navan
/
Curie-Web
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removed extra files and changed zi to zipArchive

This commit is contained in:
Navan Chauhan 2020-07-07 12:22:30 +05:30
parent c74428d94a
commit 6a67fd7e8b
5 changed files with 2 additions and 192 deletions
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99
app/backend_test.py
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@ -1,99 +0,0 @@
import mysql.connector as con
mycon = con.connect(host="navanspi.duckdns.org",user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
mycursor = mycon.cursor()
sql_select_Query = 'select * from curieweb where id="18u3r0chcf6nr6mj" 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])
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()

17
app/create_table.py
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@ -1,17 +0,0 @@
import mysql.connector as con
mycon = con.connect(host="sql12.freesqldatabase.com",user="sql12352288",password="7X35JENbK3",port=3306,database="sql12352288")
mycursor = mycon.cursor()
try:
mycursor.execute("create table curie (id INT PRIMARY KEY, email VARCHAR(255), receptor VARCHAR(255), ligand VARCHAR(255), config VARCHAR(255), date DATE, description VARCHAR(255),done TINYINT DEFAULT 0)")
except con.ProgrammingError:
print("Table Already Exists!")
try:
mycursor.execute("insert into curie values (1,'navanchauhan@gmail.com','lu.pdbqt','test.pdbqt','owo.txt',CURDATE(),'CURIE WEB TASK',0)")
except con.IntegrityError:
print("Duplicate Entry For Primary Key!")
mycon.commit()

69
app/dbTestFiller.py
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@ -1,69 +0,0 @@
import mysql.connector as con
debug = False
host = "navanspi.duckdns.org"
done = 1
if debug != False:
host = "192.168.1.6"
done = 0
mycon = con.connect(host=host,user="curieweb",password="curie-web-russian-54",port=3306,database="curie")
mycursor = mycon.cursor()
try:
mycursor.execute("create table curieweb ( id varchar(16) primary key, email nvarchar(255) NOT NULL, protein LONGBLOB NOT NULL, protein_name VARCHAR(255), ligand_pdbqt LONGBLOB, ligand_smile VARCHAR(255), ligand_name VARCHAR(255), config LONGBLOB NOT NULL, date DATE, description VARCHAR(255), done TINYINT DEFAULT 0)")
except con.ProgrammingError:
print("Table Already Exists!")
#try:
# mycursor.execute("insert into curieweb values (1,'navanchauhan@gmail.com','lu.pdbqt','test.pdbqt','owo.txt',CURDATE(),'CURIE WEB TASK',0)")
#except con.IntegrityError:
# print("Duplicate Entry For Primary Key!")
from random import choice, shuffle
from string import digits, ascii_lowercase
def gen_word(N, min_N_dig, min_N_low):
choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
choose_from.extend([digits + ascii_lowercase] * (N-min_N_low-min_N_dig))
chars = [choice(bet) for bet in choose_from]
shuffle(chars)
return ''.join(chars)
def convertToBinaryData(filename):
with open(filename, 'rb') as file:
binaryData = file.read()
return binaryData
from os.path import basename
ligand = convertToBinaryData("./static/uploads/ligands/test.pdbqt")
receptor = convertToBinaryData("static/uploads/receptor/lu.pdbqt")
config = convertToBinaryData("static/uploads/configs/owo.txt")
ligandName = "Eucalyptol"
receptorName = "6LU7"
sqlQuery = "insert into curieweb (id, email, protein, protein_name, ligand_pdbqt, ligand_name,date, config,done) values (%s,%s,%s,%s,%s,%s,CURDATE(),%s,%s) "
jobID = gen_word(16, 1, 1)
print("Succesfuly submitted Job ID:",jobID)
insert_tuple = (jobID,"navanchauhan@gmail.com",receptor,receptorName,ligand,ligandName,config,done)
try:
mycursor.execute(sqlQuery,insert_tuple)
except con.IntegrityError:
print("Oops, Collision occured. Generating new Job ID and trying again.")
jobID = gen_word(16, 1, 1)
insert_tuple = (jobID,"navanchauhan@gmail.com",receptor,receptorName,ligand,ligandName,config,done)
mycursor.execute(sqlQuery,insert_tuple)
print("Removing Test Query")
q = 'delete from curieweb where id="%s"' % (jobID)
mycursor.execute(q)
mycon.commit()
print("Database working perfectly")

4
app/dock_docker.py
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@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
records = mycursor.fetchall()
def email(zi):
def email(zipArchive):
import smtplib
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
@ -26,7 +26,7 @@ def email(zi):
msg.attach(MIMEText(body, 'plain'))
filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
attachment = open((str(zi) + ".zip"), "rb")
attachment = open((str(zipArchive) + ".zip"), "rb")
p = MIMEBase('application', 'octet-stream')
p.set_payload((attachment).read())
encoders.encode_base64(p)

5
app/test.py
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@ -1,5 +0,0 @@
import mysql.connector as con
mycon = con.connect(host="sql12.freesqldatabase.com",user="sql12352288",password="7X35JENbK3",port=3306,database="sql12352288")
mycursor = mycon.cursor()
mycursor.execute("SELECT COUNT(*) FROM curie")
id = mycursor.fetchall()[0][0]