added github action and local tests
This commit is contained in:
parent
9ef980067d
commit
a9c8e275e5
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@ -1,17 +1,50 @@
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import os
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import mysql.connector as con
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import mysql.connector as con
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from mysql.connector.errors import InterfaceError
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from mysql.connector.errors import InterfaceError
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import sys
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GitHubWorkflow = True
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try:
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print(os.environ['GITHUB_ACTIONS'])
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except:
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GitHubWorkflow = False
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def returnValue(key):
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return os.environ[key]
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if GitHubWorkflow:
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host = returnValue("CURIE_HOST")
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db = returnValue("CURIE_DB")
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user = returnValue("CURIE_USER")
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port = returnValue("CURIE_PORT")
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password = returnValue("CURIE_PASSWORD")
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fromaddr = returnValue("CURIE_EMAIL")
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emailServer = returnValue("CURIE_EMAIL_SERVER")
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emailPort = returnValye("CURIE_EMAIL_PORT")
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emailPassword = returnValye("CURIE_EMAIL_PASSWORD")
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else:
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import configparser
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import configparser
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config = configparser.ConfigParser()
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config = configparser.ConfigParser()
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config.read('config.ini')
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config.read('config.ini')
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try:
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try:
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config['DATABASE']
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config['DATABASE']
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except KeyError:
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except KeyError:
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config.read("../config.ini")
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config.read("../config.ini")
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v = config['DATABASE']
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host = v['HOST']
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db = v['NAME']
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user = v['USER']
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password = v['PASSWORD']
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port = v['PORT']
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fromaddr = config['SMTP']['EMAIL']
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emailServer = config['SMTP']['SERVER']
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emailPort = config['SMTP']['PORT']
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emailPassword = config['SMTP']['PASSWORD']
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try:
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try:
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mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
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mycon = con.connect(host=host,user=user,password=password,port=port,database=db)
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except InterfaceError:
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except InterfaceError:
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print("Could not connect to the database")
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print("Could not connect to the database")
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sys.exit(1)
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sys.exit(1)
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@ -30,7 +63,7 @@ def email(compressedFile):
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from email.mime.base import MIMEBase
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from email.mime.base import MIMEBase
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from email import encoders
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from email import encoders
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fromaddr = config['SMTP']['EMAIL']
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fromaddr = fromaddr
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toaddr = toEmail
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toaddr = toEmail
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msg = MIMEMultipart()
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msg = MIMEMultipart()
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@ -48,9 +81,9 @@ def email(compressedFile):
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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msg.attach(p)
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s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT'])
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s = smtplib.SMTP(emailServer, emailPort)
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s.starttls()
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s.starttls()
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s.login(fromaddr, config['SMTP']['PASSWORD'])
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s.login(fromaddr, emailPassword)
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text = msg.as_string()
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text = msg.as_string()
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@ -59,7 +92,7 @@ def email(compressedFile):
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receptor_name = "protein.pdbqt"
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receptor_name = "protein.pdbqt"
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ligand_name = "ligand.pdbqt"
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ligand_name = "ligand.pdbqt"
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description = "GitHub Action Test"
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description = "Test"
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#print(records[0])
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#print(records[0])
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r = records[0]
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r = records[0]
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@ -103,6 +136,7 @@ with tempfile.TemporaryDirectory() as directory:
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z = "Curie_Web_Result_"+str(jobID)
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z = "Curie_Web_Result_"+str(jobID)
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zi = os.path.join(f,z)
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zi = os.path.join(f,z)
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make_archive(zi, 'zip', directory)
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make_archive(zi, 'zip', directory)
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#email(zi)
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email(zi)
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mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
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mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
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mycon.commit()
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mycon.commit()
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@ -1,4 +1,28 @@
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import os
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import mysql.connector as con
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import mysql.connector as con
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from mysql.connector.errors import InterfaceError
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GitHubWorkflow = True
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try:
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print(os.environ['GITHUB_ACTIONS'])
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except:
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GitHubWorkflow = False
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def returnValue(key):
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return os.environ[key]
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if GitHubWorkflow:
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host = returnValue("CURIE_HOST")
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db = returnValue("CURIE_DB")
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user = returnValue("CURIE_USER")
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port = returnValue("CURIE_PORT")
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password = returnValue("CURIE_PASSWORD")
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fromaddr = returnValue("CURIE_EMAIL")
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emailServer = returnValue("CURIE_EMAIL_SERVER")
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emailPort = returnValye("CURIE_EMAIL_PORT")
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emailPassword = returnValye("CURIE_EMAIL_PASSWORD")
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else:
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import configparser
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import configparser
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config = configparser.ConfigParser()
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config = configparser.ConfigParser()
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config.read('config.ini')
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config.read('config.ini')
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@ -6,7 +30,25 @@ try:
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config['DATABASE']
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config['DATABASE']
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except KeyError:
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except KeyError:
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config.read("../config.ini")
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config.read("../config.ini")
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mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
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v = config['DATABASE']
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host = v['HOST']
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db = v['NAME']
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user = v['USER']
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password = v['PASSWORD']
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port = v['PORT']
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fromaddr = config['SMTP']['EMAIL']
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emailServer = config['SMTP']['SERVER']
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emailPort = config['SMTP']['PORT']
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emailPassword = config['SMTP']['PASSWORD']
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try:
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mycon = con.connect(host=host,user=user,password=password,port=port,database=db)
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except InterfaceError:
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print("Could not connect to the database")
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sys.exit(1)
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mycursor = mycon.cursor()
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mycursor = mycon.cursor()
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done = 1
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done = 1
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@ -1,14 +1,54 @@
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import os
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import mysql.connector as con
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import mysql.connector as con
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from mysql.connector.errors import InterfaceError
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GitHubWorkflow = True
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try:
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print(os.environ['GITHUB_ACTIONS'])
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except:
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GitHubWorkflow = False
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def returnValue(key):
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return os.environ[key]
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if GitHubWorkflow:
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host = returnValue("CURIE_HOST")
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db = returnValue("CURIE_DB")
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user = returnValue("CURIE_USER")
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port = returnValue("CURIE_PORT")
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password = returnValue("CURIE_PASSWORD")
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fromaddr = returnValue("CURIE_EMAIL")
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emailServer = returnValue("CURIE_EMAIL_SERVER")
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emailPort = returnValye("CURIE_EMAIL_PORT")
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emailPassword = returnValye("CURIE_EMAIL_PASSWORD")
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else:
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import configparser
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import configparser
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config = configparser.ConfigParser()
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config = configparser.ConfigParser()
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config.read('config.ini')
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config.read('config.ini')
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try:
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try:
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config['DATABASE']
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config['DATABASE']
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except KeyError:
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except KeyError:
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config.read("../config.ini")
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config.read("../config.ini")
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v = config['DATABASE']
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host = v['HOST']
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db = v['NAME']
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user = v['USER']
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password = v['PASSWORD']
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port = v['PORT']
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fromaddr = config['SMTP']['EMAIL']
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emailServer = config['SMTP']['SERVER']
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emailPort = config['SMTP']['PORT']
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emailPassword = config['SMTP']['PASSWORD']
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try:
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mycon = con.connect(host=host,user=user,password=password,port=port,database=db)
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except InterfaceError:
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print("Could not connect to the database")
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sys.exit(1)
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mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
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mycursor = mycon.cursor()
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mycursor = mycon.cursor()
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print("Removing Test Query")
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print("Removing Test Query")
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