diff options
Diffstat (limited to 'wqflask/tests')
11 files changed, 595 insertions, 49 deletions
diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py new file mode 100644 index 00000000..48d110c7 --- /dev/null +++ b/wqflask/tests/unit/utility/test_type_checking.py @@ -0,0 +1,54 @@ +import unittest +from utility.type_checking import is_float +from utility.type_checking import is_int +from utility.type_checking import is_str +from utility.type_checking import get_float +from utility.type_checking import get_int +from utility.type_checking import get_string + + +class TestTypeChecking(unittest.TestCase): + def test_is_float(self): + floats = [2, 1.2, '3.1'] + not_floats = ["String", None, [], ()] + for flt in floats: + results = is_float(flt) + self.assertTrue(results) + for nflt in not_floats: + results = is_float(nflt) + self.assertFalse(results) + + def test_is_int(self): + int_values = [1, 1.1] + not_int_values = ["string", None, [], "1.1"] + for int_val in int_values: + results = is_int(int_val) + self.assertTrue(results) + for not_int in not_int_values: + results = is_int(not_int) + self.assertFalse(results) + + def test_is_str(self): + string_values = [1, False, [], {}, "string_value"] + falsey_values = [None] + for string_val in string_values: + results = is_str(string_val) + self.assertTrue(results) + for non_string in falsey_values: + results = is_str(non_string) + self.assertFalse(results) + + def test_get_float(self): + vars_object = {"min_value": "12"} + results = get_float(vars_object, "min_value") + self.assertEqual(results, 12.0) + + def test_get_int(self): + vars_object = {"lx_value": "1"} + results = get_int(vars_object, "lx_value") + self.assertEqual(results, 1) + + def test_get_string(self): + string_object = {"mx_value": 1} + results = get_string(string_object, "mx_value") + self.assertEqual(results, "1") \ No newline at end of file diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py new file mode 100644 index 00000000..d0264b87 --- /dev/null +++ b/wqflask/tests/unit/wqflask/api/test_correlation.py @@ -0,0 +1,153 @@ +import unittest +from unittest import mock +from wqflask import app +from collections import OrderedDict +from wqflask.api.correlation import init_corr_params +from wqflask.api.correlation import convert_to_mouse_gene_id +from wqflask.api.correlation import do_literature_correlation_for_all_traits +from wqflask.api.correlation import get_sample_r_and_p_values +from 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("wqflask.api.correlation.g") + def test_convert_to_mouse_gene_id(self, mock_db): + + results = convert_to_mouse_gene_id(species="Other", gene_id="") + self.assertEqual(results, None) + + rat_species_results = convert_to_mouse_gene_id( + species="rat", gene_id="GH1") + + mock_db.db.execute.return_value.fetchone.side_effect = [ + AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})] + + 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("wqflask.api.correlation.g") + @mock.patch("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" + + } + mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter( + {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "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("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("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/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py new file mode 100644 index 00000000..b094294a --- /dev/null +++ b/wqflask/tests/unit/wqflask/api/test_mapping.py @@ -0,0 +1,108 @@ +import unittest +from unittest import mock +from wqflask.api.mapping import initialize_parameters +from 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 + } + + 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" + + } + + 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" + } + + self.assertEqual(results_2, expected_results) + + @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno") + @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma") + @mock.patch("wqflask.api.mapping.initialize_parameters") + @mock.patch("wqflask.api.mapping.retrieve_sample_data") + @mock.patch("wqflask.api.mapping.create_trait") + @mock.patch("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/wqflask/tests/unit/wqflask/correlation/__init__.py b/wqflask/tests/unit/wqflask/correlation/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/unit/wqflask/correlation/__init__.py diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py new file mode 100644 index 00000000..44d2e0fc --- /dev/null +++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py @@ -0,0 +1,20 @@ +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): + + @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""" + mock_class_instance = mock_class.return_value + mock_class_instance.gene_symbols = ["k1", "k2", "k3"] + mock_class_instance.get_symbol_values_pairs.return_value = { + "k1": ["v1", "v2", "v3"], "k2": ["v2", "v3"], "k3": ["k3"]} + results = get_trait_symbol_and_tissue_values( + symbol_list=["k1", "k2", "k3"]) + mock_class.assert_called_with(gene_symbols=['k1', 