commit/galaxy-central: greg: Tweak some imports.

12 Dec 2012

1 new commit in galaxy-central:


https://bitbucket.org/galaxy/galaxy-central/changeset/70f88a048ed2/
changeset:   70f88a048ed2
user:        greg
date:        2012-12-12 23:36:40
summary:     Tweak some imports.
affected #:  10 files

diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/tool_shed/install_manager.py

--- a/lib/galaxy/tool_shed/install_manager.py
+++ b/lib/galaxy/tool_shed/install_manager.py
@@ -6,6 +6,7 @@
 from galaxy.tools import ToolSection
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
+import galaxy.util.shed_util_common as suc
 from galaxy.util.odict import odict
 from galaxy.tool_shed.common_util import *
 
@@ -87,7 +88,7 @@
                 break      
         full_path = str( os.path.abspath( os.path.join( root, name ) ) )
         tool = self.toolbox.load_tool( full_path )
-        return generate_tool_guid( repository_clone_url, tool )
+        return suc.generate_tool_guid( repository_clone_url, tool )
     def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ):
         # Parse each config in self.proprietary_tool_confs (the default is tool_conf.xml) and generate a list of Elements that are
         # either ToolSection elements or Tool elements.  These will be used to generate new entries in the migrated_tools_conf.xml
@@ -177,15 +178,15 @@
             else:
                 print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \
                 % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) )
-        metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=self.app,
-                                                                                     repository=tool_shed_repository,
-                                                                                     repository_clone_url=repository_clone_url,
-                                                                                     shed_config_dict = self.shed_config_dict,
-                                                                                     relative_install_dir=relative_install_dir,
-                                                                                     repository_files_dir=None,
-                                                                                     resetting_all_metadata_on_repository=False,
-                                                                                     updating_installed_repository=False,
-                                                                                     persist=True )
+        metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=self.app,
+                                                                                         repository=tool_shed_repository,
+                                                                                         repository_clone_url=repository_clone_url,
+                                                                                         shed_config_dict = self.shed_config_dict,
+                                                                                         relative_install_dir=relative_install_dir,
+                                                                                         repository_files_dir=None,
+                                                                                         resetting_all_metadata_on_repository=False,
+                                                                                         updating_installed_repository=False,
+                                                                                         persist=True )
         tool_shed_repository.metadata = metadata_dict
         self.app.sa_session.add( tool_shed_repository )
         self.app.sa_session.flush()
@@ -217,7 +218,7 @@
                                                         tool_shed_repository,
                                                         self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
                     # Get the tool_dependencies.xml file from disk.
-                    tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repo_install_dir )
+                    tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_install_dir )
                     installed_tool_dependencies = handle_tool_dependencies( app=self.app,
                                                                             tool_shed_repository=tool_shed_repository,
                                                                             tool_dependencies_config=tool_dependencies_config,
@@ -242,7 +243,7 @@
             self.app.sa_session.add( tool_shed_repository )
             self.app.sa_session.flush()
             work_dir = tempfile.mkdtemp()
-            datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repo_install_dir )
+            datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', repo_install_dir )
             # Load proprietary data types required by tools.  The value of override is not important here since the Galaxy server will be started
             # after this installation completes.
             converter_path, display_path = alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir
@@ -294,7 +295,7 @@
                                                                           owner=self.repository_owner,
                                                                           dist_to_shed=True )
             update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING )
-            cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
+            cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
             if cloned_ok:
                 self.handle_repository_contents( tool_shed_repository=tool_shed_repository,
                                                  repository_clone_url=repository_clone_url,


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/tool_shed/update_manager.py
--- a/lib/galaxy/tool_shed/update_manager.py
+++ b/lib/galaxy/tool_shed/update_manager.py
@@ -33,7 +33,7 @@
             self.sleeper.sleep( self.seconds_to_sleep )
         log.info( 'Transfer job restarter shutting down...' )
     def check_for_update( self, repository ):
-        tool_shed_url = get_url_from_repository_tool_shed( self.app, repository )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( self.app, repository )
         url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \
             ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision )
         try:


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -1,10 +1,10 @@
 import os, tempfile, shutil, logging, urllib2
 from galaxy import util
-from shed_util_common import *
+import shed_util_common as suc
 from galaxy.tools.search import ToolBoxSearch
 from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment
-from galaxy.tool_shed.encoding_util import *
-from galaxy.model.orm import *
+from galaxy.tool_shed import encoding_util
+from galaxy.model.orm import and_
 
 from galaxy import eggs
 import pkg_resources
@@ -185,7 +185,7 @@
                 filename=os.path.join( tool_path, filename )
             # Attempt to ensure we're copying an appropriate file.
             if is_data_index_sample_file( filename ):
-                copy_sample_file( app, filename, dest_path=dest_path )
+                suc.copy_sample_file( app, filename, dest_path=dest_path )
 def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ):
     return dict( tool_shed=tool_shed,
                  repository_name=name,
@@ -204,7 +204,7 @@
         # to it being uninstalled.
         current_changeset_revision = installed_changeset_revision
     sa_session = app.model.context.current  
-    tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
+    tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url )
     if not owner:
         owner = get_repository_owner_from_clone_url( repository_clone_url )
     includes_datatypes = 'datatypes' in metadata_dict
@@ -255,7 +255,7 @@
     if shed_config_dict.get( 'tool_path' ):
         relative_install_dir = os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir )
     # Get the tool_dependencies.xml file from the repository.
-    tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir )
+    tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', relative_install_dir )
     try:
         tree = ElementTree.parse( tool_dependencies_config )
     except Exception, e:
@@ -295,8 +295,8 @@
     return tool_dependency_objects
 def generate_clone_url_for_installed_repository( trans, repository ):
     """Generate the URL for cloning a repository that has been installed into a Galaxy instance."""
-    tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-    return url_join( tool_shed_url, 'repos', repository.owner, repository.name )
+    tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
+    return suc.url_join( tool_shed_url, 'repos', repository.owner, repository.name )
 def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ):
     if tool_section is not None:
         tool_elem = SubElement( tool_section, 'tool' )
@@ -321,7 +321,7 @@
     """Generate a list of ElementTree Element objects for each section or tool."""
     elem_list = []
     tool_elem = None
-    cleaned_repository_clone_url = clean_repository_clone_url( repository_clone_url )
+    cleaned_repository_clone_url = suc.clean_repository_clone_url( repository_clone_url )
     if not owner:
         owner = get_repository_owner( cleaned_repository_clone_url )
     tool_shed = cleaned_repository_clone_url.split( 'repos' )[ 0 ].rstrip( '/' )
@@ -475,12 +475,12 @@
 def get_config( config_file, repo, ctx, dir ):
     """Return the latest version of config_filename from the repository manifest."""
     config_file = strip_path( config_file )
-    for changeset in reversed_upper_bounded_changelog( repo, ctx ):
+    for changeset in suc.reversed_upper_bounded_changelog( repo, ctx ):
         changeset_ctx = repo.changectx( changeset )
         for ctx_file in changeset_ctx.files():
             ctx_file_name = strip_path( ctx_file )
             if ctx_file_name == config_file:
-                return get_named_tmpfile_from_ctx( changeset_ctx, ctx_file, dir )
+                return suc.get_named_tmpfile_from_ctx( changeset_ctx, ctx_file, dir )
     return None
 def get_converter_and_display_paths( registration_elem, relative_install_dir ):
     """Find the relative path to data type converters and display applications included in installed tool shed repositories."""
@@ -525,7 +525,7 @@
             break
     return converter_path, display_path
 def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ):
-    url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) )
+    url = suc.url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) )
     response = urllib2.urlopen( url )
     ctx_rev = response.read()
     response.close()
@@ -552,7 +552,7 @@
         repo_path = repo_path.replace( '/', '', 1 )
     return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
 def get_repository_owner_from_clone_url( repository_clone_url ):
-    tmp_url = clean_repository_clone_url( repository_clone_url )
+    tmp_url = suc.clean_repository_clone_url( repository_clone_url )
     tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
     return get_repository_owner( tmp_url )
 def get_repository_tools_tups( app, metadata_dict ):
@@ -674,14 +674,14 @@
                      .first()
 def get_update_to_changeset_revision_and_ctx_rev( trans, repository ):
     """Return the changeset revision hash to which the repository can be updated."""
-    tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-    url = url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \
+    tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
+    url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \
         ( repository.name, repository.owner, repository.installed_changeset_revision ) )
     try:
         response = urllib2.urlopen( url )
         encoded_update_dict = response.read()
         if encoded_update_dict:
-            update_dict = tool_shed_decode( encoded_update_dict )
+            update_dict = encoding_util.tool_shed_decode( encoded_update_dict )
             changeset_revision = update_dict[ 'changeset_revision' ]
             ctx_rev = update_dict[ 'ctx_rev' ]
         response.close()
@@ -704,11 +704,11 @@
             break
     if missing_data_table_entry:
         # The repository must contain a tool_data_table_conf.xml.sample file that includes all required entries for all tools in the repository.
-        sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', relative_install_dir )
+        sample_tool_data_table_conf = suc.get_config_from_disk( 'tool_data_table_conf.xml.sample', relative_install_dir )
         if sample_tool_data_table_conf:
             # Add entries to the ToolDataTableManager's in-memory data_tables dictionary as well as the list of data_table_elems and the list of
             # data_table_elem_names.
-            error, message = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf, persist=True )
+            error, message = suc.handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf, persist=True )
             if error:
                 # TODO: Do more here than logging an exception.
                 log.debug( message )
@@ -716,7 +716,7 @@
         repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid )
         repository_tools_tups[ index ] = ( tup_path, guid, repository_tool )
         # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-        reset_tool_data_tables( app )
+        suc.reset_tool_data_tables( app )
     return repository_tools_tups
 def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups, sample_files_copied ):
     """
@@ -734,7 +734,7 @@
                 for sample_file in sample_files:
                     sample_file_name = strip_path( sample_file )
                     if sample_file_name == '%s.sample' % missing_file_name:
-                        copy_sample_file( app, sample_file )
+                        suc.copy_sample_file( app, sample_file )
                         if options.tool_data_table and options.tool_data_table.missing_index_file:
                             options.tool_data_table.handle_found_index_file( options.missing_index_file )
                         sample_files_copied.append( options.missing_index_file )
@@ -852,7 +852,7 @@
     # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later.
     metadata = repository.metadata
     repository_dict = None
-    datatypes_config = get_config_from_disk( 'datatypes_conf.xml', relative_install_dir )
+    datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', relative_install_dir )
     if datatypes_config:
         converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate )
         if converter_path or display_path:
@@ -883,10 +883,7 @@
     return False
 def pull_repository( repo, repository_clone_url, ctx_rev ):
     """Pull changes from a remote repository to a local one."""
-    commands.pull( get_configured_ui(),
-                   repo,
-                   source=repository_clone_url,
-                   rev=[ ctx_rev ] )
+    commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] )
 def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ):
     # A tool shed repository is being uninstalled so change the shed_tool_conf file.  Parse the config file to generate the entire list
     # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have
@@ -1038,7 +1035,7 @@
         trans.app.toolbox.write_integrated_tool_panel_config_file()
 def remove_tool_dependency( trans, tool_dependency ):
     dependency_install_dir = tool_dependency.installation_directory( trans.app )
-    removed, error_message = remove_tool_dependency_installation_directory( dependency_install_dir )
+    removed, error_message = suc.remove_tool_dependency_installation_directory( dependency_install_dir )
     if removed:
         tool_dependency.status = trans.model.ToolDependency.installation_status.UNINSTALLED
         tool_dependency.error_message = None
@@ -1046,7 +1043,7 @@
         trans.sa_session.flush()
     return removed, error_message
 def tool_shed_from_repository_clone_url( repository_clone_url ):
-    return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' )
+    return suc.clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' )
 def update_in_shed_tool_config( app, repository ):
     # A tool shed repository is being updated so change the shed_tool_conf file.  Parse the config file to generate the entire list
     # of config_elems instead of using the in-memory list.
@@ -1060,7 +1057,7 @@
     
     tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository )
     repository_tools_tups = get_repository_tools_tups( app, repository.metadata )
-    cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url_for_installed_repository( trans, repository ) )
+    cleaned_repository_clone_url = suc.clean_repository_clone_url( generate_clone_url_for_installed_repository( trans, repository ) )
     tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url )
     owner = repository.owner
     if not owner:


