diff options
author | Navan Chauhan <navanchauhan@gmail.com> | 2020-09-11 18:37:16 +0530 |
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committer | Navan Chauhan <navanchauhan@gmail.com> | 2020-09-11 18:37:16 +0530 |
commit | d55ef146e83a5a975cecc67183781eed25858242 (patch) | |
tree | 08248846eb8dee63099e0000d6a974bf8edd77ff | |
parent | 7381e25ef4bb2e9363f61f31712a2d5cbacf4d60 (diff) |
fixed variable name clash
-rw-r--r-- | app/dock-single.py | 18 | ||||
-rw-r--r-- | app/dock_docker.py | 16 |
2 files changed, 18 insertions, 16 deletions
diff --git a/app/dock-single.py b/app/dock-single.py index daf920c..e9ef9b2 100644 --- a/app/dock-single.py +++ b/app/dock-single.py @@ -9,15 +9,15 @@ from collections import namedtuple import mysql.connector as con import configparser -config = configparser.ConfigParser() -config.read('config.ini') +iniConfig = configparser.ConfigParser() +iniConfig.read('config.ini') try: - config['DATABASE'] + iniConfig['DATABASE'] 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() 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 import encoders - fromaddr = config['SMTP']['EMAIL'] + fromaddr = iniConfig['SMTP']['EMAIL'] msg = MIMEMultipart() msg['From'] = fromaddr @@ -200,9 +200,9 @@ def email(zipArchive): p.add_header('Content-Disposition', "attachment; filename= %s" % filename) msg.attach(p) - s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT']) + s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT']) s.starttls() - s.login(fromaddr, config['SMTP']['PASSWORD']) + s.login(fromaddr, iniConfig['SMTP']['PASSWORD']) text = msg.as_string() s.sendmail(fromaddr, toaddr, text) @@ -245,6 +245,8 @@ with tempfile.TemporaryDirectory() as directory: with open("config.txt","w") as file: file.write(configuration) 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"))) z = "Curie_Web_Result_"+str(jobID) zi = os.path.join(f,z) diff --git a/app/dock_docker.py b/app/dock_docker.py index bd6f053..712e725 100644 --- a/app/dock_docker.py +++ b/app/dock_docker.py @@ -1,15 +1,15 @@ import mysql.connector as con import configparser -config = configparser.ConfigParser() -config.read('config.ini') +iniConfig = configparser.ConfigParser() +iniConfig.read('config.ini') try: - config['DATABASE'] + iniConfig['DATABASE'] 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() 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 import encoders - fromaddr = config['SMTP']['EMAIL'] + fromaddr = iniConfig['SMTP']['EMAIL'] toaddr = toEmail msg = MIMEMultipart() @@ -46,9 +46,9 @@ def email(zipArchive): p.add_header('Content-Disposition', "attachment; filename= %s" % filename) msg.attach(p) - s = smtplib.SMTP(config['SMTP']['SERVER'], config['SMTP']['PORT']) + s = smtplib.SMTP(iniConfig['SMTP']['SERVER'], iniConfig['SMTP']['PORT']) s.starttls() - s.login(fromaddr, config['SMTP']['PASSWORD']) + s.login(fromaddr, iniConfig['SMTP']['PASSWORD']) text = msg.as_string() s.sendmail(fromaddr, toaddr, text) |