1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
|
import mysql.connector as con
from mysql.connector.errors import InterfaceError
import sys
import configparser
config = configparser.ConfigParser()
config.read('config.ini')
try:
config['DATABASE']
except KeyError:
config.read("../config.ini")
try:
mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME'])
except InterfaceError:
print("Could not connect to the database")
sys.exit(1)
mycursor = mycon.cursor()
# If we are running the CI on an actual server, try using the 6LU7 Mpro and Geraniin Job ID because Eucalyptol fails
sql_select_Query = 'select * from curieweb where id="l9xo2isr98oepcia" LIMIT 1'
mycursor.execute(sql_select_Query)
records = mycursor.fetchall()
def email(compressedFile):
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 = config['SMTP']['EMAIL']
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"
p = MIMEBase('application', 'octet-stream')
with open((str(compressedFile) + ".zip"), "rb") as attachment:
p.set_payload((attachment).read())
encoders.encode_base64(p)
p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p)
s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT'])
s.starttls()
s.login(fromaddr, config['SMTP']['PASSWORD'])
text = msg.as_string()
s.sendmail(fromaddr, toaddr, text)
s.quit()
receptor_name = "protein.pdbqt"
ligand_name = "ligand.pdbqt"
description = "GitHub Action Test"
#print(records[0])
r = records[0]
jobID = r[0]
toEmail = r[1]
targetB = r[2]
if r[3] is not None:
receptor_name = str(r[3])
if r[6] is not None:
ligand_name = str(r[6])
ligandB = r[4]
configB = r[7]
date = r[8]
if r[9] is not None:
description = r[9]
import os
cd = os.getcwd()
f = os.path.join(cd,"static/uploads")
if ".pdbqt" not in receptor_name:
receptor_name+=".pdbqt"
if ".pdbqt" not in ligand_name:
ligand_name+=".pdbqt"
print(f)
import tempfile
from shutil import make_archive
with tempfile.TemporaryDirectory() as directory:
print('The created temporary directory is %s' % directory)
os.chdir(directory)
with open(receptor_name,"wb") as file:
file.write(targetB)
with open(ligand_name,"wb") as file:
file.write(ligandB)
with open("config.txt","wb") as file:
file.write(configB)
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))
z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z)
make_archive(zi, 'zip', directory)
email(zi)
mycursor.execute('UPDATE curieweb set done=1 where id="%s"' % (jobID))
mycon.commit()
|
