Fix some errors generated by running pylint

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

1 files changed, 46 insertions, 37 deletions

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: