From b75583ea26269101f12cb29df76a23eeecf68ab5 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 9 Nov 2017 14:00:46 -0500
Subject: [PATCH] Fix post-merge lint issues

---
 lib/galaxy/config.py                  | 1 +
 lib/galaxy/jobs/__init__.py           | 2 +-
 lib/galaxy/model/orm/scripts.py       | 1 -
 lib/galaxy/util/properties.py         | 1 -
 lib/galaxy/web/stack/transport.py     | 2 +-
 lib/galaxy/webapps/galaxy/buildapp.py | 2 --
 scripts/galaxy-main                   | 1 -
 scripts/get_uwsgi_args.py             | 1 -
 scripts/manage_tool_dependencies.py   | 1 -
 9 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index b2408b28940..cd3c8045869 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -115,6 +115,7 @@ LOGGING_CONFIG_DEFAULT = {
     },
 }
 
+
 def resolve_path(path, root):
     """If 'path' is relative make absolute by prepending 'root'"""
     if not os.path.isabs(path):
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
index 65ab2fea65a..b0dee6c9a87 100644
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -207,7 +207,7 @@ class JobConfiguration(object, ConfiguresHandlers):
         # Determine the default handler(s)
         try:
             self.default_handler_id = self._get_default(self.app.config, handlers_conf, list(self.handlers.keys()))
-        except:
+        except Exception:
             log.info('No default handler specified in job config, will check for job handlers managed by application stack')
         if ((self.default_handler_id is None
                 or (len(self.handlers) == 1 and self.app.config.server_name.startswith(self.handlers.keys()[0])))
diff --git a/lib/galaxy/model/orm/scripts.py b/lib/galaxy/model/orm/scripts.py
index c37606b26d9..7a9ae93fbfc 100644
--- a/lib/galaxy/model/orm/scripts.py
+++ b/lib/galaxy/model/orm/scripts.py
@@ -3,7 +3,6 @@ Code to support database helper scripts (create_db.py, manage_db.py, etc...).
 """
 import logging
 
-from galaxy.util import listify
 from galaxy.util.path import get_ext
 from galaxy.util.properties import find_config_file, load_app_properties
 
diff --git a/lib/galaxy/util/properties.py b/lib/galaxy/util/properties.py
index aca80d4c1e8..aedfcc27e30 100644
--- a/lib/galaxy/util/properties.py
+++ b/lib/galaxy/util/properties.py
@@ -13,7 +13,6 @@ import yaml
 from six import iteritems, string_types
 from six.moves.configparser import ConfigParser
 
-from galaxy.util import listify
 from galaxy.util.path import has_ext, extensions, joinext
 
 
diff --git a/lib/galaxy/web/stack/transport.py b/lib/galaxy/web/stack/transport.py
index 394e2a36cd5..c24ab1ef756 100644
--- a/lib/galaxy/web/stack/transport.py
+++ b/lib/galaxy/web/stack/transport.py
@@ -116,7 +116,7 @@ class UWSGIFarmMessageTransport(ApplicationStackTransport):
                     self.running = False
                 else:
                     self.dispatcher.dispatch(msg)
-            except:
+            except Exception:
                 log.exception('Exception in mule message handling')
             finally:
                 self.__unlock(lock)
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 79620698b0f..4a993dcc899 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -3,13 +3,11 @@ Provides factory methods to assemble the Galaxy web application
 """
 import atexit
 import logging
-import os
 import sys
 import threading
 import traceback
 
 from paste import httpexceptions
-from six.moves import configparser
 
 import galaxy.app
 import galaxy.datatypes.registry
diff --git a/scripts/galaxy-main b/scripts/galaxy-main
index e9ee97b918c..4c82e41ecfb 100755
--- a/scripts/galaxy-main
+++ b/scripts/galaxy-main
@@ -200,7 +200,6 @@ class GalaxyConfigBuilder(object):
                     config_file,
                     dict(__file__=config_file, here=os.path.dirname(config_file))
                 )
-        root = logging.getLogger()
 
 
 def main():
diff --git a/scripts/get_uwsgi_args.py b/scripts/get_uwsgi_args.py
index 17a5eee40d0..7becdeea3af 100644
--- a/scripts/get_uwsgi_args.py
+++ b/scripts/get_uwsgi_args.py
@@ -11,7 +11,6 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
 from galaxy.script import main_factory
 from galaxy.util.path import get_ext
 from galaxy.util.properties import load_app_properties, nice_config_parser
-from galaxy.web.stack import get_app_kwds
 
 
 DESCRIPTION = "Script to determine uWSGI command line arguments"
diff --git a/scripts/manage_tool_dependencies.py b/scripts/manage_tool_dependencies.py
index 9994dcbb51a..485edf85331 100644
--- a/scripts/manage_tool_dependencies.py
+++ b/scripts/manage_tool_dependencies.py
@@ -11,7 +11,6 @@ from galaxy.config import (
 )
 from galaxy.script import main_factory
 from galaxy.tools.deps import CachedDependencyManager, DependencyManager, NullDependencyManager
-from galaxy.util.properties import find_config_file, load_app_properties
 
 DESCRIPTION = "Script to manage tool dependencies (with focus on a Conda environments)."