updated docking file and DBtester

app/dock_docker.py

@@ -0,0 +1,99 @@
+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(zi):
+    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(zi) + ".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]) + ".pdbqt"
+if r[6] != None:
+    ligand_name = str(r[6]) + ".pdbqt"
+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()