[galaxy-commits] commit/galaxy-central: inithello: Tool shed functional test enhancements. Functional tests for uninstalling, deactivating, reinstalling, and reactivating installed repositories.

21 Dec 2012

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/692a1e8b6999/
changeset:   692a1e8b6999
user:        inithello
date:        2012-12-21 18:47:30
summary:     Tool shed functional test enhancements. Functional tests for uninstalling, deactivating, reinstalling, and reactivating installed repositories.
affected #:  9 files
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d test/tool_shed/base/twilltestcase.py

--- a/test/tool_shed/base/twilltestcase.py
+++ b/test/tool_shed/base/twilltestcase.py
@@ -68,13 +68,10 @@
         for dependency in installed_repository.metadata[ 'tool_dependencies' ]:
             tool_dependency = installed_repository.metadata[ 'tool_dependencies' ][ dependency ]
             strings_displayed.extend( [ tool_dependency[ 'name' ], tool_dependency[ 'version' ], tool_dependency[ 'type' ] ] )
-            """
-            TODO: Uncomment these when Greg enhances the tool dependencies and missing tool dependencies containers to display the status.
             if dependencies_installed:
                 strings_displayed.append( 'Installed' )
             else:
                 strings_displayed.append( 'Never installed' )
-            """
         url = '/admin_toolshed/manage_repository?id=%s' % self.security.encode_id( installed_repository.id )
         self.visit_galaxy_url( url )
         self.check_for_strings( strings_displayed, strings_not_displayed )
@@ -322,6 +319,14 @@
         file( xml_filename, 'w' ).write( repository_dependency_xml )
     def generate_temp_path( self, test_script_path, additional_paths=[] ):
         return os.path.join( self.tool_shed_test_tmp_dir, test_script_path, os.sep.join( additional_paths ) )
+    def get_datatypes_count( self ):
+        url = '/admin/view_datatypes_registry'
+        self.visit_galaxy_url( url )
+        html = self.last_page()
+        datatypes_count = re.search( 'registry contains (\d+) data types', html )
+        if datatypes_count:
+            return datatypes_count.group( 1 )
+        return None
     def get_filename( self, filename, filepath=None ):
         if filepath is not None:
             return os.path.abspath( os.path.join( filepath, filename ) )
@@ -404,15 +409,16 @@
         # group(2), and the reinstalling flag in group(3) and pass them to the manage_repositories method in the Galaxy 
         # admin_toolshed controller.
         install_parameters = re.search( 'initiate_repository_installation( "([^"]+)", "([^"]+)", "([^"]+)" );', html )
-        iri_ids = install_parameters.group(1)
-        encoded_kwd = install_parameters.group(2)
-        reinstalling = install_parameters.group(3)
-        url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \
-            ( iri_ids, encoded_kwd, reinstalling )
-        self.visit_galaxy_url( url )
-    def install_repository( self, name, owner, category_name, install_tool_dependencies=False, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], **kwd ):
-        if test_db_util.get_installed_repository_by_name_owner( name, owner ) is not None:
-            return
+        if install_parameters:
+            iri_ids = install_parameters.group(1)
+            encoded_kwd = install_parameters.group(2)
+            reinstalling = install_parameters.group(3)
+            url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \
+                ( iri_ids, encoded_kwd, reinstalling )
+            self.visit_galaxy_url( url )
+    def install_repository( self, name, owner, category_name, install_tool_dependencies=False, 
+                            changeset_revision=None, strings_displayed=[], strings_not_displayed=[], 
+                            preview_strings_displayed=[], post_submit_strings_displayed=[], **kwd ):
         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=preview_strings_displayed )
@@ -435,6 +441,7 @@
         if 'shed_tool_conf' not in kwd:
             kwd[ 'shed_tool_conf' ] = self.shed_tool_conf
         self.submit_form( 1, 'select_tool_panel_section_button', **kwd )
+        self.check_for_strings( post_submit_strings_displayed, strings_not_displayed )
         self.initiate_installation_process()
         self.wait_for_repository_installation( repository, changeset_revision )
     def load_invalid_tool_page( self, repository, tool_xml, changeset_revision, strings_displayed=[], strings_not_displayed=[] ):
@@ -460,6 +467,11 @@
         self.visit_url( '/repository/preview_tools_in_changeset?repository_id=%s&changeset_revision=%s' % \
                         ( self.security.encode_id( repository.id ), changeset_revision ) )
         self.check_for_strings( strings_displayed, strings_not_displayed )
+    def reactivate_repository( self, installed_repository ):
