add test for map_api in api/test_mapping.py

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))
+
+