diff options
| -rw-r--r-- | wqflask/tests/api/__init__.py | 0 | ||||
| -rw-r--r-- | wqflask/tests/api/test_gen_menu.py | 407 | ||||
| -rw-r--r-- | wqflask/wqflask/api/gen_menu.py | 186 |
3 files changed, 500 insertions, 93 deletions
diff --git a/wqflask/tests/api/__init__.py b/wqflask/tests/api/__init__.py new file mode 100644 index 00000000..e69de29b --- /dev/null +++ b/wqflask/tests/api/__init__.py diff --git a/wqflask/tests/api/test_gen_menu.py b/wqflask/tests/api/test_gen_menu.py new file mode 100644 index 00000000..79c77fec --- /dev/null +++ b/wqflask/tests/api/test_gen_menu.py @@ -0,0 +1,407 @@ +"""Test cases for wqflask.api.gen_menu""" +import unittest +import mock + +from wqflask.api.gen_menu import gen_dropdown_json +from wqflask.api.gen_menu import get_species +from wqflask.api.gen_menu import get_groups +from wqflask.api.gen_menu import get_types +from wqflask.api.gen_menu import get_datasets +from wqflask.api.gen_menu import phenotypes_exist +from wqflask.api.gen_menu import genotypes_exist +from wqflask.api.gen_menu import build_datasets +from wqflask.api.gen_menu import build_types + + +class TestGenMenu(unittest.TestCase): + """Tests for the gen_menu module""" + + def setUp(self): + self.test_group = { + 'mouse': [ + ['H_T1', + 'H_T', + 'Family:DescriptionA' + ], + ['H_T2', "H_T'", 'Family:None'] + ], + 'human': [ + ['BXD', 'BXD', 'Family:None'], + ['HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', + 'Family:Test'] + ] + } + + self.test_type = { + 'mouse': { + 'H_T2': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']], + 'H_T1': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']] + }, + 'human': { + 'HLC': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']], + 'BXD': [('Phenotypes', + 'Traits and Cofactors', + 'Phenotypes'), + ('Genotypes', + 'DNA Markers and SNPs', + 'Genotypes'), + ['M', 'M', 'Molecular Trait Datasets']] + } + } + + @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')) + self.assertEqual(get_species(), + [['human', 'Human'], ['mouse', 'Mouse']]) + db_mock.db.execute.assert_called_once_with( + "SELECT Name, MenuName FROM Species ORDER BY OrderId" + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_get_groups(self, db_mock): + """Test that species groups are grouped correctly""" + db_mock.db.execute.return_value.fetchall.side_effect = [ + # Mouse + (('BXD', 'BXD', None), + ('HLC', 'Liver: Normal Gene Expression with Genotypes (Merck)', + 'Test')), + # Human + (('H_T1', "H_T", "DescriptionA"), + ('H_T2', "H_T'", None)) + ] + + self.assertEqual(get_groups([["human", "Human"], ["mouse", "Mouse"]]), + self.test_group) + + for name in ["mouse", "human"]: + db_mock.db.execute.assert_any_call( + ("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(name) + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_phenotypes_exist_called_with_correct_query(self, db_mock): + """Test that phenotypes_exist is called with the correct query""" + 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'" + ) + + @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""" + for x in [None, False, (), [], ""]: + db_mock.db.execute.return_value.fetchone.return_value = x + self.assertFalse(phenotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_phenotypes_exist_with_truthy_value(self, db_mock): + """Test that phenotype check returns correctly when given Truthy """ + for x in ["x", ("result"), ["result"], [1]]: + db_mock.db.execute.return_value.fetchone.return_value = (x) + self.assertTrue(phenotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_genotypes_exist_called_with_correct_query(self, db_mock): + """Test that genotypes_exist is called with the correct query""" + db_mock.db.execute.return_value.fetchone.return_value = None + genotypes_exist("test") + db_mock.db.execute.assert_called_with( + "SELECT Name FROM GenoFreeze WHERE GenoFreeze.Name = 'testGeno'" + ) + + @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""" + for x in [None, False, (), [], ""]: + db_mock.db.execute.return_value.fetchone.return_value = x + self.assertFalse(genotypes_exist("test")) + + @mock.patch('wqflask.api.gen_menu.g') + def test_genotypes_exist_with_truthy_value(self, db_mock): + """Test that genotype check returns correctly when given Truthy """ + for x in ["x", ("result"), ["result"], [1]]: + 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""" + db_mock.db.execute.return_value.fetchall.return_value = ( + (602, "BXDPublish", "BXD Published Phenotypes"), + ) + self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), + [['602', "BXDPublish", "BXD Published Phenotypes"]]) + db_mock.db.execute.assert_called_with( + "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " + + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " + + "InbredSet