+        url = '/admin_toolshed/browse_repositories?operation=activate+or+reinstall&id=%s' % self.security.encode_id( installed_repository.id )
+        self.visit_galaxy_url( url )
+        strings_displayed = [ installed_repository.name, 'repository has been activated' ]
+        self.check_for_strings( strings_displayed, [] )
     def reinstall_repository( self, installed_repository ):
         url = '/admin_toolshed/reinstall_repository?id=%s' % self.security.encode_id( installed_repository.id )
         self.visit_galaxy_url( url )
@@ -513,13 +525,16 @@
     def uninstall_repository( self, installed_repository, remove_from_disk=True ):
         url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( installed_repository.id )
         self.visit_galaxy_url( url )
-#        form = tc.browser.get_form( 'deactivate_or_uninstall_repository' )
-        tc.fv ( 1, "remove_from_disk", '1' )
-#        checkbox.readonly = False
-#        if remove_from_disk:
-#            checkbox.selected = True
+        if remove_from_disk:
+            tc.fv ( 1, "remove_from_disk", 'true' )
+        else:
+            tc.fv ( 1, "remove_from_disk", 'false' )
         tc.submit( 'deactivate_or_uninstall_repository_button' )
-        strings_displayed = [ 'has been uninstalled', 'The repository named' ]
+        strings_displayed = [ 'The repository named' ]
+        if remove_from_disk:
+            strings_displayed.append( 'has been uninstalled' )
+        else:
+            strings_displayed.append( 'has been deactivated' )
         self.check_for_strings( strings_displayed, strings_not_displayed=[] )
     def update_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ):
         url = '/admin_toolshed/check_for_updates?id=%s' % self.security.encode_id( installed_repository.id )
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d 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
@@ -26,7 +26,7 @@
     def test_0005_create_category( self ):
         """Create a category for this test suite"""
         self.create_category( name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.' )
-    def test_0010_create_freebayes_repository_name( self ):
+    def test_0010_create_freebayes_repository( self ):
         '''Create and populate freebayes_0040.'''
         self.logout()
         self.login( email=common.test_user_1_email, username=common.test_user_1_name )
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d 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
@@ -65,6 +65,7 @@
         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.'''
+        old_datatypes = self.get_datatypes_count()
         self.install_repository( 'emboss_0020', 
                                  common.test_user_1_name, 
                                  'Test 0020 Basic Repository Dependencies', 
@@ -81,6 +82,8 @@
                                                        strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'antigenic' ] )
         self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False )
         self.verify_tool_metadata_for_installed_repository( installed_repository )
+        new_datatypes = self.get_datatypes_count()
+        assert new_datatypes > old_datatypes, 'Installing emboss did not add datatypes to the registry'
     def test_0020_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( 'emboss_0020', common.test_user_1_name )
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d 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
@@ -102,11 +102,10 @@
     def test_0015_install_emboss_repository( self ):
         '''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 )
+        old_datatypes = self.get_datatypes_count()
         self.install_repository( 'emboss_0030', 
                                  common.test_user_1_name, 
                                  'Test 0030 Repository Dependency Revisions', 
-                                 changeset_revision=revisions[1], 
                                  install_tool_dependencies=False, 
                                  new_tool_panel_section='test_1030' )
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name )
@@ -121,6 +120,8 @@
         self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False )
         self.verify_tool_metadata_for_installed_repository( installed_repository )
         self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] )
+        new_datatypes = self.get_datatypes_count()
+        assert new_datatypes > old_datatypes, 'Installing emboss did not add datatypes to the registry.'
     def test_0025_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( 'emboss_0030', common.test_user_1_name )
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
--- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py
@@ -1,8 +1,8 @@
 from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
 import tool_shed.base.test_db_util as test_db_util
-class BasicToolShedFeatures( ShedTwillTestCase ):
-    '''Test installing a basic repository.'''
