diff options
Diffstat (limited to 'wqflask/tests/unit')
21 files changed, 560 insertions, 339 deletions
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py index 96563a16..66ad361d 100644 --- a/wqflask/tests/unit/base/test_data_set.py +++ b/wqflask/tests/unit/base/test_data_set.py @@ -31,14 +31,12 @@ class TestDataSetTypes(unittest.TestCase): def tearDown(self): self.app_context.pop() - @mock.patch('base.data_set.g') - def test_data_set_type(self, db_mock): + def test_data_set_type(self): """Test that DatasetType returns correctly if the Redis Instance is not empty and the name variable exists in the dictionary """ with app.app_context(): - db_mock.get = mock.Mock() redis_mock = mock.Mock() redis_mock.get.return_value = self.test_dataset self.assertEqual(DatasetType(redis_mock) @@ -89,10 +87,9 @@ class TestDataSetTypes(unittest.TestCase): '"B139_K_1206_M": "ProbeSet", ' '"B139_K_1206_R": "ProbeSet", ' '"Test": "ProbeSet"}')) - - db_mock.db.execute.assert_called_with( - ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " + - "WHERE ProbeSetFreeze.Name = \"Test\" ") + db_mock.db.execute.assert_called_once_with( + ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " + + "WHERE ProbeSetFreeze.Name = \"Test\" ") ) @mock.patch('base.data_set.g') @@ -148,9 +145,9 @@ class TestDataSetTypes(unittest.TestCase): '"Test": "Publish"}')) db_mock.db.execute.assert_called_with( - ("SELECT PublishFreeze.Name " + - "FROM PublishFreeze, InbredSet " + - "WHERE InbredSet.Name = 'Test' AND " + ("SELECT PublishFreeze.Name " + + "FROM PublishFreeze, InbredSet " + + "WHERE InbredSet.Name = 'Test' AND " "PublishFreeze.InbredSetId = InbredSet.Id") ) diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py new file mode 100644 index 00000000..9b5c023c --- /dev/null +++ b/wqflask/tests/unit/base/test_species.py @@ -0,0 +1,116 @@ +"""Tests wqflask/base/species.py""" + +import unittest +from unittest import mock +from base.species import TheSpecies +from base.species import IndChromosome +from base.species import Chromosomes +from collections import OrderedDict +from wqflask import app +from dataclasses import dataclass + + +@dataclass +class MockChromosome: + OrderId: int + Name: str + Length: int + + +@dataclass +class MockGroup: + name: str + + +@dataclass +class MockDataset: + group: MockGroup + + +class TestTheSpecies(unittest.TestCase): + """Tests for TheSpecies class""" + @mock.patch('base.species.Chromosomes') + def test_create_species_with_null_species_name(self, mock_chromosome): + """Test that TheSpecies is instantiated correctly when the +species_name is provided.""" + mock_chromosome.return_value = 1 + test_species = TheSpecies(dataset="random_dataset", species_name="a") + self.assertEqual(test_species.name, "a") + self.assertEqual(test_species.chromosomes, 1) + + @mock.patch('base.species.Chromosomes') + def test_create_species_with_species_name(self, mock_chromosome): + """Test that TheSpecies is instantiated correctly when the +species_name is not provided.""" + mock_chromosome.return_value = 1 + test_species = TheSpecies(dataset="random_dataset") + self.assertEqual(test_species.dataset, "random_dataset") + self.assertEqual(test_species.chromosomes, 1) + mock_chromosome.assert_called_once_with(dataset="random_dataset") + + +class TestIndChromosome(unittest.TestCase): + """Tests for IndChromosome class""" + + def test_create_ind_chromosome(self): + """Test that IndChromosome is instantiated correctly""" + test_ind_chromosome = IndChromosome(name="Test", length=10000000) + self.assertEqual(test_ind_chromosome.name, "Test") + self.assertEqual(test_ind_chromosome.length, 10000000) + self.assertEqual(test_ind_chromosome.mb_length, 10) + + +class TestChromosomes(unittest.TestCase): + """Tests for Chromosomes class""" + maxDiff = None + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("base.species.g") + def test_create_chromosomes_with_no_species(self, mock_db): + """Test instantiating a chromosome without a species""" + mock_db.db.execute.return_value.fetchall.return_value = [ + MockChromosome(1, "X", 100), + MockChromosome(2, "Y", 1000), + MockChromosome(3, "Z", 10000), + ] + mock_dataset = MockDataset(MockGroup("Random")) + test_chromosomes = Chromosomes(dataset=mock_dataset) + self.assertEqual( + list(test_chromosomes.chromosomes.keys()), + [1, 2, 3] + ) + self.assertEqual(test_chromosomes.dataset, mock_dataset) + mock_db.db.execute.assert_called_with( + "SELECT