'k2', 'k3']) + self.assertEqual({"k1": ["v1", "v2", "v3"], "k2": [ + "v2", "v3"], "k3": ["k3"]}, results) diff --git a/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py new file mode 100644 index 00000000..33601990 --- /dev/null +++ b/wqflask/tests/unit/wqflask/correlation/test_show_corr_results.py @@ -0,0 +1,98 @@ +import unittest +from unittest import mock +from wqflask.correlation.show_corr_results import get_header_fields +from wqflask.correlation.show_corr_results import generate_corr_json + + +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]) + + @mock.patch("wqflask.correlation.show_corr_results.hmac.data_hmac") + def test_generate_corr_json(self, mock_data_hmac): + mock_data_hmac.return_value = "hajsdiau" + + dataset = AttributeSetter({"name": "the_name"}) + this_trait = AttributeSetter( + {"name": "trait_test", "dataset": dataset}) + target_dataset = AttributeSetter({"type": "Publish"}) + corr_trait_1 = AttributeSetter({ + "name": "trait_1", + "dataset": AttributeSetter({"name": "dataset_1"}), + "view": True, + "abbreviation": "T1", + "description_display": "Trait I description", + "authors": "JM J,JYEW", + "pubmed_id": "34n4nn31hn43", + "pubmed_text": "2016", + "pubmed_link": "https://www.load", + "lod_score": "", + "mean": "", + "LRS_location_repr": "BXBS", + "additive": "", + "sample_r": 10.5, + "num_overlap": 2, + "sample_p": 5 + + + + + }) + corr_results = [corr_trait_1] + + dataset_type_other = { + "location": "cx-3-4", + "sample_4": 12.32, + "num_overlap": 3, + "sample_p": 10.34 + } + + expected_results = '[{"index": 1, "trait_id": "trait_1", "dataset": "dataset_1", "hmac": "hajsdiau", "abbreviation_display": "T1", "description": "Trait I description", "mean": "N/A", "authors_display": "JM J,JYEW", "additive": "N/A", "pubmed_id": "34n4nn31hn43", "year": "2016", "lod_score": "N/A", "lrs_location": "BXBS", "sample_r": "10.500", "num_overlap": 2, "sample_p": "5.000e+00"}]' + + results1 = generate_corr_json(corr_results=corr_results, this_trait=this_trait, + dataset=dataset, target_dataset=target_dataset, for_api=True) + self.assertEqual(expected_results, results1) + + def test_generate_corr_json_view_false(self): + trait = AttributeSetter({"view": False}) + corr_results = [trait] + this_trait = AttributeSetter({"name": "trait_test"}) + dataset = AttributeSetter({"name": "the_name"}) + + results_where_view_is_false = generate_corr_json( + corr_results=corr_results, this_trait=this_trait, dataset={}, target_dataset={}, for_api=False) + self.assertEqual(results_where_view_is_false, "[]") 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 b8c13ab4..fe2569b8 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -5,7 +5,6 @@ from unittest import mock from wqflask.marker_regression.gemma_mapping import run_gemma from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file from wqflask.marker_regression.gemma_mapping import gen_covariates_file -from wqflask.marker_regression.gemma_mapping import parse_gemma_output from wqflask.marker_regression.gemma_mapping import parse_loco_output @@ -69,11 +68,9 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), - mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] - mock_os.system.assert_has_calls(system_calls) + 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") + 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) @@ -138,31 +135,6 @@ class TestGemmaMapping(unittest.TestCase): 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("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") - def test_parse_gemma_output(self): - """add test for generating gemma output with obj returned""" - file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 -X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 -125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 -""" - with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, - {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] - mock_open.assert_called_once_with( - "/home/user/img/gema_file_output.assoc.txt") - self.assertEqual(results, expected) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_parse_gemma_output_with_empty_return(self): - """add tests for parse gemma output where nothing returned""" - output_file_results = """chr\t today""" - with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - self.assertEqual(results, []) - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.json") @@ -172,21 +144,26 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 "files": [["file_name", "user", "~/file1"], ["file_name", "user", "~/file2"]] } - return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" - return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" + 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_1).return_value, mock.mock_open(read_data=return_file_2).return_value) + 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': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { - 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + 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/snp_browser/__init__.py