diff options
Diffstat (limited to 'wqflask/tests/unit')
| -rw-r--r-- | wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py | 26 | ||||
| -rw-r--r-- | wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py | 64 |
2 files changed, 45 insertions, 45 deletions
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py index 1198740d..47377873 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -7,17 +7,17 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file class TestQtlReaperMapping(unittest.TestCase): - @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals = ["V1", "x", "V4", "V3","x"] - samples = ["S1", "S2", "S3", "S4","S5"] - trait_filename = "trait_file" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples, vals=vals, - trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") - filehandler = mock_open() - write_calls = [mock.call('Trait\t'), mock.call( - 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] + @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + vals = ["V1", "x", "V4", "V3","x"] + samples = ["S1", "S2", "S3", "S4","S5"] + trait_filename = "trait_file" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(samples=samples, vals=vals, + trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w") + filehandler = mock_open() + write_calls = [mock.call('Trait\t'), mock.call( + 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')] - filehandler.write.assert_has_calls(write_calls) + filehandler.write.assert_has_calls(write_calls) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index d69a20d3..e518ec22 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -8,35 +8,35 @@ from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names class TestRqtlMapping(unittest.TestCase): - def setUp(self): - self.app_context = app.app_context() - self.app_context.push() - - def tearDown(self): - self.app_context.pop() - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self, mock_logger, mock_db): - """test for getting trait data_type return True""" - query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value = [ - """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results = get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(query_value) - self.assertEqual(results, "fer434f") - - def test_sanitize_rqtl_phenotype(self): - """test for sanitizing rqtl phenotype""" - vals = ['f', "x", "r", "x","x"] - results = sanitize_rqtl_phenotype(vals) - expected_phenotype_string = 'c(f,NA,r,NA,NA)' - - self.assertEqual(results, expected_phenotype_string) - - def test_sanitize_rqtl_names(self): - """test for sanitzing rqtl names""" - vals = ['f', "x", "r", "x","x"] - expected_sanitized_name = "c('f',NA,'r',NA,NA)" - results = sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name, results) + def setUp(self): + self.app_context = app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + @mock.patch("wqflask.marker_regression.rqtl_mapping.g") + @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") + def test_get_trait_data(self, mock_logger, mock_db): + """test for getting trait data_type return True""" + query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value = [ + """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results = get_trait_data_type("traid_id") + mock_db.db.execute.assert_called_with(query_value) + self.assertEqual(results, "fer434f") + + def test_sanitize_rqtl_phenotype(self): + """test for sanitizing rqtl phenotype""" + vals = ['f', "x", "r", "x","x"] + results = sanitize_rqtl_phenotype(vals) + expected_phenotype_string = 'c(f,NA,r,NA,NA)' + + self.assertEqual(results, expected_phenotype_string) + + def test_sanitize_rqtl_names(self): + """test for sanitzing rqtl names""" + vals = ['f', "x", "r", "x","x"] + expected_sanitized_name = "c('f',NA,'r',NA,NA)" + results = sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name, results) |