refactor tests and pep8 formatting

2 files changed, 112 insertions, 101 deletions

diff --git a/wqflask/tests/unit/utility/test_type_checking.py b/wqflask/tests/unit/utility/test_type_checking.py
index 1ea11695..48d110c7 100644
--- a/wqflask/tests/unit/utility/test_type_checking.py
+++ b/wqflask/tests/unit/utility/test_type_checking.py
@@ -5,53 +5,50 @@ from utility.type_checking import is_str
 from utility.type_checking import get_float
 from utility.type_checking import get_int
 from utility.type_checking import get_string
-class TestTypeChecking(unittest.TestCase):
-	def test_is_float(self):
-		floats=[2,1.2,'3.1']
-		not_floats=["String",None,[],()]
-		for flt in floats:
-			results=is_float(flt)
-			self.assertTrue(results)
-		for nflt in not_floats:
-			results=is_float(nflt)
-			self.assertFalse(results)
-
-	def test_is_int(self):
-		int_values=[1,1.1]
-		not_int_values=["1sdf",None,[],"1.1"]
-		for int_val in int_values:
-			results=is_int(int_val)
-			self.assertTrue(results)
-		for not_int in not_int_values:
-			results=is_int(not_int)
-			self.assertFalse(results)
-
-	def test_is_str(self):
-		string_values=[1,False,[],{},"string_value"]
-		falsey_values=[None]
-		for string_val in string_values:
-			results=is_str(string_val)
-			self.assertTrue(results)
-		for non_string in falsey_values:
-			results=is_str(non_string)
-			self.assertFalse(results)
-
-
-	def test_get_float(self):
-		vars_object={"min_value":"12"}
-		results=get_float(vars_object,"min_value")
-		self.assertEqual(results,12.0)
-
-	def test_get_int(self):
-		vars_object={"lx_value":"1"}
-		results=get_int(vars_object,"lx_value")
-		self.assertEqual(results,1)
-
-	def test_get_string(self):
-		string_object={"mx_value":1}
-		results=get_string(string_object,"mx_value")
-		self.assertEqual(results,"1")
-
-
 
 
+class TestTypeChecking(unittest.TestCase):
+    def test_is_float(self):
+        floats = [2, 1.2, '3.1']
+        not_floats = ["String", None, [], ()]
+        for flt in floats:
+            results = is_float(flt)
+            self.assertTrue(results)
+        for nflt in not_floats:
+            results = is_float(nflt)
+            self.assertFalse(results)
+
+    def test_is_int(self):
+        int_values = [1, 1.1]
+        not_int_values = ["string", None, [], "1.1"]
+        for int_val in int_values:
+            results = is_int(int_val)
+            self.assertTrue(results)
+        for not_int in not_int_values:
+            results = is_int(not_int)
+            self.assertFalse(results)
+
+    def test_is_str(self):
+        string_values = [1, False, [], {}, "string_value"]
+        falsey_values = [None]
+        for string_val in string_values:
+            results = is_str(string_val)
+            self.assertTrue(results)
+        for non_string in falsey_values:
+            results = is_str(non_string)
+            self.assertFalse(results)
+
+    def test_get_float(self):
+        vars_object = {"min_value": "12"}
+        results = get_float(vars_object, "min_value")
+        self.assertEqual(results, 12.0)
+
+    def test_get_int(self):
+        vars_object = {"lx_value": "1"}
+        results = get_int(vars_object, "lx_value")
+        self.assertEqual(results, 1)
+
+    def test_get_string(self):
+        string_object = {"mx_value": 1}
+        results = get_string(string_object, "mx_value")
+        self.assertEqual(results, "1")
\ No newline at end of file
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 9ec32c78..496d228f 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -7,6 +7,7 @@ from wqflask.snp_browser.snp_browser import check_if_in_gene
 from wqflask.snp_browser.snp_browser import get_browser_sample_lists
 from wqflask.snp_browser.snp_browser import get_header_list
 
