from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os import logging log = logging.getLogger( __name__ ) category_name = 'Test 1460 Data Manager' category_description = 'Test script 1460 for testing Data Managers' data_manager_repository_name = 'data_manager_1460' data_manager_repository_description = 'Repository that contains a Data Manager' data_manager_repository_long_description = '%s: %s' % ( data_manager_repository_name, data_manager_repository_description ) data_manager_name = 'testing_data_manager' data_manager_tar_file = '1460_files/data_manager_files/test_data_manager.tar' ''' 1. Add a Data Manager to toolshed 2. install Data Manager 3. Check that Data Manager tool ''' #TODO: Allow testing actual Execution of installed Data Manager Tool. class TestDataManagers( ShedTwillTestCase ): '''Test installing a repository containing a Data Manager.''' 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_0010_create_data_manager_repository( self ): '''Create and populate data_manager_1460.''' ''' This is step 1 - Create repository data_manager_1460. Create and populate a repository that contains a Data manager. ''' category = self.test_db_util.get_category_by_name( category_name ) repository = self.get_or_create_repository( name=data_manager_repository_name, description=data_manager_repository_description, long_description=data_manager_repository_long_description, owner=common.test_user_1_name, category_id=self.security.encode_id( category.id ), strings_displayed=[] ) # Upload the edited tool dependency definition to the package_lapack_3_4_1440 repository. self.upload_file( repository, filename=data_manager_tar_file, filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Populate %s with a data manager configuration.' % data_manager_repository_name, strings_displayed=[], strings_not_displayed=[] ) def test_0020_install_data_manager_repository( self ): '''Install the data_manager_1460 repository to galaxy.''' ''' This is step 3 - Attempt to install the repository into a galaxy instance, verify that it is installed. ''' self.galaxy_logout() self.galaxy_login( email=common.admin_email, username=common.admin_username ) post_submit_strings_displayed = [ data_manager_repository_name ] self.install_repository( data_manager_repository_name, common.test_user_1_name, category_name, install_tool_dependencies=True, post_submit_strings_displayed=post_submit_strings_displayed ) def test_0030_verify_data_manager_tool( self ): '''Verify that the data_manager_1460 repository is installed and Data Manager tool appears in list in Galaxy.''' repository = self.test_db_util.get_installed_repository_by_name_owner( data_manager_repository_name, common.test_user_1_name ) strings_displayed = [ 'Access managed data by job' ] self.display_installed_manage_data_manager_page( repository, data_manager_names=data_manager_name, strings_displayed=strings_displayed ) def test_0040_verify_data_manager_data_table( self ): '''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.''' self.verify_installed_repository_data_table_entries( required_data_table_entries=[ 'data_manager_test_data_table' ] )