From 3b6482cb0ab7eb51756213ccf7b7c8822fbda3d5 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Tue, 7 Jul 2020 12:40:28 +0530
Subject: Fixed 10 Anti-Pattern issues

---
 app/run_docking.py   |  6 +++---
 app/run_local.py     |  8 ++++----
 app/views.py         |  5 ++---
 tests/backendTest.py | 19 ++++++++-----------
 4 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/app/run_docking.py b/app/run_docking.py
index 02e8704..1b86d92 100644
--- a/app/run_docking.py
+++ b/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 
@@ -26,9 +26,9 @@ 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') 
-    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) 
diff --git a/app/run_local.py b/app/run_local.py
index 094d024..4b902d2 100644
--- a/app/run_local.py
+++ b/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 
@@ -25,10 +25,10 @@ def email(zi):
     body = "Attached Zip contains the docked files, PLIP report and PyMOL Visualisations. If the ZIP file does not contain these files, please report this issue by replying to this email. Job was submitted on {} with the description {}".format(date, description)
     
     msg.attach(MIMEText(body, 'plain')) 
-    filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip"
-    attachment = open((str(zi) + ".zip"), "rb") 
+    filename = "Curie_Web_Results_Job_ID_" + str(jobID) + ".zip" 
     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) 
diff --git a/app/views.py b/app/views.py
index b9ab620..fd1f466 100644
--- a/app/views.py
+++ b/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")
-            f.write(buffer)
-            f.close()
+            with open("config.txt","w") as f:
+                f.write(buffer)
             ligandB = convertToBinaryData(secure_filename(ligand.filename))
             receptor = convertToBinaryData(secure_filename(target.filename))
             config = convertToBinaryData("config.txt")
diff --git a/tests/backendTest.py b/tests/backendTest.py
index 7db0d8c..33b6019 100644
--- a/tests/backendTest.py
+++ b/tests/backendTest.py
@@ -27,9 +27,9 @@ 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') 
-    p.set_payload((attachment).read()) 
+    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) 
     msg.attach(p) 
@@ -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")
-    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))
     z = "Curie_Web_Result_"+str(jobID)
     zi = os.path.join(f,z)
-- 
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