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import mysql.connector as con
mycon = con.connect(host="192.168.1.6",user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
mycursor = mycon.cursor()
sql_select_Query = "select * from curieweb where done=0 LIMIT 1"
mycursor.execute(sql_select_Query)
records = mycursor.fetchall()
def email(zipArchive):
import smtplib
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from email.mime.base import MIMEBase
from email import encoders
fromaddr = "navanchauhan@gmail.com"
toaddr = toEmail
msg = MIMEMultipart()
msg['From'] = fromaddr
msg['To'] = toaddr
msg['Subject'] = "Curie Web Results for Job ID " + str(jobID)
body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description)
msg.attach(MIMEText(body, 'plain'))
filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
attachment = open((str(zipArchive) + ".zip"), "rb")
p = MIMEBase('application', 'octet-stream')
p.set_payload((attachment).read())
encoders.encode_base64(p)
p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p)
s = smtplib.SMTP('smtp.gmail.com', 587)
s.starttls()
s.login(fromaddr, 'ircd mday avbc tice')
text = msg.as_string()
s.sendmail(fromaddr, toaddr, text)
s.quit()
receptor_name = "protein.pdbqt"
ligand_name = "ligand.pdbqt"
description = "Curie Web Task"
#print(records[0])
r = records[0]
jobID = r[0]
toEmail = r[1]
targetB = r[2]
if r[3] != None:
receptor_name = str(r[3])
if r[6] != None:
ligand_name = str(r[6])
ligandB = r[4]
configB = r[7]
date = r[8]
if r[9] != None:
description = r[9]
import os
cd = os.getcwd()
f = os.path.join(cd,"static/uploads")
#t = os.path.join(f,"receptor",target)
#r = os.path.join(f,"ligands",ligand)
#c = os.path.join(f,"configs",config)
print(f)
import tempfile
from shutil import copy
from shutil import make_archive
with tempfile.TemporaryDirectory() as directory:
print('The created temporary directory is %s' % directory)
os.chdir(directory)
# copy(t,os.getcwd())
# copy(r,os.getcwd())
# copy(c, os.getcwd())
file = open(receptor_name,"wb")
file.write(targetB)
file.close()
file = open(ligand_name,"wb")
file.write(ligandB)
file.close()
file = open("config.txt","wb")
file.write(configB)
file.close()
os.system("docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) navanchauhan/curie-cli -r %s -l %s -c config.txt -dpi" % (receptor_name,ligand_name))
#copy("report.pdf",f)
z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z)
make_archive(zi, 'zip', directory)
#copy(("Curie_Web_Result_"+str(jobID)),f)
email(zi)
#print((str(zi) + ".zip"))
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
mycon.commit()
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