pep8 formatting in wqflask/api/test_mapping.py

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))