add tests for write input for browser in marker_regression/run_mapping.py

1 files changed, 144 insertions, 133 deletions

diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
index e925ad28..6521c41d 100644
--- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
@@ -24,9 +24,11 @@ class MockDataSetGroup(AttributeSetter):
 class TestRunMapping(unittest.TestCase):
     def setUp(self):
         self.group = MockDataSetGroup(
-            {"genofile": "~/genofiles/g1_file", "name": "GP1_","species":"Human"})
-        self.dataset = AttributeSetter({"fullname":"dataser_1","group": self.group,"type":"ProbeSet"})
-        self.trait=AttributeSetter({"symbol":"IGFI","chr":"X1","mb":123313})
+            {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"})
+        self.dataset = AttributeSetter(
+            {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"})
+        self.trait = AttributeSetter(
+            {"symbol": "IGFI", "chr": "X1", "mb": 123313})
 
     def tearDown(self):
         self.dataset = AttributeSetter(
@@ -51,137 +53,146 @@ class TestRunMapping(unittest.TestCase):
         self.assertEqual(results_with_error, "False")
         self.assertEqual(results_no_error, "True")
 
-    
     def test_trim_markers_for_figure(self):
 
-
-    	markers=[{
-    	"name":"MK1",
-    	"chr":"C1",
-    	"cM":"1",
-    	"Mb":"12000",
-    	"genotypes":[],
-    	"dominance":"TT",
-    	"additive":"VA",
-    	"lod_score":0.5
-    	},
-    	{
-    	"name":"MK2",
-    	"chr":"C2",
-    	"cM":"15",
-    	"Mb":"10000",
-    	"genotypes":[],
-    	"lod_score":0.7
-    	},
-    	{
-    	"name":"MK1",
-    	"chr":"C3",
-    	"cM":"45",
-    	"Mb":"1",
-    	"genotypes":[],
-    	"dominance":"Tt",
-    	"additive":"VE",
-    	"lod_score":1
-    	}]
-
-    	marker_2=[{
-    	"name":"MK1",
-    	"chr":"C1",
-    	"cM":"1",
-    	"Mb":"12000",
-    	"genotypes":[],
-    	"dominance":"TT",
-    	"additive":"VA",
-    	"p_wald":4.6
-    	}]
-    	results=trim_markers_for_figure(markers)
-    	result_2=trim_markers_for_figure(marker_2)
-    	expected=[
-    	{
-    	"name":"MK1",
-    	"chr":"C1",
-    	"cM":"1",
-    	"Mb":"12000",
-    	"genotypes":[],
-    	"dominance":"TT",
-    	"additive":"VA",
-    	"lod_score":0.5
-    	},
-    	{
-    	"name":"MK1",
-    	"chr":"C3",
-    	"cM":"45",
-    	"Mb":"1",
-    	"genotypes":[],
-    	"dominance":"Tt",
-    	"additive":"VE",
-    	"lod_score":1
-    	}
-
-    	]
-    	self.assertEqual(results,expected)
-    	self.assertEqual(result_2,marker_2)
+        markers = [{
+            "name": "MK1",
+            "chr": "C1",
+            "cM": "1",
+            "Mb": "12000",
+            "genotypes": [],
+            "dominance":"TT",
+            "additive":"VA",
+            "lod_score":0.5
+        },
+            {
+            "name": "MK2",
+            "chr": "C2",
+            "cM": "15",
+            "Mb": "10000",
+            "genotypes": [],
+            "lod_score":0.7
+        },
+            {
+            "name": "MK1",
+            "chr": "C3",
+            "cM": "45",
+            "Mb": "1",
+            "genotypes": [],
+            "dominance":"Tt",
+            "additive":"VE",
+            "lod_score":1
+        }]
+
+        marker_2 = [{
+            "name": "MK1",
+            "chr": "C1",
+            "cM": "1",
+            "Mb": "12000",
+            "genotypes": [],
+            "dominance":"TT",
+            "additive":"VA",
+            "p_wald":4.6
+        }]
+        results = trim_markers_for_figure(markers)
+        result_2 = trim_markers_for_figure(marker_2)
+        expected = [
+            {
+                "name": "MK1",
+                "chr": "C1",
+                "cM": "1",
+                "Mb": "12000",
+                "genotypes": [],
+                "dominance":"TT",
+                "additive":"VA",
+                "lod_score":0.5
+            },
+            {
+                "name": "MK1",
+                "chr": "C3",
+                "cM": "45",
+                "Mb": "1",
+                "genotypes": [],
+                "dominance":"Tt",
+                "additive":"VE",
+                "lod_score":1
+            }
+
+        ]
+        self.assertEqual(results, expected)
+        self.assertEqual(result_2, marker_2)
 