+
 class TestSnpBrowser(unittest.TestCase):
     def setUp(self):
         self.app_context = app.app_context()
@@ -16,70 +17,83 @@ class TestSnpBrowser(unittest.TestCase):
         self.app_context.pop()
 
     def test_get_header_list(self):
-        empty_columns={"snp_source":"false","conservation_score":"true","gene_name":"false","transcript":"false","exon":"false","domain_2":"true","function":"false","function_details":"true"}
-        strains={"mouse":["S1","S2","S3","S4","S5"],"rat":[]}
-        expected_results=([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore', 'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
-
-        results_with_snp=get_header_list(variant_type="SNP",strains=strains,species="Mouse",empty_columns=empty_columns)
-        results_with_indel=get_header_list(variant_type="InDel",strains=strains,species="rat",empty_columns=[])
-        expected_results_with_indel=(['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'],0)
-
-        self.assertEqual(expected_results,results_with_snp)
-        self.assertEqual(results_with_indel,expected_results_with_indel)
-
+        empty_columns = {"snp_source": "false", "conservation_score": "true", "gene_name": "false",
+                         "transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
+        strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
+        expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
+                              'Domain 1', 'Domain 2', 'Details'], ['S1', 'S2', 'S3', 'S4', 'S5']], 5)
+
+        results_with_snp = get_header_list(
+            variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
+        results_with_indel = get_header_list(
+            variant_type="InDel", strains=strains, species="rat", empty_columns=[])
+        expected_results_with_indel = (
+            ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 
+            'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0)
+
+        self.assertEqual(expected_results, results_with_snp)
+        self.assertEqual(results_with_indel, expected_results_with_indel)
 
     @mock.patch("wqflask.snp_browser.snp_browser.g")
     def test_get_gene_id(self, mock_db):
         mock_db.db.execute.return_value.fetchone.return_value = "517d729f-aa13-4413-a885-40a3f7ff768a"
-        called_value="\n                SELECT\n                        geneId\n                FROM\n                        GeneList\n                WHERE\n                        SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'\n            "
+        db_query_value = """
+                SELECT
+                        geneId
+                FROM
+                        GeneList
+                WHERE
+                        SpeciesId = c9c0f59e-1259-4cba-91e6-831ef1a99c83 AND geneSymbol = 'INSR'
+            """
         results = get_gene_id(
             species_id="c9c0f59e-1259-4cba-91e6-831ef1a99c83", gene_name="INSR")
-        mock_db.db.execute.assert_called_once_with(called_value)
+        mock_db.db.execute.assert_called_once_with(db_query_value)
         self.assertEqual(results, "517d729f-aa13-4413-a885-40a3f7ff768a")
 