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/community/controllers/admin.py
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -5,7 +5,7 @@
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.web.form_builder import SelectField
 from galaxy.util import inflector
-from galaxy.util.shed_util_common import *
+import galaxy.util.shed_util_common as suc
 from common import *
 from repository import RepositoryGrid, CategoryGrid
 
@@ -342,8 +342,8 @@
     class RevisionColumn( grids.TextColumn ):
         def get_value( self, trans, grid, repository_metadata ):
             repository = repository_metadata.repository
-            repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
-            ctx = get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
+            repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+            ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision )
             return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision )
     class ToolsColumn( grids.TextColumn ):
         def get_value( self, trans, grid, repository_metadata ):
@@ -481,7 +481,7 @@
                     # The received id is the repository id, so we need to get the id of the user
                     # that uploaded the repository.
                     repository_id = kwd.get( 'id', None )
-                    repository = get_repository_in_tool_shed( trans, repository_id )
+                    repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'f-email' ] = repository.user.email
             elif operation == "repositories_by_category":
                 # Eliminate the current filters if any exist.
@@ -513,7 +513,7 @@
             changset_revision_str = 'changeset_revision_'
             if k.startswith( changset_revision_str ):
                 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) )
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if repository.tip( trans.app ) != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='browse_repositories',
@@ -586,7 +586,7 @@
             count = 0
             deleted_repositories = ""
             for repository_id in ids:
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if not repository.deleted:
                     repository.deleted = True
                     trans.sa_session.add( repository )
@@ -717,12 +717,12 @@
     @web.require_admin
     def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
-            kwd[ 'CONTROLLER' ] = TOOL_SHED_ADMIN_CONTROLLER
-            message, status = reset_metadata_on_selected_repositories( trans, **kwd )
+            kwd[ 'CONTROLLER' ] = suc.TOOL_SHED_ADMIN_CONTROLLER
+            message, status = suc.reset_metadata_on_selected_repositories( trans, **kwd )
         else:
             message = util.restore_text( kwd.get( 'message', ''  ) )
             status = kwd.get( 'status', 'done' )
-        repositories_select_field = build_repository_ids_select_field( trans, TOOL_SHED_ADMIN_CONTROLLER )
+        repositories_select_field = suc.build_repository_ids_select_field( trans, suc.TOOL_SHED_ADMIN_CONTROLLER )
         return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako',
                                     repositories_select_field=repositories_select_field,
                                     message=message,
@@ -740,7 +740,7 @@
             count = 0
             undeleted_repositories = ""
             for repository_id in ids:
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if repository.deleted:
                     repository.deleted = False
                     trans.sa_session.add( repository )


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -6,7 +6,7 @@
 from galaxy.util.odict import odict
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.hash_util import *
-from galaxy.util.shed_util_common import *
+import galaxy.util.shed_util_common as suc
 from galaxy.web.base.controller import *
 from galaxy.web.base.controllers.admin import *
 from galaxy.webapps.community import model
@@ -108,12 +108,12 @@
     tool_versions_dict = {}
     for tool_dict in metadata.get( 'tools', [] ):
         # We have at least 2 changeset revisions to compare tool guids and tool ids.
-        parent_id = get_parent_id( trans,
-                                   id,
-                                   tool_dict[ 'id' ],
-                                   tool_dict[ 'version' ],
-                                   tool_dict[ 'guid' ],
-                                   changeset_revisions )
+        parent_id = suc.get_parent_id( trans,
+                                       id,
+                                       tool_dict[ 'id' ],
+                                       tool_dict[ 'version' ],
+                                       tool_dict[ 'guid' ],
+                                       changeset_revisions )
         tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id
     if tool_versions_dict:
         repository_metadata.tool_versions = tool_versions_dict
@@ -130,7 +130,7 @@
         return False
     if changeset_revision == repository.tip( trans.app ):
         return True
-    file_name = strip_path( file_path )
+    file_name = suc.strip_path( file_path )
     latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision )
     can_use_disk_file = filecmp.cmp( file_path, latest_version_of_file )
     try:
@@ -140,7 +140,7 @@
     return can_use_disk_file
 def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
     """Check the malicious flag in repository metadata for a specified change set"""
-    repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+    repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
     if repository_metadata:
         return repository_metadata.malicious
     return False
@@ -191,7 +191,7 @@
                                       tool.id,
                                       tool.version )
 def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
-    stripped_file_name = strip_path( file_name )
+    stripped_file_name = suc.strip_path( file_name )
     file_path = None
     for root, dirs, files in os.walk( repo_files_dir ):
         if root.find( '.hg' ) < 0:
@@ -246,11 +246,11 @@
     This method is restricted to tool_config files rather than any file since it is likely that, with the exception of tool config files,
     multiple files will have the same name in various directories within the repository.
     """
-    stripped_filename = strip_path( filename )
-    for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+    stripped_filename = suc.strip_path( filename )
+    for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
         manifest_ctx = repo.changectx( changeset )
         for ctx_file in manifest_ctx.files():
-            ctx_file_name = strip_path( ctx_file )
+            ctx_file_name = suc.strip_path( ctx_file )
             if ctx_file_name == stripped_filename:
                 try:
                     fctx = manifest_ctx[ ctx_file ]
@@ -268,10 +268,10 @@
     return None
 def get_previous_repository_reviews( trans, repository, changeset_revision ):
     """Return an ordered dictionary of repository reviews up to and including the received changeset revision."""
-    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
     previous_reviews_dict = odict()
-    for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+    for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
         previous_changeset_revision = str( repo.changectx( changeset ) )
         if previous_changeset_revision in reviewed_revision_hashes:
             previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision )
@@ -313,9 +313,9 @@
 def get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=None ):
     if repository is None:
         repository = repository_metadata.repository
-    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     changeset_revision = repository_metadata.changeset_revision
-    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
     if ctx:
         rev = '%04d' % ctx.rev()
         label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
@@ -324,7 +324,7 @@
         label = "-1:%s" % changeset_revision
     return rev, label, changeset_revision
 def get_rev_label_from_changeset_revision( repo, changeset_revision ):
-    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
     if ctx:
         rev = '%04d' % ctx.rev()
         label = "%s:%s" % ( str( ctx.rev() ), changeset_revision )
@@ -358,8 +358,8 @@
     Return a string consisting of the human read-able 
     changeset rev and the changeset revision string.
     """
-    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
-    ctx = get_changectx_for_changeset( repo, changeset_revision )
+    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+    ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
     if ctx:
         return "%s:%s" % ( str( ctx.rev() ), changeset_revision )
     else:
@@ -389,7 +389,7 @@
     #    user is not an admin user, the email will not include any information about both HTML and image content
     #    that was included in the change set.
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( get_configured_ui(), repo_dir )
+    repo = hg.repository( suc.get_configured_ui(), repo_dir )
     smtp_server = trans.app.config.smtp_server
     if smtp_server and ( new_repo_alert or repository.email_alerts ):
         # Send email alert to users that want them.
@@ -457,9 +457,9 @@
                 log.exception( "An error occurred sending a tool shed repository update alert by email." )
 def has_previous_repository_reviews( trans, repository, changeset_revision ):
     """Determine if a repository has a changeset revision review prior to the received changeset revision."""
-    repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+    repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
     reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
-    for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ):
+    for changeset in suc.reversed_upper_bounded_changelog( repo, changeset_revision ):
         previous_changeset_revision = str( repo.changectx( changeset ) )
         if previous_changeset_revision in reviewed_revision_hashes:
             return True
@@ -471,9 +471,9 @@
     revision and the first changeset revision in the repository, searching backwards.
     """
     original_tool_data_path = trans.app.config.tool_data_path
-    repository = get_repository_in_tool_shed( trans, repository_id )
+    repository = suc.get_repository_in_tool_shed( trans, repository_id )
     repo_files_dir = repository.repo_path( trans.app )
-    repo = hg.repository( get_configured_ui(), repo_files_dir )
+    repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
     message = ''
     tool = None
     can_use_disk_file = False
@@ -482,27 +482,27 @@
     can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision )
     if can_use_disk_file:
         trans.app.config.tool_data_path = work_dir
-        tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir )
+        tool, valid, message, sample_files = suc.handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir )
         if tool is not None:
-            invalid_files_and_errors_tups = check_tool_input_params( trans.app,
-                                                                     repo_files_dir,
-                                                                     tool_config_filename,
-                                                                     tool,
-                                                                     sample_files )
+            invalid_files_and_errors_tups = suc.check_tool_input_params( trans.app,
+                                                                         repo_files_dir,
+                                                                         tool_config_filename,
+                                                                         tool,
+                                                                         sample_files )
             if invalid_files_and_errors_tups:
-                message2 = generate_message_for_invalid_tools( trans,
-                                                               invalid_files_and_errors_tups,
-                                                               repository,
-                                                               metadata_dict=None,
-                                                               as_html=True,
-                                                               displaying_invalid_tool=True )
-                message = concat_messages( message, message2 )
+                message2 = suc.generate_message_for_invalid_tools( trans,
+                                                                   invalid_files_and_errors_tups,
+                                                                   repository,
+                                                                   metadata_dict=None,
+                                                                   as_html=True,
+                                                                   displaying_invalid_tool=True )
+                message = suc.concat_messages( message, message2 )
     else:
-        tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir )
-    remove_dir( work_dir )
+        tool, message, sample_files = suc.handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir )
+    suc.remove_dir( work_dir )
     trans.app.config.tool_data_path = original_tool_data_path
     # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-    reset_tool_data_tables( trans.app )
+    suc.reset_tool_data_tables( trans.app )
     return repository, tool, message
 def new_repository_dependency_metadata_required( trans, repository, metadata_dict ):
     """
@@ -594,36 +594,36 @@
     message = ''
     status = 'done'
     encoded_id = trans.security.encode_id( repository.id )
-    repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository )
+    repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( get_configured_ui(), repo_dir )
-    metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
-                                                                                 repository=repository,
-                                                                                 repository_clone_url=repository_clone_url,
-                                                                                 relative_install_dir=repo_dir,
-                                                                                 repository_files_dir=None,
-                                                                                 resetting_all_metadata_on_repository=False,
-                                                                                 updating_installed_repository=False,
-                                                                                 persist=False )
+    repo = hg.repository( suc.get_configured_ui(), repo_dir )
+    metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                     repository=repository,
+                                                                                     repository_clone_url=repository_clone_url,
+                                                                                     relative_install_dir=repo_dir,
+                                                                                     repository_files_dir=None,
+                                                                                     resetting_all_metadata_on_repository=False,
+                                                                                     updating_installed_repository=False,
+                                                                                     persist=False )
     if metadata_dict:
-        downloadable = is_downloadable( metadata_dict )
+        downloadable = suc.is_downloadable( metadata_dict )
         repository_metadata = None
         if new_repository_dependency_metadata_required( trans, repository, metadata_dict ) or \
            new_tool_metadata_required( trans, repository, metadata_dict ) or \
            new_workflow_metadata_required( trans, repository, metadata_dict ):
             # Create a new repository_metadata table row.
-            repository_metadata = create_or_update_repository_metadata( trans,
-                                                                        encoded_id,
-                                                                        repository,
-                                                                        repository.tip( trans.app ),
-                                                                        metadata_dict )
+            repository_metadata = suc.create_or_update_repository_metadata( trans,
+                                                                            encoded_id,
+                                                                            repository,
+                                                                            repository.tip( trans.app ),
+                                                                            metadata_dict )
             # If this is the first record stored for this repository, see if we need to send any email alerts.
             if len( repository.downloadable_revisions ) == 1:
                 handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False )
         else:
             repository_metadata = get_latest_repository_metadata( trans, repository.id )
             if repository_metadata:
-                downloadable = is_downloadable( metadata_dict )
+                downloadable = suc.is_downloadable( metadata_dict )
                 # Update the last saved repository_metadata table row.
                 repository_metadata.changeset_revision = repository.tip( trans.app )
                 repository_metadata.metadata = metadata_dict
@@ -632,17 +632,17 @@
                 trans.sa_session.flush()
             else:
                 # There are no tools in the repository, and we're setting metadata on the repository tip.
-                repository_metadata = create_or_update_repository_metadata( trans,
-                                                                            encoded_id,
-                                                                            repository,
-                                                                            repository.tip( trans.app ),
-                                                                            metadata_dict )
+                repository_metadata = suc.create_or_update_repository_metadata( trans,
+                                                                                encoded_id,
+                                                                                repository,
+                                                                                repository.tip( trans.app ),
+                                                                                metadata_dict )
         if 'tools' in metadata_dict and repository_metadata and status != 'error':
             # Set tool versions on the new downloadable change set.  The order of the list of changesets is critical, so we use the repo's changelog.
             changeset_revisions = []
             for changeset in repo.changelog:
                 changeset_revision = str( repo.changectx( changeset ) )
-                if get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ):
+                if suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ):
                     changeset_revisions.append( changeset_revision )
             add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions )
     elif len( repo ) == 1 and not invalid_file_tups:
@@ -650,10 +650,10 @@
         message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."
         status = "error"
     if invalid_file_tups:
-        message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict )
+        message = suc.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict )
         status = 'error'
     # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-    reset_tool_data_tables( trans.app )
+    suc.reset_tool_data_tables( trans.app )
     return message, status
 def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ):
     # Set metadata on the repository tip.
@@ -671,7 +671,7 @@
     # Make a copy of a repository's files for browsing, remove from disk all files that are not tracked, and commit all
     # added, modified or removed files that have not yet been committed.
     repo_dir = repository.repo_path( trans.app )
-    repo = hg.repository( get_configured_ui(), repo_dir )
+    repo = hg.repository( suc.get_configured_ui(), repo_dir )
     # The following will delete the disk copy of only the files in the repository.
     #os.system( 'hg update -r null > /dev/null 2>&1' )
     files_to_remove_from_disk = []


