add tests for export_mapping_results in marker_regression/run_mapping.py

1 files changed, 167 insertions, 25 deletions

diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
index bba9de05..e925ad28 100644
--- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py
@@ -1,45 +1,187 @@
 import unittest
+import datetime
 from unittest import mock
+
 from wqflask.marker_regression.run_mapping import get_genofile_samplelist
 from wqflask.marker_regression.run_mapping import geno_db_exists
 from wqflask.marker_regression.run_mapping import write_input_for_browser
+from wqflask.marker_regression.run_mapping import export_mapping_results
+from wqflask.marker_regression.run_mapping import trim_markers_for_figure
+
 
 class AttributeSetter:
-	def __init__(self,obj):
-		for k,v in obj.items():
-			setattr(self,k,v)
+    def __init__(self, obj):
+        for k, v in obj.items():
+            setattr(self, k, v)
 
 
 class MockDataSetGroup(AttributeSetter):
-	
-	def get_genofiles(self):
-		return [{"location":"~/genofiles/g1_file","sample_list":["S1","S2","S3","S4"]}]
+
+    def get_genofiles(self):
+        return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}]
+
+
 class TestRunMapping(unittest.TestCase):
-	def setUp(self):
-		self.group=MockDataSetGroup({"genofile":"~/genofiles/g1_file","name":"GP1_"})
-		self.dataset=AttributeSetter({"group":self.group})
+    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})
+
+    def tearDown(self):
+        self.dataset = AttributeSetter(
+            {"group": {"location": "~/genofiles/g1_file"}})
+
+    def test_get_genofile_samplelist(self):
+
+        results_1 = get_genofile_samplelist(self.dataset)
+        self.assertEqual(results_1, ["S1", "S2", "S3", "S4"])
+        self.group.genofile = "~/genofiles/g2_file"
+        result_2 = get_genofile_samplelist(self.dataset)
+        self.assertEqual(result_2, [])
+
+    @mock.patch("wqflask.marker_regression.run_mapping.data_set")
+    def test_geno_db_exists(self, mock_data_set):
+        mock_data_set.create_dataset.side_effect = [
+            AttributeSetter({}), Exception()]
+        results_no_error = geno_db_exists(self.dataset)
+        results_with_error = geno_db_exists(self.dataset)
+
+        self.assertEqual(mock_data_set.create_dataset.call_count, 2)
+        self.assertEqual(results_with_error, "False")
+        self.assertEqual(results_no_error, "True")
+
+    
+    def test_trim_markers_for_figure(self):
 
-	def tearDown(self):
-		self.dataset=AttributeSetter({"group":{"location":"~/genofiles/g1_file"}})
 
-	def test_get_genofile_samplelist(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
+    	}]
 
-		results_1=get_genofile_samplelist(self.dataset)
-		self.assertEqual(results_1,["S1","S2","S3","S4"])
-		self.group.genofile="~/genofiles/g2_file"
-		result_2=get_genofile_samplelist(self.dataset)
-		self.assertEqual(result_2,[])
+    	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
+    	}
 
-	@mock.patch("wqflask.marker_regression.run_mapping.data_set")
-	def test_geno_db_exists(self,mock_data_set):
-		mock_data_set.create_dataset.side_effect=[AttributeSetter({}),Exception()]
-		results_no_error=geno_db_exists(self.dataset)
-		results_with_error=geno_db_exists(self.dataset)
+    	]
+    	self.assertEqual(results,expected)
+    	self.assertEqual(result_2,marker_2)
 
-		self.assertEqual(mock_data_set.create_dataset.call_count,2)
-		self.assertEqual(results_with_error,"False")
-		self.assertEqual(results_no_error,"True")
+    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