commit/galaxy-central: inithello: Functional tests to verify batch reset of repository metadata on tool shed and galaxy side. Made functional test scripts possible to run independently. Cleaned up common methods in tool_shed/base/twilltestcase.py. - galaxy-commits

18 Dec 2012

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e6030730bb85/
changeset:   e6030730bb85
user:        inithello
date:        2012-12-18 18:41:13
summary:     Functional tests to verify batch reset of repository metadata on tool shed and galaxy side. Made functional test scripts possible to run independently. Cleaned up common methods in tool_shed/base/twilltestcase.py.
affected #:  16 files
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/base/test_db_util.py

--- a/test/tool_shed/base/test_db_util.py
+++ b/test/tool_shed/base/test_db_util.py
@@ -14,6 +14,10 @@
 def flush( obj ):
     sa_session.add( obj )
     sa_session.flush()
+def get_all_repositories():
+    return sa_session.query( model.Repository ).all()
+def get_all_installed_repositories():
+    return ga_session.query( galaxy.model.ToolShedRepository ).all()
 def get_category_by_name( name ):
     return sa_session.query( model.Category ) \
                      .filter( model.Category.table.c.name == name ) \
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/base/twilltestcase.py
--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -139,21 +139,13 @@
             errmsg = "%i occurrences of '%s' found (min. %i, max. %i).\npage content written to '%s' " % \
                      ( pattern_count, pattern, min_count, max_count, fname )
             raise AssertionError( errmsg )
-    def create_category( self, category_name, category_description ):
+    def create_category( self, **kwd ):
+        category = test_db_util.get_category_by_name( kwd[ 'name' ] )
+        if category is not None:
+            return category
         self.visit_url( '/admin/manage_categories?operation=create' )
-        tc.fv( "1", "name", category_name )
-        tc.fv( "1", "description", category_description )
-        tc.submit( "create_category_button" )
-    def create_repository( self, repository_name, repository_description, repository_long_description=None, categories=[], strings_displayed=[], strings_not_displayed=[] ):
-        self.visit_url( '/repository/create_repository' )
-        tc.fv( "1", "name", repository_name )
-        tc.fv( "1", "description", repository_description )
-        if repository_long_description is not None:
-            tc.fv( "1", "long_description", repository_long_description )
-        for category in categories:
-            tc.fv( "1", "category_id", "+%s" % category )
-        tc.submit( "create_repository_button" )
-        self.check_for_strings( strings_displayed, strings_not_displayed )
+        self.submit_form( form_no=1, button="create_category_button", **kwd )
+        return test_db_util.get_category_by_name( kwd[ 'name' ] )
     def create_user_in_galaxy( self, cntrller='user', email='test@bx.psu.edu', password='testuser', username='admin-user', redirect='' ):
         self.visit_galaxy_url( "/user/create?cntrller=%s&use_panels=False" % cntrller )
         tc.fv( '1', 'email', email )
@@ -325,6 +317,14 @@
             return os.path.abspath( os.path.join( filepath, filename ) )
         else:
             return os.path.abspath( os.path.join( self.file_dir, filename ) )
+    def get_or_create_repository( self, owner=None, strings_displayed=[], strings_not_displayed=[], **kwd ):
+        repository = test_db_util.get_repository_by_name_and_owner( kwd[ 'name' ], owner )
+        if repository is None:
+            self.visit_url( '/repository/create_repository' )
+            self.submit_form( 1, 'create_repository_button', **kwd )
+            self.check_for_strings( strings_displayed, strings_not_displayed )
+            repository = test_db_util.get_repository_by_name_and_owner( kwd[ 'name' ], owner )
+        return repository
     def get_repo_path( self, repository ):
         # An entry in the hgweb.config file looks something like: repos/test/mira_assembler = database/community_files/000/repo_123
         lhs = "repos/%s/%s" % ( repository.user.username, repository.name )
@@ -387,7 +387,12 @@
             tc.fv( "3", "allow_push", '+%s' % username )
         tc.submit( 'user_access_button' )
         self.check_for_strings( strings_displayed, strings_not_displayed )
-    def install_repository( self, name, owner, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ):
+    def install_repository( self, name, owner, category_name, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[] ):
+        if test_db_util.get_installed_repository_by_name_owner( name, owner ) is not None:
+            return
+        self.browse_tool_shed( url=self.url )
+        self.browse_category( test_db_util.get_category_by_name( category_name ) )
+        self.preview_repository_in_tool_shed( name, common.test_user_1_name, strings_displayed=[] )
         repository = test_db_util.get_repository_by_name_and_owner( name, owner )
         repository_id = self.security.encode_id( repository.id )
         if changeset_revision is None:
@@ -446,6 +451,14 @@
         url = '/admin_toolshed/reset_repository_metadata?id=%s' % self.security.encode_id( repository.id )
         self.visit_galaxy_url( url )
         self.check_for_strings( [ 'Metadata has been reset' ] )
+    def reset_metadata_on_selected_repositories( self, repository_ids ):
+        self.visit_url( '/admin/reset_metadata_on_selected_repositories_in_tool_shed' )
+        kwd = dict( repository_ids=repository_ids )
+        self.submit_form( form_no=1, button="reset_metadata_on_selected_repositories_button", **kwd )
+    def reset_metadata_on_selected_installed_repositories( self, repository_ids ):
+        self.visit_galaxy_url( '/admin_toolshed/reset_metadata_on_selected_installed_repositories' )
+        kwd = dict( repository_ids=repository_ids )
+        self.submit_form( form_no=1, button="reset_metadata_on_selected_repositories_button", **kwd )
     def reset_repository_metadata( self, repository ):
         url = '/repository/reset_all_metadata?id=%s' % self.security.encode_id( repository.id )
         self.visit_url( url )
@@ -496,25 +509,10 @@
         self.check_for_strings( strings_displayed, strings_not_displayed )
     def verify_installed_repository_metadata_unchanged( self, name, owner ):
         installed_repository = test_db_util.get_installed_repository_by_name_owner( name, owner )
-        differs = False
         metadata = installed_repository.metadata
         self.reset_installed_repository_metadata( installed_repository )
         new_metadata = installed_repository.metadata
-        # This test assumes that the different metadata components will always appear in the same order. If this is ever not
-        # the case, this test must be updated.
-        for metadata_key in [ 'datatypes', 'tools', 'tool_dependencies', 'repository_dependencies', 'workflows' ]:
-            if ( metadata_key in metadata and metadata_key not in new_metadata ) or \
-               ( metadata_key not in metadata and metadata_key in new_metadata ):
-                differs = True
-                break
-            elif metadata_key not in metadata and metadata_key not in new_metadata:
-                continue
-            else:
-                if metadata[ metadata_key ] != new_metadata[ metadata_key ]:
-                    differs = True
-                    break
-        if differs:
-            raise AssertionError( 'Metadata for installed repository %s differs after metadata reset.' % name )
+        assert metadata == new_metadata, 'Metadata for installed repository %s differs after metadata reset.' % name
     def verify_installed_repository_on_browse_page( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ):
         url = '/admin_toolshed/browse_repositories'
         self.visit_galaxy_url( url )
@@ -544,10 +542,14 @@
             self.visit_galaxy_url( url )
             self.check_for_strings( strings, strings_not_displayed )
     def verify_unchanged_repository_metadata( self, repository ):
-        self.check_repository_changelog( repository )
-        html = self.last_page()
+        old_metadata = dict()
+        new_metadata = dict()
+        for metadata in self.get_repository_metadata( repository ):
+            old_metadata[ metadata.changeset_revision ] = metadata.metadata 
         self.reset_repository_metadata( repository )
-        self.check_repository_changelog( repository, strings_displayed=[ html ] )
+        for metadata in self.get_repository_metadata( repository ):
+            new_metadata[ metadata.changeset_revision ] = metadata.metadata
+        assert old_metadata == new_metadata, 'Metadata changed after reset on repository %s.' % repository.name 
     def visit_galaxy_url( self, url ):
         url = '%s%s' % ( self.galaxy_url, url )
         self.visit_url( url )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0000_basic_repository_features.py
--- a/test/tool_shed/functional/test_0000_basic_repository_features.py
+++ b/test/tool_shed/functional/test_0000_basic_repository_features.py
@@ -11,7 +11,7 @@
         """Create necessary user accounts and login as an admin user."""