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -9,7 +9,7 @@
 from galaxy.web.framework.helpers import time_ago, iff, grids
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.model.orm import *
-from galaxy.util.shed_util_common import *
+import galaxy.util.shed_util_common as suc
 from galaxy.tool_shed.encoding_util import *
 from common import *
 
@@ -616,7 +616,7 @@
                 else:
                     # The received id is the repository id, so we need to get the id of the user that uploaded the repository.
                     repository_id = kwd.get( 'id', None )
-                    repository = get_repository_in_tool_shed( trans, repository_id )
+                    repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'f-email' ] = repository.user.email
             elif operation == "repositories_i_own":
                 # Eliminate the current filters if any exist.
@@ -673,7 +673,7 @@
             changset_revision_str = 'changeset_revision_'
             if k.startswith( changset_revision_str ):
                 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) )
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if repository.tip( trans.app ) != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='browse_repositories',
@@ -687,10 +687,10 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
-        repository = get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repository = suc.get_repository_in_tool_shed( trans, id )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         # Update repository files for browsing.
-        update_repository( repo )
+        suc.update_repository( repo )
         is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) )
         metadata = self.get_metadata( trans, id, repository.tip( trans.app ) )
         return trans.fill_template( '/webapps/community/repository/browse_repository.mako',
@@ -748,7 +748,7 @@
             operation = kwd[ 'operation' ].lower()
             if operation == "preview_tools_in_changeset":
                 repository_id = kwd.get( 'id', None )
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 repository_metadata = get_latest_repository_metadata( trans, repository.id )
                 latest_installable_changeset_revision = repository_metadata.changeset_revision
                 return trans.response.send_redirect( web.url_for( controller='repository',
@@ -772,7 +772,7 @@
             changset_revision_str = 'changeset_revision_'
             if k.startswith( changset_revision_str ):
                 repository_id = trans.security.encode_id( int( k.lstrip( changset_revision_str ) ) )
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if repository.tip( trans.app ) != v:
                     return trans.response.send_redirect( web.url_for( controller='repository',
                                                                       action='preview_tools_in_changeset',
@@ -817,11 +817,11 @@
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repository = suc.get_repository_by_name_and_owner( trans, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         # Default to the current changeset revision.
-        update_to_ctx = get_changectx_for_changeset( repo, changeset_revision )
+        update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
         latest_changeset_revision = changeset_revision
         from_update_manager = kwd.get( 'from_update_manager', False )
         if from_update_manager:
@@ -829,9 +829,9 @@
             no_update = 'false'
         else:
             # Start building up the url to redirect back to the calling Galaxy instance.            
-            url = url_join( galaxy_url,
-                            'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
-                            ( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
+            url = suc.url_join( galaxy_url,
+                                'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \
+                                ( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) )
         if changeset_revision == repository.tip( trans.app ):
             # If changeset_revision is the repository tip, there are no additional updates.
             if from_update_manager:
@@ -839,9 +839,9 @@
             # Return the same value for changeset_revision and latest_changeset_revision.
             url += latest_changeset_revision
         else:
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, 
-                                                                                 trans.security.encode_id( repository.id ),
-                                                                                 changeset_revision )
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, 
+                                                                                     trans.security.encode_id( repository.id ),
+                                                                                     changeset_revision )
             if repository_metadata:
                 # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates.
                 if from_update_manager:
@@ -855,19 +855,19 @@
                 update_to_changeset_hash = None
                 for changeset in repo.changelog:
                     changeset_hash = str( repo.changectx( changeset ) )
-                    ctx = get_changectx_for_changeset( repo, changeset_hash )
+                    ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
                     if update_to_changeset_hash:
                         if changeset_hash == repository.tip( trans.app ):
-                            update_to_ctx = get_changectx_for_changeset( repo, changeset_hash )
+                            update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
                             latest_changeset_revision = changeset_hash
                             break
                         else:
-                            repository_metadata = get_repository_metadata_by_changeset_revision( trans,
-                                                                                                 trans.security.encode_id( repository.id ),
-                                                                                                 changeset_hash )
+                            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans,
+                                                                                                     trans.security.encode_id( repository.id ),
+                                                                                                     changeset_hash )
                             if repository_metadata:
                                 # We found a RepositoryMetadata record.
-                                update_to_ctx = get_changectx_for_changeset( repo, changeset_hash )
+                                update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
                                 latest_changeset_revision = changeset_hash
                                 break
                             else:
@@ -888,7 +888,7 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository_in_tool_shed( trans, id )
+        repository = suc.get_repository_in_tool_shed( trans, id )
         metadata = self.get_metadata( trans, id, repository.tip( trans.app ) )
         if trans.user and trans.user.email:
             return trans.fill_template( "/webapps/community/repository/contact_owner.mako",
@@ -904,7 +904,7 @@
         # Since we support both http and https, we set push_ssl to False to override the default (which is True) in the mercurial api.  The hg
         # purge extension purges all files and directories not being tracked by mercurial in the current repository.  It'll remove unknown files
         # and empty directories.  This is not currently used because it is not supported in the mercurial API.
-        repo = hg.repository( get_configured_ui(), path=repository.repo_path( trans.app ) )
+        repo = hg.repository( suc.get_configured_ui(), path=repository.repo_path( trans.app ) )
         fp = repo.opener( 'hgrc', 'wb' )
         fp.write( '[paths]\n' )
         fp.write( 'default = .\n' )
@@ -963,7 +963,7 @@
                 if not os.path.exists( repository_path ):
                     os.makedirs( repository_path )
                 # Create the local repository
-                repo = hg.repository( get_configured_ui(), repository_path, create=True )
+                repo = hg.repository( suc.get_configured_ui(), repository_path, create=True )
                 # Add an entry in the hgweb.config file for the local repository.
                 lhs = "repos/%s/%s" % ( repository.user.username, repository.name )
                 trans.app.hgweb_config_manager.add_entry( lhs, repository_path )
@@ -999,7 +999,7 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         repository_id = params.get( 'id', None )
-        repository = get_repository_in_tool_shed( trans, repository_id )
+        repository = suc.get_repository_in_tool_shed( trans, repository_id )
         mark_deprecated = util.string_as_bool( params.get( 'mark_deprecated', False ) )
         repository.deprecated = mark_deprecated
         trans.sa_session.add( repository )
@@ -1054,7 +1054,7 @@
     def download( self, trans, repository_id, changeset_revision, file_type, **kwd ):
         # Download an archive of the repository files compressed as zip, gz or bz2.
         params = util.Params( kwd )
-        repository = get_repository_in_tool_shed( trans, repository_id )
+        repository = suc.get_repository_in_tool_shed( trans, repository_id )
         # Allow hgweb to handle the download.  This requires the tool shed
         # server account's .hgrc file to include the following setting:
         # [web]
@@ -1087,7 +1087,7 @@
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
                     repository_metadata = get_repository_metadata_by_id( trans, item_id )
                     repository_id = trans.security.encode_id( repository_metadata.repository.id )
-                    repository = get_repository_in_tool_shed( trans, repository_id )
+                    repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'id' ] = repository_id
                     kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
                     if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ):
@@ -1172,7 +1172,7 @@
                     # The received id is a RepositoryMetadata id, so we have to get the repository id.
                     repository_metadata = get_repository_metadata_by_id( trans, item_id )
                     repository_id = trans.security.encode_id( repository_metadata.repository.id )
-                    repository = get_repository_in_tool_shed( trans, repository_id )
+                    repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     kwd[ 'id' ] = repository_id
                     kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision
                     if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ):
@@ -1252,11 +1252,11 @@
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repository = suc.get_repository_by_name_and_owner( trans, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         # Default to the received changeset revision and ctx_rev.
-        update_to_ctx = get_changectx_for_changeset( repo, changeset_revision )
+        update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
         ctx_rev = str( update_to_ctx.rev() )
         latest_changeset_revision = changeset_revision
         update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev )
@@ -1264,9 +1264,9 @@
             # If changeset_revision is the repository tip, there are no additional updates.
             return tool_shed_encode( update_dict )
         else:
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, 
-                                                                                 trans.security.encode_id( repository.id ),
-                                                                                 changeset_revision )
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, 
+                                                                                     trans.security.encode_id( repository.id ),
+                                                                                     changeset_revision )
             if repository_metadata:
                 # If changeset_revision is in the repository_metadata table for this repository, there are no additional updates.
                 return tool_shed_encode( update_dict )
@@ -1276,16 +1276,16 @@
                 update_to_changeset_hash = None
                 for changeset in repo.changelog:
                     changeset_hash = str( repo.changectx( changeset ) )
-                    ctx = get_changectx_for_changeset( repo, changeset_hash )
+                    ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
                     if update_to_changeset_hash:
-                        if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ):
+                        if suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ):
                             # We found a RepositoryMetadata record.
                             if changeset_hash == repository.tip( trans.app ):
                                 # The current ctx is the repository tip, so use it.
-                                update_to_ctx = get_changectx_for_changeset( repo, changeset_hash )
+                                update_to_ctx = suc.get_changectx_for_changeset( repo, changeset_hash )
                                 latest_changeset_revision = changeset_hash
                             else:
-                                update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash )
+                                update_to_ctx = suc.get_changectx_for_changeset( repo, update_to_changeset_hash )
                                 latest_changeset_revision = update_to_changeset_hash
                             break
                     elif not update_to_changeset_hash and changeset_hash == changeset_revision:
@@ -1300,10 +1300,10 @@
         repository_name = kwd[ 'name' ]
         repository_owner = kwd[ 'owner' ]
         changeset_revision = kwd[ 'changeset_revision' ]
-        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
+        repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
-        ctx = get_changectx_for_changeset( repo, changeset_revision )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
+        ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
         if ctx:
             return str( ctx.rev() )
         return ''
@@ -1312,16 +1312,16 @@
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
         trans.response.headers['Expires'] = '0'
-        return get_repository_file_contents( file_path )
+        return suc.get_repository_file_contents( file_path )
     def get_file_from_changeset_revision( self, repo_files_dir, changeset_revision, file_name, dir ):
         """Return file_name from the received changeset_revision of the repository manifest."""
         stripped_file_name = strip_path( file_name )
-        repo = hg.repository( get_configured_ui(), repo_files_dir )
-        ctx = get_changectx_for_changeset( repo, changeset_revision )
-        named_tmp_file = get_named_tmpfile_from_ctx( ctx, file_name, dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
+        ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+        named_tmp_file = suc.get_named_tmpfile_from_ctx( ctx, file_name, dir )
         return named_tmp_file
     def get_metadata( self, trans, repository_id, changeset_revision ):
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata and repository_metadata.metadata:
             return repository_metadata.metadata
         return None
@@ -1331,21 +1331,21 @@
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repository = suc.get_repository_by_name_and_owner( trans, name, owner )
         repository_id = trans.security.encode_id( repository.id )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
             metadata = repository_metadata.metadata
             if metadata:
                 # Get a dictionary of all repositories upon which the contents of the received repository depends.
-                repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans,
