Fix some errors generated by running pylint

* wqflask/wqflask/api/gen_menu.py: Apply pylint.
* wqflask/tests/api/test_gen_menu.py: Apply pylint.

2 files changed, 66 insertions, 50 deletions

diff --git a/wqflask/tests/api/test_gen_menu.py b/wqflask/tests/api/test_gen_menu.py
index 4a928d12..79c77fec 100644
--- a/wqflask/tests/api/test_gen_menu.py
+++ b/wqflask/tests/api/test_gen_menu.py
@@ -69,9 +69,11 @@ class TestGenMenu(unittest.TestCase):
 
     @mock.patch('wqflask.api.gen_menu.g')
     def test_get_species(self, db_mock):
-        """Test that assertion is raised when dataset and dataset_name are defined"""
-        db_mock.db.execute.return_value.fetchall.return_value = (('human', 'Human'),
-                                                                 ('mouse', 'Mouse'))
+        """Test that assertion is raised when dataset and dataset_name
+        are defined"""
+        db_mock.db.execute.return_value.fetchall.return_value = (
+            ('human', 'Human'),
+            ('mouse', 'Mouse'))
         self.assertEqual(get_species(),
                          [['human', 'Human'], ['mouse', 'Mouse']])
         db_mock.db.execute.assert_called_once_with(
@@ -84,7 +86,8 @@ class TestGenMenu(unittest.TestCase):
         db_mock.db.execute.return_value.fetchall.side_effect = [
             # Mouse
             (('BXD', 'BXD', None),
-             ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', 'Test')),
+             ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)',
+              'Test')),
             # Human
             (('H_T1', "H_T", "DescriptionA"),
              ('H_T2', "H_T'", None))
@@ -111,12 +114,14 @@ class TestGenMenu(unittest.TestCase):
         db_mock.db.execute.return_value.fetchone.return_value = None
         phenotypes_exist("test")
         db_mock.db.execute.assert_called_with(
-            "SELECT Name FROM PublishFreeze WHERE PublishFreeze.Name = 'testPublish'"
+            "SELECT Name FROM PublishFreeze "
+            "WHERE PublishFreeze.Name = 'testPublish'"
         )
 
     @mock.patch('wqflask.api.gen_menu.g')
     def test_phenotypes_exist_with_falsy_values(self, db_mock):
-        """Test that phenotype check returns correctly when given a None value"""
+        """Test that phenotype check returns correctly when given
+        a None value"""
         for x in [None, False, (), [], ""]:
             db_mock.db.execute.return_value.fetchone.return_value = x
             self.assertFalse(phenotypes_exist("test"))
@@ -139,7 +144,8 @@ class TestGenMenu(unittest.TestCase):
 
     @mock.patch('wqflask.api.gen_menu.g')
     def test_genotypes_exist_with_falsy_values(self, db_mock):
-        """Test that genotype check returns correctly when given a None value"""
+        """Test that genotype check returns correctly when given
+        a None value"""
         for x in [None, False, (), [], ""]:
             db_mock.db.execute.return_value.fetchone.return_value = x
             self.assertFalse(genotypes_exist("test"))
@@ -151,7 +157,6 @@ class TestGenMenu(unittest.TestCase):
             db_mock.db.execute.return_value.fetchone.return_value = (x)
             self.assertTrue(phenotypes_exist("test"))
 
-
     @mock.patch('wqflask.api.gen_menu.g')
     def test_build_datasets_with_type_phenotypes(self, db_mock):
         """Test that correct dataset is returned for a phenotype type"""
@@ -207,8 +212,9 @@ class TestGenMenu(unittest.TestCase):
         self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
                          [["635", "HLCGeno", "HLC Genotypes"]])
         db_mock.db.execute.assert_called_with(
-            "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, GenoFreeze, InbredSet " +
-            "WHERE InbredSet.Name = 'HLC' AND GenoFreeze.InbredSetId = InbredSet.Id AND " +
+            "SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
+            "GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
+            "GenoFreeze.InbredSetId = InbredSet.Id AND "
             "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
             "ORDER BY GenoFreeze.CreateTime DESC"
         )
@@ -218,7 +224,8 @@ class TestGenMenu(unittest.TestCase):
 
