diff options
5 files changed, 93 insertions, 88 deletions
diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index ed72cb33..e47c8335 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -24,6 +24,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") def test_run_gemma_first_run_loco_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"})}) @@ -50,6 +51,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + """add tests for run_gemma where first run is set to true""" chromosomes = [] for i in range(1, 5): chromosomes.append(AttributeSetter({"name": f"CH{i}"})) @@ -81,6 +83,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("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={}, genofile_name="", vals=[ "x", "w", "q", "we", "R"], trait_filename="fitr.re") @@ -97,6 +100,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") @mock.patch("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 = [] @@ -138,6 +142,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") def test_parse_gemma_output_obj_returned(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 @@ -154,6 +159,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") def test_parse_gemma_output_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") @@ -162,6 +168,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_found(self, mock_os): + """add tests for parse loco output file found""" mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" pass @@ -169,6 +176,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): + """add tests for parse loco output file not found""" mock_os.path.isfile.return_value = False file_to_write = """{"files":["file_1","file_2"]}""" diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py index a5fa0c04..428f45b9 100644 --- a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py @@ -15,6 +15,7 @@ class AttributeSetter: class TestPlinkMapping(unittest.TestCase): def test_build_line_list(self): + """testing 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"] @@ -26,6 +27,7 @@ class TestPlinkMapping(unittest.TestCase): @mock.patch("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 @@ -41,6 +43,7 @@ Expected_2\there @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") @mock.patch("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"}) @@ -62,6 +65,7 @@ Expected_2\there @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") @mock.patch("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})}) diff --git a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py index 7ece663a..b47f877a 100644 --- a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -1,13 +1,12 @@ import unittest from unittest import mock from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file -from wqflask.marker_regression.qtlreaper_mapping import natural_sort #issues some methods in genofile object are not defined #modify samples should equal to vals class TestQtlReaperMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): + def test_gen_pheno_txt_file(self): vals=["V1","x","V4","V3","x"] samples=["S1","S2","S3","S4","S5"] trait_filename="trait_file" diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py index 641644cc..9fd32a30 100644 --- a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py @@ -18,23 +18,15 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") def test_get_trait_data_type_found(self,mock_logger,mock_db): + """test for getting trait data_type return True""" caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results=get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(caller_value) self.assertEqual(results,"fer434f") - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data_type_not_found(self,mock_logger,mock_db): - caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("other") - mock_db.db.execute.assert_called_with(caller_value) - self.assertEqual(results,"numeric") - def test_sanitize_rqtl_phenotype(self): + """test for sanitizing rqtl phenotype""" vals=['f',"x","r","x","x"] results=sanitize_rqtl_phenotype(vals) expected_phenotype_string='c(f,NA,r,NA,NA)' @@ -42,6 +34,7 @@ class TestRqtlMapping(unittest.TestCase): self.assertEqual(results,expected_phenotype_string) def test_sanitize_rqtl_names(self): + """test for sanitzing rqtl names""" vals=['f',"x","r","x","x"] expected_sanitized_name="c('f',NA,'r',NA,NA)" results=sanitize_rqtl_names(vals) diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index be6e6e48..2af4c3e3 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -28,24 +28,24 @@ class TestRunMapping(unittest.TestCase): self.group = MockDataSetGroup( {"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" - }) - } + 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": "dataser_1", "group": self.group, "type": "ProbeSet"}) - self.chromosomes=AttributeSetter({"chromosomes":chromosomes}) + self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) self.trait = AttributeSetter( {"symbol": "IGFI", "chr": "X1", "mb": 123313}) @@ -142,6 +142,7 @@ class TestRunMapping(unittest.TestCase): 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) @@ -206,78 +207,78 @@ class TestRunMapping(unittest.TestCase): filehandler = mock_open() filehandler.write.assert_has_calls(write_calls) - @mock.patch("wqflask.marker_regression.run_mapping.random.choice") - def test_write_input_for_browser(self,mock_choice): - 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_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" + 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" + }, + "S2": { + "W1": "w2_value", + "W2": "w2_value" - }, - "S3":{ + }, + "S3": { - "C1":"c1_value", - "C2":"c2_value" + "C1": "c1_value", + "C2": "c2_value" - }, - - }}) + }, - results=get_perm_strata(this_trait={},sample_list=sample_list,categorical_vars=categorical_vars,used_samples=used_samples) - self.assertEqual(results,[2,1]) + }}) + results = get_perm_strata(this_trait={}, sample_list=sample_list, + categorical_vars=categorical_vars, used_samples=used_samples) + self.assertEqual(results, [2, 1]) def test_get_chr_length(self): - 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.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) + """test for getting chromosome length""" + 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.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) |