from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import logging log = logging.getLogger( __name__ ) category_name = 'Test 1430 Repair installed repository' category_description = 'Test script 1430 for repairing an installed repository.' filter_repository_name = 'filter_1430' column_repository_name = 'column_1430' filter_repository_description = "Galaxy's filter tool for test 1430" column_repository_description = 'Add a value as a new column' filter_repository_long_description = '%s: %s' % ( filter_repository_name, filter_repository_description ) column_repository_long_description = '%s: %s' % ( column_repository_name, column_repository_description ) ''' In the Tool Shed: 1) Create and populate the filter_1430 repository 2) Create and populate the column_1430 repository 3) Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository dependency on the filter_1430 repository. In Galaxy: 1) Install the column_1430 repository, making sure to check the checkbox to Handle repository dependencies so that the filter repository is also installed. Make sure to install the repositories in a specified section of the tool panel. 2) Uninstall the filter_1430 repository. 3) Repair the column_1430 repository. 4) Make sure the filter_1430 repository is reinstalled and the tool is loaded into the tool panel in the same section specified in step 1. ''' class TestRepairRepository( ShedTwillTestCase ): '''Test repairing an installed repository.''' def test_0000_initiate_users_and_category( self ): """Create necessary user accounts and login as an admin user.""" self.logout() self.login( email=common.admin_email, username=common.admin_username ) admin_user = self.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 = self.test_db_util.get_private_role( admin_user ) self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_2_email, username=common.test_user_2_name ) test_user_2 = self.test_db_util.get_user( common.test_user_2_email ) assert test_user_2 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_2_email test_user_2_private_role = self.test_db_util.get_private_role( test_user_2 ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) test_user_1 = self.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' % common.test_user_1_email test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) def test_0005_create_filter_repository( self ): '''Create and populate the filter_1430 repository.''' ''' This is step 1 - Create and populate the filter_1430 repository. This repository will be depended on by the column_1430 repository. ''' category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=filter_repository_name, description=filter_repository_description, long_description=filter_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='filtering/filtering_1.1.0.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Populate filter_1430 with version 1.1.0.', strings_displayed=[], strings_not_displayed=[] ) def test_0010_create_column_repository( self ): '''Create and populate the column_1430 repository.''' ''' This is step 2 - Create and populate the column_1430 repository. This repository will depend on the filter_1430 repository. ''' category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=column_repository_name, description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) self.upload_file( repository, filename='column_maker/column_maker.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Populate column_1430 with tool definitions.', strings_displayed=[], strings_not_displayed=[] ) def test_0015_create_repository_dependency( self ): '''Create a dependency on filter_1430.''' ''' This is step 3 - Upload a repository_dependencies.xml file to the column_1430 repository that creates a repository dependency on the filter_1430 repository. ''' column_repository = self.test_db_util.get_repository_by_name_and_owner( 'column_1430', common.test_user_1_name ) filter_repository = self.test_db_util.get_repository_by_name_and_owner( 'filter_1430', common.test_user_1_name ) tool_shed_url = self.url name = filter_repository.name owner = filter_repository.user.username changeset_revision = self.get_repository_tip( filter_repository ) repository_dependency_tuple = ( tool_shed_url, name, owner, changeset_revision ) filepath = self.generate_temp_path( '1430_repository_dependency' ) self.create_repository_dependency( column_repository, [ repository_dependency_tuple ], filepath=filepath ) def test_0020_install_column_repository( self ): '''Install the column_1430 repository into Galaxy.''' ''' This is step 1 (galaxy side) - Install the column_1430 repository, making sure to check the checkbox to handle repository dependencies so that the filter_1430 repository is also installed. Make sure to install the repositories in a specified section of the tool panel. ''' self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) post_submit_strings_displayed = [ 'column_1430', 'filter_1430' ] self.install_repository( 'column_1430', common.test_user_1_name, category_name, new_tool_panel_section_label='repair', post_submit_strings_displayed=post_submit_strings_displayed, install_tool_dependencies=False, install_repository_dependencies=True ) def test_0025_uninstall_filter_repository( self ): '''Uninstall the filter_1430 repository from Galaxy.''' ''' This is step 2 - Uninstall the filter_1430 repository. ''' installed_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name ) strings_displayed = [ 'Uninstalling this repository will result in the following' ] strings_not_displayed = [] self.uninstall_repository( installed_repository, strings_displayed=strings_displayed, strings_not_displayed=strings_not_displayed ) strings_not_displayed = [ 'filter_1430', "Galaxy's filter tool for test 1430", installed_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_not_displayed=strings_not_displayed ) def test_0030_repair_column_repository( self ): '''Repair the column_1430 repository.''' ''' This is step 3 - Repair the column_1430 repository. ''' column_repository = self.test_db_util.get_installed_repository_by_name_owner( 'column_1430', common.test_user_1_name ) self.repair_installed_repository( column_repository ) def test_0035_verify_tool_panel_section( self ): '''Check the tool panel section after repairing.''' ''' This is step 4 - Make sure the filter_1430 repository is reinstalled and the tool is loaded into the tool panel in the same section specified in step 1. ''' filter_repository = self.test_db_util.get_installed_repository_by_name_owner( 'filter_1430', common.test_user_1_name ) strings_displayed = [ 'filter_1430', "Galaxy's filter tool for test 1430", filter_repository.installed_changeset_revision ] self.display_galaxy_browse_repositories_page( strings_displayed=strings_displayed ) self.check_galaxy_repository_tool_panel_section( repository=filter_repository, expected_tool_panel_section='repair' )