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
         test_user_1 = test_db_util.get_user( common.test_user_1_email )
-        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
         test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
         self.logout()
         self.login( email=common.admin_email, username=common.admin_username )
@@ -20,22 +20,21 @@
         admin_user_private_role = test_db_util.get_private_role( admin_user )
     def test_0005_create_categories( self ):
         """Create categories for this test suite"""
-        self.create_category( 'Test 0000 Basic Repository Features 1', 'Test 0000 Basic Repository Features 1' )
-        self.create_category( 'Test 0000 Basic Repository Features 2', 'Test 0000 Basic Repository Features 2' )
+        self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
+        self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
     def test_0010_create_repository( self ):
         """Create the filtering repository"""
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        test_user_1 = test_db_util.get_user( common.test_user_1_email )
-        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
-        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
         strings_displayed = [ 'Repository %s' % "'%s'" % repository_name, 
                               'Repository %s has been created' % "'%s'" % repository_name ]
-        self.create_repository( repository_name, 
-                                repository_description, 
-                                repository_long_description=repository_long_description, 
-                                categories=[ 'Test 0000 Basic Repository Features 1' ], 
-                                strings_displayed=strings_displayed )
+        self.get_or_create_repository( name=repository_name, 
+                                       description=repository_description, 
+                                       long_description=repository_long_description, 
+                                       owner=common.test_user_1_name,
+                                       category_id=self.security.encode_id( category.id ), 
+                                       strings_displayed=strings_displayed )
     def test_0015_edit_repository( self ):
         """Edit the repository name, description, and long description"""
         repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
--- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
+++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py
@@ -21,17 +21,18 @@
         admin_user_private_role = test_db_util.get_private_role( admin_user )
     def test_0005_create_category( self ):
         """Create a category for this test suite"""
-        self.create_category( 'Test 0010 Repository With Tool Dependencies', 'Tests for a repository with tool dependencies.' )
+        self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
     def test_0010_create_freebayes_repository_and_upload_tool_xml( self ):
         '''Create freebayes repository and upload freebayes.xml without tool_data_table_conf.xml.sample. This should result in an error message and invalid tool.'''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        self.create_repository( repository_name, 
-                                repository_description, 
-                                repository_long_description=repository_long_description, 
-                                categories=[ 'Test 0010 Repository With Tool Dependencies' ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
+        category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' )
+        repository = self.get_or_create_repository( name=repository_name, 
+                                                    description=repository_description, 
+                                                    long_description=repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category.id ), 
+                                                    strings_displayed=[] )
         self.upload_file( repository, 
                           'freebayes/freebayes.xml', 
                           valid_tools_only=False,
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0020_basic_repository_dependencies.py
--- a/test/tool_shed/functional/test_0020_basic_repository_dependencies.py
+++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py
@@ -25,17 +25,18 @@
         admin_user_private_role = test_db_util.get_private_role( admin_user )
     def test_0005_create_category( self ):
         """Create a category for this test suite"""
-        self.create_category( 'Test 0020 Basic Repository Dependencies', 'Testing basic repository dependency features.' )
+        self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
     def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ):
         '''Create and populate the emboss_datatypes repository.'''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        self.create_repository( datatypes_repository_name, 
-                                datatypes_repository_description, 
-                                repository_long_description=datatypes_repository_long_description, 
-                                categories=[ 'Test 0020 Basic Repository Dependencies' ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
+        category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' )
+        repository = self.get_or_create_repository( name=datatypes_repository_name, 
+                                             description=datatypes_repository_description, 
+                                             long_description=datatypes_repository_long_description, 
+                                             owner=common.test_user_1_name,
+                                             category_id=self.security.encode_id( category.id ), 
+                                             strings_displayed=[] )
         self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
     def test_0015_verify_datatypes_in_datatypes_repository( self ):
         '''Verify that the emboss_datatypes repository contains datatype entries.'''
@@ -43,12 +44,13 @@
         self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] )
     def test_0020_create_emboss_5_repository_and_upload_files( self ):
         '''Create and populate the emboss_5_0020 repository.'''
-        self.create_repository( emboss_repository_name, 
-                                emboss_repository_description, 
-                                repository_long_description=emboss_repository_long_description, 
-                                categories=[ 'Test 0020 Basic Repository Dependencies' ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
+        category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' )
+        repository = self.get_or_create_repository( name=emboss_repository_name, 
+                                             description=emboss_repository_description, 
+                                             long_description=emboss_repository_long_description, 
+                                             owner=common.test_user_1_name,
+                                             category_id=self.security.encode_id( category.id ), 
+                                             strings_displayed=[] )
         self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
     def test_0025_generate_and_upload_repository_dependencies_xml( self ):
         '''Generate and upload the repository_dependencies.xml file'''
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0030_repository_dependency_revisions.py
--- a/test/tool_shed/functional/test_0030_repository_dependency_revisions.py
+++ b/test/tool_shed/functional/test_0030_repository_dependency_revisions.py
@@ -27,48 +27,36 @@
         admin_user_private_role = test_db_util.get_private_role( admin_user )
     def test_0005_create_category( self ):
         """Create a category for this test suite"""
-        self.create_category( 'Test 0030 Repository Dependency Revisions', 'Testing repository dependencies by revision.' )
+        self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
     def test_0010_create_repositories( self ):
         '''Create the emboss_5_0030, emboss_6_0030, emboss_datatypes_0030, and emboss_0030 repositories and populate the emboss_datatypes repository.'''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
-        if emboss_5_repository is None:
-            self.create_repository( emboss_5_repository_name, 
-                                    emboss_repository_description, 
-                                    repository_long_description=emboss_repository_long_description, 
-                                    categories=[ 'Test 0030 Repository Dependency Revisions' ], 
-                                    strings_displayed=[] )
-            emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
-            self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
-        emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
-        if emboss_6_repository is None:
-            self.create_repository( emboss_6_repository_name, 
-                                    emboss_repository_description, 
-                                    repository_long_description=emboss_repository_long_description, 
-                                    categories=[ 'Test 0030 Repository Dependency Revisions' ], 
-                                    strings_displayed=[] )
-            emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
-            self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball..' )
-        datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
-        if datatypes_repository is None:
-            self.create_repository( datatypes_repository_name, 
-                                    datatypes_repository_description, 
-                                    repository_long_description=datatypes_repository_long_description, 
-                                    categories=[ 'Test 0030 Repository Dependency Revisions' ], 
-                                    strings_displayed=[] )
-            datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
-        if self.repository_is_new( datatypes_repository ):
-            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
-        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-        if emboss_repository is None:
-            self.create_repository( emboss_repository_name, 
-                                    emboss_repository_description, 
-                                    repository_long_description=emboss_repository_long_description, 
-                                    categories=[ 'Test 0030 Repository Dependency Revisions' ], 
-                                    strings_displayed=[] )
-            emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
+        category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
+        emboss_5_repository = self.get_or_create_repository( name=emboss_5_repository_name, 
+                                                             description=emboss_repository_description, 
+                                                             long_description=emboss_repository_long_description, 
+                                                             owner=common.test_user_1_name,
+                                                             category_id=self.security.encode_id( category.id ) )
+        emboss_6_repository = self.get_or_create_repository( name=emboss_6_repository_name, 
+                                                             description=emboss_repository_description, 
+                                                             long_description=emboss_repository_long_description, 
+                                                             owner=common.test_user_1_name,
+                                                             category_id=self.security.encode_id( category.id ) )
+        datatypes_repository = self.get_or_create_repository( name=datatypes_repository_name, 
+                                                              description=emboss_repository_description, 
+                                                              long_description=emboss_repository_long_description, 
+                                                              owner=common.test_user_1_name,
+                                                              category_id=self.security.encode_id( category.id ) )
+        emboss_repository = self.get_or_create_repository( name=emboss_repository_name, 
+                                                           description=emboss_repository_description, 
+                                                           long_description=emboss_repository_long_description, 
+                                                           owner=common.test_user_1_name,
+                                                           category_id=self.security.encode_id( category.id ) )
+        self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
+        self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
+        self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+        self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
     def test_0015_generate_repository_dependencies_for_emboss_5( self ):
         '''Generate a repository_dependencies.xml file specifying emboss_datatypes and upload it to the emboss_5 repository.'''
         datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0040_repository_circular_dependencies.py
--- a/test/tool_shed/functional/test_0040_repository_circular_dependencies.py
+++ b/test/tool_shed/functional/test_0040_repository_circular_dependencies.py
@@ -25,17 +25,17 @@
         admin_user_private_role = test_db_util.get_private_role( admin_user )
     def test_0005_create_category( self ):
         """Create a category for this test suite"""
-        self.create_category( 'test_0040_repository_circular_dependencies', 'Testing handling of circular repository dependencies.' )
+        self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
     def test_0010_create_freebayes_repository_name( self ):
         '''Create and populate freebayes_0040.'''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        self.create_repository( freebayes_repository_name, 
-                                freebayes_repository_name_description, 
-                                repository_long_description=freebayes_repository_name_long_description, 
-                                categories=[ 'test_0040_repository_circular_dependencies' ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
+        repository = self.get_or_create_repository( name=freebayes_repository_name, 
+                                                    description=freebayes_repository_name_description, 
+                                                    long_description=freebayes_repository_name_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    categories=[ 'test_0040_repository_circular_dependencies' ], 
+                                                    strings_displayed=[] )
         self.upload_file( repository, 
                           'freebayes/freebayes.tar', 
                           strings_displayed=[], 
@@ -44,12 +44,12 @@
         '''Create and populate filtering_0040.'''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        self.create_repository( filtering_repository_name, 
-                                filtering_repository_description, 
-                                repository_long_description=filtering_repository_long_description, 
-                                categories=[ 'test_0040_repository_circular_dependencies' ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
+        repository = self.get_or_create_repository( name=filtering_repository_name, 
+                                                    description=filtering_repository_description, 
+                                                    long_description=filtering_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    categories=[ 'test_0040_repository_circular_dependencies' ], 
+                                                    strings_displayed=[] )
         self.upload_file( repository, 
                           'filtering/filtering_1.1.0.tar', 
                           strings_displayed=[],
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
--- /dev/null
+++ b/test/tool_shed/functional/test_0050_circular_dependencies_4_levels.py
@@ -0,0 +1,158 @@
+from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import tool_shed.base.test_db_util as test_db_util
+
+emboss_datatypes_repository_name = 'emboss_datatypes_0050'
+emboss_datatypes_repository_description = "Datatypes for emboss"
+emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
+
+emboss_repository_name = 'emboss_0050'
+emboss_repository_description = "Galaxy's emboss tool"
+emboss_repository_long_description = "Long description of Galaxy's emboss tool"
+
+filtering_repository_name = 'filtering_0050'
+filtering_repository_description = "Galaxy's filtering tool"
+filtering_repository_long_description = "Long description of Galaxy's filtering tool"
+
+freebayes_repository_name = 'freebayes_0050'
+freebayes_repository_description = "Galaxy's freebayes tool"
+freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
+
+default_category = 'test_0050_repository_n_level_circular_dependencies'
+default_category_description = 'Testing handling of circular repository dependencies to n levels.'
+
+class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
+    '''Verify that the code correctly handles circular dependencies down to n levels.'''
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
+    def test_0005_create_category( self ):
+        """Create a category for this test suite"""
+        self.create_category( name=default_category, description=default_category_description )
+    def test_0010_create_emboss_datatypes_repository( self ):
+        '''Create and populate emboss_datatypes_0050.'''
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name=emboss_datatypes_repository_name, 
+                                                    description=emboss_datatypes_repository_description, 
+                                                    long_description=emboss_datatypes_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    categories=[ default_category ], 
+                                                    strings_displayed=[] )
+        self.upload_file( repository, 
+                          'emboss/datatypes/datatypes_conf.xml', 
+                          strings_displayed=[], 
+                          commit_message='Uploaded datatypes_conf.xml.' )
+    def test_0015_create_emboss_repository( self ):
+        '''Create and populate emboss_0050.'''
+        repository = self.get_or_create_repository( name=emboss_repository_name, 
+                                                    description=emboss_repository_description, 
+                                                    long_description=emboss_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    categories=[ default_category ], 
+                                                    strings_displayed=[] )
+        self.upload_file( repository, 
+                          'emboss/emboss.tar', 
+                          strings_displayed=[], 
+                          commit_message='Uploaded tool tarball.' )
+        datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
+        repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'emboss' ] )
+        self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                 dependency_description='Emboss depends on the emboss_datatypes repository.' )
+        self.upload_file( repository, 
+                          'repository_dependencies.xml', 
+                          filepath=repository_dependencies_path, 
+                          commit_message='Uploaded dependency on emboss_datatypes.' )
+    def test_0020_create_filtering_repository( self ):
+        '''Create and populate filtering_0050.'''
+        filtering_repository = self.get_or_create_repository( name=filtering_repository_name, 
+                                                              description=filtering_repository_description, 
+                                                              long_description=filtering_repository_long_description, 
+                                                              owner=common.test_user_1_name,
+                                                              categories=[ default_category ], 
+                                                              strings_displayed=[] )
+        self.upload_file( filtering_repository, 
+                          'filtering/filtering_1.1.0.tar', 
+                          strings_displayed=[], 
+                          commit_message='Uploaded filtering.tar.' )
+        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
+        repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'filtering' ] )
+        self.generate_repository_dependency_xml( [ emboss_repository ], 
+                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                 dependency_description='Filtering depends on the emboss repository.' )
+        self.upload_file( filtering_repository, 
+                          'repository_dependencies.xml', 
+                          filepath=repository_dependencies_path, 
+                          commit_message='Uploaded dependency on emboss.' )
+    def test_0025_create_freebayes_repository( self ):
+        '''Create and populate freebayes_0050.'''
+        repository = self.get_or_create_repository( name=freebayes_repository_name, 
+                                                    description=freebayes_repository_description, 
+                                                    long_description=freebayes_repository_long_description, 
+                                                    owner=common.test_user_1_name,
+                                                    categories=[ default_category ], 
+                                                    strings_displayed=[] )
+        self.upload_file( repository, 
+                          'freebayes/freebayes.tar', 
+                          strings_displayed=[], 
+                          commit_message='Uploaded freebayes.tar.' )
+        emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
+        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
+        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
+        repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'freebayes' ] )
+        self.generate_repository_dependency_xml( [ filtering_repository ], 
+                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                 dependency_description='Emboss depends on the filtering repository.' )
+        self.upload_file( emboss_repository, 
+                          'repository_dependencies.xml', 
+                          filepath=repository_dependencies_path, 
+                          commit_message='Uploaded dependency on filtering.' )
+        previous_tip = self.get_repository_tip( repository )
+        self.generate_repository_dependency_xml( [ emboss_datatypes_repository, emboss_repository, filtering_repository, repository ], 
+                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                 dependency_description='Freebayes depends on the filtering repository.' )
+        self.upload_file( repository, 
+                          'repository_dependencies.xml', 
+                          filepath=repository_dependencies_path, 
+                          commit_message='Uploaded dependency on filtering.' )
+        self.display_manage_repository_page( repository, strings_not_displayed=[ previous_tip ] )
+    def test_0030_verify_repository_dependencies( self ):
+        '''Verify that the generated dependency circle does not cause an infinite loop.
+        
+        Expected structure:
+        
+        id: 2 key: http://localhost:8634__ESEP__freebayes_0050__ESEP__user1__ESEP__2e73d8e1b59d
+            ['http://localhost:8634', 'emboss_datatypes_0050', 'user1', '596029c334b1']
+            ['http://localhost:8634', 'emboss_0050', 'user1', '9f1503046640']
+            id: 3 key: http://localhost:8634__ESEP__filtering_0050__ESEP__user1__ESEP__eefdd8bc0db9
+                ['http://localhost:8634', 'emboss_0050', 'user1', '9f1503046640']
+            id: 4 key: http://localhost:8634__ESEP__emboss_0050__ESEP__user1__ESEP__9f1503046640
+                ['http://localhost:8634', 'emboss_datatypes_0050', 'user1', '596029c334b1']
+        '''
+        emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
+        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
+        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
+        freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
+        for repository in [ emboss_datatypes_repository, emboss_repository, filtering_repository ]:
+            self.check_repository_dependency( freebayes_repository, repository, self.get_repository_tip( repository ) )
+        for changeset_revision in self.get_repository_metadata_revisions( emboss_repository ):
+            self.check_repository_dependency( freebayes_repository, emboss_repository, changeset_revision )
+        self.display_manage_repository_page( freebayes_repository, 
+                                             strings_displayed=[ 'Freebayes depends on the filtering repository.' ] )
+    def test_0035_verify_repository_metadata( self ):
+        '''Verify that resetting the metadata does not change it.'''
