pep8 formatting and refactoring tests

1 files changed, 79 insertions, 66 deletions

diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index cbcd006d..d0264b87 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -1,7 +1,7 @@
 import unittest
 from unittest import mock
 from wqflask import app
-from collections import OrderedDict 
+from collections import OrderedDict
 from wqflask.api.correlation import init_corr_params
 from wqflask.api.correlation import convert_to_mouse_gene_id
 from wqflask.api.correlation import do_literature_correlation_for_all_traits
@@ -14,14 +14,16 @@ class AttributeSetter:
         for k, v in obj.items():
             setattr(self, k, v)
 
+
 class MockDataset(AttributeSetter):
     def get_trait_data(self):
         return None
-    def retrieve_genes(self,id=None):
+
+    def retrieve_genes(self, id=None):
         return {
-         "TT-1":"GH-1",
-         "TT-2":"GH-2",
-         "TT-3":"GH-3"
+            "TT-1": "GH-1",
+            "TT-2": "GH-2",
+            "TT-3": "GH-3"
 
         }
 
@@ -59,8 +61,9 @@ class TestCorrelations(unittest.TestCase):
         rat_species_results = convert_to_mouse_gene_id(
             species="rat", gene_id="GH1")
 
-        mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter({"mouse": "MG-1"}),AttributeSetter({"mouse":"MG-2"})]
-                                          
+        mock_db.db.execute.return_value.fetchone.side_effect = [
+            AttributeSetter({"mouse": "MG-1"}), AttributeSetter({"mouse": "MG-2"})]
+
         self.assertEqual(convert_to_mouse_gene_id(
             species="mouse", gene_id="MG-4"), "MG-4")
         self.assertEqual(convert_to_mouse_gene_id(
@@ -68,73 +71,83 @@ class TestCorrelations(unittest.TestCase):
         self.assertEqual(convert_to_mouse_gene_id(
             species="human", gene_id="H1"), "MG-2")
 
-    
-    
     @mock.patch("wqflask.api.correlation.g")
     @mock.patch("wqflask.api.correlation.convert_to_mouse_gene_id")
-    def test_do_literature_correlation_for_all_traits(self,mock_convert_to_mouse_geneid,mock_db):
-    	mock_convert_to_mouse_geneid.side_effect=["MG-1","MG-2;","MG-3","MG-4"]
-   
-
-    	trait_geneid_dict={
-    	 "TT-1":"GH-1",
-    	 "TT-2":"GH-2",
-    	 "TT-3":"GH-3"
+    def test_do_literature_correlation_for_all_traits(self, mock_convert_to_mouse_geneid, mock_db):
+        mock_convert_to_mouse_geneid.side_effect = [
+            "MG-1", "MG-2;", "MG-3", "MG-4"]
 
-    	}
-    	mock_db.db.execute.return_value.fetchone.side_effect=[AttributeSetter({"value":"V1"}),AttributeSetter({"value":"V2"}),AttributeSetter({"value":"V3"})]
+        trait_geneid_dict = {
+            "TT-1": "GH-1",
+            "TT-2": "GH-2",
+            "TT-3": "GH-3"
 
+        }
+        mock_db.db.execute.return_value.fetchone.side_effect = [AttributeSetter(
+            {"value": "V1"}), AttributeSetter({"value": "V2"}), AttributeSetter({"value": "V3"})]
 
-    	this_trait=AttributeSetter({"geneid":"GH-1"})
+        this_trait = AttributeSetter({"geneid": "GH-1"})
 
-    	target_dataset=AttributeSetter({"group":AttributeSetter({"species":"rat"})})
-    	results=do_literature_correlation_for_all_traits(this_trait=this_trait,target_dataset=target_dataset,trait_geneid_dict=trait_geneid_dict,corr_params={})
+        target_dataset = AttributeSetter(
+            {"group": AttributeSetter({"species": "rat"})})
+        results = do_literature_correlation_for_all_traits(
+            this_trait=this_trait, target_dataset=target_dataset, trait_geneid_dict=trait_geneid_dict, corr_params={})
 
-    	expected_results={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
-    	self.assertEqual(results,expected_results)
+        expected_results = {'TT-1': ['GH-1', 0],
+                            'TT-2': ['GH-2', 'V1'], 'TT-3': ['GH-3', 'V2']}
+        self.assertEqual(results, expected_results)
 
