diff options
Diffstat (limited to 'gn2/tests/unit/wqflask')
32 files changed, 2352 insertions, 0 deletions
diff --git a/gn2/tests/unit/wqflask/__init__.py b/gn2/tests/unit/wqflask/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/__init__.py diff --git a/gn2/tests/unit/wqflask/api/__init__.py b/gn2/tests/unit/wqflask/api/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/api/__init__.py diff --git a/gn2/tests/unit/wqflask/api/test_correlation.py b/gn2/tests/unit/wqflask/api/test_correlation.py new file mode 100644 index 00000000..2a1907af --- /dev/null +++ b/gn2/tests/unit/wqflask/api/test_correlation.py @@ -0,0 +1,175 @@ +import unittest +from unittest import mock +from gn2.wqflask import app +from collections import OrderedDict +from gn2.wqflask.api.correlation import init_corr_params +from gn2.wqflask.api.correlation import convert_to_mouse_gene_id +from gn2.wqflask.api.correlation import do_literature_correlation_for_all_traits +from gn2.wqflask.api.correlation import get_sample_r_and_p_values +from gn2.wqflask.api.correlation import calculate_results + + +class AttributeSetter: + def __init__(self, obj): + for k, v in obj.items(): + setattr(self, k, v) + + +class MockDataset(AttributeSetter): + def get_trait_data(self): + return None + + def retrieve_genes(self, id=None): + return {"TT-1": "GH-1", "TT-2": "GH-2", "TT-3": "GH-3"} + + +class TestCorrelations(unittest.TestCase): + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + def test_init_corr_params(self): + start_vars = {"return_count": "3", "type": "T1", "method": "spearman"} + + corr_params_results = init_corr_params(start_vars=start_vars) + expected_results = {"return_count": 3, "type": "T1", "method": "spearman"} + + self.assertEqual(corr_params_results, expected_results) + + @mock.patch("gn2.wqflask.api.correlation.database_connection") + def test_convert_to_mouse_gene_id(self, mock_db): + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchone.side_effect = [("MG-1",), ("MG-2",)] + + self.assertEqual( + convert_to_mouse_gene_id(species="Other", gene_id=""), None + ) + self.assertEqual( + convert_to_mouse_gene_id(species="mouse", gene_id="MG-4"), "MG-4" + ) + self.assertEqual( + convert_to_mouse_gene_id(species="rat", gene_id="R1"), "MG-1" + ) + self.assertEqual( + convert_to_mouse_gene_id(species="human", gene_id="H1"), "MG-2" + ) + + @mock.patch("gn2.wqflask.api.correlation.database_connection") + @mock.patch("gn2.wqflask.api.correlation.convert_to_mouse_gene_id") + def test_do_literature_correlation_for_all_traits( + self, mock_convert_to_mouse_geneid, mock_db + ): + mock_convert_to_mouse_geneid.side_effect = ["MG-1", "MG-2;", "MG-3", "MG-4"] + + trait_geneid_dict = {"TT-1": "GH-1", "TT-2": "GH-2", "TT-3": "GH-3"} + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchone.side_effect = [("V1",), ("V2",), ("V3",)] + this_trait = AttributeSetter({"geneid": "GH-1"}) + target_dataset = AttributeSetter( + {"group": AttributeSetter({"species": "rat"})} + ) + results = do_literature_correlation_for_all_traits( + this_trait=this_trait, + target_dataset=target_dataset, + trait_geneid_dict=trait_geneid_dict, + corr_params={}, + ) + expected_results = { + "TT-1": ["GH-1", 0], + "TT-2": ["GH-2", "V1"], + "TT-3": ["GH-3", "V2"], + } + self.assertEqual(results, expected_results) + + @mock.patch("gn2.wqflask.api.correlation.corr_result_helpers.normalize_values") + def test_get_sample_r_and_p_values(self, mock_normalize): + + group = AttributeSetter( + {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]} + ) + 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}), + } + 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, + ) + mock_normalize.side_effect = [ + ([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), + ([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), + ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3), + ] + + results_pearsonr = get_sample_r_and_p_values( + this_trait=this_trait, + this_dataset={}, + target_vals=target_vals, + target_dataset=target_dataset, + type="pearson", + ) + results_spearmanr = get_sample_r_and_p_values( + this_trait=this_trait, + this_dataset={}, + target_vals=target_vals, + target_dataset=target_dataset, + type="spearman", + ) + results_num_overlap = get_sample_r_and_p_values( + this_trait=this_trait, + this_dataset={}, + target_vals=target_vals, + target_dataset=target_dataset, + type="pearson", + ) + 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) + for i, val in enumerate(expected_spearmanr): + self.assertAlmostEqual(val, results_spearmanr[i], 4) + self.assertEqual(results_num_overlap, None) + + @mock.patch("gn2.wqflask.api.correlation.do_literature_correlation_for_all_traits") + def test_calculate_results(self, literature_correlation): + + literature_correlation.return_value = { + "TT-1": ["GH-1", 0], + "TT-2": ["GH-2", 3], + "TT-3": ["GH-3", 1], + } + + this_dataset = MockDataset({"group": AttributeSetter({"species": "rat"})}) + target_dataset = MockDataset({"group": AttributeSetter({"species": "rat"})}) + this_trait = AttributeSetter({"geneid": "GH-1"}) + corr_params = {"type": "literature"} + sorted_results = calculate_results( + this_trait=this_trait, + this_dataset=this_dataset, + target_dataset=target_dataset, + corr_params=corr_params, + ) + expected_results = { + "TT-2": ["GH-2", 3], + "TT-3": ["GH-3", 1], + "TT-1": ["GH-1", 0], + } + + self.assertTrue(isinstance(sorted_results, OrderedDict)) + self.assertEqual(dict(sorted_results), expected_results) diff --git a/gn2/tests/unit/wqflask/api/test_gen_menu.py b/gn2/tests/unit/wqflask/api/test_gen_menu.py new file mode 100644 index 00000000..2416b3f6 --- /dev/null +++ b/gn2/tests/unit/wqflask/api/test_gen_menu.py @@ -0,0 +1,423 @@ +"""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) diff --git a/gn2/tests/unit/wqflask/api/test_mapping.py b/gn2/tests/unit/wqflask/api/test_mapping.py new file mode 100644 index 00000000..226e2a9b --- /dev/null +++ b/gn2/tests/unit/wqflask/api/test_mapping.py @@ -0,0 +1,113 @@ +import unittest +from unittest import mock +from gn2.wqflask.api.mapping import initialize_parameters +from gn2.wqflask.api.mapping import do_mapping_for_api + + +class AttributeSetter: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) + + +class MockGroup(AttributeSetter): + def get_marker(self): + self.markers = [] + + +class TestMapping(unittest.TestCase): + + def test_initialize_parameters(self): + expected_results = { + "format": "json", + "limit_to": False, + "mapping_method": "gemma", + "maf": 0.01, + "use_loco": True, + "num_perm": 0, + "perm_check": False, + "transform": False, + "genofile": False + } + + results = initialize_parameters( + start_vars={}, dataset={}, this_trait={}) + self.assertEqual(results, expected_results) + + start_vars = { + "format": "F1", + "limit_to": "1", + "mapping_method": "rqtl", + "control_marker": True, + "pair_scan": "true", + "interval_mapping": "true", + "use_loco": "true", + "num_perm": "14", + "transform": "qnorm", + "genofile": "BXD.8.geno" + } + + results_2 = initialize_parameters( + start_vars=start_vars, dataset={}, this_trait={}) + expected_results = { + "format": "F1", + "limit_to": 1, + "mapping_method": "gemma", + "maf": 0.01, + "use_loco": True, + "num_perm": 14, + "perm_check": "ON", + "transform": "qnorm", + "genofile": "BXD.8.geno" + } + + self.assertEqual(results_2, expected_results) + + @mock.patch("gn2.wqflask.api.mapping.rqtl_mapping.run_rqtl") + @mock.patch("gn2.wqflask.api.mapping.gemma_mapping.run_gemma") + @mock.patch("gn2.wqflask.api.mapping.initialize_parameters") + @mock.patch("gn2.wqflask.api.mapping.retrieve_sample_data") + @mock.patch("gn2.wqflask.api.mapping.create_trait") + @mock.patch("gn2.wqflask.api.mapping.data_set.create_dataset") + def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno): + start_vars = { + "db": "Temp", + "trait_id": "dewf3232rff2", + "format": "F1", + "mapping_method": "gemma", + "use_loco": True + + } + sampleList = ["S1", "S2", "S3", "S4"] + samplelist = ["S1", "S2", "S4"] + dataset = AttributeSetter({"group": samplelist}) + this_trait = AttributeSetter({}) + trait_data = AttributeSetter({ + "data": { + "item1": AttributeSetter({"name": "S1", "value": "S1_value"}), + "item2": AttributeSetter({"name": "S2", "value": "S2_value"}), + "item3": AttributeSetter({"name": "S3", "value": "S3_value"}), + + } + }) + trait = AttributeSetter({ + "data": trait_data + }) + + dataset.return_value = dataset + mock_trait.return_value = this_trait + + mock_retrieve_sample.return_value = trait + mock_param.return_value = { + "format": "F1", + "limit_to": False, + "mapping_method": "gemma", + "maf": 0.01, + "use_loco": "True", + "num_perm": 14, + "perm_check": "ON" + } + + run_gemma.return_value = ["results"] + results = do_mapping_for_api(start_vars=start_vars) + self.assertEqual(results, ("results", None)) diff --git a/gn2/tests/unit/wqflask/api/test_markdown_routes.py b/gn2/tests/unit/wqflask/api/test_markdown_routes.py new file mode 100644 index 00000000..ecf64a81 --- /dev/null +++ b/gn2/tests/unit/wqflask/api/test_markdown_routes.py @@ -0,0 +1,54 @@ +"""Test functions for wqflask/api/markdown.py""" + +import unittest +from unittest import mock + +from dataclasses import dataclass +from gn2.wqflask.api.markdown import render_markdown + + +@dataclass +class MockRequests404: + status_code: int = 404 + + +@dataclass +class MockRequests200: + status_code: int = 200 + content: str = b""" +# Glossary +This is some content + +## Sub-heading +This is another sub-heading""" + + +class TestMarkdownRoutesFunctions(unittest.TestCase): + """Test cases for functions in markdown""" + + @mock.patch('gn2.wqflask.api.markdown.requests.get') + def test_render_markdown_when_fetching_locally(self, requests_mock): + requests_mock.return_value = MockRequests404() + markdown_content = render_markdown("general/glossary/glossary.md") + requests_mock.assert_called_with( + "https://raw.githubusercontent.com" + "/genenetwork/gn-docs/" + "master/general/" + "glossary/glossary.md") + self.assertRegex(markdown_content, + "Content for general/glossary/glossary.md not available.") + + @mock.patch('gn2.wqflask.api.markdown.requests.get') + def test_render_markdown_when_fetching_remotely(self, requests_mock): + requests_mock.return_value = MockRequests200() + markdown_content = render_markdown("general/glossary/glossary.md") + requests_mock.assert_called_with( + "https://raw.githubusercontent.com" + "/genenetwork/gn-docs/" + "master/general/" + "glossary/glossary.md") + self.assertEqual("""<h1>Glossary</h1> +<p>This is some content</p> +<h2>Sub-heading</h2> +<p>This is another sub-heading</p>""", + markdown_content) diff --git a/gn2/tests/unit/wqflask/correlation/__init__.py b/gn2/tests/unit/wqflask/correlation/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/correlation/__init__.py diff --git a/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py b/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py new file mode 100644 index 00000000..f76ef57e --- /dev/null +++ b/gn2/tests/unit/wqflask/correlation/test_correlation_functions.py @@ -0,0 +1,21 @@ +"""module contains tests for correlation functions""" + +import unittest +from unittest import mock + +from gn2.wqflask.correlation.correlation_functions import get_trait_symbol_and_tissue_values +from gn2.wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss + + +def test_tissue_corr_computation(mocker): + """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] + _m = mocker.patch(("gn2.wqflask.correlation.correlation_functions." + "compute_corr_coeff_p_value"), + return_value=(0.51, 0.7)) + results = cal_zero_order_corr_for_tiss(primary_values, target_values) + _m.assert_called_once_with( + primary_values=primary_values, target_values=target_values, + corr_method="pearson") + assert len(results) == 3 diff --git a/gn2/tests/unit/wqflask/correlation/test_correlation_gn3.py b/gn2/tests/unit/wqflask/correlation/test_correlation_gn3.py new file mode 100644 index 00000000..432dbc95 --- /dev/null +++ b/gn2/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 gn2.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/gn2/tests/unit/wqflask/correlation/test_show_corr_results.py b/gn2/tests/unit/wqflask/correlation/test_show_corr_results.py new file mode 100644 index 00000000..b1459dd9 --- /dev/null +++ b/gn2/tests/unit/wqflask/correlation/test_show_corr_results.py @@ -0,0 +1,42 @@ +import unittest +from unittest import mock +from gn2.wqflask.correlation.show_corr_results import get_header_fields + + +class AttributeSetter: + def __init__(self, trait_obj): + for key, value in trait_obj.items(): + setattr(self, key, value) + + +class TestShowCorrResults(unittest.TestCase): + def test_get_header_fields(self): + expected = [ + ['Index', + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Sample rho', + 'N', + 'Sample p(rho)', + 'Lit rho', + 'Tissue rho', + 'Tissue p(rho)', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'], + + ['Index', + 'ID', + 'Location', + 'Sample r', + 'N', + 'Sample p(r)'] + + ] + result1 = get_header_fields("ProbeSet", "spearman") + result2 = get_header_fields("Other", "Other") + self.assertEqual(result1, expected[0]) + self.assertEqual(result2, expected[1]) diff --git a/gn2/tests/unit/wqflask/marker_regression/__init__.py b/gn2/tests/unit/wqflask/marker_regression/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/__init__.py diff --git a/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_geno.txt diff --git a/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/genotype/bimbam/file_snps.txt