+class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
+    '''Test uninstalling and reinstalling a basic repository.'''
     def test_0000_initiate_users( self ):
         """Create necessary user accounts."""
         self.logout()
@@ -54,7 +54,6 @@
     def test_0015_uninstall_filtering_repository( self ):
         '''Uninstall the filtering repository.'''
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name )
-        old_metadata = installed_repository.metadata
         self.uninstall_repository( installed_repository, remove_from_disk=True )
         strings_not_displayed = [ installed_repository.name,
                               installed_repository.description,
@@ -84,7 +83,7 @@
     def test_0030_reactivate_filtering_repository( self ):
         '''Reactivate the filtering repository and verify that it now shows up in the list of installed repositories.'''
         installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name )
-        self.reinstall_repository( installed_repository )
+        self.reactivate_repository( installed_repository )
         strings_displayed = [ installed_repository.name,
                               installed_repository.description,
                               installed_repository.owner,
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
--- /dev/null
+++ b/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
@@ -0,0 +1,110 @@
+from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
+import tool_shed.base.test_db_util as test_db_util
+
+class UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
+    '''Test uninstalling and reinstalling a repository with tool dependencies.'''
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        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 )
+        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 the tool shed, 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_install_freebayes_repository( self ):
+        '''Install the freebayes repository into the Galaxy instance.'''
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
+        self.install_repository( 'freebayes_0010', 
+                                 common.test_user_1_name, 
+                                 'Test 0010 Repository With Tool Dependencies', 
+                                 new_tool_panel_section='test_1210' )
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+    def test_0015_uninstall_freebayes_repository( self ):
+        '''Uninstall the freebayes repository.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name )
+        self.uninstall_repository( installed_repository, remove_from_disk=True )
+        strings_not_displayed = [ installed_repository.name, installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
+    def test_0020_reinstall_freebayes_repository( self ):
+        '''Reinstall the freebayes repository.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name )
+        self.reinstall_repository( installed_repository )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+        self.display_installed_repository_manage_page( installed_repository, 
+                                                       strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] )
+        self.verify_tool_metadata_for_installed_repository( installed_repository )
+    def test_0025_deactivate_freebayes_repository( self ):
+        '''Deactivate the freebayes repository without removing it from disk.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name )
+        self.uninstall_repository( installed_repository, remove_from_disk=False )
+        strings_not_displayed = [ installed_repository.name, installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
+    def test_0030_reactivate_freebayes_repository( self ):
+        '''Reactivate the freebayes repository and verify that it now shows up in the list of installed repositories.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name )
+        self.reactivate_repository( installed_repository )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+        self.display_installed_repository_manage_page( installed_repository, 
+                                                       strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'FreeBayes' ] )
+        self.verify_tool_metadata_for_installed_repository( installed_repository )
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
--- /dev/null
+++ b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py
@@ -0,0 +1,123 @@
+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 UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
+    '''Test uninstalling and reinstalling a repository with tool dependencies.'''
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        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 )
+        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 0020 category and upload the emboss repository to the tool shed, if necessary.'''
+        category = self.create_category( name='Test 0020 Basic Repository 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 )
+        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_install_emboss_repository( self ):
+        '''Install the emboss repository into the Galaxy instance.'''
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
+        self.install_repository( emboss_repository_name, 
+                                 common.test_user_1_name, 
+                                 'Test 0020 Basic Repository Dependencies', 
+                                 new_tool_panel_section='test_1210' )
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+    def test_0015_uninstall_emboss_repository( self ):
+        '''Uninstall the emboss repository.'''
+#        old_datatypes = self.get_datatypes_count()
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.uninstall_repository( installed_repository, remove_from_disk=True )
+        strings_not_displayed = [ installed_repository.name, installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
+#        new_datatypes = self.get_datatypes_count()
+#        assert new_datatypes < old_datatypes, 'Uninstalling emboss did not remove datatypes from the registry.'
+    def test_0020_reinstall_emboss_repository( self ):
+        '''Reinstall the emboss repository.'''
+#        old_datatypes = self.get_datatypes_count()
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.reinstall_repository( installed_repository )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+        self.display_installed_repository_manage_page( installed_repository, 
+                                                       strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] )
+        self.verify_tool_metadata_for_installed_repository( installed_repository )
+#        new_datatypes = self.get_datatypes_count()
+#        assert new_datatypes > old_datatypes, 'Reinstalling emboss did not add datatypes to the registry.'