-                                                                                              repository=repository,
-                                                                                              repository_metadata=repository_metadata,
-                                                                                              toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
-                                                                                              key_rd_dicts_to_be_processed=None,
-                                                                                              all_repository_dependencies=None,
-                                                                                              handled_key_rd_dicts=None,
-                                                                                              circular_repository_dependencies=None )
+                repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
+                                                                                                  repository=repository,
+                                                                                                  repository_metadata=repository_metadata,
+                                                                                                  toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                                  key_rd_dicts_to_be_processed=None,
+                                                                                                  all_repository_dependencies=None,
+                                                                                                  handled_key_rd_dicts=None,
+                                                                                                  circular_repository_dependencies=None )
                 if repository_dependencies:
                     return tool_shed_encode( repository_dependencies )
         return ''
@@ -1361,9 +1361,9 @@
         repo_info_dicts = []
         for tup in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
             repository_id, changeset_revision = tup
-            repository = get_repository_in_tool_shed( trans, repository_id )
-            repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans, repository )
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+            repository = suc.get_repository_in_tool_shed( trans, repository_id )
+            repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
             metadata = repository_metadata.metadata
             if not includes_tools and 'tools' in metadata:
                 includes_tools = True
@@ -1372,17 +1372,17 @@
             if not includes_tool_dependencies and 'tool_dependencies' in metadata:
                 includes_tool_dependencies = True
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( get_configured_ui(), repo_dir )
-            ctx = get_changectx_for_changeset( repo, changeset_revision )
-            repo_info_dict = create_repo_info_dict( trans=trans,
-                                                    repository_clone_url=repository_clone_url,
-                                                    changeset_revision=changeset_revision,
-                                                    ctx_rev=str( ctx.rev() ),
-                                                    repository_owner=repository.user.username,
-                                                    repository_name=repository.name,
-                                                    repository=repository,
-                                                    metadata=None,
-                                                    repository_metadata=repository_metadata )      
+            repo = hg.repository( suc.get_configured_ui(), repo_dir )
+            ctx = suc.get_changectx_for_changeset( repo, changeset_revision )
+            repo_info_dict = suc.create_repo_info_dict( trans=trans,
+                                                        repository_clone_url=repository_clone_url,
+                                                        changeset_revision=changeset_revision,
+                                                        ctx_rev=str( ctx.rev() ),
+                                                        repository_owner=repository.user.username,
+                                                        repository_name=repository.name,
+                                                        repository=repository,
+                                                        metadata=None,
+                                                        repository_metadata=repository_metadata )      
             repo_info_dicts.append( tool_shed_encode( repo_info_dict ) )
         return dict( includes_tools=includes_tools,
                      includes_repository_dependencies=includes_repository_dependencies,
@@ -1397,9 +1397,9 @@
         repository_name = kwd[ 'name' ]
         repository_owner = kwd[ 'owner' ]
         changeset_revision = kwd[ 'changeset_revision' ]
-        repository = get_repository_by_name_and_owner( trans, repository_name, repository_owner )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )        
-        return build_readme_files_dict( repository_metadata )
+        repository = suc.get_repository_by_name_and_owner( trans, repository_name, repository_owner )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision )        
+        return suc.build_readme_files_dict( repository_metadata )
     @web.expose
     def get_tool_dependencies( self, trans, **kwd ):
         """Handle a request from a local Galaxy instance."""
@@ -1411,7 +1411,7 @@
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repository = suc.get_repository_by_name_and_owner( trans, name, owner )
         for downloadable_revision in repository.downloadable_revisions:
             if downloadable_revision.changeset_revision == changeset_revision:
                 break
@@ -1432,13 +1432,13 @@
         name = kwd[ 'name' ]
         owner = kwd[ 'owner' ]
         changeset_revision = kwd[ 'changeset_revision' ]
-        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repository = suc.get_repository_by_name_and_owner( trans, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         tool_version_dicts = []
         for changeset in repo.changelog:
             current_changeset_revision = str( repo.changectx( changeset ) )
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision )
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), current_changeset_revision )
             if repository_metadata and repository_metadata.tool_versions:
                 tool_version_dicts.append( repository_metadata.tool_versions )
                 if current_changeset_revision == changeset_revision:
@@ -1450,14 +1450,14 @@
         """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions."""
         encoded_id = trans.security.encode_id( repository.id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         # Initialize the tool lineage
         tool_guid_lineage = [ guid ]
         # Get all ancestor guids of the received guid.
         current_child_guid = guid
-        for changeset in reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ):
+        for changeset in suc.reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ):
             ctx = repo.changectx( changeset )
-            rm = get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) )
+            rm = suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) )
             if rm:
                 parent_guid = rm.tool_versions.get( current_child_guid, None )
                 if parent_guid:
@@ -1465,9 +1465,9 @@
                     current_child_guid = parent_guid
         # Get all descendant guids of the received guid.
         current_parent_guid = guid
-        for changeset in reversed_lower_upper_bounded_changelog( repo, repository_metadata.changeset_revision, repository.tip( trans.app ) ):
+        for changeset in suc.reversed_lower_upper_bounded_changelog( repo, repository_metadata.changeset_revision, repository.tip( trans.app ) ):
             ctx = repo.changectx( changeset )
-            rm = get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) )
+            rm = suc.get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) )
             if rm:
                 tool_versions = rm.tool_versions
                 for child_guid, parent_guid in tool_versions.items():
@@ -1566,15 +1566,15 @@
         owner = kwd.get( 'owner', None )
         galaxy_url = kwd.get( 'galaxy_url', None )
         if not repository_ids:
-            repository = get_repository_by_name_and_owner( trans, name, owner )
+            repository = suc.get_repository_by_name_and_owner( trans, name, owner )
             repository_ids = trans.security.encode_id( repository.id )
         if not galaxy_url:
             # If galaxy_url is not in the request, it had to have been stored in a cookie by the tool shed.
             galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
         # Redirect back to local Galaxy to perform install.
-        url = url_join( galaxy_url,
-                        'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \
-                        ( url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) )
+        url = suc.url_join( galaxy_url,
+                            'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \
+                            ( url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) )
         return trans.response.send_redirect( url )
     @web.expose
     def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
@@ -1586,13 +1586,13 @@
         is_malicious = changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) )
         invalid_file_tups = []
         if tool:
-            invalid_file_tups = check_tool_input_params( trans.app,
-                                                         repository.repo_path( trans.app ),
-                                                         tool_config,
-                                                         tool,
-                                                         [] )
+            invalid_file_tups = suc.check_tool_input_params( trans.app,
+                                                             repository.repo_path( trans.app ),
+                                                             tool_config,
+                                                             tool,
+                                                             [] )
         if invalid_file_tups:
-            message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True )
+            message = suc.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True )
         elif error_message:
             message = error_message
         try:
@@ -1667,9 +1667,9 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         cntrller = params.get( 'cntrller', 'repository' )
-        repository = get_repository_in_tool_shed( trans, id )
+        repository = suc.get_repository_in_tool_shed( trans, id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         repo_name = util.restore_text( params.get( 'repo_name', repository.name ) )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) )
         description = util.restore_text( params.get( 'description', repository.description ) )
@@ -1787,8 +1787,8 @@
         metadata = None
         is_malicious = False
         repository_dependencies = None
-        if changeset_revision != INITIAL_CHANGELOG_HASH:
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+        if changeset_revision != suc.INITIAL_CHANGELOG_HASH:
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
             if repository_metadata:
                 revision_label = get_revision_label( trans, repository, changeset_revision )
                 repository_metadata_id = trans.security.encode_id( repository_metadata.id )
@@ -1796,9 +1796,9 @@
                 is_malicious = repository_metadata.malicious
             else:
                 # There is no repository_metadata defined for the changeset_revision, so see if it was defined in a previous changeset in the changelog.
-                previous_changeset_revision = get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
-                if previous_changeset_revision != INITIAL_CHANGELOG_HASH:
-                    repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision )
+                previous_changeset_revision = suc.get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
+                if previous_changeset_revision != suc.INITIAL_CHANGELOG_HASH:
+                    repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision )
                     if repository_metadata:
                         revision_label = get_revision_label( trans, repository, previous_changeset_revision )
                         repository_metadata_id = trans.security.encode_id( repository_metadata.id )
@@ -1806,13 +1806,13 @@
                         is_malicious = repository_metadata.malicious
             if repository_metadata:
                 # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
-                repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans,
-                                                                                              repository=repository,
-                                                                                              repository_metadata=repository_metadata,
-                                                                                              toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
-                                                                                              key_rd_dicts_to_be_processed=None,
-                                                                                              all_repository_dependencies=None,
-                                                                                              handled_key_rd_dicts=None )
+                repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
+                                                                                                  repository=repository,
+                                                                                                  repository_metadata=repository_metadata,
+                                                                                                  toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                                  key_rd_dicts_to_be_processed=None,
+                                                                                                  all_repository_dependencies=None,
+                                                                                                  handled_key_rd_dicts=None )
         if is_malicious:
             if trans.app.security_agent.can_push( trans.app, trans.user, repository ):
                 message += malicious_error_can_push
@@ -1832,7 +1832,7 @@
             review_id = trans.security.encode_id( review.id )
         else:
             review_id = None
-        containers_dict = build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
+        containers_dict = suc.build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
         return trans.fill_template( '/webapps/community/repository/manage_repository.mako',
                                     cntrller=cntrller,
                                     repo_name=repo_name,
@@ -1903,28 +1903,28 @@
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
         trans.response.headers['Expires'] = '0'
-        return open_repository_files_folder( trans, folder_path )
+        return suc.open_repository_files_folder( trans, folder_path )
     @web.expose
     def preview_tools_in_changeset( self, trans, repository_id, **kwd ):
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository_in_tool_shed( trans, repository_id )
+        repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
             repository_metadata_id = trans.security.encode_id( repository_metadata.id ),
             metadata = repository_metadata.metadata
             # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
-            repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans,
-                                                                                          repository=repository,