     def test_export_mapping_results(self):
-    	datetime_mock=mock.Mock(wraps=datetime.datetime)
-    	datetime_mock.now.return_value=datetime.datetime(2019,9,1,10,12,12)
-
-    	markers=[{
-    	"name":"MK1",
-    	"chr":"C1",
-    	"cM":"1",
-    	"Mb":"12000",
-    	"genotypes":[],
-    	"dominance":"TT",
-    	"additive":"VA",
-    	"lod_score":3
-    	},
-    	{
-    	"name":"MK2",
-    	"chr":"C2",
-    	"cM":"15",
-    	"Mb":"10000",
-    	"genotypes":[],
-    	"lod_score":7
-    	},
-    	{
-    	"name":"MK1",
-    	"chr":"C3",
-    	"cM":"45",
-    	"Mb":"1",
-    	"genotypes":[],
-    	"dominance":"Tt",
-    	"additive":"VE",
-    	"lod_score":7
-    	}]
-
-    	with mock.patch("builtins.open", mock.mock_open()) as mock_open:
-    		
-    		# mock_open.assert_called_once_with("~/results","w+")
-    		# filehandler=mock_open()
-    		with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime",new=datetime_mock):
-    			export_mapping_results(dataset=self.dataset,trait=self.trait,markers=markers,results_path="~/results",mapping_scale="physic",score_type="-log(p)")
-
-    		
-	    		write_calls=[
-	    		mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
-	    		 mock.call('Population: Human GP1_\n'),mock.call('Data Set: dataser_1\n'),
-				 mock.call('Gene Symbol: IGFI\n'), mock.call('Location: X1 @ 123313 Mb\n'),
-				 mock.call('\n'), mock.call('Name,Chr,'),
-				 mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
-				 mock.call(',Additive'),mock.call(',Dominance'),
-				 mock.call('\n'),mock.call('MK1,C1,'),
-				 mock.call('12000,'), mock.call('1,'),
-				 mock.call('3'), mock.call(',VA'),
-				 mock.call(',TT'),mock.call('\n'),
-				 mock.call('MK2,C2,'),mock.call('10000,'),
-				 mock.call('15,'), mock.call('7'),
-				 mock.call('\n'), mock.call('MK1,C3,'),
-				 mock.call('1,'),mock.call('45,'),
-				 mock.call('7'), mock.call(',VE'),
-				 mock.call(',Tt')
-
-	    		]
-	    		mock_open.assert_called_once_with("~/results","w+")
-	    		filehandler=mock_open()
-	    		filehandler.write.assert_has_calls(write_calls)
\ No newline at end of file
+        datetime_mock = mock.Mock(wraps=datetime.datetime)
+        datetime_mock.now.return_value = datetime.datetime(
+            2019, 9, 1, 10, 12, 12)
+
+        markers = [{
+            "name": "MK1",
+            "chr": "C1",
+            "cM": "1",
+            "Mb": "12000",
+            "genotypes": [],
+            "dominance":"TT",
+            "additive":"VA",
+            "lod_score":3
+        },
+            {
+            "name": "MK2",
+            "chr": "C2",
+            "cM": "15",
+            "Mb": "10000",
+            "genotypes": [],
+            "lod_score":7
+        },
+            {
+            "name": "MK1",
+            "chr": "C3",
+            "cM": "45",
+            "Mb": "1",
+            "genotypes": [],
+            "dominance":"Tt",
+            "additive":"VE",
+            "lod_score":7
+        }]
+
+        with mock.patch("builtins.open", mock.mock_open()) as mock_open:
+
+            with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock):
+                export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers,
+                                       results_path="~/results", mapping_scale="physic", score_type="-log(p)")
+
+                write_calls = [
+                    mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
+                    mock.call('Population: Human GP1_\n'), mock.call(
+                        'Data Set: dataser_1\n'),
+                    mock.call('Gene Symbol: IGFI\n'), mock.call(
+                        'Location: X1 @ 123313 Mb\n'),
+                    mock.call('\n'), mock.call('Name,Chr,'),
+                    mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'),
+                    mock.call(',Additive'), mock.call(',Dominance'),
+                    mock.call('\n'), mock.call('MK1,C1,'),
+                    mock.call('12000,'), mock.call('1,'),
+                    mock.call('3'), mock.call(',VA'),
+                    mock.call(',TT'), mock.call('\n'),
+                    mock.call('MK2,C2,'), mock.call('10000,'),
+                    mock.call('15,'), mock.call('7'),
+                    mock.call('\n'), mock.call('MK1,C3,'),
+                    mock.call('1,'), mock.call('45,'),
+                    mock.call('7'), mock.call(',VE'),
+                    mock.call(',Tt')
+
+                ]
+                mock_open.assert_called_once_with("~/results", "w+")
+                filehandler = mock_open()
+                filehandler.write.assert_has_calls(write_calls)
+
+
+    @mock.patch("wqflask.marker_regression.run_mapping.random.choice")
+    def test_write_input_for_browser(self,mock_choice):
+    	mock_choice.side_effect=["F","i","l","e","s","x"]
+    	with mock.patch("builtins.open",mock.mock_open()) as mock_open:
+    		expected=['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT']
+
+    		results=write_input_for_browser(this_dataset=self.dataset,gwas_results={},annotations={})
+    		self.assertEqual(results,expected)