Fix Python 2.7 lint errors

lib/galaxy/auth/__init__.py

@@ -1,7 +1,6 @@
 """
 Contains implementations of the authentication logic.
 """
-import errno
 import logging
 
 from galaxy.auth.util import get_authenticators, parse_auth_results
@@ -16,7 +15,7 @@ class AuthManager(object):
     def __init__(self, app):
         self.__app = app
         self.redact_username_in_logs = app.config.redact_username_in_logs
-        self.authenticators = get_authenticators(app.config.auth_config_file)
+        self.authenticators = get_authenticators(app.config.auth_config_file, app.config.auth_config_file_set)
 
     def check_registration_allowed(self, email, username, password):
         """Checks if the provided email/username is allowed to register."""

lib/galaxy/auth/util.py

@@ -1,3 +1,4 @@
+import errno
 import logging
 import xml.etree.ElementTree
 from collections import namedtuple
@@ -24,14 +25,14 @@ AUTH_CONF_XML = """<?xml version="1.0"?>
 Authenticator = namedtuple('Authenticator', ['plugin', 'filter_template', 'options'])
 
 
-def get_authenticators(auth_config_file):
+def get_authenticators(auth_config_file, auth_config_file_set):
     __plugins_dict = plugin_config.plugins_dict(galaxy.auth.providers, 'plugin_type')
     # parse XML
     try:
         ct = xml.etree.ElementTree.parse(auth_config_file)
         conf_root = ct.getroot()
     except (OSError, IOError) as exc:
-        if exc.errno == errno.ENOENT and not app.config.auth_config_file_set:
+        if exc.errno == errno.ENOENT and not auth_config_file_set:
             conf_root = xml.etree.ElementTree.fromstring(AUTH_CONF_XML)
         else:
             raise

lib/galaxy/config/__init__.py

@@ -217,18 +217,18 @@ class BaseAppConfiguration(object):
 
     def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
         for var, defaults in defaults.items():
-            if config_kwargs.get( var, None ) is not None:
-                path = config_kwargs.get( var )
-                setattr( self, var + '_set', True )
+            if config_kwargs.get(var, None) is not None:
+                path = config_kwargs.get(var)
+                setattr(self, var + '_set', True)
             else:
                 for default in defaults:
-                    if os.path.exists( resolve_path( default, self.root ) ):
+                    if os.path.exists(resolve_path(default, self.root)):
                         path = default
                         break
                 else:
                     path = defaults[-1]
-                setattr( self, var + '_set', False )
-            setattr( self, var, resolve_path( path, self.root ) )
+                setattr(self, var + '_set', False)
+            setattr(self, var, resolve_path(path, self.root))
 
         for var, defaults in listify_defaults.items():
             paths = []
@@ -326,7 +326,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         self.oidc = []
         # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
         # and moved to the tool shed. It is created on demand.
-        self.integrated_tool_panel_config = resolve_path(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.mutable_config_dir)
+        self.integrated_tool_panel_config = resolve_path(kwargs.get('integrated_tool_panel_config', 'integrated_tool_panel.xml'), self.mutable_config_dir)
         integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory', None)
         if integrated_tool_panel_tracking_directory:
             self.integrated_tool_panel_tracking_directory = resolve_path(integrated_tool_panel_tracking_directory, self.root)
@@ -603,7 +603,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         self.tool_test_data_directories = kwargs.get("tool_test_data_directories", default_tool_test_data_directories)
         # Location for tool dependencies.
         use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \
-            parse_dependency_options(kwargs, self.root, self.dependency_resolvers_config_file)
+            parse_dependency_options(kwargs, self.data_dir, self.dependency_resolvers_config_file)
         self.use_tool_dependencies = use_tool_dependencies
         self.tool_dependency_dir = tool_dependency_dir
         self.use_cached_dependency_manager = use_cached_dependency_manager
@@ -1064,7 +1064,7 @@ def parse_dependency_options(kwargs, root, dependency_resolvers_config_file):
         tool_dependency_dir = None
 
     if tool_dependency_dir is not None:
-        tool_dependency_dir = resolve_path(tool_dependency_dir, self.data_dir)
+        tool_dependency_dir = resolve_path(tool_dependency_dir, root)
         # Setting the following flag to true will ultimately cause tool dependencies
         # to be located in the shell environment and used by the job that is executing
         # the tool.

lib/galaxy/config/script.py

@@ -166,7 +166,7 @@ def _handle_galaxy_ini(args, config_dir, data_dir):
 
     galaxy_config_template = []
     with open(GALAXY_CONFIG_TEMPLATE_FILE) as fh:
-        for line in [ l.rstrip('\n') for l in fh.readlines() ]:
+        for line in [l.rstrip('\n') for l in fh.readlines()]:
             for k, v in GALAXY_CONFIG_SUBSTITUTIONS.items():
                 if line == k:
                     line = v

lib/galaxy/model/orm/scripts.py

@@ -9,7 +9,7 @@ import sys
 from migrate.versioning.shell import main as migrate_main
 
 from galaxy.util.path import get_ext
-from galaxy.util.properties import find_config_file, get_data_dir, load_app_properties, running_from_source
+from galaxy.util.properties import find_config_file, get_data_dir, load_app_properties
 from galaxy.util.script import populate_config_args
 
 

lib/galaxy/tools/special_tools.py

@@ -1,5 +1,6 @@
-import os
 import logging
+import os
+
 log = logging.getLogger(__name__)
 
 SPECIAL_TOOLS = {

lib/galaxy/web/framework/webapp.py

@@ -968,7 +968,7 @@ class GalaxyWebTransaction(base.DefaultWebTransaction,
 
 
 def default_url_path(path):
-    return os.path.abspath(os.path.join(os.path.dirname( __file__ ), path))
+    return os.path.abspath(os.path.join(os.path.dirname(__file__), path))
 
 
 def build_native_uwsgi_app(paste_factory, config_section):

lib/tool_shed/galaxy_install/migrate/check.py

@@ -57,7 +57,7 @@ def verify_tools(app, url, galaxy_config_file=None, engine_options={}):
             if tool_shed_accessible:
                 # Automatically update the value of the migrate_tools.version database table column.
                 # FIXME: this doesn't seem right.
-                manage_tools = os.path.abspath(os.path.join(os.path.dirname( __file__ ), 'scripts', 'manage_tools.py'))
+                manage_tools = os.path.abspath(os.path.join(os.path.dirname(__file__), 'scripts', 'manage_tools.py'))
                 cmd = [executable, manage_tools, 'upgrade', 'tools']
                 if galaxy_config_file:
                     cmd[2:2] = ['-c', galaxy_config_file]

lib/tool_shed/galaxy_install/tool_migration_manager.py

@@ -3,7 +3,6 @@ Manage automatic installation of tools configured in the xxx.xml files in ~/scri
 All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed.
 """
 import errno
-import json
 import logging
 import os
 import shutil
@@ -72,7 +71,7 @@ class ToolMigrationManager(object):
         except (IOError, OSError) as exc:
             if exc.errno == errno.ENOENT:
                 with open(migrated_tools_config, 'w') as fh:
-                    fh.write( MIGRATED_TOOLS_CONF_XML.format(shed_tools_dir=self.app.config.shed_tools_dir))
+                    fh.write(MIGRATED_TOOLS_CONF_XML.format(shed_tools_dir=self.app.config.shed_tools_dir))
                 tree, error_message = xml_util.parse_xml(migrated_tools_config)
             else:
                 raise

lib/tool_shed/util/common_util.py

@@ -15,7 +15,7 @@ log = logging.getLogger(__name__)
 REPOSITORY_OWNER = 'devteam'
 TOOL_MIGRATION_SCRIPTS_DIR = os.path.abspath(os.path.join(
     os.path.dirname(__file__), os.pardir, 'galaxy_install', 'migrate', 'scripts'))
-TOOL_MIGRATION_VERSIONS_DIR = os.path.abspath( os.path.join(
+TOOL_MIGRATION_VERSIONS_DIR = os.path.abspath(os.path.join(
     os.path.dirname(__file__), os.pardir, 'galaxy_install', 'migrate', 'versions'))
 
 
@@ -30,7 +30,7 @@ def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_to
 
 def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number):
     # Get the 000x_tools.xml file associated with the current migrate_tools version number.
-    tools_xml_file_path = os.path.abspath(os.path.join(os.path.dirname( __file__ ),
+    tools_xml_file_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
                                                        os.pardir, 'galaxy_install',
                                                        'migrate', 'scripts',
                                                        '%04d_tools.xml' % latest_tool_migration_script_number))

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 
 readme = open('README.rst').read()