b/wqflask/tests/unit/wqflask/snp_browser/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/unit/wqflask/snp_browser/__init__.py diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py new file mode 100644 index 00000000..ce3e7b83 --- /dev/null +++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py @@ -0,0 +1,105 @@ +import unittest +from unittest import mock +from wqflask import app +from wqflask.snp_browser.snp_browser import get_gene_id +from wqflask.snp_browser.snp_browser import get_gene_id_name_dict +from wqflask.snp_browser.snp_browser import check_if_in_gene +from wqflask.snp_browser.snp_browser import get_browser_sample_lists +from 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("wqflask.snp_browser.snp_browser.g") + def test_get_gene_id(self, mock_db): + mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a" + db_query_value = """ + SELECT + geneId + FROM + GeneList + WHERE + SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR' + """ + results = get_gene_id( + species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR") + mock_db.db.execute.assert_called_once_with(db_query_value) + self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a") + + @mock.patch("wqflask.snp_browser.snp_browser.g") + def test_gene_id_name_dict(self, mock_db): + no_gene_names = [] + self.assertEqual("", get_gene_id_name_dict( + species_id="fregb343bui43g4", gene_name_list=no_gene_names)) + gene_name_list = ["GH1", "GH2", "GH3"] + mock_db.db.execute.return_value.fetchall.side_effect = [[], [("fsdf43-fseferger-f22", "GH1"), ("1sdf43-fsewferger-f22", "GH2"), + ("fwdj43-fstferger-f22", "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 = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3') + """ + mock_db.db.execute.assert_called_with(db_query_value) + self.assertEqual(results_found, expected_found) + self.assertEqual(no_results, {}) + + @mock.patch("wqflask.snp_browser.snp_browser.g") + def test_check_if_in_gene(self, mock_db): + mock_db.db.execute.return_value.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) + db_query_value = """SELECT geneId, geneSymbol + FROM GeneList + WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND + (txStart < 12.09 AND txEnd > 12.09); """ + gene_not_found = check_if_in_gene( + species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09) + mock_db.db.execute.assert_called_with(db_query_value) + self.assertEqual(gene_not_found, "") + + @mock.patch("wqflask.snp_browser.snp_browser.g") + def test_get_browser_sample_lists(self, mock_db): + mock_db.db.execute.return_value.fetchall.return_value = [] + + results = get_browser_sample_lists(species_id="12") + self.assertEqual(results, {'mouse': [], 'rat': []}) diff --git a/wqflask/tests/unit/wqflask/test_pbkdf2.py b/wqflask/tests/unit/wqflask/test_pbkdf2.py index a33fbd4f..7ad6c83e 100644 --- a/wqflask/tests/unit/wqflask/test_pbkdf2.py +++ b/wqflask/tests/unit/wqflask/test_pbkdf2.py @@ -11,43 +11,43 @@ class TestPbkdf2(unittest.TestCase): """ for password, salt, iterations, keylen, expected_value in [ - ('password', 'salt', 1, 20, + ('password', b'salt', 1, 20, '0c60c80f961f0e71f3a9b524af6012062fe037a6'), - ('password', 'salt', 2, 20, + ('password', b'salt', 2, 20, 'ea6c014dc72d6f8ccd1ed92ace1d41f0d8de8957'), - ('password', 'salt', 4096, 20, + ('password', b'salt', 4096, 20, '4b007901b765489abead49d926f721d065a429c1'), ('passwordPASSWORDpassword', - 'saltSALTsaltSALTsaltSALTsaltSALTsalt', + b'saltSALTsaltSALTsaltSALTsaltSALTsalt', 4096, 25, '3d2eec4fe41c849b80c8d83662c0e44a8b291a964cf2f07038'), - ('pass\x00word', 'sa\x00lt', 4096, 16, + ('pass\x00word', b'sa\x00lt', 4096, 16, '56fa6aa75548099dcc37d7f03425e0c3'), - ('password', 'ATHENA.MIT.EDUraeburn', 1, 16, + ('password', b'ATHENA.MIT.EDUraeburn', 1, 16, 'cdedb5281bb2f801565a1122b2563515'), - ('password', 'ATHENA.MIT.EDUraeburn', 1, 32, + ('password', b'ATHENA.MIT.EDUraeburn', 1, 32, ('cdedb5281bb2f80' '1565a1122b256351' '50ad1f7a04bb9f3a33' '3ecc0e2e1f70837')), - ('password', 'ATHENA.MIT.EDUraeburn', 2, 16, + ('password', b'ATHENA.MIT.EDUraeburn', 2, 16, '01dbee7f4a9e243e988b62c73cda935d'), - ('password', 'ATHENA.MIT.EDUraeburn', 2, 32, + ('password', b'ATHENA.MIT.EDUraeburn', 2, 32, ('01dbee7f4a9e243e9' '88b62c73cda935da05' '378b93244ec8f48a99' 'e61ad799d86')), - ('password', 'ATHENA.MIT.EDUraeburn', 1200, 32, + ('password', b'ATHENA.MIT.EDUraeburn', 1200, 32, ('5c08eb61fdf71e' '4e4ec3cf6ba1f55' '12ba7e52ddbc5e51' '42f708a31e2e62b1e13')), - ('X' * 64, 'pass phrase equals block size', 1200, 32, + ('X' * 64, b'pass phrase equals block size', 1200, 32, ('139c30c0966bc32ba' '55fdbf212530ac9c5' 'ec59f1a452f5cc9ad' '940fea0598ed1')), - ('X' * 65, 'pass phrase exceeds block size', 1200, 32, + ('X' * 65, b'pass phrase exceeds block size', 1200, 32, ('9ccad6d468770cd' '51b10e6a68721be6' '11a8b4d282601db3' diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py new file mode 100644 index 00000000..4f91d8ca --- /dev/null +++ b/wqflask/tests/unit/wqflask/test_server_side.py @@ -0,0 +1,31 @@ +import unittest + +from 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'}]) |