+        emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
+        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
+        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
+        freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
+        for repository in [ emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository ]:
+            self.verify_unchanged_repository_metadata( repository )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0050_circular_n_levels.py
--- a/test/tool_shed/functional/test_0050_circular_n_levels.py
+++ /dev/null
@@ -1,157 +0,0 @@
-from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
-import tool_shed.base.test_db_util as test_db_util
-
-emboss_datatypes_repository_name = 'emboss_datatypes_0050'
-emboss_datatypes_repository_description = "Datatypes for emboss"
-emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
-
-emboss_repository_name = 'emboss_0050'
-emboss_repository_description = "Galaxy's emboss tool"
-emboss_repository_long_description = "Long description of Galaxy's emboss tool"
-
-freebayes_repository_name = 'freebayes_0050'
-freebayes_repository_description = "Galaxy's freebayes tool"
-freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
-
-filtering_repository_name = 'filtering_0050'
-filtering_repository_description = "Galaxy's filtering tool"
-filtering_repository_long_description = "Long description of Galaxy's filtering tool"
-
-default_category = 'test_0050_repository_n_level_circular_dependencies'
-default_category_description = 'Testing handling of circular repository dependencies to n levels.'
-
-class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
-    '''Verify that the code correctly handles circular dependencies down to n levels.'''
-    def test_0000_initiate_users( self ):
-        """Create necessary user accounts."""
-        self.logout()
-        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        test_user_1 = test_db_util.get_user( common.test_user_1_email )
-        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
-        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
-        self.logout()
-        self.login( email=common.admin_email, username=common.admin_username )
-        admin_user = test_db_util.get_user( common.admin_email )
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
-        admin_user_private_role = test_db_util.get_private_role( admin_user )
-    def test_0005_create_category( self ):
-        """Create a category for this test suite"""
-        self.create_category( default_category, default_category_description )
-    def test_0010_create_emboss_datatypes_repository( self ):
-        '''Create and populate emboss_datatypes_0050.'''
-        self.logout()
-        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        self.create_repository( emboss_datatypes_repository_name, 
-                                emboss_datatypes_repository_description, 
-                                repository_long_description=emboss_datatypes_repository_long_description, 
-                                categories=[ default_category ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          'emboss/datatypes/datatypes_conf.xml', 
-                          strings_displayed=[], 
-                          commit_message='Uploaded datatypes_conf.xml.' )
-    def test_0015_create_emboss_repository( self ):
-        '''Create and populate emboss_0050.'''
-        self.create_repository( emboss_repository_name, 
-                                emboss_repository_description, 
-                                repository_long_description=emboss_repository_long_description, 
-                                categories=[ default_category ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          'emboss/emboss.tar', 
-                          strings_displayed=[], 
-                          commit_message='Uploaded tool tarball.' )
-        datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
-        repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'emboss' ] )
-        self.generate_repository_dependency_xml( [ datatypes_repository ], 
-                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
-                                                 dependency_description='Emboss depends on the emboss_datatypes repository.' )
-        self.upload_file( repository, 
-                          'repository_dependencies.xml', 
-                          filepath=repository_dependencies_path, 
-                          commit_message='Uploaded dependency on emboss_datatypes.' )
-    def test_0020_create_filtering_repository( self ):
-        '''Create and populate filtering_0050.'''
-        self.create_repository( filtering_repository_name, 
-                                filtering_repository_description, 
-                                repository_long_description=filtering_repository_long_description, 
-                                categories=[ default_category ], 
-                                strings_displayed=[] )
-        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
-        self.upload_file( filtering_repository, 
-                          'filtering/filtering_1.1.0.tar', 
-                          strings_displayed=[], 
-                          commit_message='Uploaded filtering.tar.' )
-        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-        repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'filtering' ] )
-        self.generate_repository_dependency_xml( [ emboss_repository ], 
-                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
-                                                 dependency_description='Filtering depends on the emboss repository.' )
-        self.upload_file( filtering_repository, 
-                          'repository_dependencies.xml', 
-                          filepath=repository_dependencies_path, 
-                          commit_message='Uploaded dependency on emboss.' )
-    def test_0025_create_freebayes_repository( self ):
-        '''Create and populate freebayes_0050.'''
-        self.create_repository( freebayes_repository_name, 
-                                freebayes_repository_description, 
-                                repository_long_description=freebayes_repository_long_description, 
-                                categories=[ default_category ], 
-                                strings_displayed=[] )
-        repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
-        self.upload_file( repository, 
-                          'freebayes/freebayes.tar', 
-                          strings_displayed=[], 
-                          commit_message='Uploaded freebayes.tar.' )
-        emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
-        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
-        repository_dependencies_path = self.generate_temp_path( 'test_0050', additional_paths=[ 'freebayes' ] )
-        self.generate_repository_dependency_xml( [ filtering_repository ], 
-                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
-                                                 dependency_description='Emboss depends on the filtering repository.' )
-        self.upload_file( emboss_repository, 
-                          'repository_dependencies.xml', 
-                          filepath=repository_dependencies_path, 
-                          commit_message='Uploaded dependency on filtering.' )
-        previous_tip = self.get_repository_tip( repository )
-        self.generate_repository_dependency_xml( [ emboss_datatypes_repository, emboss_repository, filtering_repository, repository ], 
-                                                 self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
-                                                 dependency_description='Freebayes depends on the filtering repository.' )
-        self.upload_file( repository, 
-                          'repository_dependencies.xml', 
-                          filepath=repository_dependencies_path, 
-                          commit_message='Uploaded dependency on filtering.' )
-        self.display_manage_repository_page( repository, strings_not_displayed=[ previous_tip ] )
-    def test_0030_verify_repository_dependencies( self ):
-        '''Verify that the generated dependency circle does not cause an infinite loop.
-        
-        Expected structure:
-        
-        id: 2 key: http://localhost:8634__ESEP__freebayes_0050__ESEP__user1__ESEP__2e73d8e1b59d
-            ['http://localhost:8634', 'emboss_datatypes_0050', 'user1', '596029c334b1']
-            ['http://localhost:8634', 'emboss_0050', 'user1', '9f1503046640']
-            id: 3 key: http://localhost:8634__ESEP__filtering_0050__ESEP__user1__ESEP__eefdd8bc0db9
-                ['http://localhost:8634', 'emboss_0050', 'user1', '9f1503046640']
-            id: 4 key: http://localhost:8634__ESEP__emboss_0050__ESEP__user1__ESEP__9f1503046640
-                ['http://localhost:8634', 'emboss_datatypes_0050', 'user1', '596029c334b1']
-        '''
-        emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
-        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
-        freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
-        for repository in [ emboss_datatypes_repository, emboss_repository, filtering_repository ]:
-            self.check_repository_dependency( freebayes_repository, repository, self.get_repository_tip( repository ) )
-        for changeset_revision in self.get_repository_metadata_revisions( emboss_repository ):
-            self.check_repository_dependency( freebayes_repository, emboss_repository, changeset_revision )
-        self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'Freebayes depends on the filtering repository.' ] )
-    def test_0035_verify_repository_metadata( self ):
-        '''Verify that resetting the metadata does not change it.'''
-        emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
-        emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
-        filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
-        freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
-        for repository in [ emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository ]:
-            self.verify_unchanged_repository_metadata( repository )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0060_workflows.py
--- a/test/tool_shed/functional/test_0060_workflows.py
+++ b/test/tool_shed/functional/test_0060_workflows.py
@@ -23,16 +23,17 @@
         admin_user_private_role = test_db_util.get_private_role( admin_user )
     def test_0005_create_categories( self ):
         """Create categories for this test suite"""
-        self.create_category( 'Test 0060 Workflow Features', 'Test 0060 - Workflow Features' )
+        self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
     def test_0010_create_repository( self ):
         """Create and populate the filtering repository"""
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
-        self.create_repository( repository_name, 
-                                repository_description, 
-                                repository_long_description=repository_long_description, 
-                                categories=[ 'Test 0060 Workflow Features' ], 
-                                strings_displayed=[] )
+        self.get_or_create_repository( name=repository_name, 
+                                       description=repository_description, 
+                                       long_description=repository_long_description, 
+                                       owner=common.test_user_1_name,
+                                       categories=[ 'Test 0060 Workflow Features' ], 
+                                       strings_displayed=[] )
     def test_0015_upload_workflow( self ):
         '''Upload a workflow with a missing tool, and verify that the tool specified is marked as missing.'''
         repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_0300_reset_all_metadata.py
--- /dev/null
+++ b/test/tool_shed/functional/test_0300_reset_all_metadata.py
@@ -0,0 +1,255 @@
+from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import tool_shed.base.test_db_util as test_db_util
+
+datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
+datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
+workflow_name = 'Workflow for 0060_filter_workflow_repository'
+
+class TestResetAllRepositoryMetadata( ShedTwillTestCase ):
+    '''Verify that the "Reset selected metadata" feature works.'''
