Fix linting issues

lib/galaxy/jobs/__init__.py

@@ -1771,12 +1771,12 @@ class JobWrapper( object, HasResourceParameters ):
         if self.__user_system_pwent is None:
             job = self.get_job()
 
-            if self.app.config.real_system_username == 'user_email': 
+            if self.app.config.real_system_username == 'user_email':
                 try:
                     self.__user_system_pwent = pwd.getpwnam( job.user.email.split('@')[0] )
                 except KeyError:
                     pass
-            elif self.app.config.real_system_username == 'username': 
+            elif self.app.config.real_system_username == 'username':
                 try:
                     self.__user_system_pwent = pwd.getpwnam( job.user.username )
                 except KeyError:

lib/galaxy/tools/actions/upload_common.py

@@ -283,15 +283,15 @@ def create_paramfile( trans, uploaded_datasets ):
     def _chown( path ):
         try:
             # get username from email/username
-            pwent = None        
+            pwent = None
 
-            if trans.app.config.real_system_username == 'user_email': 
+            if trans.app.config.real_system_username == 'user_email':
                 try:
                     pwent = pwd.getpwnam( trans.user.email.split('@')[0] )
                 except KeyError:
                     pass
 
-            elif trans.app.config.real_system_username == 'username': 
+            elif trans.app.config.real_system_username == 'username':
                 try:
                     pwent = pwd.getpwnam( trans.user.username )
                 except KeyError:

scripts/external_chown_script.py

@@ -7,9 +7,10 @@ import sys
 # if set to None every file can be modified by the script.
 # this can increase security in particular if write access to this
 # script is removed by the admin.
-# 
+#
 # ALLOWED_PATHS = [ "job_working_directory", "new_file_path" ]
-ALLOWED_PATHS = None 
+ALLOWED_PATHS = None
+
 
 def validate_paramters():
     if len(sys.argv) < 4:
@@ -17,7 +18,7 @@ def validate_paramters():
         exit(1)
 
     path = os.path.abspath( sys.argv[1] )
-    if ALLOWED_PATHS == None: 
+    if ALLOWED_PATHS is None:
         allowed = True
     else:
         allowed = False
@@ -26,7 +27,7 @@ def validate_paramters():
                 allowed = True
                 break
     if not allowed:
-        sys.stderr.write( "owner and group modifications in %s are not allowed\n" %path )
+        sys.stderr.write( "owner and group modifications in %s are not allowed\n" % path )
         sys.exit( 1 )
 
     galaxy_user_name = sys.argv[2]
@@ -39,20 +40,21 @@ def main():
     path, galaxy_user_name, gid = validate_paramters()
 
     cmd = [ 'chown', '-Rh', galaxy_user_name, path ]
-    p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p = os.subprocess.Popen(cmd, shell=False, stdout=os.subprocess.PIPE, stderr=os.subprocess.PIPE)
     (stdoutdata, stderrdata) = p.communicate()
     exitcode = p.returncode
     if exitcode != 0:
-       sys.stderr.write("external_chown_script: could not chown\ncmd was %s\n"% " ".join(cmd))
-       raise exit(1)
- 
+        sys.stderr.write("external_chown_script: could not chown\ncmd was %s\n" % " ".join(cmd))
+        raise exit(1)
+
     cmd = [ 'chgrp', '-Rh', gid, path ]
-    p = subprocess.Popen(cmd, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    p = os.subprocess.Popen(cmd, shell=False, stdout=os.subprocess.PIPE, stderr=os.subprocess.PIPE)
     (stdoutdata, stderrdata) = p.communicate()
     exitcode = p.returncode
     if exitcode != 0:
-       sys.stderr.write("external_chown_script: could not chgrp\ncmd was %s\n"% " ".join(cmd))
-       raise exit(1)
+        sys.stderr.write("external_chown_script: could not chgrp\ncmd was % s\n" % " ".join(cmd))
+        raise exit(1)
+
 
 if __name__ == "__main__":
     main()