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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
# This script is to generate the data for the main menus on the home page
# It needs to be run manually when database has been changed .
from __future__ import print_function, division
import sys
sys.path.insert(0, "..")
import MySQLdb
import simplejson as json
from pprint import pformat as pf
from base import webqtlConfig
# build MySql database connection
Con = MySQLdb.Connect(db=webqtlConfig.DB_NAME,host=webqtlConfig.MYSQL_SERVER,
user=webqtlConfig.DB_USER,
passwd=webqtlConfig.DB_PASSWD)
Cursor = Con.cursor()
def get_species():
"""Build species list"""
Cursor.execute("select Name, MenuName from Species order by OrderId")
species = list(Cursor.fetchall())
return species
def get_groups(species):
"""Build groups list"""
groups = {}
for species_name, _species_full_name in species:
Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet,
Species,
ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = %s
and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and
(PublishFreeze.InbredSetId = InbredSet.Id
or GenoFreeze.InbredSetId = InbredSet.Id
or ProbeFreeze.InbredSetId = InbredSet.Id)
group by InbredSet.Name
order by InbredSet.Name""", (species_name))
groups[species_name] = list(Cursor.fetchall())
return groups
def get_types(groups):
"""Build types list"""
types = {}
for species, group_dict in groups.iteritems():
types[species] = {}
for group_name, _group_full_name in group_dict:
# make group an alias to shorten the code
types[species][group_name] = [("Phenotypes", "Phenotypes"), ("Genotypes", "Genotypes")]
types[species][group_name] += build_types(species, group_name)
return types
def build_types(species, group):
Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA')
from ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species
where Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
ProbeFreeze.TissueId = Tissue.Id and
ProbeFreeze.InbredSetId = InbredSet.Id and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
ProbeSetFreeze.public > %s
order by Tissue.Name""", (species, group, webqtlConfig.PUBLICTHRESH))
return Cursor.fetchall()
def get_datasets(types):
"""Build datasets list"""
datasets = {}
for species, group_dict in types.iteritems():
datasets[species] = {}
for group, type_list in group_dict.iteritems():
datasets[species][group] = {}
for type_name, type_full_name in type_list:
datasets[species][group][type_name] = build_datasets(species, group, type_name)
return datasets
def build_datasets(species, group, type_name):
dataset_text = dataset_value = None
if type_name == "Phenotypes":
dataset_value = "%sPublish" % group
if group == 'MDP':
dataset_text = "Mouse Phenome Database"
else:
dataset_text = "%s Published Phenotypes" % group
elif type_name == "Genotypes":
dataset_value = "%sGeno" % group
dataset_text = "%s Genotypes" % group
if dataset_value:
return [(dataset_value, dataset_text)]
else:
Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
Species.Name = %s and Species.Id = InbredSet.SpeciesId and
InbredSet.Name = %s and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = %s
and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId =
InbredSet.Id and ProbeSetFreeze.public > %s order by
ProbeSetFreeze.CreateTime desc""", (
species, group, type_name, webqtlConfig.PUBLICTHRESH))
return Cursor.fetchall()
def main():
species = get_species()
groups = get_groups(species)
types = get_types(groups)
datasets = get_datasets(types)
species.append(('All Species', 'All Species'))
groups['All Species'] = [('All Groups', 'All Groups')]
types['All Species'] = {}
types['All Species']['All Groups'] = [('Phenotypes', 'Phenotypes')]
datasets['All Species'] = {}
datasets['All Species']['All Groups'] = {}
datasets['All Species']['All Groups']['Phenotypes'] = [('All Phenotypes','All Phenotypes')]
data = dict(species=species,
groups=groups,
types=types,
datasets=datasets,
)
output_file = """../wqflask/static/new/javascript/dataset_menu_structure"""
with open(output_file, 'w') as fh:
json.dump(data, fh, indent=" ", sort_keys=True)
print("\nWrote file to:", output_file)
def test_it():
types = build_types("Mouse", "BXD")
print("build_types:", pf(types))
datasets = build_datasets("Mouse", "BXD", "Hippocampus")
print("build_datasets:", pf(datasets))
if __name__ == '__main__':
main()
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