WHERE InbredSet.Name = 'BXD' AND " + + "PublishFreeze.InbredSetId = InbredSet.Id AND " + + "InfoFiles.InfoPageName = PublishFreeze.Name " + + "ORDER BY PublishFreeze.CreateTime ASC" + ) + self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), + [['602', "BXDPublish", "Mouse Phenome Database"]]) + + db_mock.db.execute.return_value.fetchall.return_value = () + db_mock.db.execute.return_value.fetchone.return_value = ( + "BXDPublish", "Mouse Phenome Database" + ) + self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"), + [["None", "BXDPublish", "Mouse Phenome Database"]]) + + @mock.patch('wqflask.api.gen_menu.g') + def test_build_datasets_with_type_phenotypes_and_no_results(self, db_mock): + """Test that correct dataset is returned for a phenotype type with no + results + + """ + db_mock.db.execute.return_value.fetchall.return_value = None + db_mock.db.execute.return_value.fetchone.return_value = (121, + "text value") + self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"), + [["None", "121", "text value"]]) + db_mock.db.execute.assert_called_with( + "SELECT PublishFreeze.Name, PublishFreeze.FullName " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = 'BXD' AND " + "PublishFreeze.InbredSetId = InbredSet.Id " + "ORDER BY PublishFreeze.CreateTime ASC" + ) + + @mock.patch('wqflask.api.gen_menu.g') + def test_build_datasets_with_type_genotypes(self, db_mock): + """Test that correct dataset is returned for a phenotype type""" + db_mock.db.execute.return_value.fetchone.return_value = ( + 635, "HLCPublish", "HLC Published Genotypes" + ) + + 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 " + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + + "ORDER BY GenoFreeze.CreateTime DESC" + ) + db_mock.db.execute.return_value.fetchone.return_value = () + self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"), + [["None", "HLCGeno", "HLC Genotypes"]]) + + @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""" + db_mock.db.execute.return_value.fetchall.return_value = ( + (112, "HC_M2_0606_P", + "Hippocampus Consortium M430v2 (Jun06) PDNN"), ) + self.assertEqual(build_datasets("Mouse", "HLC", "mRNA"), [[ + "112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN" + ]]) + db_mock.db.execute.assert_called_once_with( + "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " + + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " + + "ProbeFreeze, InbredSet, Tissue, Species WHERE " + + "Species.Name = 'Mouse' AND Species.Id = " + + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " + + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and " + + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " + + "Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id " + + "ORDER BY ProbeSetFreeze.CreateTime DESC") + + @mock.patch('wqflask.api.gen_menu.build_datasets') + @mock.patch('wqflask.api.gen_menu.g') + 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"] + ] + db_mock.db.execute.return_value.fetchall.return_value = ( + ('Mouse Tissue'), ('Human Tissue'), ('Rat Tissue') + ) + self.assertEqual(build_types('mouse', 'random group'), + [['M', 'M', 'Molecular Trait Datasets'], + ['H', 'H', 'Molecular Trait Datasets'], + ['R', 'R', 'Molecular Trait Datasets']]) + db_mock.db.execute.assert_called_once_with( + "SELECT DISTINCT Tissue.Name " + + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " + + "Tissue, Species WHERE Species.Name = 'mouse' " + + "AND Species.Id = InbredSet.SpeciesId AND " + + "InbredSet.Name = 'random group' AND " + + "ProbeFreeze.TissueId = Tissue.Id AND " + + "ProbeFreeze.InbredSetId = InbredSet.Id AND " + + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " + + "ORDER BY Tissue.Name" + ) + + @mock.patch('wqflask.api.gen_menu.build_types') + @mock.patch('wqflask.api.gen_menu.genotypes_exist') + @mock.patch('wqflask.api.gen_menu.phenotypes_exist') + def test_get_types_with_existing_genotype_and_phenotypes( + self, + phenotypes_exist_mock, + genotypes_exist_mock, + build_types_mock): + """Test that build types are constructed correctly if phenotypes and genotypes + exist + + """ + phenotypes_exist_mock.return_value = True + genotypes_exist_mock.return_value = True + + expected_result = self.test_type + + build_types_mock.return_value = [ + ['M', 'M', 'Molecular Trait Datasets'] + ] + self.assertEqual(get_types(self.test_group), expected_result) + + @mock.patch('wqflask.api.gen_menu.build_types') + @mock.patch('wqflask.api.gen_menu.genotypes_exist') + @mock.patch('wqflask.api.gen_menu.phenotypes_exist') + def test_get_types_with_buildtype_and_non_existent_genotype_and_phenotypes( + self, + phenotypes_exist_mock, + genotypes_exist_mock, + build_types_mock): + """Test