-                                                                                          repository_metadata=repository_metadata,
-                                                                                          toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
-                                                                                          key_rd_dicts_to_be_processed=None,
-                                                                                          all_repository_dependencies=None,
-                                                                                          handled_key_rd_dicts=None )
+            repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
+                                                                                              repository=repository,
+                                                                                              repository_metadata=repository_metadata,
+                                                                                              toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                              key_rd_dicts_to_be_processed=None,
+                                                                                              all_repository_dependencies=None,
+                                                                                              handled_key_rd_dicts=None )
         else:
             repository_metadata_id = None
             metadata = None
@@ -1935,7 +1935,7 @@
                                                                                  selected_value=changeset_revision,
                                                                                  add_id_to_name=False,
                                                                                  downloadable=False )
-        containers_dict = build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
+        containers_dict = suc.build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
         return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako',
                                     repository=repository,
                                     containers_dict=containers_dict,
@@ -1961,14 +1961,14 @@
         name = params.get( 'name', None )
         owner = params.get( 'owner', None )
         changeset_revision = params.get( 'changeset_revision', None )
-        repository = get_repository_by_name_and_owner( trans, name, owner )
+        repository = suc.get_repository_by_name_and_owner( trans, name, owner )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         # Get the lower bound changeset revision 
-        lower_bound_changeset_revision = get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
+        lower_bound_changeset_revision = suc.get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
         # Build the list of changeset revision hashes.
         changeset_hashes = []
-        for changeset in reversed_lower_upper_bounded_changelog( repo, lower_bound_changeset_revision, changeset_revision ):
+        for changeset in suc.reversed_lower_upper_bounded_changelog( repo, lower_bound_changeset_revision, changeset_revision ):
             changeset_hashes.append( str( repo.changectx( changeset ) ) )
         if changeset_hashes:
             changeset_hashes_str = ','.join( changeset_hashes )
@@ -1987,8 +1987,8 @@
                                                               action='browse_repositories',
                                                               message='Select a repository to rate',
                                                               status='error' ) )
-        repository = get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repository = suc.get_repository_in_tool_shed( trans, id )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         if repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='browse_repositories',
@@ -2017,10 +2017,10 @@
     def reset_all_metadata( self, trans, id, **kwd ):
         # This method is called only from the ~/templates/webapps/community/repository/manage_repository.mako template.
         # It resets all metadata on the complete changelog for a single repository in the tool shed.
-        invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd )
+        invalid_file_tups, metadata_dict = suc.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd )
         if invalid_file_tups:
-            repository = get_repository_in_tool_shed( trans, id )
-            message = generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict )
+            repository = suc.get_repository_in_tool_shed( trans, id )
+            message = suc.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, metadata_dict )
             status = 'error'
         else:
             message = "All repository metadata has been reset."
@@ -2125,9 +2125,9 @@
         message = util.restore_text( params.get( 'message', '' ) )
         status = params.get( 'status', 'done' )
         commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
-        repository = get_repository_in_tool_shed( trans, id )
+        repository = suc.get_repository_in_tool_shed( trans, id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         selected_files_to_delete = util.restore_text( params.get( 'selected_files_to_delete', '' ) )
         if params.get( 'select_files_to_delete_button', False ):
             if selected_files_to_delete:
@@ -2163,9 +2163,9 @@
                 commands.commit( repo.ui, repo, repo_dir, user=trans.user.username, message=commit_message )
                 handle_email_alerts( trans, repository )
                 # Update the repository files for browsing.
-                update_repository( repo )
+                suc.update_repository( repo )
                 # Get the new repository tip.
-                repo = hg.repository( get_configured_ui(), repo_dir )
+                repo = hg.repository( suc.get_configured_ui(), repo_dir )
                 if tip == repository.tip( trans.app ):
                     message += 'No changes to repository.  '
                     kwd[ 'message' ] = message
@@ -2187,7 +2187,7 @@
                                     status=status )
     @web.expose
     def send_to_owner( self, trans, id, message='' ):
-        repository = get_repository_in_tool_shed( trans, id )
+        repository = suc.get_repository_in_tool_shed( trans, id )
         if not message:
             message = 'Enter a message'
             status = 'error'
@@ -2237,7 +2237,7 @@
             total_alerts_removed = 0
             flush_needed = False
             for repository_id in repository_ids:
-                repository = get_repository_in_tool_shed( trans, repository_id )
+                repository = suc.get_repository_in_tool_shed( trans, repository_id )
                 if repository.email_alerts:
                     email_alerts = from_json_string( repository.email_alerts )
                 else:
@@ -2268,7 +2268,7 @@
     def set_malicious( self, trans, id, ctx_str, **kwd ):
         malicious = kwd.get( 'malicious', '' )
         if kwd.get( 'malicious_button', False ):
-            repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, ctx_str )
+            repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, ctx_str )
             malicious_checked = CheckboxField.is_checked( malicious )
             repository_metadata.malicious = malicious_checked
             trans.sa_session.add( repository_metadata )
@@ -2309,12 +2309,12 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repository = suc.get_repository_in_tool_shed( trans, id )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         changesets = []
         for changeset in repo.changelog:
             ctx = repo.changectx( changeset )
-            if get_repository_metadata_by_changeset_revision( trans, id, str( ctx ) ):
+            if suc.get_repository_metadata_by_changeset_revision( trans, id, str( ctx ) ):
                 has_metadata = True
             else:
                 has_metadata = False
@@ -2346,9 +2346,9 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
-        ctx = get_changectx_for_changeset( repo, ctx_str )
+        repository = suc.get_repository_in_tool_shed( trans, id )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
+        ctx = suc.get_changectx_for_changeset( repo, ctx_str )
         if ctx is None:
             message = "Repository does not include changeset revision '%s'." % str( ctx_str )
             status = 'error'
@@ -2362,7 +2362,7 @@
         anchors = modified + added + removed + deleted + unknown + ignored + clean
         diffs = []
         for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ):
-            diffs.append( to_safe_string( diff, to_html=True ) )
+            diffs.append( suc.to_safe_string( diff, to_html=True ) )
         is_malicious = changeset_is_malicious( trans, id, repository.tip( trans.app ) )
         metadata = self.get_metadata( trans, id, ctx_str )
         return trans.fill_template( '/webapps/community/repository/view_changeset.mako', 
@@ -2383,7 +2383,7 @@
                                     status=status )
     @web.expose
     def view_or_manage_repository( self, trans, **kwd ):
-        repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] )
+        repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         if trans.user_is_admin() or repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='manage_repository',
@@ -2398,8 +2398,8 @@
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
         cntrller = params.get( 'cntrller', 'repository' )
-        repository = get_repository_in_tool_shed( trans, id )
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repository = suc.get_repository_in_tool_shed( trans, id )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
         changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip( trans.app ) ) )
         display_reviews = util.string_as_bool( params.get( 'display_reviews', False ) )
@@ -2434,18 +2434,18 @@
                                                                                  add_id_to_name=False,
                                                                                  downloadable=False )
         revision_label = get_revision_label( trans, repository, changeset_revision )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
         if repository_metadata:
             repository_metadata_id = trans.security.encode_id( repository_metadata.id )
             metadata = repository_metadata.metadata
             # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend.
-            repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans,
-                                                                                          repository=repository,
-                                                                                          repository_metadata=repository_metadata,
-                                                                                          toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
-                                                                                          key_rd_dicts_to_be_processed=None,
-                                                                                          all_repository_dependencies=None,
-                                                                                          handled_key_rd_dicts=None )
+            repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans,
+                                                                                              repository=repository,
+                                                                                              repository_metadata=repository_metadata,
+                                                                                              toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ),
+                                                                                              key_rd_dicts_to_be_processed=None,
+                                                                                              all_repository_dependencies=None,
+                                                                                              handled_key_rd_dicts=None )
         else:
             repository_metadata_id = None
             metadata = None
@@ -2466,7 +2466,7 @@
             review_id = trans.security.encode_id( review.id )
         else:
             review_id = None
-        containers_dict = build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
+        containers_dict = suc.build_repository_containers_for_tool_shed( repository, changeset_revision, repository_dependencies, repository_metadata )
         return trans.fill_template( '/webapps/community/repository/view_repository.mako',
                                     cntrller=cntrller,
                                     repo=repo,
@@ -2491,16 +2491,16 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository_in_tool_shed( trans, repository_id )
+        repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_files_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_files_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_files_dir )
         tool_metadata_dict = {}
         tool_lineage = []
         tool = None
         guid = None
         original_tool_data_path = trans.app.config.tool_data_path
         revision_label = get_revision_label( trans, repository, changeset_revision )
-        repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
         if repository_metadata:
             metadata = repository_metadata.metadata
             if metadata:
@@ -2515,18 +2515,18 @@
                             can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision )
                             if can_use_disk_file:
                                 trans.app.config.tool_data_path = work_dir
-                                tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans,
-                                                                                                                  repo_files_dir,
-                                                                                                                  full_path_to_tool_config,
-                                                                                                                  work_dir )
+                                tool, valid, message, sample_files = suc.handle_sample_files_and_load_tool_from_disk( trans,
+                                                                                                                      repo_files_dir,
+                                                                                                                      full_path_to_tool_config,
+                                                                                                                      work_dir )
                                 if message:
                                     status = 'error'
                             else:
-                                tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans,
-                                                                                                                 repo,
-                                                                                                                 changeset_revision,
-                                                                                                                 tool_config_filename,
-                                                                                                                 work_dir )
+                                tool, message, sample_files = suc.handle_sample_files_and_load_tool_from_tmp_config( trans,
+                                                                                                                     repo,
+                                                                                                                     changeset_revision,
+                                                                                                                     tool_config_filename,
+                                                                                                                     work_dir )
                                 if message:
                                     status = 'error'
                             break