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
+    def test_0005_create_repositories_and_categories( self ):
+        category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
+        category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
+        category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
+        category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
+        category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
+        category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
+        category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' )
+        category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name='filtering_0000', 
+                                                    description="Galaxy's filtering tool", 
+                                                    long_description="Long description of Galaxy's filtering tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0000.id ) )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
+            self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0" )
+        repository = self.get_or_create_repository( name='freebayes_0010', 
+                                                    description="Galaxy's freebayes tool", 
+                                                    long_description="Long description of Galaxy's freebayes tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0000.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
+            self.upload_file( repository, 'freebayes/tool_data_table_conf.xml.sample', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
+            self.upload_file( repository, 'freebayes/sam_fa_indices.loc.sample', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
+            self.upload_file( repository, 'freebayes/tool_dependencies.xml', commit_message='Uploaded.' )
+        repository = self.get_or_create_repository( name='emboss_datatypes_0020', 
+                                                    description="Galaxy applicable data formats used by Emboss tools.", 
+                                                    long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0010.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            repository = self.get_or_create_repository( name='emboss_0020', 
+                                                 description='Galaxy wrappers for Emboss version 5.0.0 tools', 
+                                                 long_description='Galaxy wrappers for Emboss version 5.0.0 tools', 
+                                                 owner=common.test_user_1_name,
+                                                 category_id=self.security.encode_id( category_0020.id ),
+                                                 strings_displayed=[] )
+            self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
+        datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030', 
+                                                              description=datatypes_repository_description, 
+                                                              long_description=datatypes_repository_long_description, 
+                                                              owner=common.test_user_1_name,
+                                                              category_id=self.security.encode_id( category_0030.id ), 
+                                                              strings_displayed=[] )
+        if self.repository_is_new( datatypes_repository ):
+            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            emboss_5_repository = self.get_or_create_repository( name='emboss_5_0030', 
+                                                                 description=emboss_repository_description, 
+                                                                 long_description=emboss_repository_long_description, 
+                                                                 owner=common.test_user_1_name,
+                                                                 category_id=self.security.encode_id( category_0030.id ), 
+                                                                 strings_displayed=[] )
+            self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_5_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            emboss_6_repository = self.get_or_create_repository( name='emboss_6_0030', 
+                                                                 description=emboss_repository_description, 
+                                                                 long_description=emboss_repository_long_description, 
+                                                                 owner=common.test_user_1_name,
+                                                                 category_id=self.security.encode_id( category_0030.id ), 
+                                                                 strings_displayed=[] )
+            self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '6' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_6_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            emboss_repository = self.get_or_create_repository( name='emboss_0030', 
+                                                               description=emboss_repository_description, 
+                                                               long_description=emboss_repository_long_description, 
+                                                               owner=common.test_user_1_name,
+                                                               category_id=self.security.encode_id( category_0030.id ), 
+                                                               strings_displayed=[] )
+            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ emboss_5_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            self.generate_repository_dependency_xml( [ emboss_6_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+        repository = self.get_or_create_repository( name='freebayes_0040', 
+                                                    description="Galaxy's freebayes tool", 
+                                                    long_description="Long description of Galaxy's freebayes tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0040.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'freebayes/freebayes.tar', commit_message='Uploaded freebayes.tar.' )
+            repository = self.get_or_create_repository( name='filtering_0040', 
+                                                        description="Galaxy's filtering tool", 
+                                                        long_description="Long description of Galaxy's filtering tool", 
+                                                        owner=common.test_user_1_name,
+                                                        category_id=self.security.encode_id( category_0040.id ),
+                                                        strings_displayed=[] )
+            self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
+            freebayes_repository = test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
+            filtering_repository = test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name )
+            repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] )
+            self.generate_repository_dependency_xml( [ freebayes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Filtering 1.1.0 depends on the freebayes repository.' )
+            self.upload_file( filtering_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on freebayes' )
+            self.generate_repository_dependency_xml( [ filtering_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Freebayes depends on the filtering repository.' )
+            self.upload_file( freebayes_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on filtering' )
+        datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050', 
+                                                    description="Datatypes for emboss", 
+                                                    long_description="Long description of Emboss' datatypes", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0050.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( datatypes_repository ):
+            emboss_repository = self.get_or_create_repository( name='emboss_0050', 
+                                                        description="Galaxy's emboss tool", 
+                                                        long_description="Long description of Galaxy's emboss tool", 
+                                                        owner=common.test_user_1_name,
+                                                        category_id=self.security.encode_id( category_0050.id ),
+                                                        strings_displayed=[] )
+            filtering_repository = self.get_or_create_repository( name='filtering_0050', 
+                                                                  description="Galaxy's filtering tool", 
+                                                                  long_description="Long description of Galaxy's filtering tool", 
+                                                                  owner=common.test_user_1_name,
+                                                                  category_id=self.security.encode_id( category_0050.id ),
+                                                                  strings_displayed=[] )
+            freebayes_repository = self.get_or_create_repository( name='freebayes_0050', 
+                                                                  description="Galaxy's freebayes tool", 
+                                                                  long_description="Long description of Galaxy's freebayes tool", 
+                                                                  owner=common.test_user_1_name,
+                                                                  category_id=self.security.encode_id( category_0050.id ),
+                                                                  strings_displayed=[] )
+            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
+            self.upload_file( freebayes_repository, 'freebayes/freebayes.tar', commit_message='Uploaded freebayes.tar.' )
+            self.upload_file( filtering_repository, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'emboss' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Emboss depends on the emboss_datatypes repository.' )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on emboss_datatypes.' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'filtering' ] )
+            self.generate_repository_dependency_xml( [ emboss_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Filtering depends on the emboss repository.' )
+            self.upload_file( filtering_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on emboss.' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'freebayes' ] )
+            self.generate_repository_dependency_xml( [ filtering_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Emboss depends on the filtering repository.' )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on filtering.' )
+            self.generate_repository_dependency_xml( [ datatypes_repository, emboss_repository, filtering_repository, freebayes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Freebayes depends on the filtering repository.' )
+            self.upload_file( freebayes_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on filtering.' )
+        workflow_repository = self.get_or_create_repository( name='filtering_0060', 
+                                                             description="Galaxy's filtering tool", 
+                                                             long_description="Long description of Galaxy's filtering tool", 
+                                                             owner=common.test_user_1_name,
+                                                             category_id=self.security.encode_id( category_0060.id ),
+                                                             strings_displayed=[] )
+        if self.repository_is_new( workflow_repository ):
+            workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
+            workflow = workflow.replace(  '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
+            workflow_filepath = self.generate_temp_path( 'test_0360', additional_paths=[ 'filtering_workflow' ] )
+            os.makedirs( workflow_filepath )
+            file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
+            self.upload_file( workflow_repository, 
+                              workflow_filename, 
+                              filepath=workflow_filepath, 
+                              commit_message='Uploaded filtering workflow.' )
+            self.upload_file( workflow_repository, 
+                              'filtering/filtering_2.2.0.tar', 
+                              commit_message='Uploaded filtering tool.' )
+    def test_0010_reset_metadata_on_all_repositories( self ):
+        '''Reset metadata on all repositories, then verify that it has not changed.'''
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        old_metadata = dict()
+        new_metadata = dict()
+        repositories = test_db_util.get_all_repositories()
+        for repository in repositories:
+            old_metadata[ self.security.encode_id( repository.id ) ] = dict()
+            for metadata in self.get_repository_metadata( repository ):
+                old_metadata[ self.security.encode_id( repository.id ) ][ metadata.changeset_revision ] = metadata.metadata 
+        self.reset_metadata_on_selected_repositories( old_metadata.keys() )
+        for repository in repositories:
+            new_metadata[ self.security.encode_id( repository.id ) ] = dict()
+            for metadata in self.get_repository_metadata( repository ):
+                new_metadata[ self.security.encode_id( repository.id ) ][ metadata.changeset_revision ] = metadata.metadata 
+            if old_metadata[ self.security.encode_id( repository.id ) ] != new_metadata[ self.security.encode_id( repository.id ) ]:
+                raise AssertionError( 'Metadata changed after reset for repository %s.' % repository.name )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_1000_install_basic_repository.py
--- a/test/tool_shed/functional/test_1000_install_basic_repository.py
+++ b/test/tool_shed/functional/test_1000_install_basic_repository.py
@@ -5,30 +5,58 @@
     '''Test installing a basic repository.'''
     def test_0000_initiate_users( self ):
         """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
         self.galaxy_logout()
         self.galaxy_login( email=common.admin_email, username=common.admin_username )
-        admin_user = test_db_util.get_galaxy_user( common.admin_email )
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
-        admin_user_private_role = test_db_util.get_galaxy_private_role( admin_user )
-    def test_0005_browse_tool_sheds( self ):
+        galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email )
+        assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user )
+    def test_0005_ensure_repositories_and_categories_exist( self ):
+        '''Create the 0000 category and upload the filtering repository to it, if necessary.'''
