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from gn3.db.species import get_all_species
def gen_dropdown_json(conn):
"""Generates and outputs (as json file) the data for the main dropdown menus on
the home page
"""
species = get_all_species(conn)
groups = get_groups(species, conn)
types = get_types(groups, conn)
datasets = get_datasets(types, conn)
return dict(species=species,
groups=groups,
types=types,
datasets=datasets)
def get_groups(species, conn):
"""Build groups list"""
groups = {}
with conn.cursor() as cursor:
for species_name, _species_full_name in species:
groups[species_name] = []
query = ("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)
cursor.execute(query)
results = cursor.fetchall()
for result in results:
family_name = "Family:" + str(result[2])
groups[species_name].append(
[str(result[0]), str(result[1]), family_name])
return groups
def get_types(groups, conn):
"""Build types list"""
types = {}
for species, group_dict in list(groups.items()):
types[species] = {}
for group_name, _group_full_name, _family_name in group_dict:
if phenotypes_exist(group_name, conn):
types[species][group_name] = [
("Phenotypes", "Traits and Cofactors", "Phenotypes")]
if genotypes_exist(group_name, conn):
if group_name in types[species]:
types[species][group_name] += [
("Genotypes", "DNA Markers and SNPs", "Genotypes")]
else:
types[species][group_name] = [
("Genotypes", "DNA Markers and SNPs", "Genotypes")]
if group_name in types[species]:
types_list = build_types(species, group_name, conn)
if len(types_list) > 0:
types[species][group_name] += types_list
else:
types_list = build_types(species, group_name, conn)
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)
return types
def phenotypes_exist(group_name, conn):
results = []
with conn.cursor() as cursor:
cursor.execute(
("SELECT Name FROM PublishFreeze "
"WHERE PublishFreeze.Name = "
"'{}'").format(group_name + "Publish"))
results = cursor.fetchone()
return bool(results)
def genotypes_exist(group_name, conn):
with conn.cursor() as cursor:
cursor.execute(
("SELECT Name FROM GenoFreeze " +
"WHERE GenoFreeze.Name = '{}'").format(
group_name + "Geno"))
results = cursor.fetchone()
return bool(results)
def build_types(species, group, conn):
"""Fetches tissues
Gets the tissues with data for this species/group
(all types except phenotype/genotype are tissues)
"""
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 = []
with conn.cursor() as cursor:
cursor.execute(query)
for result in cursor.fetchall():
if bool(result):
these_datasets = build_datasets(species,
group, result[0], conn)
if len(these_datasets) > 0:
results.append([str(result[0]), str(result[0]),
"Molecular Traits"])
return results
def get_datasets(types, conn):
"""Build datasets list"""
datasets = {}
for species, group_dict in list(types.items()):
datasets[species] = {}
for group, type_list in list(group_dict.items()):
datasets[species][group] = {}
for type_name in type_list:
these_datasets = build_datasets(species, group,
type_name[0], conn)
if bool(these_datasets):
datasets[species][group][type_name[0]] = these_datasets
return datasets
def build_datasets(species, group, type_name, conn):
"""Gets dataset names from database"""
dataset_text = dataset_value = None
datasets = []
with conn.cursor() as cursor:
if type_name == "Phenotypes":
cursor.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))
results = cursor.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"
datasets.append([dataset_id, dataset_value, dataset_text])
else:
cursor.execute(
("SELECT PublishFreeze.Name, PublishFreeze.FullName "
"FROM PublishFreeze, InbredSet "
"WHERE InbredSet.Name = '{}' AND "
"PublishFreeze.InbredSetId = InbredSet.Id "
"ORDER BY PublishFreeze.CreateTime ASC")
.format(group))
result = cursor.fetchone()
dataset_id = "None"
dataset_value = str(result[0])
dataset_text = str(result[1])
datasets.append([dataset_id, dataset_value, dataset_text])
elif type_name == "Genotypes":
cursor.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))
results = cursor.fetchone()
dataset_id = "None"
if bool(results):
dataset_id = str(results[0])
dataset_value = "%sGeno" % group
dataset_text = "%s Genotypes" % group
datasets.append([dataset_id, dataset_value, dataset_text])
else: # for mRNA expression/ProbeSet
cursor.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 "
"AND ProbeSetFreeze.public > 0 "
"ORDER BY -ProbeSetFreeze.OrderList DESC, "
"ProbeSetFreeze.CreateTime "
"DESC").format(species, group, type_name))
results = cursor.fetchall()
datasets = []
for dataset_info in results:
this_dataset_info = []
for info in dataset_info:
this_dataset_info.append(str(info))
datasets.append(this_dataset_info)
return datasets
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