from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os 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 for test 0020' emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020' class TestBasicRepositoryDependencies( ShedTwillTestCase ): '''Testing emboss 5 with repository dependencies.''' def test_0000_initiate_users( self ): """Create necessary user accounts and login as an 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' % common.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' % common.admin_email admin_user_private_role = self.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='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 ) category = self.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, filename='emboss/datatypes/datatypes_conf.xml', filepath=None, valid_tools_only=True, uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded datatypes_conf.xml.', strings_displayed=[], strings_not_displayed=[] ) def test_0015_verify_datatypes_in_datatypes_repository( self ): '''Verify that the emboss_datatypes repository contains datatype entries.''' repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) 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.''' category = self.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, filename='emboss/emboss.tar', filepath=None, valid_tools_only=True, uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded emboss.tar', strings_displayed=[], strings_not_displayed=[] ) def test_0025_generate_and_upload_repository_dependencies_xml( self ): '''Generate and upload the repository_dependencies.xml file''' repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) repository_dependencies_path = self.generate_temp_path( 'test_0020', additional_paths=[ 'emboss', '5' ] ) repository_tuple = ( self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip( datatypes_repository ) ) self.create_repository_dependency( repository=repository, repository_tuples=[ repository_tuple ], filepath=repository_dependencies_path ) def test_0030_verify_emboss_5_dependencies( self ): '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.''' repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) changeset_revision = self.get_repository_tip( datatypes_repository ) strings_displayed = [ 'Tool dependencies', 'emboss', '5.0.0', 'package', 'emboss_datatypes_0020', 'user1', changeset_revision, 'Repository dependencies' ] self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) def test_0040_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' emboss_repository = self.test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name ) self.verify_unchanged_repository_metadata( emboss_repository ) self.verify_unchanged_repository_metadata( datatypes_repository )