100 lines
3.2 KiB
Python
100 lines
3.2 KiB
Python
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import mysql.connector as con
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mycon = con.connect(host="navanspi.duckdns.org",user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
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mycursor = mycon.cursor()
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# If we are running the CI on an actual server, try using the 6LU7 Mpro and Geraniin Job ID because Eucalyptol fails
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sql_select_Query = 'select * from curieweb where id="l9xo2isr98oepcia" LIMIT 1'
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mycursor.execute(sql_select_Query)
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records = mycursor.fetchall()
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def email(zi):
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import smtplib
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from email.mime.multipart import MIMEMultipart
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from email.mime.text import MIMEText
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from email.mime.base import MIMEBase
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from email import encoders
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fromaddr = "navanchauhan@gmail.com"
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toaddr = toEmail
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msg = MIMEMultipart()
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msg['From'] = fromaddr
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msg['To'] = toaddr
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msg['Subject'] = "Curie Web Results for Job ID " + str(jobID)
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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)
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msg.attach(MIMEText(body, 'plain'))
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filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
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attachment = open((str(zi) + ".zip"), "rb")
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p = MIMEBase('application', 'octet-stream')
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p.set_payload((attachment).read())
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encoders.encode_base64(p)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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s = smtplib.SMTP('smtp.gmail.com', 587)
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s.starttls()
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s.login(fromaddr, 'ircd mday avbc tice')
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text = msg.as_string()
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s.sendmail(fromaddr, toaddr, text)
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s.quit()
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receptor_name = "protein.pdbqt"
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ligand_name = "ligand.pdbqt"
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description = "GitHub Action Test"
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#print(records[0])
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r = records[0]
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jobID = r[0]
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toEmail = r[1]
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targetB = r[2]
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if r[3] != None:
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receptor_name = str(r[3])
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if r[6] != None:
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ligand_name = str(r[6])
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ligandB = r[4]
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configB = r[7]
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date = r[8]
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if r[9] != None:
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description = r[9]
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import os
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cd = os.getcwd()
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f = os.path.join(cd,"static/uploads")
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#t = os.path.join(f,"receptor",target)
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#r = os.path.join(f,"ligands",ligand)
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#c = os.path.join(f,"configs",config)
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print(f)
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import tempfile
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from shutil import copy
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from shutil import make_archive
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with tempfile.TemporaryDirectory() as directory:
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print('The created temporary directory is %s' % directory)
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os.chdir(directory)
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# copy(t,os.getcwd())
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# copy(r,os.getcwd())
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# copy(c, os.getcwd())
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file = open(receptor_name,"wb")
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file.write(targetB)
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file.close()
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file = open(ligand_name,"wb")
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file.write(ligandB)
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file.close()
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file = open("config.txt","wb")
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file.write(configB)
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file.close()
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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))
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#copy("report.pdf",f)
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z = "Curie_Web_Result_"+str(jobID)
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zi = os.path.join(f,z)
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make_archive(zi, 'zip', directory)
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#copy(("Curie_Web_Result_"+str(jobID)),f)
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email(zi)
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#print((str(zi) + ".zip"))
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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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