from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os, logging column_repository_name = 'column_maker_1085' column_repository_description = "Add column" column_repository_long_description = "Compute an expression on every row" convert_repository_name = 'convert_chars_1085' convert_repository_description = "Convert delimiters" convert_repository_long_description = "Convert delimiters to tab" category_name = 'Test 1085 Advanced Circular Dependencies' category_description = 'Test circular dependency features' log = logging.getLogger( __name__ ) class TestRepositoryDependencies( ShedTwillTestCase ): '''Testing the behavior of repository dependencies with tool panel sections.''' def test_0000_create_or_login_admin_user( self ): """Create necessary user accounts and login as an admin user.""" self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) galaxy_admin_user = self.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 = self.test_db_util.get_galaxy_private_role( galaxy_admin_user ) 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' % test_user_1_email test_user_1_private_role = self.test_db_util.get_private_role( test_user_1 ) 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' % admin_email admin_user_private_role = self.test_db_util.get_private_role( admin_user ) def test_0005_create_and_populate_column_repository( self ): """Create a category for this test suite and add repositories to it.""" category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_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=[] ) if self.repository_is_new( repository ): 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='Uploaded column_maker tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0010_create_and_populate_convert_repository( self ): self.logout() self.login( email=common.admin_email, username=common.admin_username ) category = self.create_category( name=category_name, description=category_description ) self.logout() self.login( email=common.test_user_1_email, username=common.test_user_1_name ) repository = self.get_or_create_repository( name=convert_repository_name, description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) if self.repository_is_new( repository ): self.upload_file( repository, filename='convert_chars/convert_chars.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded convert_chars tarball.', strings_displayed=[], strings_not_displayed=[] ) def test_0015_create_and_upload_dependency_files( self ): convert_repository = self.test_db_util.get_repository_by_name_and_owner( convert_repository_name, common.test_user_1_name ) column_repository = self.test_db_util.get_repository_by_name_and_owner( column_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_1085', additional_paths=[ 'column' ] ) repository_tuple = ( self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip( convert_repository ) ) self.create_repository_dependency( repository=column_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) repository_tuple = ( self.url, column_repository.name, column_repository.user.username, self.get_repository_tip( column_repository ) ) self.create_repository_dependency( repository=convert_repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) def test_0020_install_repositories( self ): '''Install column_maker into column_maker tool panel section and install repository dependencies.''' self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) self.install_repository( column_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=False, install_repository_dependencies=True, new_tool_panel_section_label='column_maker', strings_displayed=[ 'install_repository_dependencies' ] ) installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) browse_strings_displayed = [ 'convert_chars_1085', 'Convert delimiters', self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, 'column_maker_1085', 'Add column', installed_column_repository.installed_changeset_revision ] strings_displayed = [ 'convert_chars_1085', 'Convert delimiters', self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision, 'column_maker_1085', installed_column_repository.installed_changeset_revision, 'Installed repository dependencies' ] self.display_galaxy_browse_repositories_page( strings_displayed=browse_strings_displayed ) self.display_installed_repository_manage_page( installed_convert_repository, strings_displayed=strings_displayed ) def test_0025_uninstall_column_repository( self ): '''uninstall column_maker, verify same section''' installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_column_repository ) self.test_db_util.ga_refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' ) def test_0030_uninstall_convert_repository( self ): installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_convert_repository ) self.test_db_util.ga_refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'column_maker' ) def test_0035_reinstall_column_repository( self ): '''reinstall column_maker into new section 'new_column_maker' (no_changes = false), no dependencies''' installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_column_repository, install_tool_dependencies=False, install_repository_dependencies=False, new_tool_panel_section_label='new_column_maker', no_changes=False ) strings_displayed = [ 'column_maker_1085', 'Add column', self.url.replace( 'http://', '' ), installed_column_repository.installed_changeset_revision ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) def test_0040_reinstall_convert_repository( self ): '''reinstall convert_chars into new section 'new_convert_chars' (no_changes = false), no dependencies''' installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) self.reinstall_repository( installed_convert_repository, install_tool_dependencies=False, install_repository_dependencies=False, new_tool_panel_section_label='new_convert_chars', no_changes=False ) strings_displayed = [ 'convert_chars_1085', 'Convert delimiters', self.url.replace( 'http://', '' ), installed_convert_repository.installed_changeset_revision ] self.display_installed_repository_manage_page( installed_convert_repository, strings_displayed=strings_displayed ) def test_0045_uninstall_and_verify_tool_panel_sections( self ): '''uninstall both and verify tool panel sections''' installed_convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) installed_column_repository = self.test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_convert_repository ) self.uninstall_repository( installed_column_repository ) self.test_db_util.ga_refresh( installed_convert_repository ) self.test_db_util.ga_refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'new_column_maker' ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'new_convert_chars' )