diff options
Diffstat (limited to 'wqflask/tests/unit')
3 files changed, 46 insertions, 45 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py index b094294a..159c982b 100644 --- a/wqflask/tests/unit/wqflask/api/test_mapping.py +++ b/wqflask/tests/unit/wqflask/api/test_mapping.py @@ -58,7 +58,7 @@ class TestMapping(unittest.TestCase): self.assertEqual(results_2, expected_results) - @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno") + @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl") @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma") @mock.patch("wqflask.api.mapping.initialize_parameters") @mock.patch("wqflask.api.mapping.retrieve_sample_data") 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..9d13e943 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 +1,43 @@ 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 dataclasses import dataclass +from wqflask.marker_regression.rqtl_mapping import run_rqtl -class TestRqtlMapping(unittest.TestCase): +@dataclass +class MockGroup: + name: str + genofile: str + +@dataclass +class MockDataset: + group: MockGroup - 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) +class TestRqtlMapping(unittest.TestCase): + """Tests for functions in rqtl_mapping.py""" + @mock.patch("wqflask.marker_regression.rqtl_mapping.requests.post") + @mock.patch("wqflask.marker_regression.rqtl_mapping.locate") + @mock.patch("wqflask.marker_regression.rqtl_mapping.write_phenotype_file") + def test_run_rqtl_with_perm(self, mock_write_pheno_file, mock_locate, mock_post): + """Test for run_rqtl with permutations > 0""" + dataset_group = MockGroup("GP1", "file_geno") + dataset = MockDataset(dataset_group) + + mock_write_pheno_file.return_value = "pheno_filename" + mock_locate.return_value = "geno_filename" + mock_post.return_value = mock.Mock(ok=True) + mock_post.return_value.json.return_value = {"perm_results": [], + "suggestive": 3, + "significant": 4, + "results" : []} + + 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() + + self.assertEqual(results, ([], 3, 4, [])) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py index 78cd3be9..c220a072 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -229,20 +229,20 @@ class TestRunMapping(unittest.TestCase): used_samples = ["S1", "S2"] sample_list = AttributeSetter({"sample_attribute_values": { "S1": { - "C1": "c1_value", - "C2": "c2_value", - "W1": "w1_value" + "c1": "c1_value", + "c2": "c2_value", + "w1": "w1_value" }, "S2": { - "W1": "w2_value", - "W2": "w2_value" + "w1": "w2_value", + "w2": "w2_value" }, "S3": { - "C1": "c1_value", - "C2": "c2_value" + "c1": "c1_value", + "c2": "c2_value" }, |