diff --git a/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py new file mode 100644 index 00000000..580d79cf --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/test_display_mapping_results.py @@ -0,0 +1,159 @@ +import unittest + +import htmlgen as HT +from gn2.wqflask.marker_regression.display_mapping_results import ( + DisplayMappingResults, + HtmlGenWrapper +) + + +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, + (245, 211, 211)) + + +class TestHtmlGenWrapper(unittest.TestCase): + """Test Wrapper around HTMLGen""" + + def test_create_image(self): + """Test HT.Image method""" + self.assertEqual( + str(HtmlGenWrapper.create_image_tag(src="test.png", + alt="random", + border="0", + width="10", + height="13", + usemap="#webqtlmap")), + ("""<img alt="random" border="0" height="13" """ + """src="test.png" usemap="#webqtlmap" """ + """width="10"/>""") + ) + + def test_create_form(self): + """Test HT.Form method""" + test_form = HtmlGenWrapper.create_form_tag( + cgi="/testing/", + enctype='multipart/form-data', + name="formName", + submit=HtmlGenWrapper.create_input_tag( + type_='hidden', name='Default_Name') + ) + test_image = HtmlGenWrapper.create_image_tag( + src="test.png", + alt="random", + border="0", + width="10", + height="13", + usemap="#webqtlmap" + ) + self.assertEqual( + str(test_form).replace("\n", ""), + ("""<form action="/testing/" enctype="multipart/form-data" """ + """method="POST" """ + """name="formName"><input name="Default_Name" """ + """type="hidden"/></form>""")) + hddn = { + 'FormID': 'showDatabase', + 'ProbeSetID': '_', + 'database': "TestGeno", + 'CellID': '_', + 'RISet': "Test", + 'incparentsf1': 'ON' + } + for key in hddn.keys(): + test_form.append( + HtmlGenWrapper.create_input_tag( + name=key, + value=hddn[key], + type_='hidden')) + test_form.append(test_image) + + self.assertEqual(str(test_form).replace("\n", ""), ( + """<form action="/testing/" enctype="multipart/form-data" """ + """method="POST" name="formName">""" + """<input name="Default_Name" type="hidden"/>""" + """<input name="FormID" type="hidden" value="showDatabase"/>""" + """<input name="ProbeSetID" type="hidden" value="_"/>""" + """<input name="database" type="hidden" value="TestGeno"/>""" + """<input name="CellID" type="hidden" value="_"/>""" + """<input name="RISet" type="hidden" value="Test"/>""" + """<input name="incparentsf1" type="hidden" value="ON"/>""" + """<img alt="random" border="0" height="13" src="test.png" """ + """usemap="#webqtlmap" width="10"/>""" + """</form>""")) + + def test_create_paragraph(self): + """Test HT.Paragraph method""" + test_p_element = HtmlGenWrapper.create_p_tag(id="smallSize") + par_text = ( + "Mapping using genotype data as " + "a trait will result in infinity LRS at one locus. " + "In order to display the result properly, all LRSs " + "higher than 100 are capped at 100." + ) + self.assertEqual( + str(test_p_element), + """<p id="smallSize"></p>""" + ) + test_p_element.append(HtmlGenWrapper.create_br_tag()) + test_p_element.append(par_text) + self.assertEqual( + str(test_p_element), + """<p id="smallSize"><br/>{}</p>""".format(par_text) + ) + + def test_create_br_tag(self): + """Test HT.BR() method""" + self.assertEqual(str(HtmlGenWrapper.create_br_tag()), + "<br/>") + + def test_create_input_tag(self): + """Test HT.Input method""" + self.assertEqual( + str(HtmlGenWrapper.create_input_tag( + type_="hidden", + name="name", + value="key", + Class="trait trait_")).replace("\n", ""), + ("""<input class="trait trait_" name="name" """ + """type="hidden" value="key"/>""")) + + def test_create_map_tag(self): + """Test HT.Map method""" + self.assertEqual(str(HtmlGenWrapper.create_map_tag( + name="WebqTLImageMap")).replace("\n", ""), + """<map name="WebqTLImageMap"></map>""") + gifmap = HtmlGenWrapper.create_map_tag(name="test") + gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect", + coords='1 2 3', href='#area1')) + gifmap.append(HtmlGenWrapper.create_area_tag(shape="rect", + coords='1 2 3', href='#area2')) + self.assertEqual( + str(gifmap).replace("\n", ""), + ("""<map name="test">""" + """<area coords="1 2 3" """ + """href="#area1" shape="rect"/>""" + """<area coords="1 2 3" href="#area2" shape="rect"/>""" + """</map>""")) + + def test_create_area_tag(self): + """Test HT.Area method""" + self.assertEqual( + str(HtmlGenWrapper.create_area_tag( + shape="rect", + coords="1 2", + href="http://test.com", + title="Some Title")).replace("\n", ""), + ("""<area coords="1 2" href="http://test.com" """ + """shape="rect" title="Some Title"/>""")) + + def test_create_link_tag(self): + """Test HT.HREF method""" + self.assertEqual( + str(HtmlGenWrapper.create_link_tag( + "www.test.com", "test", target="_blank")).replace("\n", ""), + """<a href="www.test.com" target="_blank">test</a>""") diff --git a/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py new file mode 100644 index 00000000..b4d80ad7 --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -0,0 +1,188 @@ +# test for wqflask/marker_regression/gemma_mapping.py +import os +import unittest +import random +from unittest import mock +from gn2.wqflask.marker_regression.gemma_mapping import run_gemma +from gn2.wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file +from gn2.wqflask.marker_regression.gemma_mapping import gen_covariates_file +from gn2.wqflask.marker_regression.gemma_mapping import parse_loco_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + + +class MockGroup(AttributeSetter): + def get_samplelist(self, redis_conn): + return None + + +class TestGemmaMapping(unittest.TestCase): + + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.parse_loco_output") + def test_run_gemma_firstrun_set_false(self, mock_parse_loco): + """add tests for gemma function where first run is set to false""" + dataset = AttributeSetter( + {"group": AttributeSetter({"genofile": "genofile.geno"})}) + + output_file = "file1" + mock_parse_loco.return_value = [] + this_trait = AttributeSetter({"name": "t1"}) + + result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ + ], covariates="", use_loco=True, first_run=False, output_files=output_file) + + expected_results = ([], "file1") + self.assertEqual(expected_results, result) + + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", + os.path.join(os.path.dirname(__file__), "user/data")) + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.parse_loco_output") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.gen_covariates_file") + @mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os") + @mock.patch("gn2.