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-rw-r--r--app/dock_docker.py19
1 files changed, 8 insertions, 11 deletions
diff --git a/app/dock_docker.py b/app/dock_docker.py
index e1b17d1..54f413c 100644
--- a/app/dock_docker.py
+++ b/app/dock_docker.py
@@ -26,9 +26,9 @@ def email(zipArchive):
msg.attach(MIMEText(body, 'plain'))
filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
- attachment = open((str(zipArchive) + ".zip"), "rb")
p = MIMEBase('application', 'octet-stream')
- p.set_payload((attachment).read())
+ with open((str(zipArchive) + ".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)
@@ -78,15 +78,12 @@ with tempfile.TemporaryDirectory() as 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()
+ 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))
#copy("report.pdf",f)
z = "Curie_Web_Result_"+str(jobID)