From b808d0f36c299120b175b20d7158c926ebbe3f55 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Mon, 6 Jul 2020 18:57:35 +0530
Subject: updated docking file and DBtester

---
 app/dock_docker.py | 99 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 99 insertions(+)
 create mode 100644 app/dock_docker.py

(limited to 'app/dock_docker.py')

diff --git a/app/dock_docker.py b/app/dock_docker.py
new file mode 100644
index 0000000..2e13253
--- /dev/null
+++ b/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()    
\ No newline at end of file
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