that build types are constructed correctly if phenotypes_exist and + genotypes_exist are false but build_type is falsy + + """ + phenotypes_exist_mock.return_value = False + genotypes_exist_mock.return_value = False + + build_types_mock.return_value = [] + self.assertEqual(get_types(self.test_group), { + 'mouse': {}, + 'human': {} + }) + + @mock.patch('wqflask.api.gen_menu.build_types') + @mock.patch('wqflask.api.gen_menu.genotypes_exist') + @mock.patch('wqflask.api.gen_menu.phenotypes_exist') + def test_get_types_with_non_existent_genotype_phenotypes_and_buildtype( + self, + phenotypes_exist_mock, + genotypes_exist_mock, + build_types_mock): + """Test that build types are constructed correctly if phenotypes_exist, + genotypes_exist and build_types are truthy + + """ + phenotypes_exist_mock.return_value = False + genotypes_exist_mock.return_value = False + + build_types_mock.return_value = [ + ['M', 'M', 'Molecular Trait Datasets'] + ] + expected_result = { + 'mouse': { + 'H_T2': [['M', 'M', 'Molecular Trait Datasets']], + 'H_T1': [['M', 'M', 'Molecular Trait Datasets']]}, + 'human': { + 'HLC': [['M', 'M', 'Molecular Trait Datasets']], + 'BXD': [['M', 'M', 'Molecular Trait Datasets']]}} + self.assertEqual(get_types(self.test_group), + expected_result) + + @mock.patch('wqflask.api.gen_menu.build_datasets') + def test_get_datasets_with_existent_datasets(self, + build_datasets_mock): + """Test correct dataset is returned with existent build_datasets""" + build_datasets_mock.return_value = "Test" + expected_result = { + 'mouse': { + 'H_T2': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}, + 'H_T1': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}}, + 'human': {'HLC': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}, + 'BXD': {'Genotypes': 'Test', + 'M': 'Test', + 'Phenotypes': 'Test'}}} + self.assertEqual(get_datasets(self.test_type), + expected_result) + + @mock.patch('wqflask.api.gen_menu.build_datasets') + def test_get_datasets_with_non_existent_datasets(self, + build_datasets_mock): + """Test correct dataset is returned with non-existent build_datasets""" + build_datasets_mock.return_value = None + expected_result = { + 'mouse': { + 'H_T2': {}, + 'H_T1': {}}, + 'human': {'HLC': {}, + 'BXD': {}}} + self.assertEqual(get_datasets(self.test_type), + expected_result) + + @mock.patch('wqflask.api.gen_menu.get_datasets') + @mock.patch('wqflask.api.gen_menu.get_types') + @mock.patch('wqflask.api.gen_menu.get_groups') + @mock.patch('wqflask.api.gen_menu.get_species') + def test_gen_dropdown_json(self, + species_mock, + groups_mock, + types_mock, + datasets_mock): + "Test that the correct dictionary is constructed properly" + species_mock.return_value = ("speciesA speciesB speciesC speciesD" + .split(" ")) + datasets_mock.return_value = ("datasetA datasetB datasetC datasetD" + .split(" ")) + groups_mock.return_value = ("groupA groupB groupC groupD" + .split(" ")) + types_mock.return_value = ("typeA typeB typeC typeD" + .split(" ")) + datasets_mock.return_value = ("datasetA datasetB datasetC datasetD" + .split(" ")) + + expected_result = { + 'datasets': ['datasetA', 'datasetB', 'datasetC', 'datasetD'], + 'types': ['typeA', 'typeB', 'typeC', 'typeD'], + 'groups': ['groupA', 'groupB', 'groupC', 'groupD'], + 'species': ['speciesA', 'speciesB', 'speciesC', 'speciesD']} + + self.assertEqual(gen_dropdown_json(), expected_result) diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py index cfce0c8e..cc11e14b 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) @@ -29,11 +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: @@ -41,25 +32,31 @@ def get_species(): return species + def get_groups(species): """Build groups list""" groups = {} for species_name, _species_full_name in 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() + 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() 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 = {} @@ -68,48 +65,45 @@ 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: types[species][group_name] += types_list - else: - if not phenotypes_exist(group_name) and not genotypes_exist(group_name): - types[species].pop(group_name, None) - groups[species] = list(group for group in groups[species] if group[0] != group_name) - else: #ZS: This whole else statement might be unnecessary, need to check + else: types_list = build_types(species, group_name) if len(types_list) > 0: 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() + results = g.db.execute( + ("SELECT Name FROM PublishFreeze " + "WHERE PublishFreeze.Name = " + "'{}'").format(group_name+"Publish")).fetchone() + return bool(results) - if results != None: - return True - else: - return False def genotypes_exist(group_name): - results = g.db.execute("""SELECT Name - FROM GenoFreeze - WHERE GenoFreeze.Name = '{}'""".format(group_name+"Geno")).fetchone() + results = g.db.execute( + ("SELECT Name FROM GenoFreeze " + + "WHERE GenoFreeze.Name = '{}'").format(group_name+"Geno")).fetchone() + return bool(results) - if results != None: - return True - else: - return False def build_types(species, group): """Fetches tissues @@ -119,25 +113,26 @@ def build_types(species, group): """ - query = """SELECT DISTINCT Tissue.Name - FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species - WHERE Species.Name = '{0}' AND - Species.Id = InbredSet.SpeciesId AND - InbredSet.Name = '{1}' AND - ProbeFreeze.TissueId = Tissue.Id AND - ProbeFreeze.InbredSetId = InbredSet.Id AND - ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id - ORDER BY Tissue.Name""".format(species, group) + query = ("SELECT DISTINCT Tissue.Name " + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " + "Tissue, Species WHERE Species.Name = '{0}' " + "AND Species.Id = InbredSet.SpeciesId AND " + "InbredSet.Name = '{1}' AND ProbeFreeze.TissueId = " + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id " + "AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " + "ORDER BY Tissue.Name").format(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 = {} @@ -147,7 +142,7 @@ def get_datasets(types): datasets[species][group] = {} for type_name in type_list: these_datasets = build_datasets(species, group, type_name[0]) - if len(these_datasets) > 0: + if bool(these_datasets): datasets[species][group][type_name[0]] = these_datasets return datasets @@ -158,29 +153,30 @@ def build_datasets(species, group, type_name): dataset_text = dataset_value = None datasets = [] if type_name == "Phenotypes": - results = g.db.execute("""SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, PublishFreeze.FullName - FROM InfoFiles, PublishFreeze, InbredSet - WHERE InbredSet.Name = '{}' AND - PublishFreeze.InbredSetId = InbredSet.Id AND - InfoFiles.InfoPageName = PublishFreeze.Name - ORDER BY PublishFreeze.CreateTime ASC""".format(group)).fetchall() - - if len(results) > 0: + results = g.db.execute( + ("SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " + "InbredSet WHERE InbredSet.Name = '{}' AND " + "PublishFreeze.InbredSetId = InbredSet.Id AND " + "InfoFiles.InfoPageName = PublishFreeze.Name " + "ORDER BY PublishFreeze.CreateTime ASC").format(group)).fetchall() + if bool(results): for result in results: dataset_id = str(result[0]) dataset_value = str(result[1]) + dataset_text = str(result[2]) if group == 'MDP': dataset_text = "Mouse Phenome Database" - else: - #dataset_text = "%s Phenotypes" % group - dataset_text = str(result[2]) + datasets.append([dataset_id, dataset_value, dataset_text]) else: - result = g.db.execute("""SELECT PublishFreeze.Name, PublishFreeze.FullName - FROM PublishFreeze, InbredSet - WHERE InbredSet.Name = '{}' AND - PublishFreeze.InbredSetId = InbredSet.Id - ORDER BY PublishFreeze.CreateTime ASC""".format(group)).fetchone() + result = g.db.execute( + ("SELECT PublishFreeze.Name, PublishFreeze.FullName " + "FROM PublishFreeze, InbredSet " + "WHERE InbredSet.Name = '{}' AND " + "PublishFreeze.InbredSetId = InbredSet.Id " + "ORDER BY PublishFreeze.CreateTime ASC") + .format(group)).fetchone() dataset_id = "None" dataset_value = str(result[0]) @@ -188,30 +184,34 @@ def build_datasets(species, group, type_name): datasets.append([dataset_id, dataset_value, dataset_text]) elif type_name == "Genotypes": - results = g.db.execute("""SELECT InfoFiles.GN_AccesionId - FROM InfoFiles, GenoFreeze, InbredSet - WHERE InbredSet.Name = '{}' AND - GenoFreeze.InbredSetId = InbredSet.Id AND - InfoFiles.InfoPageName = GenoFreeze.ShortName - ORDER BY GenoFreeze.CreateTime DESC""".format(group)).fetchone() - - if results != None: + results = g.db.execute( + ("SELECT InfoFiles.GN_AccesionId " + + "FROM InfoFiles, GenoFreeze, InbredSet " + + "WHERE InbredSet.Name = '{}' AND " + + "GenoFreeze.InbredSetId = InbredSet.Id AND " + + "InfoFiles.InfoPageName = GenoFreeze.ShortName " + + "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone() + + dataset_id = "None" + if bool(results): dataset_id = str(results[0]) - else: - dataset_id = "None" + dataset_value = "%sGeno" % group dataset_text = "%s Genotypes" % group datasets.append([dataset_id, dataset_value, dataset_text]) - 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() + 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() datasets = [] for dataset_info in results: @@ -220,4 +220,4 @@ def build_datasets(species, group, type_name): this_dataset_info.append(str(info)) datasets.append(this_dataset_info) - return datasets
\ No newline at end of file + return datasets |