.build_datasets')
def test_get_datasets_with_non_existent_datasets(self,
build_datasets_mock):
"""Test correct dataset is returned with non-existent build_datasets"""
build_datasets_mock.return_value = None
expected_result = {
'mouse': {
'H_T2': {},
'H_T1': {}},
'human': {'HLC': {},
'BXD': {}}}
self.assertEqual(get_datasets(self.test_type, mock.MagicMock()),
expected_result)
@mock.patch('gn2.wqflask.api.gen_menu.get_datasets')
@mock.patch('gn2.wqflask.api.gen_menu.get_types')
@mock.patch('gn2.wqflask.api.gen_menu.get_groups')
@mock.patch('gn2.wqflask.api.gen_menu.get_all_species')
def test_gen_dropdown_json(self,
species_mock,
groups_mock,
types_mock,
datasets_mock):
"Test that the correct dictionary is constructed properly"
species_mock.return_value = ("speciesA speciesB speciesC speciesD"
.split(" "))
datasets_mock.return_value = ("datasetA datasetB datasetC datasetD"
.split(" "))
groups_mock.return_value = ("groupA groupB groupC groupD"
.split(" "))
types_mock.return_value = ("typeA typeB typeC typeD"
.split(" "))
datasets_mock.return_value = ("datasetA datasetB datasetC datasetD"
.split(" "))
expected_result = {
'datasets': ['datasetA', 'datasetB', 'datasetC', 'datasetD'],
'types': ['typeA', 'typeB', 'typeC', 'typeD'],
'groups': ['groupA', 'groupB', 'groupC', 'groupD'],
'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']}
self.assertEqual(gen_dropdown_json(mock.MagicMock()), expected_result)