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): + """add tests for run_gemma where first run is set to true""" + this_chromosomes = {} + for i in range(1, 5): + this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"})) + chromosomes = AttributeSetter({"chromosomes": lambda cursor: this_chromosomes}) + + dataset_group = MockGroup( + {"name": "GP1", "genofile": "file_geno"}) + dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", + "species": AttributeSetter({"chromosomes": chromosomes})}) + trait = AttributeSetter({"name": "trait1"}) + samples = [] + mock_gen_pheno_txt.return_value = None + mock_os.path.isfile.return_value = True + mock_gen_covar.return_value = None + mock_choice.return_value = "R" + mock_flat_files.return_value = os.path.join( + os.path.dirname(__file__), "genotype/bimbam") + mock_parse_loco.return_value = [] + results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ + ], vals=[], covariates="", use_loco=True) + mock_gen_pheno_txt.assert_called_once() + 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(results, ([], "GP1_GWA_RRRRRR")) + + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") + 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=AttributeSetter({"name": "A"}), + genofile_name="", vals=[ + "x", "w", "q", "we", "R"]) + mock_open.assert_called_once_with( + '/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( + 'q\n'), mock.call('we\n'), mock.call('R\n')] + + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.create_trait") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.create_dataset") + def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): + """add tests for generating covariates files""" + covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" + samplelist = ["X1", "X2", "X3", "X4"] + create_dataset_side_effect = [] + create_trait_side_effect = [] + + for i in range(4): + create_dataset_side_effect.append( + AttributeSetter({"name": f'name_{i}'})) + create_trait_side_effect.append( + AttributeSetter({"data": [f'data_{i}']})) + + create_dataset.side_effect = create_trait_side_effect + create_trait.side_effect = create_trait_side_effect + + group = MockGroup({"name": "group_X", "samplelist": samplelist}) + this_dataset = AttributeSetter({"group": group, "name": "dataset1_name"}) + flat_files.return_value = "Home/Genenetwork" + + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_covariates_file(this_dataset=this_dataset, covariates=covariates, + samples=["x1", "x2", "X3"]) + + create_dataset.assert_has_calls( + [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) + mock_calls = [] + trait_names = ["X1", "Y1", "M1", "V1"] + + for i, trait in enumerate(create_trait_side_effect): + mock_calls.append( + mock.call(dataset=trait, name=trait_names[i], cellid=None)) + + create_trait.assert_has_calls(mock_calls) + + flat_files.assert_called_once_with('mapping') + mock_open.assert_called_once_with( + 'Home/Genenetwork/COVAR_npKxIOnq3azWdgYixtd9IQ.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')]) + + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.json") + def test_parse_loco_outputfile_found(self, mock_json, mock_os): + """add tests for parse loco output file found""" + mock_json.load.return_value = { + "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 +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""" + + return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4""" + mock_os.path.isfile.return_value = True + file_to_write = """{"files":["file_1","file_2"]}""" + with mock.patch("builtins.open") as mock_open: + + handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( + read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value) + 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': -11.65, 'lod_score': 0.07058107428570727}, + {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, + 'additive': -12.0, 'lod_score': 0.3010299956639812}, + {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, + 'additive': -5.8, 'lod_score': 0.1549019599857432}, + {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': -10.55, 'lod_score': 0.22184874961635637}] + self.assertEqual(expected_results, results) + + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("gn2.wqflask.marker_regression.gemma_mapping.os") + def test_parse_loco_outputfile_not_found(self, mock_os): + """add tests for parse loco output where output file not found""" + + mock_os.path.isfile.return_value = False + file_to_write = """{"files":["file_1","file_2"]}""" + + with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open: + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + self.assertEqual(results, []) diff --git a/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py new file mode 100644 index 00000000..7542e15a --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -0,0 +1,86 @@ +# test for wqflask/marker_regression/plink_mapping.py +import unittest +from unittest import mock +from gn2.wqflask.marker_regression.plink_mapping import build_line_list +from gn2.wqflask.marker_regression.plink_mapping import get_samples_from_ped_file +from gn2.wqflask.marker_regression.plink_mapping import flat_files +from gn2.wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink +from gn2.wqflask.marker_regression.plink_mapping import parse_plink_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + + +class TestPlinkMapping(unittest.TestCase): + + def test_build_line_list(self): + """test for building line list""" + line_1 = "this is line one test" + irregular_line = " this is an, irregular line " + exp_line1 = ["this", "is", "line", "one", "test"] + + results = build_line_list(irregular_line) + self.assertEqual(exp_line1, build_line_list(line_1)) + self.assertEqual([], build_line_list()) + self.assertEqual(["this", "is", "an,", "irregular", "line"], results) + + @mock.patch("gn2.wqflask.marker_regression.plink_mapping.flat_files") + def test_get_samples_from_ped_file(self, mock_flat_files): + """test for getting samples from ped file""" + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + file_sample = """Expected_1\tline test +Expected_2\there + Expected_3\tthree""" + mock_flat_files.return_value = "/home/user/" + with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open: + results = get_samples_from_ped_file(dataset) + mock_flat_files.assert_called_once_with("mapping") + mock_open.assert_called_once_with("/home/user/n_1.ped", "r") + self.assertEqual( + ["Expected_1", "Expected_2", "Expected_3"], results) + + @mock.patch("gn2.wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("gn2.wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") + def test_gen_pheno_txt_file_plink(self, mock_samples): + """test for getting gen_pheno txt file""" + mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] + + trait = AttributeSetter({"name": "TX"}) + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + vals = ["value=K1", "value=K2", "value=K3"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset, + vals=vals, pheno_filename="ph_file") + mock_open.assert_called_once_with( + "/home/user/data/ph_file.txt", "wb") + filehandler = mock_open() + calls_expected = [mock.call('FID\tIID\tTX\n'), + mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')] + + filehandler.write.assert_has_calls(calls_expected) + + filehandler.close.assert_called_once() + + @mock.patch("gn2.wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("gn2.wqflask.marker_regression.plink_mapping.build_line_list") + def test_parse_plink_output(self, mock_line_list): + """test for parsing plink output""" + chromosomes = [0, 34, 110, 89, 123, 23, 2] + species = AttributeSetter( + {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) + + fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA""" + + mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ + "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] + with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: + parse_results = parse_plink_output( + output_filename="P1_file", species=species) + mock_open.assert_called_once_with( + "/home/user/data/P1_file.qassoc", "rb") + expected = (2, {'AACCAT': 0.89, 'AATA': 0.3}) + + self.assertEqual(parse_results, expected) diff --git a/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py new file mode 100644 index 00000000..c2753141 --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -0,0 +1,24 @@ +import unittest +from unittest import mock +from gn2.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 + + +class TestQtlReaperMapping(unittest.TestCase): + @mock.patch("gn2.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/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py new file mode 100644 index 00000000..9f646fb0 --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -0,0 +1,43 @@ +import unittest +from unittest import mock +from dataclasses import dataclass + +from gn2.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("gn2.wqflask.marker_regression.rqtl_mapping.requests.post") + @mock.patch("gn2.wqflask.marker_regression.rqtl_mapping.locate") + @mock.patch("gn2.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, pair_scan=False, 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/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py new file mode 100644 index 00000000..817bf2b9 --- /dev/null +++ b/gn2/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -0,0 +1,288 @@ +import unittest +import datetime +from unittest import mock + +from gn2.wqflask.marker_regression.run_mapping import get_genofile_samplelist +from gn2.wqflask.marker_regression.run_mapping import geno_db_exists +from gn2.wqflask.marker_regression.run_mapping import write_input_for_browser +from gn2.wqflask.marker_regression.run_mapping import export_mapping_results +from gn2.wqflask.marker_regression.run_mapping import trim_markers_for_figure +from gn2.wqflask.marker_regression.run_mapping import get_perm_strata +from gn2.wqflask.marker_regression.run_mapping import get_chr_lengths + + +class AttributeSetter: + def __init__(self, obj): + for k, v in obj.items(): + setattr(self, k, v) + + +class MockGroup(AttributeSetter): + + def get_genofiles(self): + return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] + + +class TestRunMapping(unittest.TestCase): + def setUp(self): + + self.group = MockGroup( + {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) + chromosomes = { + "3": AttributeSetter({ + "name": "C1", + "length": "0.04" + }), + "4": AttributeSetter({ + "name": "C2", + "length": "0.03" + }), + "5": AttributeSetter({ + "name": "C4", + "length": "0.01" + }) + } + self.dataset = AttributeSetter( + {"fullname": "dataset_1", "group": self.group, "type": "ProbeSet"}) + + self.chromosomes = AttributeSetter({"chromosomes": lambda cur: chromosomes}) + self.trait = AttributeSetter( + {"symbol": "IGFI", "chr": "X1", "mb": 123313, "display_name": "Test Name"}) + + def tearDown(self): + self.dataset = AttributeSetter( + {"group": {"location": "~/genofiles/g1_file"}}) + + def test_get_genofile_samplelist(self): + + results_1 = get_genofile_samplelist(self.dataset) + self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) + self.group.genofile = "~/genofiles/g2_file" + result_2 = get_genofile_samplelist(self.dataset) + self.assertEqual(result_2, []) + + @mock.patch("gn2.wqflask.marker_regression.run_mapping.data_set") + def test_if_geno_db_exists(self, mock_data_set): + mock_data_set.create_dataset.side_effect = [ + AttributeSetter({}), Exception()] + results_no_error = geno_db_exists(self.dataset) + results_with_error = geno_db_exists(self.dataset) + + self.assertEqual(mock_data_set.create_dataset.call_count, 2) + self.assertEqual(results_with_error, "False") + self.assertEqual(results_no_error, "True") + + def test_trim_markers_for_figure(self): + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":0.7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + }] + + marker_2 = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "p_wald":4.6 + }] + results = trim_markers_for_figure(markers) + result_2 = trim_markers_for_figure(marker_2) + expected = [ + { + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + } + + ] + self.assertEqual(results, expected) + self.assertEqual(result_2, marker_2) + + def test_export_mapping_results(self): + """test for exporting mapping results""" + datetime_mock = mock.Mock(wraps=datetime.datetime) + datetime_mock.now.return_value = datetime.datetime( + 2019, 9, 1, 10, 12, 12) + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":3 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":7 + }] + + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + + with mock.patch("gn2.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_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: 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,-logP'), + mock.call(',Additive'), mock.call(',Dominance'), + mock.call('\n'), mock.call('MK1,C1,'), + 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('7'), + mock.call(',VE'), mock.call(',Tt') + ] + mock_open.assert_called_once_with("~/results", "w+") + filehandler = mock_open() + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("gn2.wqflask.marker_regression.run_mapping.random.choice") + def test_write_input_for_browser(self, mock_choice): + """test for writing input for browser""" + mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] + + results = write_input_for_browser( + this_dataset=self.dataset, gwas_results={}, annotations={}) + self.assertEqual(results, expected) + + def test_get_perm_strata(self): + categorical_vars = ["C1", "C2", "W1"] + used_samples = ["S1", "S2"] + sample_list = AttributeSetter({"sample_attribute_values": { + "S1": { + "c1": "c1_value", + "c2": "c2_value", + "w1": "w1_value" + }, + "S2": { + "w1": "w2_value", + "w2": "w2_value" + }, + "S3": { + + "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, [1, 1]) + + def test_get_chr_length(self): + """test for getting chromosome length""" + cursor = mock.MagicMock() + chromosomes = AttributeSetter({"chromosomes": self.chromosomes}) + dataset = AttributeSetter({"species": chromosomes}) + results = get_chr_lengths( + mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[]) + chr_lengths = [] + for key, chromo in self.chromosomes.chromosomes(cursor).items(): + chr_lengths.append({"chr": chromo.name, "size": chromo.length}) + + self.assertEqual(chr_lengths, results) + + qtl_results = [{ + "chr": "16", + "cM": "0.2" + }, + { + "chr": "12", + "cM": "0.5" + }, + { + "chr": "18", + "cM": "0.1" + }, + { + "chr": "22", + "cM": "0.4" + }, + ] + + result_with_other_mapping_scale = get_chr_lengths( + mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results) + expected_value = [{'chr': '1', 'size': '0'}, { + 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] + + self.assertEqual(result_with_other_mapping_scale, expected_value) diff --git a/gn2/tests/unit/wqflask/show_trait/__init__.py b/gn2/tests/unit/wqflask/show_trait/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/show_trait/__init__.py diff --git a/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py new file mode 100644 index 00000000..1ecf394b --- /dev/null +++ b/gn2/tests/unit/wqflask/show_trait/test_export_trait_data.py @@ -0,0 +1,151 @@ +import datetime +import unittest +from unittest import mock +from gn2.wqflask.show_trait.export_trait_data import dict_to_sorted_list +from gn2.wqflask.show_trait.export_trait_data import cmp_samples +from gn2.wqflask.show_trait.export_trait_data import export_sample_table +from gn2.wqflask.show_trait.export_trait_data import get_export_metadata + + +class AttributesSetter: + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) + + +class TestExportTraits(unittest.TestCase): + """Test methods for exporting traits and metadata""" + + @mock.patch("gn2.wqflask.show_trait.export_trait_data.datetime") + @mock.patch("gn2.wqflask.show_trait.export_trait_data.create_trait") + @mock.patch("gn2.wqflask.show_trait.export_trait_data.data_set") + def test_get_export_metadata(self, data_mock, trait_mock, date_mock): + """test for exporting metadata with dataset.type=Publish""" + mock_dataset = AttributesSetter({"type": "Publish", + "name": "HC_M2_0606_P", + "dataset_name": "HC_M2_0606_P"}) + + mock_dataset.group = AttributesSetter({"name": "C"}) + data_mock.create_dataset.return_value = mock_dataset + + trait_data = { + "symbol": "Nr3c1", + "description_display": "nuclear receptor subfamily 3,group C, member 1 (glucocorticoid receptor); distal 3' UTR", + "title": "Trait_1 title", + + "authors": "XL_1", + "journal": "" + + } + + date_mock.datetime.now.return_value = datetime.datetime( + 2022, 8, 8, 19, 2, 31, 628813) + trait_mock.return_value = AttributesSetter(trait_data) + + results = get_export_metadata({ + "trait_id": "1460303_at", + "trait_display_name": "1460303_at", + "dataset": "HC_M2_0606_P", + "group": "BXD", + }) + + expected = [["Phenotype ID:", "1460303_at"], + ["Phenotype URL: ", "http://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P"], + ["Group: ", "C"], + ["Phenotype: ", + 'nuclear receptor subfamily 3","group C"," member 1 (glucocorticoid receptor); distal 3\' UTR'], + ["Authors: ", "XL_1"], + ["Title: ", "Trait_1 title"], + ["Journal: ", "N/A"], + ["Dataset Link: ", "http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=HC_M2_0606_P"], + ["Export Date: ", "August 08, 2022"], + ["Export Time: ", "19:02 GMT"]] + + self.assertEqual(results, expected) + + def test_dict_to_sortedlist(self): + """test for conversion of dict to sorted list""" + sample1 = { + "other": "exp1", + "name": "exp2" + } + sample2 = { + "se": 1, + "num_cases": 4, + "value": 6, + "name": 3 + + } + rever = { + "name": 3, + "value": 6, + "num_cases": 4, + "se": 1 + } + oneItem = { + "item1": "one" + } + + self.assertEqual(["exp2", "exp1"], dict_to_sorted_list(sample1)) + self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(sample2)) + self.assertEqual([3, 6, 1, 4], dict_to_sorted_list(rever)) + self.assertEqual(["one"], dict_to_sorted_list(oneItem)) + """test that the func returns the values not the keys""" + self.assertFalse(["other", "name"] == dict_to_sorted_list(sample1)) + + def test_cmp_samples(self): + """test for comparing samples function""" + sampleA = [ + [ + ("value", "other"), + ("name", "test_name") + ] + ] + sampleB = [ + [ + ("value", "other"), + ("unknown", "test_name") + ] + ] + sampleC = [ + [("other", "value"), + ("name", "value") + ], + [ + ("name", "value"), + ("value", "name") + ], + [ + ("other", "value"), + ("name", "value" + )], + [ + ("name", "name1"), + ("se", "valuex") + ], + [( + "value", "name1"), + ("se", "valuex") + ], + [( + "other", "name1"), + ("se", "valuex" + ) + ], + [( + "name", "name_val"), + ("num_cases", "num_val") + ], + [( + "other_a", "val_a"), + ("other_b", "val" + ) + ] + ] + results = [cmp_samples(val[0], val[1]) for val in sampleA] + resultB = [cmp_samples(val[0], val[1]) for val in sampleB] + resultC = [cmp_samples(val[0], val[1]) for val in sampleC] + + self.assertEqual(1, *results) + self.assertEqual(-1, *resultB) + self.assertEqual([1, -1, 1, -1, -1, 1, -1, -1], resultC) diff --git a/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py new file mode 100644 index 00000000..45484f17 --- /dev/null +++ b/gn2/tests/unit/wqflask/show_trait/test_get_max_digits.py @@ -0,0 +1,15 @@ +import pytest +import unittest + +from gn2.wqflask.show_trait.show_trait import get_max_digits + +@unittest.skip("Too complicated") +@pytest.mark.parametrize( + "trait_vals,expected", + ((( + (0, 1345, 92, 734), + (234253, 33, 153, 5352), + (3542, 24, 135)), + [3, 5, 3]),)) +def test_get_max_digits(trait_vals, expected): + assert get_max_digits(trait_vals) == expected diff --git a/gn2/tests/unit/wqflask/snp_browser/__init__.py b/gn2/tests/unit/wqflask/snp_browser/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/snp_browser/__init__.py diff --git a/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py b/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py new file mode 100644 index 00000000..bf0421c0 --- /dev/null +++ b/gn2/tests/unit/wqflask/snp_browser/test_snp_browser.py @@ -0,0 +1,206 @@ +import unittest +from unittest import mock +from gn2.wqflask import app +from gn2.wqflask.snp_browser.snp_browser import get_gene_id +from gn2.wqflask.snp_browser.snp_browser import get_gene_id_name_dict +from gn2.wqflask.snp_browser.snp_browser import check_if_in_gene +from gn2.wqflask.snp_browser.snp_browser import get_browser_sample_lists +from gn2.wqflask.snp_browser.snp_browser import get_header_list + + +class TestSnpBrowser(unittest.TestCase): + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + def test_get_header_list(self): + empty_columns = { + "snp_source": "false", + "conservation_score": "true", + "gene_name": "false", + "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", + ], + ) + + results_with_snp = get_header_list( + variant_type="SNP", + strains=strains, + species="Mouse", + empty_columns=empty_columns, + ) + results_with_indel = get_header_list( + 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", + ], + ) + + self.assertEqual(expected_results, results_with_snp) + self.assertEqual(expected_results_with_indel, results_with_indel) + + @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection") + def test_get_gene_id(self, mock_db): + db_query_value = ( + "SELECT geneId FROM GeneList WHERE " "SpeciesId = %s AND geneSymbol = %s" + ) + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchone.return_value = ( + ("517d729f-aa13-4413" "-a885-40a3f7ff768a"), + ) + + results = get_gene_id( + species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR" + ) + cursor.execute.assert_called_once_with( + db_query_value, ("c9c0f59e-1259-4cba-91e6-831ef1a99c83", "INSR") + ) + self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a") + + @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection") + def test_gene_id_name_dict(self, mock_db): + no_gene_names = [] + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchall.side_effect = [ + [], + [ + ("fsdf43-fseferger-f22", "GH1"), + ("1sdf43-fsewferger-f22", "GH2"), + ("fwdj43-fstferger-f22", "GH3"), + ], + ] + self.assertEqual( + "", + get_gene_id_name_dict( + species_id="fregb343bui43g4", gene_name_list=no_gene_names + ), + ) + gene_name_list = ["GH1", "GH2", "GH3"] + no_results = get_gene_id_name_dict( + species_id="ret3-32rf32", gene_name_list=gene_name_list + ) + results_found = get_gene_id_name_dict( + species_id="ret3-32rf32", gene_name_list=gene_name_list + ) + expected_found = { + "GH1": "fsdf43-fseferger-f22", + "GH2": "1sdf43-fsewferger-f22", + "GH3": "fwdj43-fstferger-f22", + } + db_query_value = ( + "SELECT geneId, geneSymbol FROM GeneList WHERE " + "SpeciesId = %s AND geneSymbol in (%s, %s, %s)" + ) + cursor.execute.assert_called_with( + db_query_value, ("ret3-32rf32", "GH1", "GH2", "GH3") + ) + self.assertEqual(results_found, expected_found) + self.assertEqual(no_results, {}) + + @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection") + def test_check_if_in_gene(self, mock_db): + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.fetchone.side_effect = [("fsdf-232sdf-sdf", "GHA"), ""] + results_found = check_if_in_gene( + species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr_="CH1", mb=12.09 + ) + self.assertEqual(results_found, ["fsdf-232sdf-sdf", "GHA"]) + db_query_value = ( + "SELECT geneId, geneSymbol FROM GeneList " + "WHERE SpeciesId = %s AND chromosome = %s " + "AND (txStart < %s AND txEnd > %s)" + ) + gene_not_found = check_if_in_gene( + species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr_="CH1", mb=12.09 + ) + cursor.execute.assert_has_calls( + [ + mock.call( + db_query_value, + ("517d729f-aa13-4413-a885-40a3f7ff768a", "CH1", 12.09, 12.09), + ), + mock.call( + db_query_value, + ("517d729f-aa13-4413-a885-40a3f7ff768a", "CH1", 12.09, 12.09), + ), + ] + ) + self.assertEqual(gene_not_found, "") + + @mock.patch("gn2.wqflask.snp_browser.snp_browser.database_connection") + def test_get_browser_sample_lists(self, mock_db): + conn = mock.MagicMock() + mock_db.return_value.__enter__.return_value = conn + with conn.cursor() as cursor: + cursor.execute.return_value.fetchall.return_value = [] + results = get_browser_sample_lists(species_id="12") + self.assertEqual(results, {"mouse": [], "rat": []}) diff --git a/gn2/tests/unit/wqflask/test_collect.py b/gn2/tests/unit/wqflask/test_collect.py new file mode 100644 index 00000000..6c1bafa5 --- /dev/null +++ b/gn2/tests/unit/wqflask/test_collect.py @@ -0,0 +1,75 @@ +"""Test cases for some methods in collect.py""" + +import unittest +from unittest import mock + +from flask import Flask +from gn2.wqflask.collect import process_traits + +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 + + @property + def logged_in(self): + return self.is_logged_in + + +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 + + @property + def user_session(self): + if self.is_logged_in: + return MockSession(is_logged_in=True) + return MockSession() + + +class TestCollect(unittest.TestCase): + + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("gn2.wqflask.collect.g", MockFlaskG()) + def test_process_traits_with_bytestring(self): + """ + Test that the correct traits are returned when the user is logged + out and bytes are used. + """ + self.assertEqual(sorted(process_traits( + b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,' + b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,' + b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,' + b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5')), + sorted(['1429252_at:HC_M2_0606_P', + '1451401_a_at:HC_M2_0606_P', + '1452447_at:HC_M2_0606_P', + '1452452_at:HC_M2_0606_P'])) + + @mock.patch("gn2.wqflask.collect.g", MockFlaskG()) + def test_process_traits_with_normal_string(self): + """ + Test that the correct traits are returned when the user is logged + out and a normal string is used. + """ + self.assertEqual(sorted(process_traits( + '1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,' + '1452447_at:HC_M2_0606_P:eeece8fceb67072debea,' + '1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,' + '1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5')), + sorted(['1429252_at:HC_M2_0606_P', + '1451401_a_at:HC_M2_0606_P', + '1452447_at:HC_M2_0606_P', + '1452452_at:HC_M2_0606_P'])) diff --git a/gn2/tests/unit/wqflask/test_pbkdf2.py b/gn2/tests/unit/wqflask/test_pbkdf2.py new file mode 100644 index 00000000..ed4eff4f --- /dev/null +++ b/gn2/tests/unit/wqflask/test_pbkdf2.py @@ -0,0 +1,61 @@ +"""Test cases pbkdf2""" + +import unittest +from gn2.wqflask.pbkdf2 import pbkdf2_hex + + +class TestPbkdf2(unittest.TestCase): + def test_pbkdf2_hex(self): + """ + Test pbkdf2_hex function + """ + + for password, salt, iterations, keylen, expected_value in [ + ('password', b'salt', 1, 20, + '0c60c80f961f0e71f3a9b524af6012062fe037a6'), + ('password', b'salt', 2, 20, + 'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957'), + ('password', b'salt', 4096, 20, + '4b007901b765489abead49d926f721d065a429c1'), + ('passwordPASSWORDpassword', + b'saltSALTsaltSALTsaltSALTsaltSALTsalt', + 4096, 25, + '3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038'), + ('pass\x00word', b'sa\x00lt', 4096, 