deepSepsis/preprocessing.py at master · cbmi-uthsc/deepSepsis · GitHub

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''' This file will be used to pre process the data from the CITI site

    Using the tutorial provided in the eICU site

    Getting the data using login credentials '''

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import psycopg2
import getpass
import pdvega

# for configuring connection
from configobj import ConfigObj
import os


config='../db/config.ini'

# connection info
conn_info = dict()
if os.path.isfile(config):
    config = ConfigObj(config)
    conn_info["sqluser"] = config['username']
    conn_info["sqlpass"] = config['password']
    conn_info["sqlhost"] = config['host']
    conn_info["sqlport"] = config['port']
    conn_info["dbname"] = config['dbname']
    conn_info["schema_name"] = config['schema_name']
else:
    conn_info["sqluser"] = 'postgres'
    conn_info["sqlpass"] = ''
    conn_info["sqlhost"] = 'localhost'
    conn_info["sqlport"] = 5432
    conn_info["dbname"] = 'eicu'
    conn_info["schema_name"] = 'public,eicu_crd'

# Connect to the eICU database
print('Database: {}'.format(conn_info['dbname']))
print('Username: {}'.format(conn_info["sqluser"]))
if conn_info["sqlpass"] == '':
    # try connecting without password, i.e. peer or OS authentication
    try:
        if (conn_info["sqlhost"] == 'localhost') & (conn_info["sqlport"]=='5432'):
            con = psycopg2.connect(dbname=conn_info["dbname"],
                                   user=conn_info["sqluser"])
        else:
            con = psycopg2.connect(dbname=conn_info["dbname"],
                                   host=conn_info["sqlhost"],
                                   port=conn_info["sqlport"],
                                   user=conn_info["sqluser"])
    except:
        conn_info["sqlpass"] = getpass.getpass('Password: ')

        con = psycopg2.connect(dbname=conn_info["dbname"],
                               host=conn_info["sqlhost"],
                               port=conn_info["sqlport"],
                               user=conn_info["sqluser"],
                               password=conn_info["sqlpass"])
query_schema = 'set search_path to ' + conn_info['schema_name'] + ';'


# After acquiring login credential pre processing can be done on data using apache spark or pandas