import argparse
import os

from py2neo import Graph
import mysql.connector
import parser

user = "neo4j"
pwd = "neo5j"
DATAPORTAL_DB = Graph("bolt://dataportal.europdx.eu:7687", auth=(user, pwd), secure=True)

def load_neo4j_data():
    pdxmodels_cna = DATAPORTAL_DB.run(
        "MATCH(mc:ModelCreation)--(s:Sample)--(mo:MolecularCharacterization)--(ma:MarkerAssociation)--(m:Marker) "
        "WHERE (mo.type=\"copy number alteration\") RETURN mc.sourcePdxId, ma.cnaLog2RCNA, ma.copyNumberStatus, "
        "m.ncbiGeneId")
    pdxmodels_mut = DATAPORTAL_DB.run(
        "MATCH(mc:ModelCreation)--(s:Sample)--(mo:MolecularCharacterization)--(ma:MarkerAssociation)--(m:Marker) "
        "WHERE (mo.type=\"mutation\") RETURN mc, ma, m")


    # cna[0] == ModelCreation, cna[1] == MarkerAssociation, cna[2] == Marker
    # ========== CNA =============
    print("CNA")
    cna_list = []  # [modelID, valueOf, entrezID]}
    for cna in pdxmodels_cna:
        copy_number_status = cna[2]
        gistic_val = ""
        if copy_number_status:
            copy_number_status = copy_number_status.lower()
            if copy_number_status == "amplification":
                gistic_val = 2
            if copy_number_status == "gain":
                gistic_val = 1
            if copy_number_status == "normal":
                gistic_val = 0
            if copy_number_status == "heterozygous loss":
                gistic_val = -1
            if copy_number_status == "homozygous deletion":
                gistic_val = -2

        if gistic_val:
            cna_list.append([cna[0], gistic_val, cna[2]["ncbiGeneId"], "gistic"])
        if cna[1]:
            cna_list.append([cna[0], cna[1], cna[3], "log2CNA"])

    # ========== CNA =============

    # ========== Mutation =============
    print("MUT")
    mut_list = []
    for mut in pdxmodels_mut:
        mut_list.append([
            mut[0]["sourcePdxId"],  # Model ID
            mut[2]["hgncSymbol"],   # hugo
            mut[2]["ncbiGeneId"],   # entrez
            mut[1]["chromosome"],
            mut[1]['seq_start_position'],
            mut[1]["consequence"],
            mut[1]["amino_acid_change"]
            ]
        )

    # ========== Mutation =============
    return cna_list, mut_list


def import_SQL_cna(cna_data, mydb, cursor):
    stable_id_command = "SELECT StableID.id From StableID JOIN PDXmodel ON PDXmodel.id=StableID.pdxmodel_ID WHERE PDXmodel.pdxmodel_id=%s AND StableID.stable_id=%s"
    insert_cna_command = "INSERT INTO CNA (stable_id_ID, entrez_gene_id, value_of) VALUES (%s, %s, %s)"
    print("import CNA")
    for cna in cna_data:
        cursor.execute(stable_id_command,(cna[0], cna[3]))
        stable_id_id = cursor.fetchall()[0][0]
        if stable_id_id:
            cursor.execute(insert_cna_command, (stable_id_id, cna[2], cna[1]))
        if not stable_id_id:
            print("not for " + cna[0] )
            stable_id_id = parser.create_stable(cna[0],cna[3],cursor)
            cursor.execute(insert_cna_command, (stable_id_id, cna[2], cna[1]))
    print("import CNA done")
    mydb.commit()


def import_SQL_mut(mut_data, mydb, cursor, ncbi_build):
    pdxmodel_in_db_command = "SELECT * FROM PDXmodel WHERE PDXmodel.pdxmodel_id=%s"
    insert_mutation_command = "INSERT INTO Mutation (pdxmodel_ID, hugo_symbol, entrez_gene_id, chromosome, start_position, variant_classification, HGVSp_Short, ncbi_build) VALUES (%s, %s, %s, %s, %s, %s, %s, %s)"
    print("import mut")
    for mut in mut_data:
        cursor.execute(pdxmodel_in_db_command, (mut[0],))
        result = cursor.fetchall()
        pdxmodel_database_id = result[0][0]
        ncbi_gene_id = mut[2]
        if ncbi_gene_id == "":
            ncbi_gene_id = None
        cursor.execute(insert_mutation_command, (pdxmodel_database_id, mut[1], ncbi_gene_id, mut[3], mut[4], mut[5], mut[6], ncbi_build))
    print("import mut done")
    mydb.commit()

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("-host", help="database host")
    parser.add_argument("-database", help="database name")
    args = parser.parse_args()
    HOST = args.host
    USER = 'dhuser'
    PASSWD = 'dhpwd'
    DATABASE = args.database

    if os.environ.get('HOST') is not None:
        HOST=os.environ.get('HOST')

    if os.environ.get('DATABASE') is not None:
        DATABASE=os.environ.get('DATABASE')
    mydb = mysql.connector.connect(
        host=HOST,
        user=USER,
        passwd=PASSWD,
        db=DATABASE
    )
    cursor = mydb.cursor(buffered=True)
    mydb.autocommit = True

    cnas, muts = load_neo4j_data()
    import_SQL_cna(cnas, mydb, cursor)
    import_SQL_mut(muts, mydb, cursor)
    print()


if __name__ == "__main__":
    main()