Chr_Length.Name, Chr_Length.OrderId, Length " + "FROM Chr_Length, InbredSet WHERE " + "Chr_Length.SpeciesId = InbredSet.SpeciesId AND " + "InbredSet.Name = 'Random' ORDER BY OrderId" + ) + + @mock.patch("base.species.g") + def test_create_chromosomes_with_species(self, mock_db): + """Test instantiating a chromosome with a species""" + mock_db.db.execute.return_value.fetchall.return_value = [ + MockChromosome(1, "X", 100), + MockChromosome(2, "Y", 1000), + MockChromosome(3, "Z", 10000), + ] + mock_dataset = MockDataset(MockGroup("Random")) + test_chromosomes = Chromosomes(dataset=mock_dataset, + species="testSpecies") + self.assertEqual( + list(test_chromosomes.chromosomes.keys()), + [1, 2, 3] + ) + mock_db.db.execute.assert_called_with( + "SELECT Chr_Length.Name, Chr_Length.OrderId, Length " + "FROM Chr_Length, Species WHERE " + "Chr_Length.SpeciesId = Species.SpeciesId AND " + "Species.Name = 'Testspecies' ORDER BY OrderId" + ) diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py index 8e8ba482..e1555cb4 100644 --- a/wqflask/tests/unit/base/test_webqtl_case_data.py +++ b/wqflask/tests/unit/base/test_webqtl_case_data.py @@ -4,15 +4,16 @@ import unittest from wqflask import app # Required because of utility.tools in webqtlCaseData.py from base.webqtlCaseData import webqtlCaseData + class TestWebqtlCaseData(unittest.TestCase): """Tests for WebqtlCaseData class""" def setUp(self): self.w = webqtlCaseData(name="Test", - value=0, - variance=0.0, - num_cases=10, - name2="Test2") + value=0, + variance=0.0, + num_cases=10, + name2="Test2") def test_webqtl_case_data_repr(self): self.assertEqual( diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py index fff5fd8f..024ab43f 100644 --- a/wqflask/tests/unit/utility/test_authentication_tools.py +++ b/wqflask/tests/unit/utility/test_authentication_tools.py @@ -5,6 +5,7 @@ from unittest import mock from utility.authentication_tools import check_resource_availability from utility.authentication_tools import add_new_resource + class TestResponse: """Mock Test Response after a request""" @property @@ -18,7 +19,7 @@ class TestUser: @property def user_id(self): """Mockes user id. Used in Flask.g.user_session.user_id""" - return "Jane" + return b"Jane" class TestUserSession: diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py index 8d90a1ec..1d349193 100644 --- a/wqflask/tests/unit/utility/test_chunks.py +++ b/wqflask/tests/unit/utility/test_chunks.py @@ -7,6 +7,7 @@ from utility.chunks import divide_into_chunks class TestChunks(unittest.TestCase): "Test Utility method for chunking" + def test_divide_into_chunks(self): "Check that a list is chunked correctly" self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3), diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py index d0264b87..1089a36f 100644 --- a/wqflask/tests/unit/wqflask/api/test_correlation.py +++ b/wqflask/tests/unit/wqflask/api/test_correlation.py @@ -105,10 +105,10 @@ class TestCorrelations(unittest.TestCase): target_dataset = AttributeSetter({"group": group}) target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6] - trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}), - "S3": AttributeSetter( - {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}), - "S6": AttributeSetter({"value": 5.0})} + trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}), + "S3": AttributeSetter( + {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}), + "S6": AttributeSetter({"value": 5.0})} this_trait = AttributeSetter({"data": trait_data}) mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0], [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6) @@ -127,9 +127,9 @@ class TestCorrelations(unittest.TestCase): expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6] expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6] for i, val in enumerate(expected_pearsonr): - self.assertAlmostEqual(val, results_pearsonr[i],4) + self.assertAlmostEqual(val, results_pearsonr[i], 4) for i, val in enumerate(expected_spearmanr): - self.assertAlmostEqual(val, results_spearmanr[i],4) + self.assertAlmostEqual(val, results_spearmanr[i], 4) self.assertEqual(results_num_overlap, None) @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits") diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py index 57eb1650..7e477da2 100644 --- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py +++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py @@ -2,9 +2,7 @@ import unittest from unittest import mock -from wqflask import app from wqflask.api.gen_menu import gen_dropdown_json -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 @@ -18,8 +16,6 @@ class TestGenMenu(unittest.TestCase): """Tests for the gen_menu module""" def setUp(self): - self.app_context = app.app_context() - self.app_context.push() self.test_group = { 'mouse': [ ['H_T1', @@ -70,212 +66,225 @@ 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): - """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): + def test_get_groups(self): """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.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'" ) - @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): + 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 - @mock.patch('wqflask.api.gen_menu.g') - def test_genotypes_exist_with_truthy_value(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(genotypes_exist("test", 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 +306,9 @@ 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 +326,8 @@ 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 +354,7 @@ 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 +376,7 @@ 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') @@ -381,13 +390,13 @@ 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') @mock.patch('wqflask.api.gen_menu.get_types') @mock.patch('wqflask.api.gen_menu.get_groups') - @mock.patch('wqflask.api.gen_menu.get_species') + @mock.patch('wqflask.api.gen_menu.get_all_species') def test_gen_dropdown_json(self, species_mock, groups_mock, @@ -411,4 +420,4 @@ 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) diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py index b094294a..159c982b 100644 --- a/wqflask/tests/unit/wqflask/api/test_mapping.py +++ b/wqflask/tests/unit/wqflask/api/test_mapping.py @@ -58,7 +58,7 @@ class TestMapping(unittest.TestCase): self.assertEqual(results_2, expected_results) - @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno") + @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl") @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma") @mock.patch("wqflask.api.mapping.initialize_parameters") @mock.patch("wqflask.api.mapping.retrieve_sample_data") diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py index 44d2e0fc..a8cf6006 100644 --- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py +++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py @@ -1,11 +1,31 @@ +"""module contains tests for correlation functions""" + import unittest from unittest import mock + from wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss class TestCorrelationFunctions(unittest.TestCase): - + """test for correlation helper functions""" + + @mock.patch("wqflask.correlation.correlation_functions.compute_corr_coeff_p_value") + def test_tissue_corr_computation(self, mock_tiss_corr_computation): + """test for cal_zero_order_corr_for_tiss""" + + primary_values = [9.288, 9.313, 8.988, 9.660, 8.21] + target_values = [9.586, 8.498, 9.362, 8.820, 8.786] + + mock_tiss_corr_computation.return_value = (0.51, 0.7) + + results = cal_zero_order_corr_for_tiss(primary_values, target_values) + mock_tiss_corr_computation.assert_called_once_with( + primary_values=primary_values, target_values=target_values, + corr_method="pearson") + + self.assertEqual(len(results), 3) + @mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData") def test_get_trait_symbol_and_tissue_values(self, mock_class): """test for getting trait symbol and tissue_values""" diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py new file mode 100644 index 00000000..e1bd6d86 --- /dev/null +++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_gn3.py @@ -0,0 +1,14 @@ +"""this module contains tests for code used in integrating to gn3 api""" +from unittest import TestCase +from base.data_set import create_dataset + +class TestCorrelation(TestCase): + + def test_create_dataset(self): + """test for creating datasets""" + + pass + def test_fetch_dataset_info(self): + """test for fetching dataset info data""" + + pass diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py index 8ae0f09f..f4869c45 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py @@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import ( class TestDisplayMappingResults(unittest.TestCase): """Basic Methods to test Mapping Results""" + def test_pil_colors(self): """Test that colors use PILLOW color format""" self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR, @@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase): class TestHtmlGenWrapper(unittest.TestCase): """Test Wrapper around HTMLGen""" + def test_create_image(self): """Test HT.Image method""" self.assertEqual( @@ -37,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase): cgi="/testing/", enctype='multipart/form-data', name="formName", - submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name') + submit=HtmlGenWrapper.create_input_tag( + type_='hidden', name='Default_Name') ) test_image = HtmlGenWrapper.create_image_tag( src="test.png", diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py index fe2569b8..58a44b2a 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -47,11 +47,11 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco): """add tests for run_gemma where first run is set to true""" - this_chromosomes={} + this_chromosomes = {} for i in range(1, 5): - this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"})) + this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"})) chromosomes = AttributeSetter({"chromosomes": this_chromosomes}) dataset_group = MockGroup( @@ -68,9 +68,10 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - self.assertEqual(mock_os.system.call_count,2) + self.assertEqual(mock_os.system.call_count, 2) mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True) + mock_parse_loco.assert_called_once_with( + dataset, "GP1_GWA_RRRRRR", True) mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) self.assertEqual(mock_flat_files.call_count, 4) @@ -80,10 +81,12 @@ class TestGemmaMapping(unittest.TestCase): def test_gen_pheno_txt_file(self): """add tests for generating pheno txt file""" with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ - "x", "w", "q", "we", "R"], trait_filename="fitr.re") + gen_pheno_txt_file( + this_dataset=AttributeSetter({"name": "A"}), + genofile_name="", vals=[ + "x", "w", "q", "we", "R"]) mock_open.assert_called_once_with( - '/home/user/data/gn2/fitr.re.txt', 'w') + '/home/user/data/gn2/PHENO_KiAEKlCvM6iGTM9Kh_TAlQ.txt', 'w') filehandler = mock_open() values = ["x", "w", "q", "we", "R"] write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( @@ -102,7 +105,8 @@ class TestGemmaMapping(unittest.TestCase): create_trait_side_effect = [] for i in range(4): - create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) + create_dataset_side_effect.append( + AttributeSetter({"name": f'name_{i}'})) create_trait_side_effect.append( AttributeSetter({"data": [f'data_{i}']})) @@ -110,7 +114,7 @@ class TestGemmaMapping(unittest.TestCase): create_trait.side_effect = create_trait_side_effect group = MockGroup({"name": "group_X", "samplelist": samplelist}) - this_dataset = AttributeSetter({"group": group}) + this_dataset = AttributeSetter({"group": group, "name": "A"}) flat_files.return_value = "Home/Genenetwork" with mock.patch("builtins.open", mock.mock_open())as mock_open: @@ -130,7 +134,7 @@ class TestGemmaMapping(unittest.TestCase): flat_files.assert_called_once_with('mapping') mock_open.assert_called_once_with( - 'Home/Genenetwork/group_X_covariates.txt', 'w') + 'Home/Genenetwork/COVAR_anFZ_LfZYV0Ulywo+7tRCw.txt', 'w') filehandler = mock_open() filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) @@ -144,7 +148,7 @@ class TestGemmaMapping(unittest.TestCase): "files": [["file_name", "user", "~/file1"], ["file_name", "user", "~/file2"]] } - return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t + return_file = """X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5 Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7 X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" @@ -159,11 +163,14 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6""" mock_open.side_effect = handles results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") - expected_results= [ - {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727}, - {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812}, - {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432}, - {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] + expected_results = [ + {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, + 'additive': 23.3, 'lod_score': 0.07058107428570727}, + {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, + 'additive': 24.0, 'lod_score': 0.3010299956639812}, + {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, + 'additive': 11.6, 'lod_score': 0.1549019599857432}, + {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}] self.assertEqual(expected_results, results) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py index 5eec93f1..fd21a825 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -12,9 +12,10 @@ class AttributeSetter: def __init__(self, obj): for key, val in obj.items(): setattr(self, key, val) -class TestPlinkMapping(unittest.TestCase): +class TestPlinkMapping(unittest.TestCase): + def test_build_line_list(self): """test for building line list""" line_1 = "this is line one test" diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index b47f877a..8b4337ec 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -1,21 +1,24 @@ import unittest -from unittest import mock -from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file +from unittest import mock +from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file + +# issues some methods in genofile object are not defined +# modify samples should equal to vals -#issues some methods in genofile object are not defined -#modify samples should equal to vals -class TestQtlReaperMapping(unittest.TestCase): - @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals=["V1","x","V4","V3","x"] - samples=["S1","S2","S3","S4","S5"] - trait_filename="trait_file" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") - filehandler=mock_open() - write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] - filehandler.write.assert_has_calls(write_calls) +class TestQtlReaperMapping(unittest.TestCase): + @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + vals = ["V1", "x", "V4", "V3", "x"] + samples = ["S1", "S2", "S3", "S4", "S5"] + trait_filename = "trait_file" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(samples=samples, vals=vals, + trait_filename=trait_filename) + mock_open.assert_called_once_with( + "/home/user/data/gn2/trait_file.txt", "w") + filehandler = mock_open() + write_calls = [mock.call('Trait\t'), mock.call( + 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] - + filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index c585f1df..9d13e943 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -1,48 +1,43 @@ import unittest from unittest import mock -from wqflask import app -from wqflask.marker_regression.rqtl_mapping import get_trait_data_type -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names +from dataclasses import dataclass -class TestRqtlMapping(unittest.TestCase): - - def setUp(self): - self.app_context=app.app_context() - self.app_context.push() - - def tearDown(self): - self.app_context.pop() - - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self,mock_logger,mock_db): - """test for getting trait data_type return True""" - query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(query_value) - self.assertEqual(results,"fer434f") - - def test_sanitize_rqtl_phenotype(self): - """test for sanitizing rqtl phenotype""" - vals=['f',"x","r","x","x"] - results=sanitize_rqtl_phenotype(vals) - expected_phenotype_string='c(f,NA,r,NA,NA)' - - self.assertEqual(results,expected_phenotype_string) - - def test_sanitize_rqtl_names(self): - """test for sanitzing rqtl names""" - vals=['f',"x","r","x","x"] - expected_sanitized_name="c('f',NA,'r',NA,NA)" - results=sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name,results) - - - - +from wqflask.marker_regression.rqtl_mapping import run_rqtl +@dataclass +class MockGroup: + name: str + genofile: str +@dataclass +class MockDataset: + group: MockGroup +class TestRqtlMapping(unittest.TestCase): + """Tests for functions in rqtl_mapping.py""" + @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post") + @mock.patch("wqflask.marker_regression.rqtl_mapping.locate") + @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file") + def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post): + """Test for run_rqtl with permutations > 0""" + dataset_group = MockGroup("GP1", "file_geno") + dataset = MockDataset(dataset_group) + + mock_write_pheno_file.return_value = "pheno_filename" + mock_locate.return_value = "geno_filename" + mock_post.return_value = mock.Mock(ok=True) + mock_post.return_value.json.return_value = {"perm_results": [], + "suggestive": 3, + "significant": 4, + "results" : []} + + results = run_rqtl(trait_name="the_trait", vals=[], samples=[], + dataset=dataset, mapping_scale="cM", model="normal", method="hk", + num_perm=5, perm_strata_list=[], do_control="false", control_marker="", + manhattan_plot=True, cofactors="") + + mock_write_pheno_file.assert_called_once() + mock_locate.assert_called_once() + mock_post.assert_called_once() + + self.assertEqual(results, ([], 3, 4, [])) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py index a29d8cfb..868b0b0b 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -43,11 +43,11 @@ class TestRunMapping(unittest.TestCase): }) } self.dataset = AttributeSetter( - {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"}) self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) self.trait = AttributeSetter( - {"symbol": "IGFI", "chr": "X1", "mb": 123313}) + {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"}) def tearDown(self): self.dataset = AttributeSetter( @@ -180,33 +180,36 @@ class TestRunMapping(unittest.TestCase): with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, - results_path="~/results", mapping_scale="physic", score_type="-log(p)", - transform="qnorm", covariates="Dataset1:Trait1,Dataset2:Trait2", n_samples="100") + results_path="~/results", mapping_method="gemma", mapping_scale="physic", + score_type="-logP", transform="qnorm", + covariates="Dataset1:Trait1,Dataset2:Trait2", + n_samples="100", vals_hash="") write_calls = [ mock.call('Time/Date: 09/01/19 / 10:12:12\n'), mock.call('Population: Human GP1_\n'), mock.call( - 'Data Set: dataser_1\n'), - mock.call('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'), + 'Data Set: dataset_1\n'), + mock.call('Trait: Test Name\n'), + mock.call('Trait Hash: \n'), + mock.call('N Samples: 100\n'), + mock.call('Mapping Tool: gemma\n'), + mock.call('Transform - Quantile Normalized\n'), mock.call('Gene Symbol: IGFI\n'), mock.call( 'Location: X1 @ 123313 Mb\n'), mock.call('Cofactors (dataset - trait):\n'), mock.call('Trait1 - Dataset1\n'), mock.call('Trait2 - Dataset2\n'), mock.call('\n'), mock.call('Name,Chr,'), - mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call('Mb,-logP'), mock.call(',Additive'), mock.call(',Dominance'), mock.call('\n'), mock.call('MK1,C1,'), - mock.call('12000,'), mock.call('1,'), - mock.call('3'), mock.call(',VA'), - mock.call(',TT'), mock.call('\n'), - mock.call('MK2,C2,'), mock.call('10000,'), - mock.call('15,'), mock.call('7'), + mock.call('12000,'), mock.call('3'), + mock.call(',VA'), mock.call(',TT'), + mock.call('\n'), mock.call('MK2,C2,'), + mock.call('10000,'), mock.call('7'), mock.call('\n'), mock.call('MK1,C3,'), - mock.call('1,'), mock.call('45,'), - mock.call('7'), mock.call(',VE'), - mock.call(',Tt') - + mock.call('1,'), mock.call('7'), + mock.call(',VE'), mock.call(',Tt') ] mock_open.assert_called_once_with("~/results", "w+") filehandler = mock_open() @@ -228,28 +231,23 @@ class TestRunMapping(unittest.TestCase): used_samples = ["S1", "S2"] sample_list = AttributeSetter({"sample_attribute_values": { "S1": { - "C1": "c1_value", - "C2": "c2_value", - "W1": "w1_value" - + "c1": "c1_value", + "c2": "c2_value", + "w1": "w1_value" }, "S2": { - "W1": "w2_value", - "W2": "w2_value" - + "w1": "w2_value", + "w2": "w2_value" }, "S3": { - "C1": "c1_value", - "C2": "c2_value" - + "c1": "c1_value", + "c2": "c2_value" }, - }}) - results = get_perm_strata(this_trait={}, sample_list=sample_list, categorical_vars=categorical_vars, used_samples=used_samples) - self.assertEqual(results, [2, 1]) + self.assertEqual(results, [1, 1]) def test_get_chr_length(self): """test for getting chromosome length""" diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py index ce3e7b83..89442c47 100644 --- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py +++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py @@ -21,11 +21,11 @@ class TestSnpBrowser(unittest.TestCase): "transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"} strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []} expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', - 'Domain 1', 'Domain 2', 'Details'], - ['S1', 'S2', 'S3', 'S4', 'S5']], 5, - ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', - 