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Curie-Web
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fix file open anti-pattern

This commit is contained in:
Navan Chauhan 2020-07-07 12:27:10 +05:30
parent 6a67fd7e8b
commit 59e56bb76e
1 changed files with 8 additions and 11 deletions
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19
app/dock_docker.py
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@ -26,9 +26,9 @@ def email(zipArchive):
msg.attach(MIMEText(body, 'plain')) msg.attach(MIMEText(body, 'plain'))
filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
attachment = open((str(zipArchive) + ".zip"), "rb")
p = MIMEBase('application', 'octet-stream') 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) encoders.encode_base64(p)
p.add_header('Content-Disposition', "attachment; filename= %s" % filename) p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
msg.attach(p) msg.attach(p)
@ -78,15 +78,12 @@ with tempfile.TemporaryDirectory() as directory:
# copy(t,os.getcwd()) # copy(t,os.getcwd())
# copy(r,os.getcwd()) # copy(r,os.getcwd())
# copy(c, os.getcwd()) # copy(c, os.getcwd())
file = open(receptor_name,"wb") with open(receptor_name,"wb") as file:
file.write(targetB) file.write(targetB)
file.close() with open(ligand_name,"wb") as file:
file = open(ligand_name,"wb") file.write(ligandB)
file.write(ligandB) with open("config.txt","wb") as file:
file.close() file.write(configB)
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)) 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) #copy("report.pdf",f)
z = "Curie_Web_Result_"+str(jobID) z = "Curie_Web_Result_"+str(jobID)