diff options
Diffstat (limited to 'wqflask/tests')
| -rw-r--r-- | wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py | 76 |
1 files changed, 40 insertions, 36 deletions
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 91d2c587..5c679c05 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -1,42 +1,46 @@ import unittest from unittest import mock -from wqflask import app -from wqflask.marker_regression.rqtl_mapping import get_trait_data_type -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names +from wqflask.marker_regression.rqtl_mapping import run_rqtl +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + +class MockGroup(AttributeSetter): + def get_samplelist(self): + return None 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) + @mock.patch("wqflask.marker_regression.rqtl_mapping.process_rqtl_results") + @mock.patch("wqflask.marker_regression.rqtl_mapping.process_perm_results") + @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post") + @mock.patch("wqflask.marker_regression.rqtl_mapping.locate") + @mock.patch("wqflask.marker_regression.gemma_mapping.write_phenotype_file") + def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post, mock_process_perm, mock_process_rqtl): + """Test for run_rqtl with permutations > 0""" + dataset_group = MockGroup( + {"name": "GP1", "genofile": "file_geno"}) + + dataset = AttributeSetter({"group": dataset_group}) + + mock_write_pheno_file.return_value = "pheno_filename" + mock_locate.return_value = "geno_filename" + + mock_post.return_value = "output_filename" + + mock_process_perm.return_value = [[], 3, 4] + mock_process_rqtl.return_value = [] + + results = run_rqtl(trait_name="the_trait", vals=[], samples=[], + dataset=dataset, 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() + mock_process_perm.assert_called_once() + mock_process_rqtl.assert_called_once() + self.assertEqual(results, ([], 3, 4, []))
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