     @mock.patch('wqflask.api.gen_menu.g')
     def test_build_datasets_with_type_mrna(self, db_mock):
-        """Test that correct dataset is returned for a mRNA expression/ Probeset"""
+        """Test that correct dataset is returned for a mRNA
+        expression/ Probeset"""
         db_mock.db.execute.return_value.fetchall.return_value = (
             (112, "HC_M2_0606_P",
              "Hippocampus Consortium M430v2 (Jun06) PDNN"), )
@@ -241,7 +248,8 @@ class TestGenMenu(unittest.TestCase):
     def test_build_types(self, db_mock, datasets_mock):
         """Test that correct tissue metadata is returned"""
         datasets_mock.return_value = [
-            ["112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"]
+            ["112", 'HC_M2_0606_P',
+                "Hippocampus Consortium M430v2 (Jun06) PDNN"]
         ]
         db_mock.db.execute.return_value.fetchall.return_value = (
             ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue')
@@ -352,7 +360,6 @@ class TestGenMenu(unittest.TestCase):
                       'BXD': {'Genotypes': 'Test',
                               'M': 'Test',
                               'Phenotypes': 'Test'}}}
-        self.maxDiff = None
         self.assertEqual(get_datasets(self.test_type),
                          expected_result)
 
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 82c5d9be..45814ed9 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -1,21 +1,12 @@
 from __future__ import print_function, division
 
-import sys
-
 from flask import g
 
-from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
-from utility.benchmark import Bench
-
-import MySQLdb
-
-import urlparse
-
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
 
 def gen_dropdown_json():
-    """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+    """Generates and outputs (as json file) the data for the main dropdown menus on
+    the home page
+    """
 
     species = get_species()
     groups = get_groups(species)
@@ -29,9 +20,11 @@ def gen_dropdown_json():
 
     return data
 
+
 def get_species():
     """Build species list"""
-    results = g.db.execute("SELECT Name, MenuName FROM Species ORDER BY OrderId").fetchall()
+    results = g.db.execute(
+        "SELECT Name, MenuName FROM Species ORDER BY OrderId").fetchall()
 
     species = []
     for result in results:
@@ -39,6 +32,7 @@ def get_species():
 
     return species
 
+
 def get_groups(species):
     """Build groups list"""
     groups = {}
@@ -46,18 +40,23 @@ def get_groups(species):
         groups[species_name] = []
 
         results = g.db.execute(
-            ("SELECT InbredSet.Name, InbredSet.FullName, IFNULL(InbredSet.Family, 'None') " +
-             "FROM InbredSet, Species WHERE Species.Name = '{}' AND InbredSet.SpeciesId = " +
-             "Species.Id GROUP by InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " +
-             "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, InbredSet.FullName) ASC, " +
-             "InbredSet.FullName ASC, InbredSet.MenuOrderId ASC").format(species_name)).fetchall()
+            ("SELECT InbredSet.Name, InbredSet.FullName, "
+             "IFNULL(InbredSet.Family, 'None') "
+             "FROM InbredSet, Species WHERE Species.Name = '{}' "
+             "AND InbredSet.SpeciesId = Species.Id GROUP by InbredSet.Name "
+             "ORDER BY IFNULL(InbredSet.FamilyOrder, InbredSet.FullName) "
+             "ASC, IFNULL(InbredSet.Family, InbredSet.FullName) ASC, "
+             "InbredSet.FullName ASC, InbredSet.MenuOrderId ASC")
+            .format(species_name)).fetchall()
 
