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Curie-Web
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Fixed 10 Anti-Pattern issues

This commit is contained in:
Navan Chauhan 2020-07-07 12:40:28 +05:30
parent bb73018258
commit 3b6482cb0a
4 changed files with 17 additions and 21 deletions
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6
app/run_docking.py
View File

@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
records = mycursor.fetchall() records = mycursor.fetchall()
def email(zi): def email(zipArchive):
import smtplib import smtplib
from email.mime.multipart import MIMEMultipart from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText from email.mime.text import MIMEText
@ -26,9 +26,9 @@ def email(zi):
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(zi) + ".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)

6
app/run_local.py
View File

@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
records = mycursor.fetchall() records = mycursor.fetchall()
def email(zi): def email(zipArchive):
import smtplib import smtplib
from email.mime.multipart import MIMEMultipart from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText from email.mime.text import MIMEText
@ -26,9 +26,9 @@ def email(zi):
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(zi) + ".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)

5
app/views.py
View File

@ -105,9 +105,8 @@ def dock_upload():
target.save(secure_filename(target.filename)) target.save(secure_filename(target.filename))
ligand.save(secure_filename(ligand.filename)) ligand.save(secure_filename(ligand.filename))
buffer = "center_x="+cx+"\ncenter_y="+cy+"\ncenter_z="+cz+"\nsize_x="+sx+"\nsize_y="+sy+"\nsize_z="+sz buffer = "center_x="+cx+"\ncenter_y="+cy+"\ncenter_z="+cz+"\nsize_x="+sx+"\nsize_y="+sy+"\nsize_z="+sz
f = open("config.txt","w") with open("config.txt","w") as f:
f.write(buffer) f.write(buffer)
f.close()
ligandB = convertToBinaryData(secure_filename(ligand.filename)) ligandB = convertToBinaryData(secure_filename(ligand.filename))
receptor = convertToBinaryData(secure_filename(target.filename)) receptor = convertToBinaryData(secure_filename(target.filename))
config = convertToBinaryData("config.txt") config = convertToBinaryData("config.txt")

19
tests/backendTest.py
View File

@ -27,9 +27,9 @@ def email(compressedFile):
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(compressedFile) + ".zip"), "rb")
p = MIMEBase('application', 'octet-stream') p = MIMEBase('application', 'octet-stream')
p.set_payload((attachment).read()) with open((str(zi) + ".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)
@ -79,15 +79,12 @@ from shutil import make_archive
with tempfile.TemporaryDirectory() as directory: with tempfile.TemporaryDirectory() as directory:
print('The created temporary directory is %s' % directory) print('The created temporary directory is %s' % directory)
os.chdir(directory) os.chdir(directory)
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))
z = "Curie_Web_Result_"+str(jobID) z = "Curie_Web_Result_"+str(jobID)
zi = os.path.join(f,z) zi = os.path.join(f,z)