+        category = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
+        self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name='filtering_0000', 
+                                                    description="Galaxy's filtering tool", 
+                                                    long_description="Long description of Galaxy's filtering tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category.id ) )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
+            self.upload_file( repository, 'filtering/filtering_0000.txt', commit_message="Uploaded readme for 1.1.0", remove_repo_files_not_in_tar='No' )
+            self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' )
+            self.upload_file( repository, 'readme.txt', commit_message="Uploaded readme for 2.2.0", remove_repo_files_not_in_tar='No' )
+    def test_0010_browse_tool_sheds( self ):
         """Browse the available tool sheds in this Galaxy instance."""
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
         self.visit_galaxy_url( '/admin_toolshed/browse_tool_sheds' )
         self.check_page_for_string( 'Embedded tool shed for functional tests' )
         self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0000 Basic Repository Features 1', 'Test 0000 Basic Repository Features 2' ] )
-    def test_0010_browse_test_0000_category( self ):
+    def test_0015_browse_test_0000_category( self ):
         '''Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test.'''
         category = test_db_util.get_category_by_name( 'Test 0000 Basic Repository Features 1' )
         self.browse_category( category, strings_displayed=[ 'filtering_0000' ] )
-    def test_0015_preview_filtering_repository( self ):
+    def test_0020_preview_filtering_repository( self ):
         '''Load the preview page for the filtering_0000 repository in the tool shed.'''
         self.preview_repository_in_tool_shed( 'filtering_0000', common.test_user_1_name, strings_displayed=[ 'filtering_0000', 'Valid tools' ] )
-    def test_0020_install_filtering_repository( self ):
-        self.install_repository( 'filtering_0000', common.test_user_1_name )
+    def test_0025_install_filtering_repository( self ):
+        self.install_repository( 'filtering_0000', common.test_user_1_name, 'Test 0000 Basic Repository Features 1' )
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name )
         self.verify_installed_repository_on_browse_page( installed_repository )
         self.display_installed_repository_manage_page( installed_repository, 
                                                        strings_displayed=[ 'Installed tool shed repository', 'Tools', 'Filter1' ] )
         self.verify_tool_metadata_for_installed_repository( installed_repository )
-    def test_0025_verify_installed_repository_metadata( self ):
+    def test_0030_verify_installed_repository_metadata( self ):
         '''Verify that resetting the metadata on an installed repository does not change the metadata.'''
         self.verify_installed_repository_metadata_unchanged( 'filtering_0000', common.test_user_1_name )
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
--- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
+++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
@@ -10,15 +10,62 @@
         admin_user = test_db_util.get_galaxy_user( common.admin_email )
         assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
         admin_user_private_role = test_db_util.get_galaxy_private_role( admin_user )
-    def test_0005_browse_tool_shed( self ):
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
+    def test_0005_ensure_repositories_and_categories_exist( self ):
+        '''Create the 0010 category and upload the freebayes repository to it, if necessary.'''
+        category = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name='freebayes_0010', 
+                                                    description="Galaxy's freebayes tool", 
+                                                    long_description="Long description of Galaxy's freebayes tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category.id ) )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 
+                              'freebayes/freebayes.xml', 
+                              valid_tools_only=False, 
+                              commit_message="Uploaded freebayes.xml." )
+            self.upload_file( repository, 
+                              'freebayes/tool_data_table_conf.xml.sample', 
+                              valid_tools_only=False,
+                              commit_message="Uploaded tool_data_table_conf.xml.", 
+                              remove_repo_files_not_in_tar='No' )
+            self.upload_file( repository, 
+                              'freebayes/sam_fa_indices.loc.sample', 
+                              commit_message="Uploaded sam_fa_indices.loc.sample.", 
+                              valid_tools_only=False,
+                             remove_repo_files_not_in_tar='No' )
+            self.upload_file( repository, 
+                              'freebayes/invalid_tool_dependencies/tool_dependencies.xml', 
+                              valid_tools_only=False,
+                              commit_message="Uploaded invalid_tool_dependencies/tool_dependencies.xml.", 
+                              remove_repo_files_not_in_tar='No' )
+            self.upload_file( repository, 
+                              'freebayes/tool_dependencies.xml', 
+                              valid_tools_only=False,
+                              commit_message="Uploaded tool_dependencies.xml", 
+                              remove_repo_files_not_in_tar='No' )
+    def test_0010_browse_tool_shed( self ):
         """Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
         self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0010 Repository With Tool Dependencies' ] )
         category = test_db_util.get_category_by_name( 'Test 0010 Repository With Tool Dependencies' )
         self.browse_category( category, strings_displayed=[ 'freebayes_0010' ] )
         self.preview_repository_in_tool_shed( 'freebayes_0010', common.test_user_1_name, strings_displayed=[ 'freebayes_0010', 'Valid tools' ] )
     def test_0015_install_freebayes_repository( self ):
         '''Install the freebayes repository without installing tool dependencies.'''
-        self.install_repository( 'freebayes_0010', common.test_user_1_name, install_tool_dependencies=False )
+        self.install_repository( 'freebayes_0010', common.test_user_1_name, 'Test 0010 Repository With Tool Dependencies', install_tool_dependencies=False )
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name )
         self.verify_installed_repository_on_browse_page( installed_repository )
         self.display_installed_repository_manage_page( installed_repository,
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
--- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
+++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
@@ -1,24 +1,71 @@
 from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
 import tool_shed.base.test_db_util as test_db_util
+datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
+datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+
+emboss_repository_name = 'emboss_0020'
+emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+
 class ToolWithRepositoryDependencies( ShedTwillTestCase ):
     '''Test installing a repository with repository dependencies.'''
     def test_0000_initiate_users( self ):
         """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
         self.galaxy_logout()
         self.galaxy_login( email=common.admin_email, username=common.admin_username )
-        admin_user = test_db_util.get_galaxy_user( common.admin_email )
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
-        admin_user_private_role = test_db_util.get_galaxy_private_role( admin_user )
-    def test_0005_browse_tool_shed( self ):
+        galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email )
+        assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user )
+    def test_0005_ensure_repositories_and_categories_exist( self ):
+        '''Create the 0020 category and any missing repositories.'''
+        category = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Test 0020 Basic Repository Dependencies' )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        datatypes_repository = self.get_or_create_repository( name=datatypes_repository_name, 
+                                                              description=datatypes_repository_description, 
+                                                              long_description=datatypes_repository_long_description, 
+                                                              owner=common.test_user_1_name,
+                                                              category_id=self.security.encode_id( category.id ), 
+                                                              strings_displayed=[] )
+        if self.repository_is_new( datatypes_repository ):
+            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            emboss_repository = self.get_or_create_repository( name=emboss_repository_name, 
+                                                               description=emboss_repository_description, 
+                                                               long_description=emboss_repository_long_description, 
+                                                               owner=common.test_user_1_name,
+                                                               category_id=self.security.encode_id( category.id ), 
+                                                               strings_displayed=[] )
+            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_1020', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+    def test_0010_browse_tool_shed( self ):
         """Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
         self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0020 Basic Repository Dependencies' ] )
         category = test_db_util.get_category_by_name( 'Test 0020 Basic Repository Dependencies' )
         self.browse_category( category, strings_displayed=[ 'emboss_0020' ] )
         self.preview_repository_in_tool_shed( 'emboss_0020', common.test_user_1_name, strings_displayed=[ 'emboss_0020', 'Valid tools' ] )
     def test_0015_install_emboss_repository( self ):
         '''Install the emboss repository without installing tool dependencies.'''