     @mock.patch("wqflask.snp_browser.snp_browser.g")
-    def test_gene_id_name_dict(self,mock_db):
-    	no_gene_names=[]
-    	self.assertEqual("",get_gene_id_name_dict(species_id="fregb343bui43g4",gene_name_list=no_gene_names))
-    	gene_name_list=["GH1","GH2","GH3"]
-    	mock_db.db.execute.return_value.fetchall.side_effect=[[],[("fsdf43-fseferger-f22","GH1"),("1sdf43-fsewferger-f22","GH2"),
-    	("fwdj43-fstferger-f22","GH3")]]
-    	no_results=get_gene_id_name_dict(species_id="ret3-32rf32",gene_name_list=gene_name_list)
-    	results_found=get_gene_id_name_dict(species_id="ret3-32rf32",gene_name_list=gene_name_list)
-    	expected_found= {'GH1': 'fsdf43-fseferger-f22', 'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
-    	db_query_value="\n                SELECT\n                        geneId, geneSymbol\n                FROM\n                        GeneList\n                WHERE\n                        SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')\n            "
-    	mock_db.db.execute.assert_called_with(db_query_value)
-    	self.assertEqual(results_found,expected_found)
-    	self.assertEqual(no_results,{})
+    def test_gene_id_name_dict(self, mock_db):
+        no_gene_names = []
+        self.assertEqual("", get_gene_id_name_dict(
+            species_id="fregb343bui43g4", gene_name_list=no_gene_names))
+        gene_name_list = ["GH1", "GH2", "GH3"]
+        mock_db.db.execute.return_value.fetchall.side_effect = [[], [("fsdf43-fseferger-f22", "GH1"), ("1sdf43-fsewferger-f22", "GH2"),
+                                                                     ("fwdj43-fstferger-f22", "GH3")]]
+        no_results = get_gene_id_name_dict(
+            species_id="ret3-32rf32", gene_name_list=gene_name_list)
+        results_found = get_gene_id_name_dict(
+            species_id="ret3-32rf32", gene_name_list=gene_name_list)
+        expected_found = {'GH1': 'fsdf43-fseferger-f22',
+                          'GH2': '1sdf43-fsewferger-f22', 'GH3': 'fwdj43-fstferger-f22'}
+        db_query_value = """
+                SELECT
+                        geneId, geneSymbol
+                FROM
+                        GeneList
+                WHERE
+                        SpeciesId = ret3-32rf32 AND geneSymbol in ('GH1','GH2','GH3')
+            """
+        mock_db.db.execute.assert_called_with(db_query_value)
+        self.assertEqual(results_found, expected_found)
+        self.assertEqual(no_results, {})
 
     @mock.patch("wqflask.snp_browser.snp_browser.g")
-    def test_check_if_in_gene(self,mock_db):
-    	mock_db.db.execute.return_value.fetchone.side_effect=[("fsdf-232sdf-sdf","GHA"),""]
-    	results_found=check_if_in_gene(species_id="517d729f-aa13-4413-a885-40a3f7ff768a",chr="CH1",mb=12.09)
-    	db_query_value="SELECT geneId, geneSymbol\n                   FROM GeneList\n                   WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND\n                        (txStart < 12.09 AND txEnd > 12.09); "
-    	gene_not_found=check_if_in_gene(species_id="517d729f-aa13-4413-a885-40a3f7ff768a",chr="CH1",mb=12.09)
-    	mock_db.db.execute.assert_called_with(db_query_value)
-    	self.assertEqual(gene_not_found,"")
+    def test_check_if_in_gene(self, mock_db):
+        mock_db.db.execute.return_value.fetchone.side_effect = [
+            ("fsdf-232sdf-sdf", "GHA"), ""]
+        results_found = check_if_in_gene(
+            species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+        db_query_value = """SELECT geneId, geneSymbol
+                   FROM GeneList
+                   WHERE SpeciesId = 517d729f-aa13-4413-a885-40a3f7ff768a AND chromosome = 'CH1' AND
+                        (txStart < 12.09 AND txEnd > 12.09); """
+        gene_not_found = check_if_in_gene(
+            species_id="517d729f-aa13-4413-a885-40a3f7ff768a", chr="CH1", mb=12.09)
+        mock_db.db.execute.assert_called_with(db_query_value)
+        self.assertEqual(gene_not_found, "")
 
     @mock.patch("wqflask.snp_browser.snp_browser.g")
-    def test_get_browser_sample_lists(self,mock_db):
-    	mock_db.db.execute.return_value.fetchall.return_value=[]
-
-    	results=get_browser_sample_lists(species_id="12")
-    	self.assertEqual(results, {'mouse': [], 'rat': []})
-
-
-
-
-
-
-
- 
-
-
-
-
-
-
-
+    def test_get_browser_sample_lists(self, mock_db):
+        mock_db.db.execute.return_value.fetchall.return_value = []
 
+        results = get_browser_sample_lists(species_id="12")
+        self.assertEqual(results, {'mouse': [], 'rat': []})