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/community/controllers/repository_review.py
--- a/lib/galaxy/webapps/community/controllers/repository_review.py
+++ b/lib/galaxy/webapps/community/controllers/repository_review.py
@@ -4,12 +4,12 @@
 from galaxy.web.form_builder import SelectField, CheckboxField
 from galaxy.webapps.community import model
 from galaxy.web.framework.helpers import time_ago, iff, grids
-from galaxy.model.orm import *
+from galaxy.model.orm import and_
 from sqlalchemy.sql.expression import func
 from common import *
 from galaxy.webapps.community.util.container_util import STRSEP
 from repository import RepositoryGrid
-from galaxy.util.shed_util_common import *
+import galaxy.util.shed_util_common as suc
 from galaxy.util.odict import odict
 
 from galaxy import eggs
@@ -56,7 +56,7 @@
             # Restrict to revisions that have been reviewed.
             if repository.reviews:
                 rval = ''
-                repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+                repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
                 for review in repository.reviews:
                     changeset_revision = review.changeset_revision
                     rev, label = get_rev_label_from_changeset_revision( repo, changeset_revision )
@@ -311,7 +311,7 @@
         status = params.get( 'status', 'done' )
         review = get_review( trans, kwd[ 'id' ] )
         repository = review.repository
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         rev, changeset_revision_label = get_rev_label_from_changeset_revision( repo, review.changeset_revision )
         return trans.fill_template( '/webapps/community/repository_review/browse_review.mako',
                                     repository=repository,
@@ -384,7 +384,7 @@
                     message = "You have already created a review for revision <b>%s</b> of repository <b>%s</b>." % ( changeset_revision, repository.name )
                     status = "error"
                 else:
-                    repository = get_repository_in_tool_shed( trans, repository_id )
+                    repository = suc.get_repository_in_tool_shed( trans, repository_id )
                     # See if there are any reviews for previous changeset revisions that the user can copy.
                     if not create_without_copying and not previous_review_id and has_previous_repository_reviews( trans, repository, changeset_revision ):
                         return trans.response.send_redirect( web.url_for( controller='repository_review',
@@ -392,7 +392,7 @@
                                                                           **kwd ) )
                     # A review can be initially performed only on an installable revision of a repository, so make sure we have metadata associated
                     # with the received changeset_revision.
-                    repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+                    repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
                     if repository_metadata:
                         metadata = repository_metadata.metadata
                         if metadata:
@@ -470,7 +470,7 @@
         for component in get_components( trans ):
             components_dict[ component.name ] = dict( component=component, component_review=None )
         repository = review.repository
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         for component_review in review.component_reviews:
             if component_review and component_review.component:
                 component_name = component_review.component.name
@@ -653,9 +653,9 @@
         status = params.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         if repository_id:
-            repository = get_repository_in_tool_shed( trans, repository_id )
+            repository = suc.get_repository_in_tool_shed( trans, repository_id )
             repo_dir = repository.repo_path( trans.app )
-            repo = hg.repository( get_configured_ui(), repo_dir )
+            repo = hg.repository( suc.get_configured_ui(), repo_dir )
             metadata_revision_hashes = [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
             reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ]
             reviews_dict = odict()
@@ -669,7 +669,7 @@
                         repository_reviews = get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision )
                         # Determine if the current user can add a review to this revision.
                         can_add_review = trans.user not in [ repository_review.user for repository_review in repository_reviews ]
-                        repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+                        repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
                         if repository_metadata:
                             repository_metadata_reviews = util.listify( repository_metadata.reviews )
                         else:
@@ -700,9 +700,9 @@
         status = params.get( 'status', 'done' )
         repository_id = kwd.get( 'id', None )
         changeset_revision = kwd.get( 'changeset_revision', None )
-        repository = get_repository_in_tool_shed( trans, repository_id )
+        repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ]
         rev, changeset_revision_label = get_rev_label_from_changeset_revision( repo, changeset_revision )
         reviews = get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision )
@@ -765,9 +765,9 @@
         params = util.Params( kwd )
         message = util.restore_text( params.get( 'message', ''  ) )
         status = params.get( 'status', 'done' )
-        repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] )
+        repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         changeset_revision = kwd.get( 'changeset_revision', None )
-        repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
+        repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) )
         previous_reviews_dict = get_previous_repository_reviews( trans, repository, changeset_revision )
         rev, changeset_revision_label = get_rev_label_from_changeset_revision( repo, changeset_revision )
         return trans.fill_template( '/webapps/community/repository_review/select_previous_review.mako',
@@ -780,7 +780,7 @@
     @web.expose
     @web.require_login( "view or manage repository" )
     def view_or_manage_repository( self, trans, **kwd ):
-        repository = get_repository_in_tool_shed( trans, kwd[ 'id' ] )
+        repository = suc.get_repository_in_tool_shed( trans, kwd[ 'id' ] )
         if trans.user_is_admin() or repository.user == trans.user:
             return trans.response.send_redirect( web.url_for( controller='repository',
                                                               action='manage_repository',


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/community/controllers/upload.py
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -3,7 +3,7 @@
 from galaxy.model.orm import *
 from galaxy.datatypes.checkers import *
 from common import *
-from galaxy.util.shed_util_common import *
+import galaxy.util.shed_util_common as suc
 
 from galaxy import eggs
 eggs.require('mercurial')
@@ -28,9 +28,9 @@
         category_ids = util.listify( params.get( 'category_id', '' ) )
         categories = get_categories( trans )
         repository_id = params.get( 'repository_id', '' )
-        repository = get_repository_in_tool_shed( trans, repository_id )
+        repository = suc.get_repository_in_tool_shed( trans, repository_id )
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         uncompress_file = util.string_as_bool( params.get( 'uncompress_file', 'true' ) )
         remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) )
         uploaded_file = None
@@ -53,7 +53,7 @@
                 uploaded_directory = tempfile.mkdtemp()
                 repo_url = 'http%s' % url[ len( 'hg' ): ]
                 repo_url = repo_url.encode( 'ascii', 'replace' )
-                commands.clone( get_configured_ui(), repo_url, uploaded_directory )
+                commands.clone( suc.get_configured_ui(), repo_url, uploaded_directory )
             elif url:
                 valid_url = True
                 try:
@@ -146,7 +146,7 @@
                     if full_path.endswith( 'tool_data_table_conf.xml.sample' ):
                         # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries
                         # to the in-memory trans.app.tool_data_tables dictionary.
-                        error, error_message = handle_sample_tool_data_table_conf_file( trans.app, full_path )
+                        error, error_message = suc.handle_sample_tool_data_table_conf_file( trans.app, full_path )
                         if error:
                             message = '%s<br/>%s' % ( message, error_message )
                     # See if the content of the change set was valid.
@@ -154,7 +154,7 @@
                     handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
                 if ok:
                     # Update the repository files for browsing.
-                    update_repository( repo )
+                    suc.update_repository( repo )
                     # Get the new repository tip.
                     if tip == repository.tip( trans.app ):
                         message = 'No changes to repository.  '
@@ -181,8 +181,8 @@
                                 message += "  %d files were removed from the repository root.  " % len( files_to_remove )
                         kwd[ 'message' ] = message
                         set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd )
-                    #provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to e.g. a requirement tag mismatch
-                    if get_config_from_disk( 'tool_dependencies.xml', repo_dir ):
+                    # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to e.g. a requirement tag mismatch
+                    if suc.get_config_from_disk( 'tool_dependencies.xml', repo_dir ):
                         if repository.metadata_revisions:
                             metadata_dict = repository.metadata_revisions[0].metadata
                         else:
@@ -192,7 +192,7 @@
                             status = 'warning'
                             log.debug( 'Error in tool dependencies for repository %s: %s.' % ( repository.id, repository.name ) )
                     # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-                    reset_tool_data_tables( trans.app )
+                    suc.reset_tool_data_tables( trans.app )
                     trans.response.send_redirect( web.url_for( controller='repository',
                                                                action='browse_repository',
                                                                id=repository_id,
@@ -202,7 +202,7 @@
                 else:
                     status = 'error'
                 # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file.
-                reset_tool_data_tables( trans.app )
+                suc.reset_tool_data_tables( trans.app )
         selected_categories = [ trans.security.decode_id( id ) for id in category_ids ]
         return trans.fill_template( '/webapps/community/repository/upload.mako',
                                     repository=repository,
@@ -214,7 +214,7 @@
                                     status=status )
     def upload_directory( self, trans, repository, uploaded_directory, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ):
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         undesirable_dirs_removed = 0
         undesirable_files_removed = 0
         if upload_point is not None:
@@ -250,7 +250,7 @@
     def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ):
         # Upload a tar archive of files.
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         undesirable_dirs_removed = 0
         undesirable_files_removed = 0
         ok, message = self.__check_archive( tar )
@@ -283,7 +283,7 @@
             return self.__handle_directory_changes(trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed)
     def __handle_directory_changes( self, trans, repository, full_path, filenames_in_archive, remove_repo_files_not_in_tar, new_repo_alert, commit_message, undesirable_dirs_removed, undesirable_files_removed ):    
         repo_dir = repository.repo_path( trans.app )
-        repo = hg.repository( get_configured_ui(), repo_dir )
+        repo = hg.repository( suc.get_configured_ui(), repo_dir )
         content_alert_str = ''
         files_to_remove = []
         filenames_in_archive = [ os.path.join( full_path, name ) for name in filenames_in_archive ]
@@ -339,7 +339,7 @@
             if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ):
                 # Handle the special case where a tool_data_table_conf.xml.sample file is being uploaded by parsing the file and adding new entries
                 # to the in-memory trans.app.tool_data_tables dictionary.
-                error, message = handle_sample_tool_data_table_conf_file( trans.app, filename_in_archive )
+                error, message = suc.handle_sample_tool_data_table_conf_file( trans.app, filename_in_archive )
                 if error:
                     return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
         commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/community/controllers/workflow.py
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -10,7 +10,7 @@
 from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps
 from galaxy.model.orm import *
 from common import *
-from galaxy.util.shed_util_common import *
+import galaxy.util.shed_util_common as suc
 from galaxy.tool_shed.encoding_util import *
 
