diff options
| -rw-r--r-- | wqflask/tests/unit/wqflask/api/test_mapping.py | 154 |
1 files changed, 75 insertions, 79 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py index 5455b215..b094294a 100644 --- a/wqflask/tests/unit/wqflask/api/test_mapping.py +++ b/wqflask/tests/unit/wqflask/api/test_mapping.py @@ -5,108 +5,104 @@ from wqflask.api.mapping import do_mapping_for_api class AttributeSetter: - def __init__(self,obj): - for key,value in obj.items(): - setattr(self,key,value) + def __init__(self, obj): + for key, value in obj.items(): + setattr(self, key, value) + class MockGroup(AttributeSetter): def get_marker(self): - self.markers=[] + self.markers = [] + + class TestMapping(unittest.TestCase): - + def test_initialize_parameters(self): - expected_results={ - "format":"json", - "limit_to":False, - "mapping_method":"gemma", - "maf":0.01, - "use_loco":True, - "num_perm":0, - "perm_check":False + expected_results = { + "format": "json", + "limit_to": False, + "mapping_method": "gemma", + "maf": 0.01, + "use_loco": True, + "num_perm": 0, + "perm_check": False } - results=initialize_parameters(start_vars={},dataset={},this_trait={}) - self.assertEqual(results,expected_results) + results = initialize_parameters( + start_vars={}, dataset={}, this_trait={}) + self.assertEqual(results, expected_results) - start_vars={ - "format":"F1", - "limit_to":"1", - "mapping_method":"rqtl", - "control_marker":True, - "pair_scan":"true", - "interval_mapping":"true", - "use_loco":"true", - "num_perm":"14" + start_vars = { + "format": "F1", + "limit_to": "1", + "mapping_method": "rqtl", + "control_marker": True, + "pair_scan": "true", + "interval_mapping": "true", + "use_loco": "true", + "num_perm": "14" } - results_2=initialize_parameters(start_vars=start_vars,dataset={},this_trait={}) - expected_results={ - "format":"F1", - "limit_to":1, - "mapping_method":"gemma", - "maf":0.01, - "use_loco":True, - "num_perm":14, - "perm_check":"ON" + results_2 = initialize_parameters( + start_vars=start_vars, dataset={}, this_trait={}) + expected_results = { + "format": "F1", + "limit_to": 1, + "mapping_method": "gemma", + "maf": 0.01, + "use_loco": True, + "num_perm": 14, + "perm_check": "ON" } - self.assertEqual(results_2,expected_results) + self.assertEqual(results_2, expected_results) - @mock.patch("wqflask.api.mapping.rqtl_mapping.run_rqtl_geno") @mock.patch("wqflask.api.mapping.gemma_mapping.run_gemma") @mock.patch("wqflask.api.mapping.initialize_parameters") @mock.patch("wqflask.api.mapping.retrieve_sample_data") @mock.patch("wqflask.api.mapping.create_trait") @mock.patch("wqflask.api.mapping.data_set.create_dataset") - def test_do_mapping_for_api(self,mock_create_dataset,mock_trait,mock_retrieve_sample,mock_param,run_gemma - ,run_rqtl_geno): - start_vars={ - "db":"Temp", - "trait_id":"dewf3232rff2", - "format":"F1", - "mapping_method":"gemma", - "use_loco":True + def test_do_mapping_for_api(self, mock_create_dataset, mock_trait, mock_retrieve_sample, mock_param, run_gemma, run_rqtl_geno): + start_vars = { + "db": "Temp", + "trait_id": "dewf3232rff2", + "format": "F1", + "mapping_method": "gemma", + "use_loco": True } - sampleList=["S1","S2","S3","S4"] - samplelist=["S1","S2","S4"] - dataset=AttributeSetter({"group":samplelist}) - this_trait=AttributeSetter({}) - trait_data=AttributeSetter({ - "data":{ - "item1":AttributeSetter({"name":"S1","value":"S1_value"}), - "item2":AttributeSetter({"name":"S2","value":"S2_value"}), - "item3":AttributeSetter({"name":"S3","value":"S3_value"}), + sampleList = ["S1", "S2", "S3", "S4"] + samplelist = ["S1", "S2", "S4"] + dataset = AttributeSetter({"group": samplelist}) + this_trait = AttributeSetter({}) + trait_data = AttributeSetter({ + "data": { + "item1": AttributeSetter({"name": "S1", "value": "S1_value"}), + "item2": AttributeSetter({"name": "S2", "value": "S2_value"}), + "item3": AttributeSetter({"name": "S3", "value": "S3_value"}), } - }) - trait=AttributeSetter({ - "data":trait_data - }) - - dataset.return_value=dataset - mock_trait.return_value=this_trait - - mock_retrieve_sample.return_value=trait - mock_param.return_value={ - "format":"F1", - "limit_to":False, - "mapping_method":"gemma", - "maf":0.01, - "use_loco":"True", - "num_perm":14, - "perm_check":"ON" + }) + trait = AttributeSetter({ + "data": trait_data + }) + + dataset.return_value = dataset + mock_trait.return_value = this_trait + + mock_retrieve_sample.return_value = trait + mock_param.return_value = { + "format": "F1", + "limit_to": False, + "mapping_method": "gemma", + "maf": 0.01, + "use_loco": "True", + "num_perm": 14, + "perm_check": "ON" } - run_gemma.return_value=["results"] - results=do_mapping_for_api(start_vars=start_vars) - self.assertEqual(results,("results",None)) - - - - - - - + run_gemma.return_value = ["results"] + results = do_mapping_for_api(start_vars=start_vars) + self.assertEqual(results, ("results", None)) |