From 8fa2d7cc9d3d6599d1c44a6f5e76decf932b2cbd Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Mon, 3 Aug 2020 16:54:57 +0300 Subject: Fix some errors generated by running pylint * wqflask/wqflask/api/gen_menu.py: Apply pylint. * wqflask/tests/api/test_gen_menu.py: Apply pylint. --- wqflask/tests/api/test_gen_menu.py | 33 +++++++++------ wqflask/wqflask/api/gen_menu.py | 83 +++++++++++++++++++++----------------- 2 files changed, 66 insertions(+), 50 deletions(-) (limited to 'wqflask') 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: -- cgit v1.2.3