 class RepoInputDataModule( InputDataModule ):
@@ -145,7 +145,7 @@
         message = kwd.get( 'message', '' )
         status = kwd.get( 'status', 'done' )
         repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
-        repository = get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) )
+        repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) )
         return trans.fill_template( "/webapps/community/repository/view_workflow.mako",
                                     repository=repository,
                                     changeset_revision=repository_metadata.changeset_revision,


diff -r ae60aaaf6a139e88b2849abf97fd47af711341fd -r 70f88a048ed2b565d60250ca66302fd03a7852ff lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -2,6 +2,7 @@
 from admin import *
 from galaxy.util.json import from_json_string, to_json_string
 from galaxy.util.shed_util import *
+import galaxy.util.shed_util_common as suc
 from galaxy.tool_shed.encoding_util import *
 from galaxy import eggs, tools
 
@@ -423,7 +424,7 @@
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = url_for( '/', qualified=True )
-        url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) )
+        url = suc.url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
@@ -439,10 +440,10 @@
     def check_for_updates( self, trans, **kwd ):
         # Send a request to the relevant tool shed to see if there are any updates.
         repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-        url = url_join( tool_shed_url,
-                        'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
-                        ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
+        url = suc.url_join( tool_shed_url,
+                            'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
+                            ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
@@ -531,14 +532,14 @@
     def find_tools_in_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = url_for( '/', qualified=True )
-        url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url )
+        url = suc.url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
     def find_workflows_in_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
         galaxy_url = url_for( '/', qualified=True )
-        url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url )
+        url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url )
         return trans.response.send_redirect( url )
     def generate_tool_path( self, repository_clone_url, changeset_revision ):
         """
@@ -547,20 +548,20 @@
         <tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision>
         http://test@bx.psu.edu:9009/repos/test/filter
         """
-        tmp_url = clean_repository_clone_url( repository_clone_url )
+        tmp_url = suc.clean_repository_clone_url( repository_clone_url )
         # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
         items = tmp_url.split( 'repos' )
         tool_shed_url = items[ 0 ]
         repo_path = items[ 1 ]
         tool_shed_url = clean_tool_shed_url( tool_shed_url )
-        return url_join( tool_shed_url, 'repos', repo_path, changeset_revision )
+        return suc.url_join( tool_shed_url, 'repos', repo_path, changeset_revision )
     @web.json
     @web.require_admin
     def get_file_contents( self, trans, file_path ):
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
         trans.response.headers['Expires'] = '0'
-        return get_repository_file_contents( file_path )
+        return suc.get_repository_file_contents( file_path )
     @web.expose
     @web.require_admin
     def get_repository_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ):
@@ -570,10 +571,10 @@
         need it so that we can derive the tool shed from which it was installed.
         """
         repository = get_installed_tool_shed_repository( trans, repository_id )
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-        url = url_join( tool_shed_url,
-                        'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \
-                         ( repository_name, repository_owner, changeset_revision ) )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
+        url = suc.url_join( tool_shed_url,
+                            'repository/get_repository_dependencies?name=%s&owner=%s&changeset_revision=%s' % \
+                            ( repository_name, repository_owner, changeset_revision ) )
         response = urllib2.urlopen( url )
         raw_text = response.read()
         response.close()
@@ -612,7 +613,7 @@
         message = ''
         tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository
         # Get the tool_dependencies.xml file from the repository.
-        tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) )
+        tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', tool_shed_repository.repo_path( trans.app ) )
         installed_tool_dependencies = handle_tool_dependencies( app=trans.app,
                                                                 tool_shed_repository=tool_shed_repository,
                                                                 tool_dependencies_config=tool_dependencies_config,
@@ -697,15 +698,15 @@
             clone_dir = os.path.join( tool_path, relative_clone_dir )
             relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
             install_dir = os.path.join( tool_path, relative_install_dir )
-            cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
+            cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev )
             if cloned_ok:
                 if reinstalling:
                     # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated.
                     current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository )
                     if current_ctx_rev != ctx_rev:
-                        repo = hg.repository( get_configured_ui(), path=os.path.abspath( install_dir ) )
+                        repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) )
                         pull_repository( repo, repository_clone_url, current_changeset_revision )
-                        update_repository( repo, ctx_rev=current_ctx_rev )
+                        suc.update_repository( repo, ctx_rev=current_ctx_rev )
                 self.handle_repository_contents( trans,
                                                  tool_shed_repository=tool_shed_repository,
                                                  tool_path=tool_path,
@@ -722,10 +723,10 @@
                     update_tool_shed_repository_status( trans.app,
                                                         tool_shed_repository,
                                                         trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS )
-                    tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
-                    url = url_join( tool_shed_url,
-                                    '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
-                                    ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
+                    tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
+                    url = suc.url_join( tool_shed_url,
+                                        '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
+                                        ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) )
                     response = urllib2.urlopen( url )
                     text = response.read()
                     response.close()
@@ -744,7 +745,7 @@
                                                         tool_shed_repository,
                                                         trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES )
                     # Get the tool_dependencies.xml file from the repository.
-                    tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir )
+                    tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir )
                     installed_tool_dependencies = handle_tool_dependencies( app=trans.app,
                                                                             tool_shed_repository=tool_shed_repository,
                                                                             tool_dependencies_config=tool_dependencies_config,
@@ -774,15 +775,15 @@
         when an admin is installing a new repository or reinstalling an uninstalled repository.
         """
         shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf )
-        metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
-                                                                                     repository=tool_shed_repository,
-                                                                                     repository_clone_url=repository_clone_url,
-                                                                                     shed_config_dict=shed_config_dict,
-                                                                                     relative_install_dir=relative_install_dir,
-                                                                                     repository_files_dir=None,
-                                                                                     resetting_all_metadata_on_repository=False,
-                                                                                     updating_installed_repository=False,
-                                                                                     persist=True )
+        metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                         repository=tool_shed_repository,
+                                                                                         repository_clone_url=repository_clone_url,
+                                                                                         shed_config_dict=shed_config_dict,
+                                                                                         relative_install_dir=relative_install_dir,
+                                                                                         repository_files_dir=None,
+                                                                                         resetting_all_metadata_on_repository=False,
+                                                                                         updating_installed_repository=False,
+                                                                                         persist=True )
         tool_shed_repository.metadata = metadata_dict
         trans.sa_session.add( tool_shed_repository )
         trans.sa_session.flush()
@@ -824,7 +825,7 @@
             files_dir = relative_install_dir
             if shed_config_dict.get( 'tool_path' ):
                 files_dir = os.path.join( shed_config_dict['tool_path'], files_dir )
-            datatypes_config = get_config_from_disk( 'datatypes_conf.xml', files_dir )
+            datatypes_config = suc.get_config_from_disk( 'datatypes_conf.xml', files_dir )
             # Load data types required by tools.
             converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, files_dir, override=False )
             if converter_path or display_path:
@@ -859,13 +860,10 @@
                                                               **kwd ) )
         if repository.can_install and operation == 'install':
             # Send a request to the tool shed to install the repository.
-            tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-            url = url_join( tool_shed_url,
-                            'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
-                            ( repository.name,
-                              repository.owner,
-                              repository.installed_changeset_revision,
-                              ( url_for( '/', qualified=True ) ) ) )
+            tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
+            url = suc.url_join( tool_shed_url,
+                                'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
+                                ( repository.name, repository.owner, repository.installed_changeset_revision, ( url_for( '/', qualified=True ) ) ) )
             return trans.response.send_redirect( url )
         description = util.restore_text( params.get( 'description', repository.description ) )
         shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository )
@@ -1049,7 +1047,7 @@
         # Avoid caching
         trans.response.headers['Pragma'] = 'no-cache'
         trans.response.headers['Expires'] = '0'
-        return open_repository_files_folder( trans, folder_path )
+        return suc.open_repository_files_folder( trans, folder_path )
     @web.expose
     @web.require_admin
     def prepare_for_install( self, trans, **kwd ):
@@ -1081,9 +1079,9 @@
             repository_ids = kwd.get( 'repository_ids', None )
             changeset_revisions = kwd.get( 'changeset_revisions', None )
             # Get the information necessary to install each repository.
-            url = url_join( tool_shed_url,
-                            'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \
-                            ( repository_ids, changeset_revisions ) )
+            url = suc.url_join( tool_shed_url,
+                                'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \
+                                ( repository_ids, changeset_revisions ) )
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
@@ -1240,21 +1238,21 @@
                 repository_dependencies = None
             elif len( repo_info_tuple ) == 7:
                 description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
-            url = url_join( tool_shed_url,
-                            'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
-                            ( name, repository_owner, changeset_revision ) )
+            url = suc.url_join( tool_shed_url,
+                                'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
+                                ( name, repository_owner, changeset_revision ) )
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
             readme_files_dict = from_json_string( raw_text )
-            containers_dict = build_repository_containers_for_galaxy( trans=trans,
-                                                                      toolshed_base_url=tool_shed_url,
-                                                                      repository_name=name,
-                                                                      repository_owner=repository_owner,
-                                                                      changeset_revision=changeset_revision,
-                                                                      readme_files_dict=readme_files_dict,
-                                                                      repository_dependencies=repository_dependencies,
-                                                                      tool_dependencies=tool_dependencies )
+            containers_dict = suc.build_repository_containers_for_galaxy( trans=trans,
+                                                                          toolshed_base_url=tool_shed_url,
+                                                                          repository_name=name,
+                                                                          repository_owner=repository_owner,
+                                                                          changeset_revision=changeset_revision,
+                                                                          readme_files_dict=readme_files_dict,
+                                                                          repository_dependencies=repository_dependencies,
+                                                                          tool_dependencies=tool_dependencies )
         else:
             containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None )
         # Handle tool dependencies chack box.
@@ -1300,7 +1298,7 @@
         repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository )
         clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) )
         relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
         tool_section = None
         tool_panel_section_key = None
         metadata = tool_shed_repository.metadata
@@ -1377,17 +1375,17 @@
                                                                         repository_name=tool_shed_repository.name,
                                                                         repository_owner=tool_shed_repository.owner,
                                                                         changeset_revision=tool_shed_repository.installed_changeset_revision )
-            repo = hg.repository( get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) )
-            repo_info_dict = create_repo_info_dict( trans=trans,
-                                                    repository_clone_url=repository_clone_url,
-                                                    changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                    ctx_rev=ctx_rev,
-                                                    repository_owner=tool_shed_repository.owner,
-                                                    repository_name=tool_shed_repository.name,
-                                                    repository=None,
-                                                    repository_metadata=None,
-                                                    metadata=metadata,
-                                                    repository_dependencies=repository_dependencies )
+            repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( tool_shed_repository.repo_path( trans.app ) ) )
+            repo_info_dict = suc.create_repo_info_dict( trans=trans,
+                                                        repository_clone_url=repository_clone_url,
+                                                        changeset_revision=tool_shed_repository.installed_changeset_revision,
+                                                        ctx_rev=ctx_rev,
+                                                        repository_owner=tool_shed_repository.owner,
+                                                        repository_name=tool_shed_repository.name,
+                                                        repository=None,
+                                                        repository_metadata=None,
+                                                        metadata=metadata,
+                                                        repository_dependencies=repository_dependencies )
             repo_info_dict = tool_shed_encode( repo_info_dict )
         new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies,
                         includes_tools=tool_shed_repository.includes_tools,
@@ -1439,12 +1437,12 @@
             repository_dependencies = None
         elif len( repo_info_tuple ) == 7:
             description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
-        tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
+        tool_shed = suc.get_tool_shed_from_clone_url( repository_clone_url )
         # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset
         # revision to see if it was previously installed using one of them.
-        url = url_join( tool_shed_url,
-                        'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
-                        ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) )
+        url = suc.url_join( tool_shed_url,
+                            'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
+                            ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) )
         response = urllib2.urlopen( url )
         text = response.read()
         response.close()
@@ -1466,7 +1464,7 @@
         repository_id = kwd[ 'id' ]
         tool_shed_repository = get_installed_tool_shed_repository( trans, repository_id )
         metadata = tool_shed_repository.metadata
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
         ctx_rev = get_ctx_rev( tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision )
         repository_clone_url = generate_clone_url_for_installed_repository( trans, tool_shed_repository )
         repository_dependencies = self.get_repository_dependencies( trans=trans,
@@ -1474,16 +1472,16 @@
                                                                     repository_name=tool_shed_repository.name,
                                                                     repository_owner=tool_shed_repository.owner,
                                                                     changeset_revision=tool_shed_repository.installed_changeset_revision )
-        repo_info_dict = create_repo_info_dict( trans=trans,
-                                                repository_clone_url=repository_clone_url,
-                                                changeset_revision=tool_shed_repository.installed_changeset_revision,
-                                                ctx_rev=ctx_rev,
-                                                repository_owner=tool_shed_repository.owner,
-                                                repository_name=tool_shed_repository.name,
-                                                repository=None,
-                                                repository_metadata=None,
-                                                metadata=metadata,
-                                                repository_dependencies=repository_dependencies )
+        repo_info_dict = suc.create_repo_info_dict( trans=trans,
+                                                    repository_clone_url=repository_clone_url,
+                                                    changeset_revision=tool_shed_repository.installed_changeset_revision,
+                                                    ctx_rev=ctx_rev,
+                                                    repository_owner=tool_shed_repository.owner,
+                                                    repository_name=tool_shed_repository.name,
+                                                    repository=None,
+                                                    repository_metadata=None,
+                                                    metadata=metadata,
+                                                    repository_dependencies=repository_dependencies )
         # Get the location in the tool panel in which the tool was originally loaded.
         if 'tool_panel_section' in metadata:
             tool_panel_dict = metadata[ 'tool_panel_section' ]
@@ -1513,21 +1511,21 @@
             message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section."
             status = 'warning'
         if metadata and 'readme_files' in metadata:
-            url = url_join( tool_shed_url,
-                            'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
-                            ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) )
+            url = suc.url_join( tool_shed_url,
+                                'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \
+                                ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) )
             response = urllib2.urlopen( url )
             raw_text = response.read()
             response.close()
             readme_files_dict = from_json_string( raw_text )
-            containers_dict = build_repository_containers_for_galaxy( trans=trans,
-                                                                      toolshed_base_url=tool_shed_url,
-                                                                      repository_name=name,
-                                                                      repository_owner=repository_owner,
-                                                                      changeset_revision=changeset_revision,
-                                                                      readme_files_dict=readme_files_dict,
-                                                                      repository_dependencies=repository_dependencies,
-                                                                      tool_dependencies=tool_dependencies )
+            containers_dict = suc.build_repository_containers_for_galaxy( trans=trans,
+                                                                          toolshed_base_url=tool_shed_url,
+                                                                          repository_name=name,
+                                                                          repository_owner=repository_owner,
+                                                                          changeset_revision=changeset_revision,
+                                                                          readme_files_dict=readme_files_dict,
+                                                                          repository_dependencies=repository_dependencies,
+                                                                          tool_dependencies=tool_dependencies )
         else:
             containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None )
         # Handle repository dependencies check box.
@@ -1558,12 +1556,12 @@
     @web.require_admin
     def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ):
         if 'reset_metadata_on_selected_repositories_button' in kwd:
-            kwd[ 'CONTROLLER' ] = GALAXY_ADMIN_TOOL_SHED_CONTROLLER
-            message, status = reset_metadata_on_selected_repositories( trans, **kwd )
+            kwd[ 'CONTROLLER' ] = suc.GALAXY_ADMIN_TOOL_SHED_CONTROLLER
+            message, status = suc.reset_metadata_on_selected_repositories( trans, **kwd )
         else:
             message = util.restore_text( kwd.get( 'message', ''  ) )
             status = kwd.get( 'status', 'done' )
-        repositories_select_field = build_repository_ids_select_field( trans, GALAXY_ADMIN_TOOL_SHED_CONTROLLER )
+        repositories_select_field = suc.build_repository_ids_select_field( trans, suc.GALAXY_ADMIN_TOOL_SHED_CONTROLLER )
         return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako',
                                     repositories_select_field=repositories_select_field,
                                     message=message,
@@ -1573,20 +1571,20 @@
     def reset_repository_metadata( self, trans, id ):
         """Reset all metadata on a single installed tool shed repository."""
         repository = get_installed_tool_shed_repository( trans, id )
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
         repository_clone_url = generate_clone_url_for_installed_repository( trans, repository )
         tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app )
         if relative_install_dir:
             original_metadata_dict = repository.metadata
-            metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
-                                                                                         repository=repository,
-                                                                                         repository_clone_url=repository_clone_url,
-                                                                                         shed_config_dict = repository.get_shed_config_dict( trans.app ),
-                                                                                         relative_install_dir=relative_install_dir,
-                                                                                         repository_files_dir=None,
-                                                                                         resetting_all_metadata_on_repository=False,
-                                                                                         updating_installed_repository=False,
-                                                                                         persist=False )
+            metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                             repository=repository,
+                                                                                             repository_clone_url=repository_clone_url,
+                                                                                             shed_config_dict = repository.get_shed_config_dict( trans.app ),
+                                                                                             relative_install_dir=relative_install_dir,
+                                                                                             repository_files_dir=None,
+                                                                                             resetting_all_metadata_on_repository=False,
+                                                                                             updating_installed_repository=False,
+                                                                                             persist=False )
             repository.metadata = metadata_dict
             if metadata_dict != original_metadata_dict:
                 update_in_shed_tool_config( trans.app, repository )
@@ -1645,10 +1643,10 @@
     def set_tool_versions( self, trans, **kwd ):
         # Get the tool_versions from the tool shed for each tool in the installed change set.
         repository = get_installed_tool_shed_repository( trans, kwd[ 'id' ] )
-        tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
-        url = url_join( tool_shed_url,
-                        'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
-                        ( repository.name, repository.owner, repository.changeset_revision ) )
+        tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
+        url = suc.url_join( tool_shed_url,
+                            'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \
+                            ( repository.name, repository.owner, repository.changeset_revision ) )
         response = urllib2.urlopen( url )
         text = response.read()
         response.close()
@@ -1757,21 +1755,21 @@
                         repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) )
                     else:
                         repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) )
-                    repo = hg.repository( get_configured_ui(), path=repo_files_dir )
+                    repo = hg.repository( suc.get_configured_ui(), path=repo_files_dir )
                     repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
                     pull_repository( repo, repository_clone_url, latest_ctx_rev )
-                    update_repository( repo, latest_ctx_rev )
+                    suc.update_repository( repo, latest_ctx_rev )
                     tool_shed = clean_tool_shed_url( tool_shed_url )
                     # Update the repository metadata.
-                    metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app,
-                                                                                                 repository=repository,
-                                                                                                 repository_clone_url=repository_clone_url,
-                                                                                                 shed_config_dict = repository.get_shed_config_dict( trans.app ),
-                                                                                                 relative_install_dir=relative_install_dir,
-                                                                                                 repository_files_dir=None,
-                                                                                                 resetting_all_metadata_on_repository=False,
-                                                                                                 updating_installed_repository=True,
-                                                                                                 persist=True )
+                    metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app,
+                                                                                                     repository=repository,
+                                                                                                     repository_clone_url=repository_clone_url,
+                                                                                                     shed_config_dict = repository.get_shed_config_dict( trans.app ),
+                                                                                                     relative_install_dir=relative_install_dir,
+                                                                                                     repository_files_dir=None,
+                                                                                                     resetting_all_metadata_on_repository=False,
+                                                                                                     updating_installed_repository=True,
+                                                                                                     persist=True )
                     repository.metadata = metadata_dict
                     # Update the repository changeset_revision in the database.
                     repository.changeset_revision = latest_changeset_revision

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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