-        self.install_repository( 'emboss_0020', common.test_user_1_name, install_tool_dependencies=False )
+        self.install_repository( 'emboss_0020', common.test_user_1_name, 'Test 0020 Basic Repository Dependencies', install_tool_dependencies=False )
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0020', common.test_user_1_name )
         self.verify_installed_repository_on_browse_page( installed_repository )
         self.display_installed_repository_manage_page( installed_repository,
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
--- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
+++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
@@ -1,17 +1,100 @@
 from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
 import tool_shed.base.test_db_util as test_db_util
+datatypes_repository_name = 'emboss_datatypes_0030'
+datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
+datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+
+emboss_repository_name = 'emboss_0030'
+emboss_5_repository_name = 'emboss_5_0030'
+emboss_6_repository_name = 'emboss_6_0030'
+emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+
 class RepositoryWithDependencyRevisions( ShedTwillTestCase ):
     '''Test installing a repository with dependency revisions.'''
     def test_0000_initiate_users( self ):
         """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
         self.galaxy_logout()
         self.galaxy_login( email=common.admin_email, username=common.admin_username )
-        admin_user = test_db_util.get_galaxy_user( common.admin_email )
-        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
-        admin_user_private_role = test_db_util.get_galaxy_private_role( admin_user )
-    def test_0005_browse_tool_shed( self ):
+        galaxy_admin_user = test_db_util.get_galaxy_user( common.admin_email )
+        assert galaxy_admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
+        galaxy_admin_user_private_role = test_db_util.get_galaxy_private_role( galaxy_admin_user )
+    def test_0005_ensure_repositories_and_categories_exist( self ):
+        '''Create the 0030 category and add repositories to it, if necessary.'''
+        category = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Test 0030 Repository Dependency Revisions' )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        datatypes_repository = self.get_or_create_repository( name=datatypes_repository_name, 
+                                                              description=datatypes_repository_description, 
+                                                              long_description=datatypes_repository_long_description, 
+                                                              owner=common.test_user_1_name,
+                                                              category_id=self.security.encode_id( category.id ), 
+                                                              strings_displayed=[] )
+        if self.repository_is_new( datatypes_repository ):
+            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            emboss_5_repository = self.get_or_create_repository( name=emboss_5_repository_name, 
+                                                                 description=emboss_repository_description, 
+                                                                 long_description=emboss_repository_long_description, 
+                                                                 owner=common.test_user_1_name,
+                                                                 category_id=self.security.encode_id( category.id ), 
+                                                                 strings_displayed=[] )
+            self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_1030', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_5_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            emboss_6_repository = self.get_or_create_repository( name=emboss_6_repository_name, 
+                                                                 description=emboss_repository_description, 
+                                                                 long_description=emboss_repository_long_description, 
+                                                                 owner=common.test_user_1_name,
+                                                                 category_id=self.security.encode_id( category.id ), 
+                                                                 strings_displayed=[] )
+            self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_1030', additional_paths=[ 'emboss', '6' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_6_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            emboss_repository = self.get_or_create_repository( name=emboss_repository_name, 
+                                                               description=emboss_repository_description, 
+                                                               long_description=emboss_repository_long_description, 
+                                                               owner=common.test_user_1_name,
+                                                               category_id=self.security.encode_id( category.id ), 
+                                                               strings_displayed=[] )
+            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_1030', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ emboss_5_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            self.generate_repository_dependency_xml( [ emboss_6_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+    def test_0010_browse_tool_shed( self ):
         """Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
         self.browse_tool_shed( url=self.url, strings_displayed=[ 'Test 0030 Repository Dependency Revisions' ] )
         category = test_db_util.get_category_by_name( 'Test 0030 Repository Dependency Revisions' )
         self.browse_category( category, strings_displayed=[ 'emboss_0030' ] )
@@ -20,7 +103,11 @@
         '''Install the emboss repository without installing tool dependencies.'''
         repository = test_db_util.get_repository_by_name_and_owner( 'emboss_0030', common.test_user_1_name )
         revisions = self.get_repository_metadata_revisions( repository )
-        self.install_repository( 'emboss_0030', common.test_user_1_name, changeset_revision=revisions[1], install_tool_dependencies=False )
+        self.install_repository( 'emboss_0030', 
+                                 common.test_user_1_name, 
+                                 'Test 0030 Repository Dependency Revisions', 
+                                 changeset_revision=revisions[1], 
+                                 install_tool_dependencies=False )
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name )
         self.verify_installed_repository_on_browse_page( installed_repository )
         self.display_installed_repository_manage_page( installed_repository,
diff -r 8e1eec8c56cc5f62f5541c754f31607675347285 -r e6030730bb85b532534f7229c79751efadcd1eb7 test/tool_shed/functional/test_1300_reset_all_metadata.py
--- /dev/null
+++ b/test/tool_shed/functional/test_1300_reset_all_metadata.py
@@ -0,0 +1,269 @@
+from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import tool_shed.base.test_db_util as test_db_util
+
+datatypes_repository_name = 'emboss_datatypes_0020'
+datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
+datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools.  This repository contains no tools."
+emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
+workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
+workflow_name = 'Workflow for 0060_filter_workflow_repository'
+
+class TestResetInstalledRepositoryMetadata( ShedTwillTestCase ):
+    '''Verify that the "Reset selected metadata" feature works.'''
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        test_user_1 = test_db_util.get_user( common.test_user_1_email )
+        assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % test_user_1_email
+        test_user_1_private_role = test_db_util.get_private_role( test_user_1 )
+        self.logout()
+        self.login( email=common.admin_email, username=common.admin_username )
+        admin_user = test_db_util.get_user( common.admin_email )
+        assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
+        admin_user_private_role = test_db_util.get_private_role( admin_user )
+    def test_0005_create_repositories_and_categories( self ):
+        '''Ensure that the necessary categories and repositories exist for these tests.'''
+        category_0000 = self.create_category( name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1' )
+        category_0001 = self.create_category( name='Test 0000 Basic Repository Features 2', description='Test 0000 Basic Repository Features 2' )
+        category_0010 = self.create_category( name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.' )
+        category_0020 = self.create_category( name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.' )
+        category_0030 = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.' )
+        category_0040 = self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
+        category_0050 = self.create_category( name='test_0050_repository_n_level_circular_dependencies', description='Testing handling of circular repository dependencies to n levels.' )
+        category_0060 = self.create_category( name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features' )
+        self.logout()
+        self.login( email=common.test_user_1_email, username=common.test_user_1_name )
+        repository = self.get_or_create_repository( name='filtering_0000', 
+                                                    description="Galaxy's filtering tool", 
+                                                    long_description="Long description of Galaxy's filtering tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0000.id ) )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" )
+            self.upload_file( repository, 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0" )
+        repository = self.get_or_create_repository( name='freebayes_0010', 
+                                                    description="Galaxy's freebayes tool", 
+                                                    long_description="Long description of Galaxy's freebayes tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0010.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
+            self.upload_file( repository, 'freebayes/tool_data_table_conf.xml.sample', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
+            self.upload_file( repository, 'freebayes/sam_fa_indices.loc.sample', valid_tools_only=False, commit_message='Uploaded.', strings_displayed=[] )
+            self.upload_file( repository, 'freebayes/tool_dependencies.xml', commit_message='Uploaded.' )
+        repository = self.get_or_create_repository( name='emboss_datatypes_0020', 
+                                                    description="Galaxy applicable data formats used by Emboss tools.", 
+                                                    long_description="Galaxy applicable data formats used by Emboss tools. This repository contains no tools.", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0010.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            repository = self.get_or_create_repository( name='emboss_0020', 
+                                                 description='Galaxy wrappers for Emboss version 5.0.0 tools', 
+                                                 long_description='Galaxy wrappers for Emboss version 5.0.0 tools', 
+                                                 owner=common.test_user_1_name,
+                                                 category_id=self.security.encode_id( category_0020.id ),
+                                                 strings_displayed=[] )
+            self.upload_file( repository, 'emboss/emboss.tar', commit_message='Uploaded emboss_5.tar' )
+        datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0030', 
+                                                              description=datatypes_repository_description, 
+                                                              long_description=datatypes_repository_long_description, 
+                                                              owner=common.test_user_1_name,
+                                                              category_id=self.security.encode_id( category_0030.id ), 
+                                                              strings_displayed=[] )
+        if self.repository_is_new( datatypes_repository ):
+            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            emboss_5_repository = self.get_or_create_repository( name='emboss_5_0030', 
+                                                                 description=emboss_repository_description, 
+                                                                 long_description=emboss_repository_long_description, 
