# 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)
#
# Created by GeneNetwork Core Team 2010/08/10
# Updated on Lei Yan 2011/02/08
# created by Lei Yan 02/08/2011

"""
Script responsible for updating the GenerRIF_BASIC table
"""

import os
import sys
import MySQLdb

path1 = os.path.abspath(os.path.dirname(__file__))
path2 = path1 + "/.."
path3 = path1 + "/../../tmp"
sys.path.insert(0, path2)


def fetchrif():
    """ TODO: break this down into modules """
    try:
        con = MySQLdb.Connect(db="gn3", host="localhost", user="gn2", passwd="password")
        cursor = con.cursor()
        print("You have successfully connected to mysql.\n")
    except:
        print("You entered incorrect password.\n")
        sys.exit(0)

    tax_ids = {"10090": 1, "9606": 4, "10116": 2, "3702": 3}
    tax_id_keys = tax_ids.keys()

    os.chdir(path3)
    print(f"path3: {path3}")
    genedict = {}

    os.system("rm -vf gene_info")
    os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz")
    os.system("gunzip gene_info.gz")

    with open("gene_info", "r") as file:
        i = 0
        for line1 in file:
            line1 = line1.strip()
            if line1.startswith("#"):
                continue
            line2 = line1.strip().split("\t")
            if line2[0] in tax_id_keys:
                genedict[line2[1]] = line2[2]
            i += 1
            if i % 1000000 == 0:
                print(f"finished: {i}")
        print(f"finished all: {i}")

    os.system("rm -vf generifs_basic")
    os.system("wget ftp://ftp.ncbi.nlm.nih.gov/gene/GeneRIF/generifs_basic.gz")
    os.system("gunzip generifs_basic.gz")

    with open("generifs_basic", "r") as file:
        i = 0
        for line1 in file:
            line1 = line1.strip()
            if line1.startswith("#"):
                continue
            line2 = line1.strip().split("\t")
            if line2[0] in tax_id_keys and len(line2) >= 5:
                line2[0] = tax_ids[line2[0]]
                try:
                    symbol = genedict[line2[1]]
                except:
                    symbol = ""
                sql = """
                                    SELECT COUNT(*)
                                    FROM GeneRIF_BASIC
                                    WHERE GeneRIF_BASIC.`SpeciesId`=%s
                                    AND GeneRIF_BASIC.`GeneId`=%s
                                    AND GeneRIF_BASIC.`PubMed_ID`=%s
                                    AND GeneRIF_BASIC.`createtime`=%s
                                    AND GeneRIF_BASIC.`comment`=%s
                                    """
                cursor.execute(sql, (line2[0], line2[1], line2[2], line2[3], line2[4]))
                count = cursor.fetchone()[0]
                if count == 0:
                    print("to insert...")
                    sql = """
                                            INSERT INTO GeneRIF_BASIC
                                            SET GeneRIF_BASIC.`SpeciesId`=%s,
                                                    GeneRIF_BASIC.`GeneId`=%s,
                                                    GeneRIF_BASIC.`symbol`=%s,
                                                    GeneRIF_BASIC.`PubMed_ID`=%s,
                                                    GeneRIF_BASIC.`createtime`=%s,
                                                    GeneRIF_BASIC.`comment`=%s
                                            """
                    cursor.execute(
                        sql, (line2[0], line2[1], symbol, line2[2], line2[3], line2[4])
                    )
            i += 1
            if i % 100000 == 0:
                print(f"finished: {i}")
        print(f"finished all: {i}")
        cursor.close()


# /usr/bin/python addRif.py

if __name__ == "__main__":
    print(f"command line arguments:\n\t{sys.argv}")
    fetchrif()
    print("exit successfully")