diff options
| -rw-r--r-- | wqflask/tests/unit/wqflask/api/test_mapping.py | 145 |
1 files changed, 99 insertions, 46 deletions
diff --git a/wqflask/tests/unit/wqflask/api/test_mapping.py b/wqflask/tests/unit/wqflask/api/test_mapping.py index 4da1725f..5455b215 100644 --- a/wqflask/tests/unit/wqflask/api/test_mapping.py +++ b/wqflask/tests/unit/wqflask/api/test_mapping.py @@ -1,57 +1,110 @@ import unittest from unittest import mock from wqflask.api.mapping import initialize_parameters +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): - return None -class TestMock(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 - } - - 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" - - } - - 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) - + def get_marker(self): + 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 + } + + 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" + + } + + 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) + + + @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 + + } + 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" + } + + run_gemma.return_value=["results"] + results=do_mapping_for_api(start_vars=start_vars) + self.assertEqual(results,("results",None)) + + |