'conservation_score', 'domain_1', 'domain_2', - 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5']) + 'Domain 1', 'Domain 2', 'Details'], + ['S1', 'S2', 'S3', 'S4', 'S5']], 5, + ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', + 'conservation_score', 'domain_1', 'domain_2', + 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5']) results_with_snp = get_header_list( variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns) @@ -33,9 +33,9 @@ class TestSnpBrowser(unittest.TestCase): variant_type="InDel", strains=strains, species="rat", empty_columns=[]) expected_results_with_indel = ( ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', - 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0, - ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', - 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']) + 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0, + ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', + 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']) self.assertEqual(expected_results, results_with_snp) self.assertEqual(expected_results_with_indel, results_with_indel) diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py index 9a36132d..2a914fb2 100644 --- a/wqflask/tests/unit/wqflask/test_collect.py +++ b/wqflask/tests/unit/wqflask/test_collect.py @@ -11,6 +11,7 @@ app = Flask(__name__) class MockSession: """Helper class for mocking wqflask.collect.g.user_session.logged_in""" + def __init__(self, is_logged_in=False): self.is_logged_in = is_logged_in @@ -21,6 +22,7 @@ class MockSession: class MockFlaskG: """Helper class for mocking wqflask.collect.g.user_session""" + def __init__(self, is_logged_in=False): self.is_logged_in = is_logged_in diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py index 4f91d8ca..be7ca2df 100644 --- a/wqflask/tests/unit/wqflask/test_server_side.py +++ b/wqflask/tests/unit/wqflask/test_server_side.py @@ -17,15 +17,18 @@ class TestServerSideTableTests(unittest.TestCase): def test_get_page(self): rows_count = 3 table_rows = [ - {'first': 'd', 'second': 4, 'third': 'zz'}, - {'first': 'b', 'second': 2, 'third': 'aa'}, + {'first': 'd', 'second': 4, 'third': 'zz'}, + {'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, ] headers = ['first', 'second', 'third'] - request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} + request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', + 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'} - test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page() + test_page = ServerSideTable( + rows_count, table_rows, headers, request_args).get_page() self.assertEqual(test_page['sEcho'], '1') self.assertEqual(test_page['iTotalRecords'], 'nan') self.assertEqual(test_page['iTotalDisplayRecords'], '3') - self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}]) + self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, { + 'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}]) diff --git a/wqflask/tests/unit/wqflask/wgcna/__init__.py b/wqflask/tests/unit/wqflask/wgcna/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/unit/wqflask/wgcna/__init__.py diff --git a/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py new file mode 100644 index 00000000..8e947e2f --- /dev/null +++ b/wqflask/tests/unit/wqflask/wgcna/test_wgcna.py @@ -0,0 +1,50 @@ + +"""module contains for processing gn3 wgcna data""" +from unittest import TestCase + +from wqflask.wgcna.gn3_wgcna import process_wgcna_data + + +class DataProcessingTests(TestCase): + """class contains data processing tests""" + + def test_data_processing(self): + """test for parsing data for datatable""" + output = { + "input": { + "sample_names": ["BXD1", "BXD2", "BXD3", "BXD4", "BXD5", "BXD6"], + + }, + "output": { + "ModEigens": { + "MEturquoise": [ + 0.0646677768085351, + 0.137200224277058, + 0.63451113720732, + -0.544002665501479, + -0.489487590361863, + 0.197111117570427 + ], + "MEgrey": [ + 0.213, + 0.214, + 0.3141, + -0.545, + -0.423, + 0.156, + ] + }}} + + row_data = [['BXD1', 0.065, 0.213], + ['BXD2', 0.137, 0.214], + ['BXD3', 0.635, 0.314], + ['BXD4', -0.544, -0.545], + ['BXD5', -0.489, -0.423], + ['BXD6', 0.197, 0.156]] + + expected_results = { + "col_names": ["sample_names", "MEturquoise", "MEgrey"], + "mod_dataset": row_data + } + + self.assertEqual(process_wgcna_data(output), expected_results) |