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"""Test cases for wqflask.api.gen_menu"""
import unittest
import mock
from wqflask.api.gen_menu import get_species
from wqflask.api.gen_menu import get_groups
from wqflask.api.gen_menu import get_types
from wqflask.api.gen_menu import phenotypes_exist
from wqflask.api.gen_menu import genotypes_exist
from wqflask.api.gen_menu import build_datasets
from 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']
]
}
@mock.patch('wqflask.api.gen_menu.g')
def test_get_species(self, db_mock):
"""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)
)
@mock.patch('wqflask.api.gen_menu.g')
def test_phenotypes_exist_called_with_correct_query(self, db_mock):
"""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):
"""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):
"""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"))
@mock.patch('wqflask.api.gen_menu.g')
def test_genotypes_exist_with_truthy_value(self, db_mock):
"""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"))
@mock.patch('wqflask.api.gen_menu.g')
def test_build_datasets_with_type_phenotypes(self, db_mock):
"""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_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"]])
@mock.patch('wqflask.api.gen_menu.g')
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.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):
"""Test that correct tissue metadata is returned"""
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 Trait Datasets'],
['H', 'H', 'Molecular Trait Datasets'],
['R', 'R', 'Molecular Trait Datasets']])
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"
)
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@mock.patch('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 = {
'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']]
}
}
build_types_mock.return_value = [
['M', 'M', 'Molecular Trait Datasets']
]
self.assertEqual(get_types(self.test_group), expected_result)
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@mock.patch('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), {
'mouse': {},
'human': {}
})
@mock.patch('wqflask.api.gen_menu.build_types')
@mock.patch('wqflask.api.gen_menu.genotypes_exist')
@mock.patch('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),
expected_result)
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