"""Script that generates the data for the main dropdown menus on the home page

Writes out data as /static/new/javascript/dataset_menu_structure.json
It needs to be run manually when database has been changed.

"""

# 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
# at rwilliams@uthsc.edu 
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)

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):
    """Fetches tissues
    
    Gets the tissues with data for this species/group
    (all types except phenotype/genotype are tissues)
     
    """
    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):
    """Gets dataset names from database"""
    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():
    """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
    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)

    print("\nWrote file to:", output_file)


def _test_it():
    """Used for internal testing only"""
    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()