Fixed 10 Anti-Pattern issues

app/run_docking.py

@@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
 
 records = mycursor.fetchall()
 
-def email(zi):
+def email(zipArchive):
     import smtplib 
     from email.mime.multipart import MIMEMultipart 
     from email.mime.text import MIMEText 
@@ -26,8 +26,8 @@ def email(zi):
     
     msg.attach(MIMEText(body, 'plain')) 
     filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
-    attachment = open((str(zi) + ".zip"), "rb") 
     p = MIMEBase('application', 'octet-stream') 
+    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) 

app/run_local.py

@@ -8,7 +8,7 @@ mycursor.execute(sql_select_Query)
 
 records = mycursor.fetchall()
 
-def email(zi):
+def email(zipArchive):
     import smtplib 
     from email.mime.multipart import MIMEMultipart 
     from email.mime.text import MIMEText 
@@ -26,8 +26,8 @@ def email(zi):
     
     msg.attach(MIMEText(body, 'plain')) 
     filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" 
-    attachment = open((str(zi) + ".zip"), "rb") 
     p = MIMEBase('application', 'octet-stream') 
+    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) 

app/views.py

@@ -105,9 +105,8 @@ def dock_upload():
             target.save(secure_filename(target.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
-            f = open("config.txt","w")
+            with open("config.txt","w") as f:
                 f.write(buffer)
-            f.close()
             ligandB = convertToBinaryData(secure_filename(ligand.filename))
             receptor = convertToBinaryData(secure_filename(target.filename))
             config = convertToBinaryData("config.txt")

tests/backendTest.py

@@ -27,8 +27,8 @@ def email(compressedFile):
     
     msg.attach(MIMEText(body, 'plain')) 
     filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
-    attachment = open((str(compressedFile) + ".zip"), "rb") 
     p = MIMEBase('application', 'octet-stream') 
+    with open((str(zi) + ".zip"), "rb") as attachment:
         p.set_payload((attachment).read()) 
     encoders.encode_base64(p) 
     p.add_header('Content-Disposition', "attachment; filename= %s" % filename) 
@@ -79,15 +79,12 @@ from shutil import make_archive
 with tempfile.TemporaryDirectory() as directory:
     print('The created temporary directory is %s' % directory)
     os.chdir(directory)
-    file = open(receptor_name,"wb")
+    with open(receptor_name,"wb") as file:
         file.write(targetB)
-    file.close()
-    file = open(ligand_name,"wb")
+    with open(ligand_name,"wb") as file:
         file.write(ligandB)
-    file.close()
-    file = open("config.txt","wb")
+    with open("config.txt","wb") as file:
         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))
     z = "Curie_Web_Result_"+str(jobID)
     zi = os.path.join(f,z)