+    def test_0025_deactivate_emboss_repository( self ):
+        '''Deactivate the emboss repository without removing it from disk.'''
+#        old_datatypes = self.get_datatypes_count()
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.uninstall_repository( installed_repository, remove_from_disk=False )
+        strings_not_displayed = [ installed_repository.name,
+                                  installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
+#        new_datatypes = self.get_datatypes_count()
+#        assert new_datatypes < old_datatypes, 'Deactivating emboss did not remove datatypes from the registry.'
+    def test_0030_reactivate_emboss_repository( self ):
+        '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.'''
+#        old_datatypes = self.get_datatypes_count()
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.reactivate_repository( installed_repository )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+        self.display_installed_repository_manage_page( installed_repository, 
+                                                       strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] )
+        self.verify_tool_metadata_for_installed_repository( installed_repository )
+#        new_datatypes = self.get_datatypes_count()
+#        assert new_datatypes > old_datatypes, 'Reactivating emboss did not add datatypes to the registry.'
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
--- /dev/null
+++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
@@ -0,0 +1,146 @@
+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 UninstallingAndReinstallingRepositories( ShedTwillTestCase ):
+    '''Test uninstalling and reinstalling a repository with repository dependency revisions.'''
+    def test_0000_initiate_users( self ):
+        """Create necessary user accounts."""
+        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 )
+        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 0030 category and upload the emboss repository to the tool shed, if necessary.'''
+        category = self.create_category( name='Test 0030 Repository Dependency Revisions', description='Tests for a repository with tool 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_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_install_emboss_repository( self ):
+        '''Install the emboss repository into the Galaxy instance.'''
+        self.galaxy_logout()
+        self.galaxy_login( email=common.admin_email, username=common.admin_username )
+        self.install_repository( emboss_repository_name, 
+                                 common.test_user_1_name, 
+                                 'Test 0030 Repository Dependency Revisions', 
+                                 new_tool_panel_section='test_1210' )
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+    def test_0015_uninstall_emboss_repository( self ):
+        '''Uninstall the emboss repository.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.uninstall_repository( installed_repository, remove_from_disk=True )
+        strings_not_displayed = [ installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
+    def test_0020_reinstall_emboss_repository( self ):
+        '''Reinstall the emboss repository.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.reinstall_repository( installed_repository )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+        self.display_installed_repository_manage_page( installed_repository, 
+                                                       strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] )
+        self.verify_tool_metadata_for_installed_repository( installed_repository )
+    def test_0025_deactivate_emboss_repository( self ):
+        '''Deactivate the emboss repository without removing it from disk.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.uninstall_repository( installed_repository, remove_from_disk=False )
+        strings_not_displayed = [ installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed )
+    def test_0030_reactivate_emboss_repository( self ):
+        '''Reactivate the emboss repository and verify that it now shows up in the list of installed repositories.'''
+        installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name )
+        self.reactivate_repository( installed_repository )
+        strings_displayed = [ installed_repository.name,
+                              installed_repository.description,
+                              installed_repository.owner, 
+                              installed_repository.tool_shed, 
+                              installed_repository.installed_changeset_revision ]
+        self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed )
+        self.display_installed_repository_manage_page( installed_repository, 
+                                                       strings_displayed=[ 'Installed tool shed repository', 'Valid tools', 'emboss' ] )
+        self.verify_tool_metadata_for_installed_repository( installed_repository )
diff -r b268bc0bbc63f525a981547d06c20911f553f1b2 -r 692a1e8b69998d99465838cb5c8b1d56f3a37d2d test/tool_shed/functional_tests.py
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -270,7 +270,7 @@
                                                file_path = galaxy_file_path,
                                                tool_path = tool_path,
                                                tool_data_path = tool_data_path,
-                                               shed_tool_path=galaxy_shed_tool_path,
+                                               shed_tool_path = galaxy_shed_tool_path,
                                                update_integrated_tool_panel = False,
                                                tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
                                                tool_sheds_config_file = galaxy_tool_sheds_conf_file,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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[galaxy-commits] commit/galaxy-central: inithello: Tool shed functional test enhancements. Functional tests for uninstalling, deactivating, reinstalling, and reactivating installed repositories.