     @mock.patch("wqflask.api.correlation.corr_result_helpers.normalize_values")
-    def test_get_sample_r_and_p_values(self,mock_normalize):
-
-        group=AttributeSetter({"samplelist":["S1","S2","S3","S4","S5","S6","S7"]})
-        target_dataset=AttributeSetter({"group":group})
-
-        target_vals=[3.4, 6.2, 4.1,3.4,1.2,5.6]
-        trait_data={"S1":AttributeSetter({"value":2.3}),"S2":AttributeSetter({"value":1.1}),"S3":AttributeSetter({"value":6.3}),"S4":AttributeSetter({"value":3.6}),"S5":AttributeSetter({"value":4.1}),"S6":AttributeSetter({"value":5.0})}
-        this_trait=AttributeSetter({"data":trait_data})
-        mock_normalize.return_value=([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6)
-        mock_normalize.side_effect=[([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,6.3,3.6,4.1,5.0], [3.4,6.2,4.1,3.4,1.2,5.6], 6),([2.3,1.1,1.4], [3.4,6.2,4.1], 3)]
-
-        results_pearsonr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
-        results_spearmanr=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="spearman")
-        results_num_overlap=get_sample_r_and_p_values(this_trait=this_trait,this_dataset={},target_vals=target_vals,target_dataset=target_dataset,type="pearson")
-        expected_pearsonr=[-0.21618688834430866, 0.680771605997119, 6]
-        expected_spearmanr=[-0.11595420713048969, 0.826848213385815, 6]
-        for i,val in enumerate(expected_pearsonr):
-            self.assertAlmostEqual(val,results_pearsonr[i])
-        for i,val in enumerate(expected_spearmanr):
-            self.assertAlmostEqual(val,results_spearmanr[i])
-        self.assertEqual(results_num_overlap,None)
+    def test_get_sample_r_and_p_values(self, mock_normalize):
+
+        group = AttributeSetter(
+            {"samplelist": ["S1", "S2", "S3", "S4", "S5", "S6", "S7"]})
+        target_dataset = AttributeSetter({"group": group})
+
+        target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
+        trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}), 
+        "S3": AttributeSetter(
+            {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}), 
+        "S6": AttributeSetter({"value": 5.0})}
+        this_trait = AttributeSetter({"data": trait_data})
+        mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+                                       [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
+        mock_normalize.side_effect = [([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+                                       [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+                                      ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
+                                       [3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6),
+                                      ([2.3, 1.1, 1.4], [3.4, 6.2, 4.1], 3)]
+
+        results_pearsonr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+        }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+        results_spearmanr = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+        }, target_vals=target_vals, target_dataset=target_dataset, type="spearman")
+        results_num_overlap = get_sample_r_and_p_values(this_trait=this_trait, this_dataset={
+        }, target_vals=target_vals, target_dataset=target_dataset, type="pearson")
+        expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
+        expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
+        for i, val in enumerate(expected_pearsonr):
+            self.assertAlmostEqual(val, results_pearsonr[i],4)
+        for i, val in enumerate(expected_spearmanr):
+            self.assertAlmostEqual(val, results_spearmanr[i],4)
+        self.assertEqual(results_num_overlap, None)
 
     @mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
-    def test_calculate_results(self,literature_correlation):
- 
-        literature_correlation.return_value={'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
-
-
-
-        this_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})})
-        target_dataset=MockDataset({"group":AttributeSetter({"species":"rat"})})
-        this_trait=AttributeSetter({"geneid":"GH-1"})
-        corr_params={"type":"literature"}
-        sorted_results=calculate_results(this_trait=this_trait,this_dataset=this_dataset,target_dataset=target_dataset,corr_params=corr_params)
-        expected_results={'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
-
-        self.assertTrue(isinstance(sorted_results,OrderedDict))
-        self.assertEqual(dict(sorted_results),expected_results)
-
-
-
-            
-
-
+    def test_calculate_results(self, literature_correlation):
+
+        literature_correlation.return_value = {
+            'TT-1': ['GH-1', 0], 'TT-2': ['GH-2', 3], 'TT-3': ['GH-3', 1]}
+
+        this_dataset = MockDataset(
+            {"group": AttributeSetter({"species": "rat"})})
+        target_dataset = MockDataset(
+            {"group": AttributeSetter({"species": "rat"})})
+        this_trait = AttributeSetter({"geneid": "GH-1"})
+        corr_params = {"type": "literature"}
+        sorted_results = calculate_results(
+            this_trait=this_trait, this_dataset=this_dataset, target_dataset=target_dataset, corr_params=corr_params)
+        expected_results = {'TT-2': ['GH-2', 3],
+                            'TT-3': ['GH-3', 1], 'TT-1': ['GH-1', 0]}
+
+        self.assertTrue(isinstance(sorted_results, OrderedDict))
+        self.assertEqual(dict(sorted_results), expected_results)