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Curie-Web
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fixed variable name clash

This commit is contained in:
Navan Chauhan 2020-09-11 18:37:16 +05:30
parent 7381e25ef4
commit d55ef146e8
2 changed files with 18 additions and 16 deletions
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18
app/dock-single.py
View File

@ -9,15 +9,15 @@ from collections import namedtuple
import mysql.connector as con import mysql.connector as con
import configparser import configparser
config = configparser.ConfigParser() iniConfig = configparser.ConfigParser()
config.read('config.ini') iniConfig.read('config.ini')
try: try:
config['DATABASE'] iniConfig['DATABASE']
except KeyError: except KeyError:
config.read("../config.ini") iniConfig.read("../config.ini")
mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME']) mycon = con.connect(host=iniConfig['DATABASE']['HOST'],user=iniConfig['DATABASE']['USER'],password=iniConfig['DATABASE']['PASSWORD'],port=iniConfig['DATABASE']['PORT'],database=iniConfig['DATABASE']['NAME'])
mycursor = mycon.cursor() mycursor = mycon.cursor()
sql_select_Query = "SELECT id,email,pdb,ligand_smile,ligand_name,description,date FROM curieweb WHERE pdb IS NOT NULL AND done=0 LIMIT 1" sql_select_Query = "SELECT id,email,pdb,ligand_smile,ligand_name,description,date FROM curieweb WHERE pdb IS NOT NULL AND done=0 LIMIT 1"
@ -183,7 +183,7 @@ def email(zipArchive):
from email.mime.base import MIMEBase from email.mime.base import MIMEBase
from email import encoders from email import encoders
fromaddr = config['SMTP']['EMAIL'] fromaddr = iniConfig['SMTP']['EMAIL']
msg = MIMEMultipart() msg = MIMEMultipart()
msg['From'] = fromaddr msg['From'] = fromaddr
@ -200,9 +200,9 @@ def email(zipArchive):
p.add_header('Content-Disposition', "attachment; filename= %s" % filename) p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p) msg.attach(p)
s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT']) s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT'])
s.starttls() s.starttls()
s.login(fromaddr, config['SMTP']['PASSWORD']) s.login(fromaddr, iniConfig['SMTP']['PASSWORD'])
text = msg.as_string() text = msg.as_string()
s.sendmail(fromaddr, toaddr, text) s.sendmail(fromaddr, toaddr, text)
@ -245,6 +245,8 @@ with tempfile.TemporaryDirectory() as directory:
with open("config.txt","w") as file: with open("config.txt","w") as file:
file.write(configuration) file.write(configuration)
os.system('obabel -:"%s" --gen3d -opdbqt -O%s.pdbqt' % (records[3],records[4])) os.system('obabel -:"%s" --gen3d -opdbqt -O%s.pdbqt' % (records[3],records[4]))
print("Ligand:",records[4])
print(str(records[4]+".pdbqt"))
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" % (pdbqt,str(records[4]+".pdbqt"))) 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" % (pdbqt,str(records[4]+".pdbqt")))
z = "Curie_Web_Result_"+str(jobID) z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z) zi = os.path.join(f,z)

16
app/dock_docker.py
View File

@ -1,15 +1,15 @@
import mysql.connector as con import mysql.connector as con
import configparser import configparser
config = configparser.ConfigParser() iniConfig = configparser.ConfigParser()
config.read('config.ini') iniConfig.read('config.ini')
try: try:
config['DATABASE'] iniConfig['DATABASE']
except KeyError: except KeyError:
config.read("../config.ini") iniConfig.read("../config.ini")
mycon = con.connect(host=config['DATABASE']['HOST'],user=config['DATABASE']['USER'],password=config['DATABASE']['PASSWORD'],port=config['DATABASE']['PORT'],database=config['DATABASE']['NAME']) mycon = con.connect(host=iniConfig['DATABASE']['HOST'],user=iniConfig['DATABASE']['USER'],password=iniConfig['DATABASE']['PASSWORD'],port=iniConfig['DATABASE']['PORT'],database=iniConfig['DATABASE']['NAME'])
mycursor = mycon.cursor() mycursor = mycon.cursor()
sql_select_Query = "select * from curieweb where done=0 LIMIT 1" sql_select_Query = "select * from curieweb where done=0 LIMIT 1"
@ -28,7 +28,7 @@ def email(zipArchive):
from email.mime.base import MIMEBase from email.mime.base import MIMEBase
from email import encoders from email import encoders
fromaddr = config['SMTP']['EMAIL'] fromaddr = iniConfig['SMTP']['EMAIL']
toaddr = toEmail toaddr = toEmail
msg = MIMEMultipart() msg = MIMEMultipart()
@ -46,9 +46,9 @@ def email(zipArchive):
p.add_header('Content-Disposition', "attachment; filename= %s" % filename) p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p) msg.attach(p)
s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT']) s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT'])
s.starttls() s.starttls()
s.login(fromaddr, config['SMTP']['PASSWORD']) s.login(fromaddr, iniConfig['SMTP']['PASSWORD'])
text = msg.as_string() text = msg.as_string()
s.sendmail(fromaddr, toaddr, text) s.sendmail(fromaddr, toaddr, text)