16, + '56fa6aa75548099dcc37d7f03425e0c3'), + ('password', b'ATHENA.MIT.EDUraeburn', 1, 16, + 'cdedb5281bb2f801565a1122b2563515'), + ('password', b'ATHENA.MIT.EDUraeburn', 1, 32, + ('cdedb5281bb2f80' + '1565a1122b256351' + '50ad1f7a04bb9f3a33' + '3ecc0e2e1f70837')), + ('password', b'ATHENA.MIT.EDUraeburn', 2, 16, + '01dbee7f4a9e243e988b62c73cda935d'), + ('password', b'ATHENA.MIT.EDUraeburn', 2, 32, + ('01dbee7f4a9e243e9' + '88b62c73cda935da05' + '378b93244ec8f48a99' + 'e61ad799d86')), + ('password', b'ATHENA.MIT.EDUraeburn', 1200, 32, + ('5c08eb61fdf71e' + '4e4ec3cf6ba1f55' + '12ba7e52ddbc5e51' + '42f708a31e2e62b1e13')), + ('X' * 64, b'pass phrase equals block size', 1200, 32, + ('139c30c0966bc32ba' + '55fdbf212530ac9c5' + 'ec59f1a452f5cc9ad' + '940fea0598ed1')), + ('X' * 65, b'pass phrase exceeds block size', 1200, 32, + ('9ccad6d468770cd' + '51b10e6a68721be6' + '11a8b4d282601db3' + 'b36be9246915ec82a')) + ]: + self.assertEqual( + pbkdf2_hex(data=password, + salt=salt, + iterations=iterations, + keylen=keylen), + expected_value) diff --git a/gn2/tests/unit/wqflask/test_resource_manager.py b/gn2/tests/unit/wqflask/test_resource_manager.py new file mode 100644 index 00000000..a4b3a0ee --- /dev/null +++ b/gn2/tests/unit/wqflask/test_resource_manager.py @@ -0,0 +1,94 @@ +"""Test cases for wqflask/resource_manager.py""" +import json +import unittest + +from unittest import mock +from gn3.authentication import get_user_membership +from gn3.authentication import get_highest_user_access_role +from gn3.authentication import DataRole +from gn3.authentication import AdminRole + + +class TestGetUserMembership(unittest.TestCase): + """Test cases for `get_user_membership`""" + + def setUp(self): + conn = mock.MagicMock() + conn.hgetall.return_value = { + '7fa95d07-0e2d-4bc5-b47c-448fdc1260b2': ( + '{"name": "editors", ' + '"admins": ["8ad942fe-490d-453e-bd37-56f252e41604", "rand"], ' + '"members": ["8ad942fe-490d-453e-bd37-56f252e41603", ' + '"rand"], ' + '"changed_timestamp": "Oct 06 2021 06:39PM", ' + '"created_timestamp": "Oct 06 2021 06:39PM"}')} + self.conn = conn + + def test_user_is_group_member_only(self): + """Test that a user is only a group member""" + self.assertEqual( + get_user_membership( + conn=self.conn, + user_id="8ad942fe-490d-453e-bd37-56f252e41603", + group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"), + {"member": True, + "admin": False}) + + def test_user_is_group_admin_only(self): + """Test that a user is a group admin only""" + self.assertEqual( + get_user_membership( + conn=self.conn, + user_id="8ad942fe-490d-453e-bd37-56f252e41604", + group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"), + {"member": False, + "admin": True}) + + def test_user_is_both_group_member_and_admin(self): + """Test that a user is both an admin and member of a group""" + self.assertEqual( + get_user_membership( + conn=self.conn, + user_id="rand", + group_id="7fa95d07-0e2d-4bc5-b47c-448fdc1260b2"), + {"member": True, + "admin": True}) + + +class TestCheckUserAccessRole(unittest.TestCase): + """Test cases for `get_highest_user_access_role`""" + + @mock.patch("gn2.wqflask.resource_manager.requests.get") + def test_edit_access(self, requests_mock): + """Test that the right access roles are set""" + response = mock.PropertyMock(return_value=json.dumps( + { + 'data': ['no-access', 'view', 'edit', ], + 'metadata': ['no-access', 'view', 'edit', ], + 'admin': ['not-admin', 'edit-access', ], + } + )) + type(requests_mock.return_value).content = response + self.assertEqual(get_highest_user_access_role( + resource_id="0196d92e1665091f202f", + user_id="8ad942fe-490d-453e-bd37"), + {"data": DataRole.EDIT, + "metadata": DataRole.EDIT, + "admin": AdminRole.EDIT_ACCESS}) + + @mock.patch("gn2.wqflask.resource_manager.requests.get") + def test_no_access(self, requests_mock): + response = mock.PropertyMock(return_value=json.dumps( + { + 'data': ['no-access', ], + 'metadata': ['no-access', ], + 'admin': ['not-admin', ], + } + )) + type(requests_mock.return_value).content = response + self.assertEqual(get_highest_user_access_role( + resource_id="0196d92e1665091f202f", + user_id=""), + {"data": DataRole.NO_ACCESS, + "metadata": DataRole.NO_ACCESS, + "admin": AdminRole.NOT_ADMIN}) diff --git a/gn2/tests/unit/wqflask/test_server_side.py b/gn2/tests/unit/wqflask/test_server_side.py new file mode 100644 index 00000000..b3e90eb9 --- /dev/null +++ b/gn2/tests/unit/wqflask/test_server_side.py @@ -0,0 +1,34 @@ +import unittest + +from gn2.wqflask.server_side import ServerSideTable + + +class TestServerSideTableTests(unittest.TestCase): + """ + Test the ServerSideTable class + + test table: + first, second, third + 'd', 4, 'zz' + 'b', 2, 'aa' + 'c', 1, 'ss' + """ + + def test_get_page(self): + rows_count = 3 + table_rows = [ + {'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'} + + 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'}]) diff --git a/gn2/tests/unit/wqflask/test_user_login.py b/gn2/tests/unit/wqflask/test_user_login.py new file mode 100644 index 00000000..84e25d45 --- /dev/null +++ b/gn2/tests/unit/wqflask/test_user_login.py @@ -0,0 +1,21 @@ +"""Test cases for some methods in login.py""" + +import unittest +from gn2.wqflask.user_login import encode_password + + +class TestUserLogin(unittest.TestCase): + def test_encode_password(self): + """ + Test encode password + """ + pass_gen_fields = { + "salt": "salt", + "hashfunc": "sha1", + "iterations": 4096, + "keylength": 20, + } + self.assertEqual( + encode_password(pass_gen_fields, + "password").get("password"), + '4b007901b765489abead49d926f721d065a429c1') diff --git a/gn2/tests/unit/wqflask/test_user_session.py b/gn2/tests/unit/wqflask/test_user_session.py new file mode 100644 index 00000000..944e5b6a --- /dev/null +++ b/gn2/tests/unit/wqflask/test_user_session.py @@ -0,0 +1,15 @@ +"""Test cases for some methods in user_session.py""" + +import unittest +from gn2.wqflask.user_session import verify_cookie + + +class TestUserSession(unittest.TestCase): + def test_verify_cookie(self): + """ + Test cookie verification + """ + self.assertEqual( + "3f4c1dbf-5b56-4260-87d6-f35445bda37e", + verify_cookie(("3f4c1dbf-5b56-4260-87d6-" + "f35445bda37e:af4fcf5eace9e7c864ce"))) diff --git a/gn2/tests/unit/wqflask/wgcna/__init__.py b/gn2/tests/unit/wqflask/wgcna/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/gn2/tests/unit/wqflask/wgcna/__init__.py diff --git a/gn2/tests/unit/wqflask/wgcna/test_wgcna.py b/gn2/tests/unit/wqflask/wgcna/test_wgcna.py new file mode 100644 index 00000000..2ed5e08f --- /dev/null +++ b/gn2/tests/unit/wqflask/wgcna/test_wgcna.py @@ -0,0 +1,50 @@ + +"""module contains for processing gn3 wgcna data""" +from unittest import TestCase + +from gn2.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) |