         for result in results:
             family_name = "Family:" + str(result[2])
-            groups[species_name].append([str(result[0]), str(result[1]), family_name])
+            groups[species_name].append(
+                [str(result[0]), str(result[1]), family_name])
 
     return groups
 
+
 def get_types(groups):
     """Build types list"""
     types = {}
@@ -66,12 +65,15 @@ def get_types(groups):
         types[species] = {}
         for group_name, _group_full_name, _family_name in group_dict:
             if phenotypes_exist(group_name):
-                types[species][group_name] = [("Phenotypes", "Traits and Cofactors", "Phenotypes")]
+                types[species][group_name] = [
+                    ("Phenotypes", "Traits and Cofactors", "Phenotypes")]
             if genotypes_exist(group_name):
                 if group_name in types[species]:
-                    types[species][group_name] += [("Genotypes", "DNA Markers and SNPs", "Genotypes")]
+                    types[species][group_name] += [
+                        ("Genotypes", "DNA Markers and SNPs", "Genotypes")]
                 else:
-                    types[species][group_name] = [("Genotypes", "DNA Markers and SNPs", "Genotypes")]
+                    types[species][group_name] = [
+                        ("Genotypes", "DNA Markers and SNPs", "Genotypes")]
             if group_name in types[species]:
                 types_list = build_types(species, group_name)
                 if len(types_list) > 0:
@@ -82,13 +84,17 @@ def get_types(groups):
                     types[species][group_name] = types_list
                 else:
                     types[species].pop(group_name, None)
-                    groups[species] = list(group for group in groups[species] if group[0] != group_name)
+                    groups[species] = list(
+                        group for group in groups[species]
+                        if group[0] != group_name)
     return types
 
+
 def phenotypes_exist(group_name):
     results = g.db.execute(
-        ("SELECT Name FROM PublishFreeze " +
-         "WHERE PublishFreeze.Name = '{}'").format(group_name+"Publish")).fetchone()
+        ("SELECT Name FROM PublishFreeze "
+         "WHERE PublishFreeze.Name = "
+         "'{}'").format(group_name+"Publish")).fetchone()
     return bool(results)
 
 
@@ -118,13 +124,15 @@ def build_types(species, group):
 
     results = []
     for result in g.db.execute(query).fetchall():
-        if len(result):
+        if bool(result):
             these_datasets = build_datasets(species, group, result[0])
             if len(these_datasets) > 0:
-                results.append([str(result[0]), str(result[0]), "Molecular Trait Datasets"])
+                results.append([str(result[0]), str(result[0]),
+                                "Molecular Trait Datasets"])
 
     return results
 
+
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
@@ -192,17 +200,18 @@ def build_datasets(species, group, type_name):
         dataset_text = "%s Genotypes" % group
         datasets.append([dataset_id, dataset_value, dataset_text])
 
-    else: # for mRNA expression/ProbeSet
+    else:  # for mRNA expression/ProbeSet
         results = g.db.execute(
-            ("SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
-             "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
-             "ProbeFreeze, InbredSet, Tissue, Species WHERE " +
-             "Species.Name = '{0}' AND Species.Id = " +
-             "InbredSet.SpeciesId AND InbredSet.Name = '{1}' " +
-             "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " +
-             "and Tissue.Name = '{2}' AND ProbeFreeze.TissueId = " +
-             "Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id " +
-             "ORDER BY ProbeSetFreeze.CreateTime DESC").format(species, group, type_name)).fetchall()
+            ("SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+             "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+             "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+             "Species.Name = '{0}' AND Species.Id = "
+             "InbredSet.SpeciesId AND InbredSet.Name = '{1}' "
+             "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+             "and Tissue.Name = '{2}' AND ProbeFreeze.TissueId = "
+             "Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id "
+             "ORDER BY ProbeSetFreeze.CreateTime "
+             "DESC").format(species, group, type_name)).fetchall()
 
         datasets = []
         for dataset_info in results: