"""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 get_datasets 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'] ] } 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']] } } @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) @mock.patch('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.maxDiff = None self.assertEqual(get_datasets(self.test_type), expected_result) @mock.patch('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), expected_result)