Fixed 10 Anti-Pattern issues
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parent
bb73018258
commit
3b6482cb0a
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@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
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records = mycursor.fetchall()
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def email(zi):
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def email(zipArchive):
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import smtplib
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from email.mime.multipart import MIMEMultipart
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from email.mime.text import MIMEText
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@ -26,9 +26,9 @@ def email(zi):
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msg.attach(MIMEText(body, 'plain'))
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filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
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attachment = open((str(zi) + ".zip"), "rb")
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p = MIMEBase('application', 'octet-stream')
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p.set_payload((attachment).read())
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with open((str(zipArchive) + ".zip"), "rb") as attachment:
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p.set_payload((attachment).read())
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encoders.encode_base64(p)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
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records = mycursor.fetchall()
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def email(zi):
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def email(zipArchive):
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import smtplib
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from email.mime.multipart import MIMEMultipart
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from email.mime.text import MIMEText
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@ -26,9 +26,9 @@ def email(zi):
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msg.attach(MIMEText(body, 'plain'))
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filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
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attachment = open((str(zi) + ".zip"), "rb")
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p = MIMEBase('application', 'octet-stream')
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p.set_payload((attachment).read())
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with open((str(zipArchive) + ".zip"), "rb") as attachment:
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p.set_payload((attachment).read())
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encoders.encode_base64(p)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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@ -105,9 +105,8 @@ def dock_upload():
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target.save(secure_filename(target.filename))
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ligand.save(secure_filename(ligand.filename))
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buffer = "center_x="+cx+"\ncenter_y="+cy+"\ncenter_z="+cz+"\nsize_x="+sx+"\nsize_y="+sy+"\nsize_z="+sz
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f = open("config.txt","w")
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f.write(buffer)
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f.close()
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with open("config.txt","w") as f:
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f.write(buffer)
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ligandB = convertToBinaryData(secure_filename(ligand.filename))
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receptor = convertToBinaryData(secure_filename(target.filename))
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config = convertToBinaryData("config.txt")
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@ -27,9 +27,9 @@ def email(compressedFile):
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msg.attach(MIMEText(body, 'plain'))
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filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
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attachment = open((str(compressedFile) + ".zip"), "rb")
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p = MIMEBase('application', 'octet-stream')
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p.set_payload((attachment).read())
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with open((str(zi) + ".zip"), "rb") as attachment:
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p.set_payload((attachment).read())
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encoders.encode_base64(p)
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p.add_header('Content-Disposition', "attachment; filename= %s" % filename)
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msg.attach(p)
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@ -79,15 +79,12 @@ from shutil import make_archive
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with tempfile.TemporaryDirectory() as directory:
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print('The created temporary directory is %s' % directory)
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os.chdir(directory)
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file = open(receptor_name,"wb")
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file.write(targetB)
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file.close()
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file = open(ligand_name,"wb")
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file.write(ligandB)
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file.close()
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file = open("config.txt","wb")
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file.write(configB)
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file.close()
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with open(receptor_name,"wb") as file:
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file.write(targetB)
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with open(ligand_name,"wb") as file:
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file.write(ligandB)
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with open("config.txt","wb") as file:
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file.write(configB)
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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))
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z = "Curie_Web_Result_"+str(jobID)
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zi = os.path.join(f,z)
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