# 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
            group = types[species][group_name] = [("Phenotypes", "Phenotypes"),
                                                  ("Genotypes", "Genotypes")]           
            Cursor.execute("""select distinct Tissue.Name, concat(Tissue.Name, ' mRNA') from
                       ProbeFreeze,
                       ProbeSetFreeze, InbredSet, Tissue where ProbeFreeze.TissueId = Tissue.Id and
                       ProbeFreeze.InbredSetId = InbredSet.Id and
                       InbredSet.Name = %s and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
                       ProbeSetFreeze.public > %s
                       order by Tissue.Name""", (group_name, webqtlConfig.PUBLICTHRESH))
            group += Cursor.fetchall()
    return types


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:
                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:
                    datasets[species][group][type_name] = [(dataset_value, dataset_text)]
                else:
                    Cursor.execute("""select ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
                                ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue where
                                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""", (type_name,
                                                                    webqtlConfig.PUBLICTHRESH))
                    datasets[species][group][type_name] = Cursor.fetchall()
            
    return datasets


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.json"""
    
    with open(output_file, 'w') as fh:
        json.dump(data, fh, indent="   ", sort_keys=True)
    

if __name__ == '__main__':
    main()