+                                                                 owner=common.test_user_1_name,
+                                                                 category_id=self.security.encode_id( category_0030.id ), 
+                                                                 strings_displayed=[] )
+            self.upload_file( emboss_5_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_5_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            emboss_6_repository = self.get_or_create_repository( name='emboss_6_0030', 
+                                                                 description=emboss_repository_description, 
+                                                                 long_description=emboss_repository_long_description, 
+                                                                 owner=common.test_user_1_name,
+                                                                 category_id=self.security.encode_id( category_0030.id ), 
+                                                                 strings_displayed=[] )
+            self.upload_file( emboss_6_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '6' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_6_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            emboss_repository = self.get_or_create_repository( name='emboss_0030', 
+                                                               description=emboss_repository_description, 
+                                                               long_description=emboss_repository_long_description, 
+                                                               owner=common.test_user_1_name,
+                                                               category_id=self.security.encode_id( category_0030.id ), 
+                                                               strings_displayed=[] )
+            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded emboss.tar' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0330', additional_paths=[ 'emboss', '5' ] )
+            self.generate_repository_dependency_xml( [ emboss_5_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+            self.generate_repository_dependency_xml( [ emboss_6_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ) )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded repository_dependencies.xml' )
+        repository = self.get_or_create_repository( name='freebayes_0040', 
+                                                    description="Galaxy's freebayes tool", 
+                                                    long_description="Long description of Galaxy's freebayes tool", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0040.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( repository ):
+            self.upload_file( repository, 'freebayes/freebayes.tar', commit_message='Uploaded freebayes.tar.' )
+            repository = self.get_or_create_repository( name='filtering_0040', 
+                                                        description="Galaxy's filtering tool", 
+                                                        long_description="Long description of Galaxy's filtering tool", 
+                                                        owner=common.test_user_1_name,
+                                                        category_id=self.security.encode_id( category_0040.id ),
+                                                        strings_displayed=[] )
+            self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
+            freebayes_repository = test_db_util.get_repository_by_name_and_owner( 'freebayes_0040', common.test_user_1_name )
+            filtering_repository = test_db_util.get_repository_by_name_and_owner( 'filtering_0040', common.test_user_1_name )
+            repository_dependencies_path = self.generate_temp_path( 'test_0340', additional_paths=[ 'dependencies' ] )
+            self.generate_repository_dependency_xml( [ freebayes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Filtering 1.1.0 depends on the freebayes repository.' )
+            self.upload_file( filtering_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on freebayes' )
+            self.generate_repository_dependency_xml( [ filtering_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Freebayes depends on the filtering repository.' )
+            self.upload_file( freebayes_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on filtering' )
+        datatypes_repository = self.get_or_create_repository( name='emboss_datatypes_0050', 
+                                                    description="Datatypes for emboss", 
+                                                    long_description="Long description of Emboss' datatypes", 
+                                                    owner=common.test_user_1_name,
+                                                    category_id=self.security.encode_id( category_0050.id ),
+                                                    strings_displayed=[] )
+        if self.repository_is_new( datatypes_repository ):
+            emboss_repository = self.get_or_create_repository( name='emboss_0050', 
+                                                        description="Galaxy's emboss tool", 
+                                                        long_description="Long description of Galaxy's emboss tool", 
+                                                        owner=common.test_user_1_name,
+                                                        category_id=self.security.encode_id( category_0050.id ),
+                                                        strings_displayed=[] )
+            filtering_repository = self.get_or_create_repository( name='filtering_0050', 
+                                                                  description="Galaxy's filtering tool", 
+                                                                  long_description="Long description of Galaxy's filtering tool", 
+                                                                  owner=common.test_user_1_name,
+                                                                  category_id=self.security.encode_id( category_0050.id ),
+                                                                  strings_displayed=[] )
+            freebayes_repository = self.get_or_create_repository( name='freebayes_0050', 
+                                                                  description="Galaxy's freebayes tool", 
+                                                                  long_description="Long description of Galaxy's freebayes tool", 
+                                                                  owner=common.test_user_1_name,
+                                                                  category_id=self.security.encode_id( category_0050.id ),
+                                                                  strings_displayed=[] )
+            self.upload_file( datatypes_repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' )
+            self.upload_file( emboss_repository, 'emboss/emboss.tar', commit_message='Uploaded tool tarball.' )
+            self.upload_file( freebayes_repository, 'freebayes/freebayes.tar', commit_message='Uploaded freebayes.tar.' )
+            self.upload_file( filtering_repository, 'filtering/filtering_1.1.0.tar', commit_message='Uploaded filtering.tar.' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'emboss' ] )
+            self.generate_repository_dependency_xml( [ datatypes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Emboss depends on the emboss_datatypes repository.' )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on emboss_datatypes.' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'filtering' ] )
+            self.generate_repository_dependency_xml( [ emboss_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Filtering depends on the emboss repository.' )
+            self.upload_file( filtering_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on emboss.' )
+            repository_dependencies_path = self.generate_temp_path( 'test_0350', additional_paths=[ 'freebayes' ] )
+            self.generate_repository_dependency_xml( [ filtering_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Emboss depends on the filtering repository.' )
+            self.upload_file( emboss_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on filtering.' )
+            self.generate_repository_dependency_xml( [ datatypes_repository, emboss_repository, filtering_repository, freebayes_repository ], 
+                                                     self.get_filename( 'repository_dependencies.xml', filepath=repository_dependencies_path ), 
+                                                     dependency_description='Freebayes depends on the filtering repository.' )
+            self.upload_file( freebayes_repository, 
+                              'repository_dependencies.xml', 
+                              filepath=repository_dependencies_path, 
+                              commit_message='Uploaded dependency on filtering.' )
+        workflow_repository = self.get_or_create_repository( name='filtering_0060', 
+                                                             description="Galaxy's filtering tool", 
+                                                             long_description="Long description of Galaxy's filtering tool", 
+                                                             owner=common.test_user_1_name,
+                                                             category_id=self.security.encode_id( category_0060.id ),
+                                                             strings_displayed=[] )
+        if self.repository_is_new( workflow_repository ):
+            workflow = file( self.get_filename( 'filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga' ), 'r' ).read()
+            workflow = workflow.replace(  '__TEST_TOOL_SHED_URL__', self.url.replace( 'http://', '' ) )
+            workflow_filepath = self.generate_temp_path( 'test_0360', additional_paths=[ 'filtering_workflow' ] )
+            os.makedirs( workflow_filepath )
+            file( os.path.join( workflow_filepath, workflow_filename ), 'w+' ).write( workflow )
+            self.upload_file( workflow_repository, 
+                              workflow_filename, 
+                              filepath=workflow_filepath, 
+                              commit_message='Uploaded filtering workflow.' )
+            self.upload_file( workflow_repository, 
+                              'filtering/filtering_2.2.0.tar', 
+                              commit_message='Uploaded filtering tool.' )
+    def test_0010_install_all_missing_repositories( self ):
+        '''Call the install_repository method to ensure that all required repositories are installed.'''
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
+        category_0000 = 'Test 0000 Basic Repository Features 1'
+        category_0001 = 'Test 0000 Basic Repository Features 2'
+        category_0010 = 'Test 0010 Repository With Tool Dependencies'
+        category_0020 = 'Test 0020 Basic Repository Dependencies'
+        category_0030 = 'Test 0030 Repository Dependency Revisions'
+        category_0040 = 'test_0040_repository_circular_dependencies'
+        category_0050 = 'test_0050_repository_n_level_circular_dependencies'
+        category_0060 = 'Test 0060 Workflow Features'
+        self.install_repository( 'filtering_0000', common.test_user_1_name, category_0000, strings_displayed=[] )
+        self.install_repository( 'freebayes_0010', common.test_user_1_name, category_0010, strings_displayed=[] )
+        self.install_repository( 'emboss_0020', common.test_user_1_name, category_0020, strings_displayed=[] )
+        self.install_repository( 'emboss_5_0030', common.test_user_1_name, category_0030, strings_displayed=[] )
+        self.install_repository( 'filtering_0040', common.test_user_1_name, category_0040, strings_displayed=[] )
+        self.install_repository( 'freebayes_0050', common.test_user_1_name, category_0050, strings_displayed=[] )
+        self.install_repository( 'filtering_0060', common.test_user_1_name, category_0060, strings_displayed=[] )
+    def test_0015_reset_metadata_on_all_repositories( self ):
+        '''Reset metadata on all repositories, then verify that it has not changed.'''
+        repository_metadata = dict()
+        repositories = test_db_util.get_all_installed_repositories()
+        for repository in repositories:
+            repository_metadata[ self.security.encode_id( repository.id ) ] = repository.metadata
+        self.reset_metadata_on_selected_installed_repositories( repository_metadata.keys() )
+        for repository in repositories:
+            test_db_util.ga_refresh( repository )
+            old_metadata = repository_metadata[ self.security.encode_id( repository.id ) ]
+            assert repository.metadata == old_metadata, 'Metadata for installed repository %s changed after reset.' % repository.name
+ 
\ No newline at end of file
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