From 6b885b0b4dcdfed744b1996bd767bb9f20fdf633 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Sat, 5 Dec 2020 13:35:43 +0300 Subject: modify tests for run_gemma --- .../unit/wqflask/marker_regression/test_gemma_mapping.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) (limited to 'wqflask/tests') 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 5b621264..3d00dd7c 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -43,18 +43,18 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - @mock.patch("wqflask.marker_regression.gemma_mapping.logger") @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco): """add tests for run_gemma where first run is set to true""" - chromosomes = [] + this_chromosomes={} for i in range(1, 5): - chromosomes.append(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": chromosomes}) + this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"})) + chromo = AttributeSetter({"chromosomes": this_chromosomes}) + dataset_group = MockGroup( {"name": "GP1", "genofile": "file_geno"}) dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", @@ -76,7 +76,6 @@ class TestGemmaMapping(unittest.TestCase): mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count, 2) self.assertEqual(mock_flat_files.call_count, 4) self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) -- cgit v1.2.3 From 54fc88f3f0f4966608fccdba76b49871eef50553 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Sat, 5 Dec 2020 13:43:23 +0300 Subject: add pep8 formatting --- wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'wqflask/tests') 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 3d00dd7c..b8c13ab4 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -53,12 +53,12 @@ class TestGemmaMapping(unittest.TestCase): this_chromosomes={} for i in range(1, 5): this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": this_chromosomes}) + chromosomes = AttributeSetter({"chromosomes": this_chromosomes}) dataset_group = MockGroup( {"name": "GP1", "genofile": "file_geno"}) dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", - "species": AttributeSetter({"chromosomes": chromo})}) + "species": AttributeSetter({"chromosomes": chromosomes})}) trait = AttributeSetter({"name": "trait1"}) samples = [] mock_gen_pheno_txt.return_value = None -- cgit v1.2.3