29 lines
1.5 KiB
Python
29 lines
1.5 KiB
Python
import pandas as pd
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import configparser
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import subprocess
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import os
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# read database credentials
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group = snakemake.params["group"]
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config = configparser.ConfigParser()
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config.read(snakemake.input["db_credentials"])
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# bash command to create table and restore tables from sql file
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checkdb_cmd = "mysql -h " + config[group]["host"] + " -u " + config[group]["user"] + " -p" + config[group]["password"] + " -e use " + config[group]["database"]
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create_cmd = "mysql -h " + config[group]["host"] + " -u " + config[group]["user"] + " -p" + config[group]["password"] + " -e \"CREATE DATABASE IF NOT EXISTS " + config[group]["database"] + ";\""
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restore_cmd = "mysql -h " + config[group]["host"] + " -u " + config[group]["user"] + " -p" + config[group]["password"] + " " + config[group]["database"] + " < data/external/rapids_example.sql"
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try:
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print("Checking if " + config[group]["database"] + " database exists")
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subprocess.run(checkdb_cmd.split(), check = True, stdout=subprocess.DEVNULL, stderr=subprocess.STDOUT)
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except subprocess.CalledProcessError:
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print(config[group]["database"] + " database does not exist")
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print("Creating " + config[group]["database"] + " database")
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os.system(create_cmd)
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print(config[group]["database"] + " database created")
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print("Restoring rapids_example.sql")
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os.system(restore_cmd)
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print("rapids_example.sql restored in " + config[group]["database"] + " database")
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else:
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raise ValueError(config[group]["database"] + " DB already exists")
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