22 lines
999 B
Python
22 lines
999 B
Python
|
import pandas as pd
|
||
|
|
import configparser
|
||
|
|
import os
|
||
|
|
|
||
|
|
# read database credentials
|
||
|
|
group = snakemake.params["group"]
|
||
|
|
config = configparser.ConfigParser()
|
||
|
|
config.read(snakemake.input["db_credentials"])
|
||
|
|
|
||
|
|
# bash command to create table and restore tables from sql file
|
||
|
|
checkdb_cmd = "mysql -h " + config[group]["host"] + " -u " + config[group]["user"] + " -p" + config[group]["password"] + " -e \"use " + config[group]["database"] + "\""
|
||
|
|
create_cmd = "mysql -h " + config[group]["host"] + " -u " + config[group]["user"] + " -p" + config[group]["password"] + " -e \"CREATE DATABASE IF NOT EXISTS " + config[group]["database"] + ";\""
|
||
|
|
restore_cmd = "mysql -h " + config[group]["host"] + " -u " + config[group]["user"] + " -p" + config[group]["password"] + " " + config[group]["database"] + " < data/external/" + config[group]["database"] + ".sql"
|
||
|
|
|
||
|
|
try:
|
||
|
|
os.system(checkdb_cmd)
|
||
|
|
except:
|
||
|
|
print(config[group]["database"] + " DB already exists.")
|
||
|
|
else:
|
||
|
|
os.system(create_cmd)
|
||
|
|
os.system(restore_cmd)
|